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Impact of farming practices on soil diatoms and testate amoebae: A pilot study in the DOK-trial at Therwil, Switzerland
Abstract
Testate amoebae (Arcellinida and Euglyphida) and diatoms (Bacillariophyta) respond to different
ecological gradients. These protists are useful tools for biomonitoring and paleoecological studies in
aquatic and terrestrial ecosystems. However, little is known about the responses of these microeukaryotes
to soil management practices. We analyzed the testate amoeba and diatom communities
from the DOK-trial (D: biodynamic, O: bio-organic, K: german ‘‘konventionell’’ integrated conventional)
agricultural experiment at Therwil, Switzerland. Soil samples were collected from biodynamic and
conventional plots and subsequently incubated for four months in a growth chamber. The diatom
diversity tended to be higher in the biodynamic than in the two conventional systems. Redundancy
analysis (RDA) suggested that diatom community structure differed between organic and the two
conventional systems. Testate amoeba abundance was about five times higher in biodynamic than in
conventional systems (P < 0.05) but no significant differences in diversity were reported between
treatments. Altogether, these data suggest that diatoms and testate amoebae are sensitive to farming
systems. As direct analyses of soil samples are time-consuming, molecular tools would be very useful for
further development of the use of protists in bioindication.
... Though these communities seem to be widespread and ubiquitous like aquatic diatom communities, soil diatoms are rather scarce. Scanty researches made the use of soil diatoms more popular on the basis of two principle areas: first as indicators of anthropogenic disturbances in different ecosystems (Dorokhova 2007;Heger et al. 2012;Fazlutdinova and Sukhanova 2014;Vacht et al. 2014;Antonelli et al. 2017;Blanco et al. 2017) and the other one as hydrological tracers to assess terrestrial-aquatic connectivity (Pfister et al. 2009;Klaus et al. 2015;Martínez-Carreras et al. 2015;Coles et al. 2016). Barragán et al. (2018) showed that the terrestrial diatom communities are a dynamic biota that is ready-to-use for implementing quality assessment methods for soils. ...
... Moreover, ecological studies of diatom communities on soils are also quite responsive as well as sensitive to several environmental variables such as soil moisture and pH (Lund 1945;Hayek and Hulbary 1956;Van De Vijver and Beyens 1998;Van Kerckvoorde et al. 2000;Van de Vijver et al. 2002;Souffreau et al. 2010;Antonelli et al. 2017). Foets et al. (2021) showed that the environmental parameters (soil moisture and pH) and disturbances caused by farming practices play a vital role in structuring terrestrial diatom assemblages (Heger et al. 2012;Stanek-Tarkowska and Noga 2012;Vacht et al. 2014;Antonelli et al. 2017;Foets et al. 2020a). Apart from these factors, diatom communities are also affected by the other parameters like organic matter, nitrogen, and carbon content in the soil (Gärtner 1996;Kokfelt et al. 2009;Nielsen et al. 2011;Binoy and Ray 2016;Stanek-Tarkowska et al. 2018;Foets et al. 2021). ...
... However, a few groups of soil microorganisms such as microalgae especially diatoms remain poorly studied (Geisen et al. 2018;Guilland et al. 2018). These soil diatom communities are sensitive to many anthropogenic factors (VanLandingham 1968;Sukhanova et al. 2000;Berard et al. 2004;Zancan et al. 2006;Heger et al. 2012;Stanek-Tarkowska and Noga 2012;Uhr 2013;Antonelli et al. 2017). Some researchers studied in relation to different types of disturbance such as oil pollution (Dorokhova 2007), animal disturbance (Moravcová et al. 2010), agricultural activities (Zancan et al. 2006;Heger et al. 2012), and herbicides effect (Zurek 1981;Berard et al. 2004). ...
Diatoms have long been utilized as robust ecological indicators for aquatic ecosystems. Ecological data of aquatic diatoms have been well documented. Autecological and biotic indices have extensively used for ecoassessment of water bodies throughout the world. In spite of the fact that diatoms are quite abundant in terrestrial environments and respond quickly to soil environment fluctuations, ecological studies on these entities are substantially lacking as compared to their aquatic counterparts. Of late researchers have investigated certain aspects of soil diatom ecology from some parts of the world. Terrestrial diatoms have been found to be quite responsive to soil environmental conditions, anthropogenic disturbances and agricultural practices. This review attempts to assemble the diverse findings associated with the terrestrial diatoms and their response towards various stressors and explores the future prospects of soil diatom ecology.KeywordsTerrestrial diatomsSoil microbiomeAgricultural practices
... They are used in ecological monitoring, palaeoecological reconstruction, stratigraphic correlation (Mann, 1999) and environmental assessment . They are one of the chief producers of atmospheric oxygen (Singh et al., 2010), biogenic silica (Mann, 1999) and biofuels (Amato, 2010).Diatoms play a major role in the biogeochemical cycles (Mann, 1999) and serve as the major food for protozoa in the soil food web (Heger et al., 2011). They assist as organic carbon stalk of soils (Hunt et al., 1979). ...
... Diadesmis species is a typical cosmopolitan soil diatom, which is adapted to live in very low light conditions (Van de Vijver & Beyens, 1998 Lund (1946) diatoms are growing in moist soil and their abundance can be decreased during summer droughts. Available water is the primary factor in determining the abundance of algae (Broady, 1979) in general, especially diatoms that live at the surface of the soil are very sensitive to desiccation and dryness adversely affects the abundance of them in soils (Heger et al., 2011). The present investigation has confirmed the above observation that diatoms are abundant in moist soil. ...
... Distribution of diatoms is affected by many environmental factors (Kokfelt et al., 2009) and agricultural practices (Heger et al., 2011). According to Chaib et al. (2001), anthropogenic pressures affect spatial distribution patterns of diatom communities. ...
... As photoautotrophs, soil algae are thought to be important contributors to the organic carbon content of soil (Hunt et al., 1979) which, in turn, can alter both productivity and community structure of many terrestrial ecosystems (Samaritani, 2013) through its impact on microbial biomass. Soil algae contribute to the formation and stabilization of soils (King and Ward, 1977), reduce erosion by regulating the soil water flow (Abdel-Raouf et al., 2012), increase the organic matter level of soil by fixing CO 2 photosynthetically (Chang and Alexander, 1983;Zaady et al., 2000), and constitute food sources for heterotrophic soil organisms (Heger et al., 2012;Schmidt et al., 2016;Stanek-Tarkowska and Noga, 2012). Organic matter productions ranging from 0.0123 to 0.0450 g m −2 year −1 have been determined for terrestrial algae in different habitats (San Jose and Bravo, 1991). ...
... Soil diatom communities observed in this study appear to be sensitive to experimentally induced perturbations. It is well known that undisturbed sites support more diverse and abundant algal communities (Heger et al., 2012;Zancan et al., 2006). Contrastingly, the results of this experiment concerning Bacteria, Archaea, Fungi or Protozoa revealed no clear response patterns to CO 2 increase in terms of functionality, diversity or abundance. ...
... Multivariate analysis presented here revealed that the response to different CO 2 fluxes is species-dependent (Heger et al., 2012;Steven et al., 2010). This confirms our hypothesis that the response of the soil diatom assemblage to CO 2 leakages is not merely quantitative but also qualitative. ...
... They are one of the chief producers of atmospheric oxygen (Singh et al., 2010), biogenic silica (Mann, 1999) and biofuels (Amato, 2010). Diatoms play a major role in the biogeochemical cycles (Mann, 1999) and serve as the major food for protozoa in the soil food web (Heger et al., 2011). They assist as organic carbon stalk of soils (Hunt et al., 1979). ...
... 3.2.3.1 Eolimna minima (Grunow) Lange-Bertalot (Plate 2- Fig. 5; Guiry &Guiry, 2012;Heger et al., 2011) was a very common species of diatoms in these soils. It was found in field soils of natural forest and plantations during all seasons and also observed in the culture of those soils. ...
... Diadesmis species is a typical cosmopolitan soil diatom, which is adapted to live in very low light conditions (Van de Vijver & Beyens, 1998 Lund (1946) diatoms are growing in moist soil and their abundance can be decreased during summer droughts. Available water is the primary factor in determining the abundance of algae (Broady, 1979) in general, especially diatoms that live at the surface of the soil are very sensitive to desiccation and dryness adversely affects the abundance of them in soils (Heger et al., 2011). The present investigation has confirmed the above observation that diatoms are abundant in moist soil. ...
Diatoms represent an ecologically specialized group of Protistan algae found in all environments. This is the
first description of ecology and diversity of diatoms of the Western Ghats of South India, one of the biodiversity hot spots of the world. Soils under three different kinds of vegetation such as forests, rubber plantation, and teak plantation during three seasons of a year were investigated for diatoms directly observable in field soil samples as well as in the culture of soils in nutrient media. Identification was based on the morphology, using ordinary microscopic and scanning electron microscopic studies. Correlations of diversity to vegetation, season and physico-chemical characters of soil were found out. Relative abundance, speciesrichness, evenness and diversity-index are also described. Altogether nine well-known species and
quite a new variety of diatom species were observed in this part of South India. However, compared to the
other groups of algae, quite low diversity of diatoms was observed in these soils. Soils of natural forest
and teak plantations showed more diatoms than that of the rubber plantation. Apart from positive correlations of diversity index to carbon and soil moisture content, no significant correlations were found between diatoms and other soil parameters.
... In addition to soil type and texture, geology, vegetation cover and land use, these environmental factors affect the diversity, density and distribution of soil species (Van Kerckvoorde et al. 2000, Antonelli et al. 2017, Zhang et al. 2020. Indeed, several investigations of soil diatom assemblages in an agricultural setting showed changes in community structure in response to different agricultural practices (irrigation, organic and conventional fertilization, tillage) (Bérard et al. 2004, Zancan et al. 2006, Heger et al. 2012, Stanek-Tarkowska & Noga 2012, Lin et al. 2013). These activities lead to variation in soil properties (pH, moisture, organic matter and nutrient content) that influence the composition of terrestrial diatom communities. ...
... Several works (Hofmmann 1989, Van de Vijver & Beyens 1998, Van Kerckvoorde et al. 2000, Van de Vijver et al. 2002, Heger et al. 2012, Vijayan & Ray 2016, Zhang et al. 2020 reported that soil moisture, soil type and texture, pH, organic matter, nutrient availability, land use and vegetation type affect biocrust algal diversity and biomass, especially diatoms. ...
Microscopic algae especially diatoms (Class Bacillariophyceae) are an important component of biological soil crusts (or biocrust) communities in arid and semi-arid environments. In Morocco, a largely arid and semi-arid African Mediterranean country, the soil diatom diversity and ecology remain unexplored, unlike aquatic diatoms. This study aims to understand the spatial distribution of soil diatoms and to investigate the effects of soil properties and land use on their diversity and taxonomic composition in the region of Marrakesh (Morocco). Five sampling sites with different land use and vegetation cover were selected along a natural altitudinal gradient in the Ourika watershed (from the humid mountain highlands of Oukaimeden at 2634 m (High Atlas) to the arid Haouz plain at 765 m). Biological soil crusts were taken and soil physicochemical characteristics (soil moisture and texture, pH, electrical conductivity, total organic carbon, ammoniacal nitrogen, available phosphorus) were measured at five locations and two seasons (February and May). The spatial distribution of soil diatom communities and associated influencing factors were investigated via statistical analysis using Canonical Correspondence Analysis (CCA). A total of 27 diatom taxa belonging to 16 genera were recorded. The results showed that the distribution of soil diatoms was mainly influenced by altitude, bioclimate, substratum type, land use and vegetation cover. These environmental factors induce spatial variability in the soil physicochemical properties. Diatom composition and species richness were correlated with soil moisture, pH, texture, conductivity, nutrient and organic matter content. Diatoms showed higher species richness in siliceous soils of high altitudinal humid grassland dominated by acidophilous and neutral taxa with a preference for low conductivity. In contrast diatom communities of forests and sedimentary lowland arid steppe were relatively species poor, dominated by typically alkaliphilous and halophilous soil species. This exploratory survey provides a first account of the diatom assemblages of biological soil crusts over an altitudinal range in Morocco, necessary for understanding their structure and ecological function, including improving soil condition and sustainable fertility management.
... qualitative data) and researchers often used culturing methods prior to microscope examination. Due to the latter, many diatom species were overlooked, and relative abundances were not reflecting the prevailing environmental conditions (Broady, 1979 showed that soil diatoms are quite responsive to agricultural practices (Heger et al., 2012;Stanek-Tarkowska et al., 2018;Stanek-Tarkowska and Noga, 2012). It was even possible to separate those different land use types based on IPS values (Antonelli et al., 2017). ...
... Also, Lund (1945), who sampled 66 different soils in the UK, was able to determine tolerance ranges of pH for 24 taxa. In addition to soil moisture and pH, disturbances caused by farming practices also play a key role in structuring terrestrial diatom assemblages (Antonelli et al., 2017;Foets et al., 2020a;Heger et al., 2012;Stanek-Tarkowska and Noga, 2012;Vacht et al., 2014). Foets et al. (2020a found that disturbed areas were less diverse, and that land uses with different disturbance levels could be differentiated solely based on the community composition. ...
Diatoms are unicellular, microscopic algae characterized by a siliceous cell wall. They live in almost all habitats containing water (e.g. lakes, streams, soils, rocks) and count among the most common algal groups in both freshwater and marine ecosystems. Their diversity and sensitivity to several environmental variables have made them indispensable in water quality assessment. Because of those characteristics, recent research explored the use of terrestrial diatoms (i.e. diatoms living on soils) as tracers of hydrological connectivity during runoff events. Although the results were promising, further use was hampered by the lack of ecological knowledge on terrestrial diatoms and the large number of samples needed. To overcome the former, the spatial and temporal variability of diatom communities and their absolute abundances on soils were investigated and the occurrences of common soil diatoms were tested to an extensive set of environmental variables. Also, in order to reduce the number of samples, the Phillips sampler, a time-integrated mass-flux sampler, was explored for sampling drift diatom communities in streams during rainfall-runoff events. The results of the thesis allow to reduce the sampling effort and speed up the analysis of diatom-based hydrological tracer studies. They also indicate that many more diatoms can be used as environmental markers in hydrological tracing, that more locations can be sampled, and that the number of stream sampling sites can be increased in the future. The work thus improved the use of terrestrial diatoms as hydrological tracers.
... /eje-2018 Heikens et al. 2001). Diatoms, mostly known from their bioindication abilities in water (Dickman 1998), are so far less used for in soil ecological research, but can still be considered as potential indicators of soil habitat properties (van Kerckvoorde et al. 2000; Van de Vijver et al. 2008;Heger et al. 2012;Vacht et al. 2014). Based on previous studies from urban areas and traffic related disturbances (Santorufo et al. 2012) the following hypotheses were set: Although, microarthropod and diatom communities vary between the airfields the communities at the studied airfields also share a substantial percentage of species which can be considered typical to areas affected by intensive traffic related disturbances such as airfields; Diatom and microarthropod (Collembola and oribatid mites) species indicative of specific airfields and the purpose of different airfield areas can be identified. ...
... The dominant diatom species were the cosmopolitan H. amphioxys, A. granulata and L. mutica. All the studied airfields contained the same base soil community, that has also previously been found from many soil habitats both in Estonia (Vacht et al. 2014) and elsewhere (Soare & Dobrescu 2010;Heger et al. 2012) that represent a tolerant algal community which has little bioindication value that is particular to airfields. Nevertheless, the shared species of the three airfields (e.g. ...
Even though airfields, which are often anthropologically modified natural areas, are continuously influenced by human activities, their soils are still dynamic ecosystems containing various habitats for microscopic groups of organisms which are often ignored. In this exploratory study, the microarthropod fauna, Collembola (Hexapoda) and oribatid mites (Acari: Oribatida), and diatom (Bacillariophyta) flora were identified in three Estonian airfields, both runway sides and snow-melting sites were investigated. The communities of these airfields shared approximately 10-60% of the species belonging to each studied bioindicator group. The shared species were generally characteristic of a broad habitat spectrum. Communities were also characterized based on their species richness and diversity and in relation to location and the purpose of different airfield areas (e.g. snow-melting sites vs. runway sides). Also, species indicative of a specific airfield or purpose of the area within the airfield were identified using Indicator Species Analysis. Some possible linkages between airfield properties and communities, e.g. airfield that had highest pollutant concentrations had also maintained high diversity and species richness, were noted. Despite the contamination levels the airfield soils had still maintained a functioning soil ecosystem.
... For example, new approaches were proposed in soil microbiology, such as taking into account functional ecology concepts, i.e. vigour, organisation, stability, suppressiveness and redundancy (Garbisu et al. 2011), or organisms rarely used, e.g. testate amoebae or diatoms (Heger et al. 2012), which are good bioindicators (Payne 2013) and sensitive to farming practices (Heger et al. 2012). Functional traits of soil macro-invertebrates are also increasingly used (Yan et al. 2012). ...
... For example, new approaches were proposed in soil microbiology, such as taking into account functional ecology concepts, i.e. vigour, organisation, stability, suppressiveness and redundancy (Garbisu et al. 2011), or organisms rarely used, e.g. testate amoebae or diatoms (Heger et al. 2012), which are good bioindicators (Payne 2013) and sensitive to farming practices (Heger et al. 2012). Functional traits of soil macro-invertebrates are also increasingly used (Yan et al. 2012). ...
Many authors have discussed the concept of soil fertility. Despite some disagreement on the exact terminology, soil fertility retrospectively appeared to focus generally on the use of soil for agriculture. It was defined some 150 years ago, while agricultural sciences mostly focused on soil physical and chemical properties. More recently, with the increasing awareness of environmental issues related to agricultural land use and the development of new knowledge on ecosystems, more comprehensive approaches to soil quality were developed. Since the 1980s, growing knowledge on the roles of soil organic matter and living organisms has emphasised the importance of understanding and assessing the biological components of the soil and their functions alongside the physical and chemical components. Soil is described as a living system that fulfils several functions, such as primary production, environmental filter and climate regulation. Following the metaphor of a complex living ‘organism’, the term ‘soil health’ is thus used by some authors instead of soil quality. Soil quality is hence defined as the soil fitness for use, which cannot be measured directly. It must be assessed in a sensitive and holistic way that accounts for both inherent properties and dynamic responses to management and resistance to environmental stress. Several sets of indicators and more integrated methods have been developed. However, further research is still needed to consolidate assessment guidelines that would help to model better the impact of agricultural practices on soil quality and to define strategies for a sustainable management of soil quality.
... Diatoms are rarely identified in soil algae studied [10][11][12][13][14][15][16][17][18][19][20]. Although some research has been carried out on the ecology and species composition of soil diatoms [10,13,[21][22][23][24][25][26][27][28], no studies have been found which concern soils developed on fallow land. Also, no research studies have been conducted on the diversity of soil diatom communities in the area of the Małopolska region (southern Poland). ...
... borealis; it always reached an over 20% share in the assemblage, while in April and July even more than 60%. Hantzschia amphioxys (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27).5%) and Stauroneis borrichii also occurred numerously, reaching the highest percentage in August -32%, while Luticola nivalis were numerous only in autumn (Tab. 3). ...
The aim of this work was to investigate the species diversity of diatoms growing on fallow fields on loose sand. The study site was located in the western part of Pogórska Wola near Tarnów (southern Poland). Samples were collected from fallow land once a month from April to December 2011. 57 diatom taxa from 19 different genera were found. The most numerous genera were Fragilaria (8) and Luticola (7). The highest species richness was observed in December, November and July, while the highest values of species diversity (Shannon–Wiener index) were recorded between August and October. Four taxa – Pinnularia borealis Ehrenb. var. borealis, Stauroneis borrichii (Petersen) Lund, Hantzschia amphioxys (Ehrenb.) Grunow, and Luticola nivalis (Ehrenb.) D.G. Mann, were found to be the dominant species. Neutral species (a pH of about 7) dominated in all months (from April to December), reaching an over 90% share in the assemblage. In terms of nitrogen content, nitrogen-autotrophic taxa, tolerating an elevated concentration of organically bound nitrogen, occurred most abundantly, as was indicated by the low content of nitrogen in the soil.
... Although mostly known for their short response times to environmental changes and indicator abilities in water (e.g. Kobayasi and Mayama, 1982;Eloranta and Soininen, 2002;de la Rey et al., 2004;Levkov et al., 2007;Beyene et al., 2014), diatoms can also be found in soils and are considered to be potentially good environmental indicators of terrestrial ecosystem properties (van Kerckvoorde et al., 2000;Berard et al., 2004;Van de Vijver et al., 2008;Kabirov and Gaisina, 2009;Moravcová et al., 2009;Heger et al., 2012). For example, soil diatoms have been studied in relation to agricultural activities (Heger et al., 2012), oil pollution (Dorokhova, 2007), and in polar areas in the context of vegetation type (van Kerckvoorde et al., 2000;Van de Vijver et al., 2008) and animal perturbation (Moravcová et al., 2009). ...
... Kobayasi and Mayama, 1982;Eloranta and Soininen, 2002;de la Rey et al., 2004;Levkov et al., 2007;Beyene et al., 2014), diatoms can also be found in soils and are considered to be potentially good environmental indicators of terrestrial ecosystem properties (van Kerckvoorde et al., 2000;Berard et al., 2004;Van de Vijver et al., 2008;Kabirov and Gaisina, 2009;Moravcová et al., 2009;Heger et al., 2012). For example, soil diatoms have been studied in relation to agricultural activities (Heger et al., 2012), oil pollution (Dorokhova, 2007), and in polar areas in the context of vegetation type (van Kerckvoorde et al., 2000;Van de Vijver et al., 2008) and animal perturbation (Moravcová et al., 2009). ...
Riparian soils are affected by both natural and anthropogenic disturbances occurring in the water bodies and on the catchment area. These riparian areas are also rich in microhabitats and therefore host various soil biota, including diatoms. Diatoms are known for their bioindication abilities in water and could potentially be used in that context in the riparian zone. Therefore the possibility of riparian soil diatoms acting as indicators of both terrestrial and aquatic disturbances is worth discussion. We analysed diatom community structure and their variability between different study areas and sites. We also quantified diatom species diversity and richness and evenness of the riparian topsoils. Possible effects of various anthropogenic disturbances on diatom communities, alkaline air pollution, and the effects of mining waters pumped into the area were studied in northeastern Estonia. These results were compared with results from an area with low human influence in south-eastern Estonia. Additionally, we evaluated the potential of diatoms as indicators of various anthropogenic disturbance levels and a water contamination gradient based on sulphate concentrations. Community parameters, including species richness, diversity, and evenness, indicated some differences between the studied communities both when the separate study sites and distinguishable anthropogenic disturbance levels were compared. Diatom assemblages also showed moderate variability between the study sites, which could be influenced by variable moisture conditions, variable organic matter content, and the trophic level of the water body. Despite the variable levels of human influence the two compared areas shared about 51.4% of the species. Our findings show that the diatom community composition of riparian soils could potentially indicate anthropogenic disturbance levels, especially through the abundance, absence, or presence of specific species (e.g. Hantzschia amphioxys, Fragilaria zeilleri var. elliptica, Pinnularia lata).
... In addition to soil type and texture, geology, vegetation cover and land use, these environmental factors affect the diversity, density and distribution of soil species (Van Kerckvoorde et al. 2000, Antonelli et al. 2017, Zhang et al. 2020. Indeed, several investigations of soil diatom assemblages in an agricultural setting showed changes in community structure in response to different agricultural practices (irrigation, organic and conventional fertilization, tillage) (Bérard et al. 2004, Zancan et al. 2006, Heger et al. 2012, Stanek-Tarkowska & Noga 2012, Lin et al. 2013). These activities lead to variation in soil properties (pH, moisture, organic matter and nutrient content) that influence the composition of terrestrial diatom communities. ...
... Several works (Hofmmann 1989, Van de Vijver & Beyens 1998, Van Kerckvoorde et al. 2000, Van de Vijver et al. 2002, Heger et al. 2012, Vijayan & Ray 2016, Zhang et al. 2020 reported that soil moisture, soil type and texture, pH, organic matter, nutrient availability, land use and vegetation type affect biocrust algal diversity and biomass, especially diatoms. ...
Bioactive products of the multicellular filamentous benthic cyanobacterium, Pseudanabaena species, isolated from wastewater stabilization ponds at Marrakech, were tested against some pathogenic micro-organisms. Extracellular and intracellular products released by this blue-green alga in the stationary, growth phase, reduced the survival of Escherichia coli, Salmonella sp., Staphylococcus aureus and Candida albicans, and stimulated the growth of non-O1 V. cholerae, whereas no significant effect was noted on the growth of Candida tropicalis. Intracellular substances (methanolic extract) had a stronger inhibitory effect on these micro-organisms than that produced by extracellular substances. These antibacterial and antifungal substances may have a pharmacological value. They may have an important ecological effect on the composition of the bacterial community in Marrakech stabilization ponds when blooms of Pseudanabaena species occurred in this sewage treatment ecosystem during hot periods.
... Результаты исследований дают основание предположить, что внесение в почву навозных стоков обеспечивает благоприятную экологическую нишу для активного развития Bacillariophyta. Считается, что эти МО являются хорошими продуцентами ор- ганического вещества и играют важную роль в формировании и стабилизации почвенных агрегатов [22]. На сообщества почвенных ЦБ наиболее существенное влияние оказал техногенный фактор. ...
Algocyanoflora is an important component of soil microbiota. Anthopogenic pressure causes considerable transformation of natural microbiological communities. Thus there are certain negative consequences. We compare the microphototroph species content in soils differ in the character of the anthropogenic pressure: site 1 – nature reserve soils; site 2 – technogenic soils; site 3 – soils used in agricultural holdings, farms. As a result the richest microphototrophic species composition was in nature reserve soils. Soil management and heavy fertilizing with swine manure slurry decreased microphototrophic biodiversity by 30%. Technogenic pressure decreased biodiversity almost by 50%. Leptolyngbya angustissima, Nostoc punctiforme (Cyanobacteria), Chlamydomonas gloeogama, Ch. minutissima, Chlorococcum infusionum, Chlorella vulgaris, Chloroplana terricola, Klebsormidium flaccidum, Kl. nitens (Chlorophyta), and Hantzschia amphioxys (Bacillariophyta) are the most tolerant to anthropogenic pressure. Ochrophyte microalgae species are the least tolerant to anthropogenic pressure, while green algae are most tolerant ones. Technogenic factor greatly affects the soil microphototrophic communities. At the technogenically stressed site microphototroph species diversity is almost two times lower compared to the control site (nature reserve). The microphototroph biodiversity in nutrient-rich agrozems is just a bit less than in nature reserve (35 and 49 spesies, respectively). Algoindiaction according to algae and cyanobacteria communities is an informative and sensitive quick-test in assessing the soil status. Changes in the species composition and aboudance of microphototrophs are a response to changes in environmental conditions.
... Diatoms are important contributors to organic compounds and play a crucial role in the formation and stability of soil aggregates (Meetting, 1981). It remains unclear if soil diatoms can be used to monitor agricultural soil quality, however, there is evidence that diatom community composition is sensitive to land use (Heger et al., 2012;Foets et al., 2020a). ...
... External disturbances promote rapid changes in their community structure and diversity, outpacing the responsiveness of large animals residing in the soil matrix (Bamforth et al., 2005;Foissner, 2005). This rapid response makes soil ciliates sentinel organisms of environmental changes, coupled with ease of culture and observation, can be used as dynamic indicators to assess soil environmental health (Heger et al., 2012;Debastiani et al., 2016). In addition, soil ciliates can decompose organic matter in the soil and maintain the stability of the soil environment (Xiong et al., 2018), a key role that can affect the ecological balance and overall health of the soil (Azam et al., 1983;Geisen et al., 2015). ...
Introduction: Soil ciliates, as protozoa, play a crucial role in biogeochemical cycling and the soil food web, yet they are highly sensitive to environmental fluctuations in soil conditions. The diversity and biogeographic characteristics of soil ciliates in the Tibetan Plateau remain poorly understood. As part of a regional survey focused on soil ciliate diversity, we investigated the composition and spatiotemporal variations of soil ciliate communities along the Yarlung Zangbo River, a representative soil habitat in the Tibetan Plateau.
Methods: A total of 290 soil samples were collected from four habitat types of grassland, shrubland, forestland and wetland in the middle reaches of the Yarlung Zangbo River during the wet and dry seasons, and 138 species of ciliates were identified.
Results: Soil ciliate diversity exhibited greater variation across habitat types than seasons. Moreover, soil ciliate diversity was higher during the wet season compared to the dry season, with the wetland habitat showing the highest diversity and the grassland habitat displaying the lowest. We observed spatiotemporal heterogeneity in the composition of soil ciliate communities across different seasons and habitat types. Notably, Litostomatea, Karyorelictea, and Prostomatea predominated in ciliate communities during the wet season and in grassland habitat. Phyllopharyngers dominated during dry seasons and in forested regions, while Spirotrichea species were prevalent in wetland and forested areas. The co-occurrence network analysis showed that soil ciliate community was more complex in wet season than in dry season, and the stability of soil ciliate community in wet season was higher than that in dry season. The stability of soil ciliate community in wetland was higher than that in forestland, shrubland and grassland, and the anti-interference ability was stronger. Soil temperature (ST), Total nitrogen (TN), Soil organic matter (SOM) and Soil water content (SWC) are important factors affecting the structure of soil ciliate community. By influencing the metabolic rate and nutrient acquisition of soil ciliates, the distribution pattern of soil ciliate community diversity in the middle reaches of Yarlung Zangbo River is shaped.
Discussion: In summary, this study revealed the distribution pattern of soil ciliate community diversity in the Yarlung Zangbo River Basin, and the key factors affecting the spatial and temporal differences and stability of the community, enhancing our understanding of how ciliates adapt to environmental conditions in soil habitats across the Tibetan Plateau.
... Як тест-об'єкти в оцінці стану ґрунтів дослідниками пропонується використовувати такі мікрооб'єкти: Tetrahymena pyriformis штам GL [17]; Escherichia соli [24]; Bacillus subtilis [25]; Saccharomyces cerevisiae [26]; Chlorella vulgaris [27]; Paramecium caudatum [17]. ...
... It increased from T0 to T2 in Org, and at T2, it was also statistically different between management systems ( Table 1). The higher value of this index in the Organic system as against the Integrated one agreed with the study of Heger et al. [24]. The change in the agricultural system affected the diatom community composition; indeed, it was different at T0 relative to T1 and T2 only in the Organic system ( Figure 3). ...
The use of conservation and sustainable practices could restore the abundance and richness of soil organisms in agroecosystems. Fitting in this context, this study aimed to highlight whether and how different soil living communities reacted to the conversion from an integrated to an organic orchard. The metataxonomic approach for fungi and bacteria and the determination of biological forms of diatoms and microarthropods were applied. Soil analyses were carried out in order to evaluate the effect of soil chemical features on four major soil living communities. Our results showed that the different taxa reacted with different speeds to the management changes. Fungi responded quickly to the changes, suggesting that modification in agricultural practices had a greater impact on fungal communities. Bacteria and microarthropods were more affected by abiotic parameters and less by the management. The diatom composition seemed to be affected by seasonality but the highest H’ (Shannon index) value was measured in the organic system. Fungi, but also diatoms, seemed to be promising for monitoring changes in the soil since they were sensitive to both the soil features and the anthropic impact. Our study showed that soil biodiversity could be affected by the conversion to sustainable management practices from the early years of an orchard onwards. Therefore, better ecological orchard management may strengthen soil sustainability and resilience in historically agricultural regions.
... Protists are valuable tools for biomonitoring studies in terrestrial ecosystems. They are sensitive to farming systems and contribute significantly to mineralization processes and key ecosystem functions in soil (Heger et al., 2012;Domonell et al., 2013). Changes in soil ciliate community structure have also been suggested as bioindicators of environmental stress, improvements in soil quality, CO 2 flux increments in soil, and peat-bog restoration (Lüftenegger et al.,1985;Yeates et al., 1991;Foissner, 1999;Mayzlish and Steiberger, 2004;Mieczan et al., 2017;Gabilondo et al., 2018;Abraham et al., 2019). ...
A 1-year baseline survey was conducted in north-western China to evaluate the ecological restoration quality of grain for green (GFG) using soil ciliate communities. The aims of this study were focused on analyzing the changes of soil ciliate communities in four plots (A, GFG for 15 years; B, GFG for 13 years; C, layland; D, cultivated land) for GFG environmental assessment. Simultaneously we studied the effects of vegetation communities and physical-chemical variables with GFG changes on soil ciliates. A total of 114 species of ciliates were identified among the four sample sites, representing 9 classes, 14 orders, 22 families and 37 genera. The community patterns of the soil ciliates were significantly correlated with the individual abundance of aboveground plants, soil water content, and soil porosity. The contents of total nitrogen were the main factor affecting the soil ciliate community composition. The species number, individual abundance, and diversity index of the ciliates were each in the order A>B>C>D; that is, the community composition of ciliates was complicated with the implementation of the GFG. It was shown that the succession of ciliate community shifts toward promoting the complexity with the progress of GFG. These findings demonstrate that soil ciliate communities may be used as a useful indicator to evaluate the effects of the ecological restoration quality of GFG.
... Human disturbance of Sphagnum peatland ecosystems is mainly associated with agricultural uses of the landscape, since this usually entails hydrological alterations and a greater water deficit. The greater runoff contribution and increased nutrient levels modify the main chemical parameters of water (pH, electrical conductivity, and nutrients), therefore causing a substitution of testate amoeba communities (Figure 3), as has been experimentally observed in N-and P-fertilized Sphagnum peatlands or sedge tundra [36,74] and in surface soils subjected to agricultural use [75]. Historically, population density and intensive agricultural activities have been higher in lowlands near coastal areas of Portugal (http://www.ine.pt; ...
Testate amoebae are one of the most studied groups of microorganisms in Sphagnum peatland ecosystems and, therefore, one of the most reliable bioindicators of their ecological status. Peatland ecosystems are supported by a delicate biogeochemical balance that leads to the formation of peat, one of the main sinks of C, as a result of soil–atmosphere interaction, but currently they are one of the most threatened wetland types at their southern distribution limit. In the European continent, where climatic conditions limit peat formation, they have endured significant anthropic pressure for centuries, and the risk of loss of biodiversity linked to these ecosystems is critical. In addition, peatlands are poorly known ecosystems in the Iberian Peninsula compared with other wetlands; therefore, we have studied the chemical parameters of water and the diversity patterns of testate amoebae in the western Iberian Peninsula to better understand the current status of these ecosystems. The analysis of testate amoeba communities showed an inverse relationship between the diversity and conservation status of these peatlands, both in relation to chemical parameters (i.e., pH, electrical conductivity, phosphates) and to the proportion of anthropized area, with a marked geographical pattern in the degree of anthropogenic disturbance.
... Also, Lund (1945), who sampled 66 different soils in the UK, was able to determine tolerance ranges to pH for 24 taxa. In addition to soil moisture and pH, disturbances caused by farming practices also play a key role in structuring terrestrial diatom assemblages Foets et al., 2020a;Heger et al., 2012;Stanek-Tarkowska and Noga, 2012;Vacht et al., 2014). Foets et al. (2020a) found that disturbed areas were less diverse and that land uses with different disturbance levels could be differentiated solely based on the community composition. ...
Like aquatic diatoms, terrestrial diatoms are sensitive to multiple environmental factors such as pH, anthropic disturbances, soil moisture and nitrogen. While most aquatic diatom species have well-known autecological values for several important variables, qualifying them as biological indicators, this potential has not yet been untapped for terrestrial diatoms. Here, we aim to establish autecological values for pH and soil moisture content using weighted averaging for common, widespread terrestrial diatoms and compare them with previous calculated indicator values and tolerance ranges. In order to provide robust autecological values, we combined the data of ecological studies carried out across a range of climate conditions. We found that our validation metrics improved considerably after removing samples collected in anthropic disturbed habitats, suggesting that an-thropic disturbance is the principal factor defining taxon occurrences. Besides our results showing similarities with previous studies, they also showed a significant improvement on the existing indicator values. Moreover, we expanded the list of terrestrial diatoms to 249 taxa that may serve as environmental markers in different research fields.
... Based on this, he identified indicators for different soil types and also compiled extensive lists of ecological preferences for soil testate amoebae (Bonnet, 1976a(Bonnet, , 1984(Bonnet, , 1985(Bonnet, , 1986(Bonnet, , 1988(Bonnet, , 1989(Bonnet, , 1991a(Bonnet, ,b, 1992. The ecology of testate amoebae was also studied in agro-ecosystems and the impact of farming practices and pesticides on community structure was assessed (Foissner, 1987(Foissner, , 1997(Foissner, , 1999Heger et al., 2012). These studies generally showed a negative impact of intensive farming on the diversity and abundance of testate amoebae. ...
This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology and paleoecology has gained in popularity in recent years, with research showing that morphological characteristics provide complementary information to the commonly used environmental inferences based on testate amoeba (morpho-)species data. We provide a broad overview of testate amoeba morphological and functional traits and trait-environment relationships in the context of ecology, evolution, genetics, biogeography, and paleoecology. As examples we report upon previous ecological and paleoecological studies that used trait-based approaches, and describe key testate amoebae traits that can be used to improve the interpretation of environmental studies. We also highlight knowledge gaps and speculate on potential future directions for the application of trait-based approaches in testate amoeba research.
... Functional traits such as biovolume, shell compression, aperture, and test material origin of Testate amoeba in combination with environmental variables can be used for bioindication (Fournier et al. 2012). Testate amoeba can also be a potential indicator for agricultural soil (Heger et al. 2012), hydrological variation and paleohydrological reconstruction (Song et al. 2014), and for peatland restoration (Creevy et al. 2018). Soil ciliates are eminent tools to detect soil recovery, pollution, and disturbances (Luftenegger et al. 1985;Foissner 1994). ...
Soil quality is the competence of soil to perform necessary functions that are able to maintain animal and plant productivity of the soil. Soil consists of various physical, chemical, and biological parameters, and all these parameters are involved in the critical functioning of soil. There is a need for continuous assessment of soil quality as soil is a complex and dynamic constituent of Earth’s biosphere that is continuously changing by natural and anthropogenic disturbances. Any perturbations in the soil cause disturbances in the physical (soil texture, bulk density, etc.), chemical (pH, salinity, organic carbon, etc.), and biological (microbes and enzymes) parameters. These physical, chemical, and biological parameters can serve as indicators for soil quality assessment. However, soil quality assessment cannot be possible by evaluating only one parameter out of physical, chemical, or biological. So, there is an emergent need to establish a minimum dataset (MDS) which shall include physical, chemical, and biological parameters to assess the quality of the given soil. This review attempts to describe various physical, chemical, and biological parameters, combinations of which can be used in the establishment of MDS.
... Although soils are harsh terrestrial conditions for diatoms, high species richness has been found in soil habitats, such as 251 diatom species observed in the Attert River basin [26] and 165 taxa found in the subantarctic region [13]. These studies revealed that diatom communities were closely linked to soil acidity [13], organic matter content [29] and moisture [17]. In addition, diatoms act an important role on the silica cycle in soils [30,31]. ...
Diatoms constitute a major part of microbial biomass and species richness in soil habitats. However, in spite of a growing interest on soil diatoms, variations in soil diatom communities across different types of soil are poorly known. We hypothesize that diatom communities are different in distinct soil types and can serve as a potential bioindicator for soil environmental assessment. Thirty-four soil samples were collected from Wuhan (yellow brown soil, n = 11), Xi'an (yellow cinnamon soil, n = 10), Korla and Karamay cities (brown calcic soil, n = 13) in central-west China. Diatom flora and thirteen environmental variables were analysed in these soil samples. In total, 66 taxa belonging to 30 genera were identified. Analysis of similarity (ANOSIM) revealed that diatom communities are significantly different among the three types of soil. The indicator species of yellow brown soil in Wuhan City included Pinnularia microstauron, Nitzschia amphibia, Sellaphora nigri, Pinnularia borealis and Humidophila contenta. Brown calcic soil in Korla and Karamay cities was characterized by Luticola suecorum, Luticola cohnii, Luticola nivalis and Luticola mutica. Yellow cinnamon soil in Xi'an City was featured by Stauroneis lundii and three unidentified Luticola species. Results of RDA showed that diatom communities were significantly correlated with magnesia, total phosphorus, organic phosphorus and conductivity, suggestive of the effects of nutrients and ionic strength on soil diatom distribution. Our results reveal high diatom diversity in soil habitats and highlight the potential of diatoms as a bioindicator for soil environmental assessment.
... Wanner et al., 2015), TA abundances (as reflected in protozoic Si pool quantities) and biodiversity (as reflected by numbers of taxa) significantly differed between natural/undisturbed (peatland) and drained/disturbed (cropland) areas. This is in line with the findings of Foissner (1997), who found TA biodiversity (species richness) in (disturbed) agricultural soils to be significantly lower (≥50%) compared to undisturbed soils, whereas TA respond relatively quickly to reduced disturbance (reflected by increased numbers of TA taxa in soils under no-tillage management; Adl et al., 2006) and are sensitive to farming practices (TA abundance was found to be about five times higher in biodynamic than in conventional systems; Heger et al., 2012). Our results are further corroborated by the findings of Creevy et al. (2016), who found significant correlations between taxon richness of TA and corresponding protozoic Si pools in soils of Mere Sands Wood Nature Reserve, an artificial, post sand-mined catchment, in NW England. ...
Many peatlands have been damaged by human activities like Sphagnum harvesting and draining reflected in reduced peatland areas and ecosystem functioning. Peatlands generally play an important role in global silicon (Si) cycling and maintain huge numbers of testate amoebae (TA). However, there is a lack of knowledge on (i) the quantity of protozoic Si pools (represented by siliceous shells of TA) in peatlands and (ii) how these pools respond to land use changes caused by human influence. In our study, we quantified protozoic Si pools in the Dajiuhu National Wetland Park, China, with a focus on the comparison between peatland and cropland areas (i.e., former peatland drained for agriculture). We found protozoic Si pools to (i) represent an important biogenic silica fraction in peatlands and (ii) significantly differ between peatlands and croplands with soil moisture as a key factor for protozoic Si pool quantity showing a significant decrease of these pools in drained areas (i.e., in croplands). From our results we concluded the decrease of protozoic Si pools due to land-use change to represent another example (apart from the loss of phytogenic Si) for anthropogenic desilication in agricultural biogeosystems in general.
... In the DOC experiment, biodynamic management, further, led to a higher proportion of more stable organic matter fractions ( Birkhofer et al. 2007), higher biological activity ( Birkhofer et al. 2007;Fließbach et al. 2007), a change in bacterial populations ( Heger et al. 2012), and a better utilization of carbon by the microbial biomass ( Fließbach et al. 2007) compared to the non-biodynamic treatments. Changes in bacterial populations (Faust et al. 2017;Joergensen et al. 2009) and a more efficient use of soil organic carbon by microbes (Sradnick et al. 2018) were also reported from the experiment at Darmstadt. ...
Research into biodynamic food and farming has a long history within the biodynamic movement. Whilst the basic aim of this research has always been to provide knowledge for furthering the development of this farming approach, recently interest has increased in sharing research activities and results with the global scientific community. After commencing with an introduction to biodynamic agriculture, this review gives an overview of peer-reviewed publications on issues in biodynamic food and farming that have been published between 2006 and 2017. The time before this period is covered by the reviews of Leiber et al. (2006) and Turinek et al. (2009).
Overall, 86 articles were included into this review. The most recognized topics were soil quality and soil health in biodynamic vs. conventional and organic farming, effects of biodynamic preparations, food quality, and viticulture. The studies provide substantial evidence for positive effects of biodynamic management on agroecosystems and food quality:
1) Biodynamic management creates system effects on soils, where compost application plays a crucial role.
2) Biodynamic preparations create effects on food chemical composition and food quality.
3) Biodynamic production can improve the value of food with regard to nutritive properties, taste and human health and well-being.
4) Biodynamic management improves grape quality and plant traits compared to non-biodynamic management.
Until now, the effects of biodynamic management have usually been studied with classical analytical methods in natural and life sciences through disciplinary and reductionist study designs. An application of study designs or specific methods that are conducive for a more holistic analysis are rarely implemented. Thus, we identify the development of appropriate methods and study designs for a holistic examination as a major challenge of future research in biodynamic food and farming.
... Whereas in the study of Antonelli et al. (2017) pH and anthropic disturbances caused by farming practices were seen as the principal explanatory variables. Similarly, studies comparing different disturbance factors showed that soil diatoms are quite responsive to agricultural practices (Heger, Straub & Mitchell, 2012;Stanek-Tarkowska et al., 2018;Stanek-Tarkowska & Noga, 2012). It was even possible to separate those different land use types based on IPS values . ...
Diatoms are generally regarded as inhabitants of water bodies. However, numerous taxa are able to survive and reproduce in a variety of non-aquatic ecosystems. Although terrestrial diatoms are discussed extensively in the literature, most of those studies covered floristic aspects and few information exists on their ecology. This lack of knowledge thwarts their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal patterns and the role of different disturbances on the community composition. We collected soil diatom samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 14 months. Our results indicate that forests create a stable microhabitat for diatoms and that temporal variation of the diatom communities is mainly controlled by farming practices rather than seasonal changes in environmental variables. We also found out that communities need one to 2 months to reestablish a new, stable community after a significant change in the environment. We were able to confirm the applicability of the Pollution-Sensitivity Index (IPS) to identify anthropic disturbances.
... Uitdehaag et al. [23] extracted diatoms from clothes in a criminal investigation. A study dealing with farming practices [24] investigated testate amoebae and diatoms in arable soils, but it used different methods for these protists (permanent slides from chemically cleaned diatom frustules vs. wet mounts from testate amoebae obtained from sieved soil samples). ...
... This may reflect the greater increase in nutrient availability provided by manure treatments, which are known to primarily affect bacterial communities but have indirect effects on predatory protists (Frostegård et al. 1997). It was also suggested that both mineral (NPK) and organic (farmyard manure) fertilization affect the community composition of diatoms and testate amoebae (Heger et al. 2012), although no comparison to unfertilized soils was undertaken in this study. Notably, our results contradict those of previous studies on fungal communities in the surface layers of farmyard manure-amended soils. ...
My thesis intended to develop methods to facilitate the study of soil eukaryotic microbes as well as to enhance the understanding of their ecological role in the soil food web and nutrient cycles of agroecosystems. A cell extraction method was first developed and evaluated for its quantitative and qualitative ability to recover eukaryotic microbial cells in a particle free suspension. Cells were sorted based on their natural fluorescence by mean of flow cytometry, thus allowing the separation of photo-autotrophic and heterotrophic organisms. Deep molecular characterisation based on a multiple barcoding approach was also applied to assess the long term effect of crop fertilisation on the diversity and community composition of different groups of soil eukaryotic microbes. The comparison between group specific barcodes and a universal eukaryotic barcode further aimed to challenge the accuracy of the latter approach to measure soil microbial eukaryotic diversity. At a final stage, the diversity and community composition of micro-algae and fungi in the sorted cell fractions were compared to their originated soil. Micro-algal and fungal biomarkers associated with the different organic and mineral long term fertilisation treatments were uncovered and their co-occurrence patterns in relation to fertilisation were assessed.
... Therefore, it seems reasonable to think that their use could be equally widespread. Recent research is making the use of soil diatoms more popular in two principal areas: as indicators of anthropogenic disturbances in different ecosystems (Dorokhova 2007;Heger et al. 2012;Fazlutdinova and Sukhanova 2014;Vacht et al. 2014;Antonelli et al. 2017;Blanco et al. 2017) and as hydrological tracers to assess terrestrial-aquatic connectivity (Pfister et al. 2009;Klaus et al. 2015;Martínez-Carreras et al. 2015;Coles et al. 2016). ...
Terrestrial diatom communities are dynamic, partially unknown and potential bioindicators of the soil ecological quality. Many different sampling methods for soil algae can be found in the literature. However, so far none of them have been tested for their performance with soil diatom communities and given recommendations for obtaining a representative diatom sample for bioindication purposes. The aim of this study was to develop a standardized sampling protocol for terrestrial diatoms and test the spatial variability of the communities to ensure the representativeness of the samples obtained. Sampling was performed in four different sampling sites in the Attert River basin (NW Luxembourg), using metal cylinders (Ø 5.6 cm) to extract soil cores. Our objective was to determine whether a single cylinder or a mix of several is needed to obtain a representative sample of the community of a certain site. Different statistical analyses (ANOVA, PerMANOVA and Mantel test) have been carried out to assess the reliability of the sampling method and give some recommendations for a routine sampling. Inside each site, no differences were found between single and mixed samples for their species composition or diatom-based quality index values. However, the species richness and diversity had significant differences in the only natural (forest) sampled site. The method here presented has proven to be useful for obtaining representative soil diatom samples and its use is recommended following the advices presented in this work.
... Therefore, it seems reasonable to think that their use could be equally widespread. Recent research is making the use of soil diatoms more popular in two principal areas: as indicators of anthropogenic disturbances in different ecosystems ( Dorokhova 2007;Heger et al. 2012;Fazlutdinova and Sukhanova 2014;Vacht et al. 2014;Antonelli et al. 2017;Blanco et al. 2017) and as hydrological tracers to assess terrestrial-aquatic connectivity ( Pfister et al. 2009;Klaus et al. 2015;Martínez-Carreras et al. 2015;Coles et al. 2016). The applications of these organisms are just awakening the awareness of their potential, and so are the sampling methods. ...
The analysis of samples taken in different aerial microhabitats in Europe (Germany and Luxembourg) revealed the presence of a new and interesting small-celled naviculoid diatom species. Based on detailed light and scanning electron microscopy, one taxon previously misidentified as Sellaphora saugerresii is here described as Mayamaea petersenii sp. nov. The ecological preferences and a detailed analysis of its frustule ultrastructure lead to propose its generic placement in Mayamaea, followed by a discussion concerning key characters of the genera Sellaphora, Eolimna and Chamaepinnularia.
... Protist communities differed significantly between all treatments one-year post application. Organic fertilizer-treated soil contained a fundamentally different protist community structure compared (Heger et al., 2012;Murase et al., 2015). Organic fertilizer (OF) amendment enhanced the relative abundance of the most abundant protist taxonomic groups, that is, Stramenopiles, Alveolata, Rhizaria, Excavata and Amoebozoa (Figure 1b), most of which are predators of other microbes. ...
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
... Furthermore, information on dynamics and quantities of different BSi pools will be helpful for the evaluation of anthropogenic influences on Si cycling (e.g., Struyf and Conley, 2012). In general, land-use changes have been recognized as important human influences on (especially phytogenic) BSi (e.g., Keller et al., 2012), but there are no studies on, e.g., protophytic or protozoic Si pools, although soil diatoms and TA were found to be promising bioindicators in agricultural soils (Heger et al., 2012). ...
... This may reflect the greater increase in nutrient availability provided by manure treatments, which are known to primarily affect bacterial communities but have indirect effects on predatory protists (Frosteg ard et al. 1997). It was also suggested that both mineral (NPK) and organic (farmyard manure) fertilization affect the community composition of diatoms and testate amoebae (Heger et al. 2012), although no comparison to unfertilized soils was undertaken in this study. Notably, our results contradict those of previous studies on fungal communities in the surface layers of farmyard manure-amended soils. ...
Corlissina maricaensis gen. nov., sp. nov. was obtained from samples of sediment collected in a brackish lagoon of Maricá city, in Rio de Janeiro state. The morphological description was based on live observations, after protargol staining, and scanning electron microscopy. The new species has a cylindrical body shape that is slightly contractile, 230-550 × 35-65 µm in size, a cytoplasm with many globular inclusions, one row of irregular cortical granules between each somatic kinety, approximately 40-62 somatic kineties, two globular macronuclei measuring 9-24 µm and one micronucleus of approximately 4-9 µm. A subapical oral cavity was approximately 20-80 × 9-25 µm, with an adoral zone on the left side of the buccal field, which was composed by 32-60 polykineties and a paroral at right side that was composed by 40-57 short polykineties. The new genus is distinguished from other geleiids by a loop-shaped posterior end of the paroral ciliature, constituted by two rows of short polykineties, and the oralization of the central superior kinety (K0i), forming a row of dikinetids that internally borders the adoral zone, followed by several rows of monokinetids. In the phylogenetic analyses, the new species was recovered as the sister group of Parduczia orbis with full support values based on 18S rDNA gene sequences. This work also indicates some problems in the definitions of Geleiidae and proposes a new diagnosis for this karyorelictid family.
... Lara 2011). Heger et al. (2012) have already suggested this may turn out to be a more time efficient approach when using both testates and diatoms to monitor the state of agricultural soils. Another potential advantage with this approach is that it could allow the use of other protist (or prokaryotic) taxa which are more difficult to identify during direct counts under a microscope. ...
The nature conservation, and wider environmental importance of peatlands, particularly in relation to carbon management, has led to there being a growing interest in attempting to manage degraded peatlands in a way that will restore them to fully functioning peatland ecosystems. Much of this management is concerned with the rewetting of these sites therefore it has become important to monitor the surface wetness of these bogs and if possible compare current wetness with previous, pre-damage, conditions. We present previously unpublished case studies of the use of testate amoebae to monitor bog restoration schemes in N.W. England (Holcroft Moss, Cheshire) and Ireland (Ardagullion Bog, Co. Longford). In addition we summarise the key conservation related conclusions of our previously published work on two other sites in N.W. England - Astley Moss (in the Chat Moss complex of Greater Manchester) and Danes Moss (Cheshire). At Holcroft the record of lead pollution from the peat core allows us to date recent changes in the testate community preserved in a peat core and relate these to both conservation management and other changes in the landscape around the bog in over the last 50 years. Ardagullion Bog provides an illustration of the utility of using multiple peat cores in the testate monitoring of peat bog restoration and illustrates that a bog that has only suffered limited 'damage' is able to be restored to something close to pre damage conditions on a decadal time scale. We also summarise what we see as the main lessons from testate studies of bog restoration - both from the case studies described in this paper and from the wider literature - and discuss the conditions under which testate amoebae may be of particular use in peatland restoration.
... One difficulty highlighted by this study was the very time-consuming nature of identifying and counting diatoms and testate amoeba by direct counts of soil slides. Because of this Heger et al. (2012) suggested that molecular methods may be the way forward in this area. Diatoms are not the only eukaryotic algae found in soils, indeed often green algae are the most common soil algal group -even more common than cyanobacteria (Zancan et al. 2006). ...
This essay introduces the special issue of this journal on the ecology of soil protists. This issue marks approximately the first 100 years of soil protistology as a discipline as some of the first studies to show that protozoa were an important part of soil ecology took place at Rothamsted, in southern England, towards the end of the first decade of the twentieth century. Much of the work on soil protists - and indeed the papers in this special issue - concentrate on traditional protozoa. In addition it is now realised that slime molds (eumycetozoans) can potentially make an important contribution to the numbers and diversity of soil amoebae. We also argue that diatoms and other algae are likely important in soils and in need of more detailed study. By its nature microbiology (including soil protist ecology) is a science limited by technology - for example the subject could not really exist before the invention of the microscope. We suggest ways in which newer technologies (molecular methods, stable isotopes etc.) may contribute to future studies on the ecology of soil protists.
... A particular motivator for greater quantities of fundamental research has been the increasing recognition of the potential of TA as bioindicators (Payne 2013). TA have been shown to respond to a long list of anthropogenic factors ranging from air pollution (Meyer et al. 2012), to farming systems (Heger et al. 2012), to chemical weapons disposal (Stoiko et al. 2006). Although most research remains restricted to demonstration studies there is considerable potential for TA to be used routinely in a variety of biomonitoring applications (Payne 2013). ...
Testate amoebae are an abundant group of microorganisms which make a significant contribution to the diversity of protist life. Most of the world's potential habitats for testate amoebae have been barely studied and when such places are investigated they frequently reveal novel communities and species. Here we consider the testate amoeba communities associated with boreal forest epiphytes (mosses and lichens); an environment which we argue has been under-researched. We present a dataset of 165 samples from four regions of western Russia and analyse these data in relation to micro-habitat position and selected environmental data. The testate amoebae of epiphytes are abundant but dominated by ubiquitous species. We show that there are trends toward a lower species richness and test concentration with greater elevation on the trunk and in lichens compared to mosses. There are considerable differences in community composition between sampling regions. Of all measured environmental variables only moisture content showed a significant relationship with testate amoeba community structure. Our data highlight how little is known about testate amoeba communities of this habitat and call for greater research efforts, particularly in less-studied regions and biomes.
... As noted above, Widmer et al (2006) had earlier 539 similarly found within this trial bacterial community structure to be only weakly 540 influenced by farming system, when compared to the effects of manure and crop 541 rotations. The DOK long-term trial also recently provided an opportunity to conduct one 542 of the few studies to date on farming system influence on protists (Heger et al., 2012). 543 While results were based on a spring sampling alone, testate amoebae (Arcellinida and 544 Euglyphida) and diatoms (Bacillariophyta) appeared to respond to farming system 545 treatments. ...
... This may reflect the greater increase in nutrient availability provided by manure treatments, which are known to primarily affect bacterial communities but have indirect effects on predatory protists (Frosteg ard et al. 1997). It was also suggested that both mineral (NPK) and organic (farmyard manure) fertilization affect the community composition of diatoms and testate amoebae (Heger et al. 2012), although no comparison to unfertilized soils was undertaken in this study. Notably, our results contradict those of previous studies on fungal communities in the surface layers of farmyard manure-amended soils. ...
In order to understand the fine scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long term fertilization experiment. We performed PCR-amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced and a total of 88,706 quality filtered reads were clustered in to 1,232 operational taxonomic units (OTU) across the six datasets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There was only little differences in OTU richness observed between organic- (farmyard manure), mineral- and non-fertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all datasets other than that generated using the universal eukaryotic 18S rRNA primers, whereas mineral fertilization had only a minor effect. In addition, a co-occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, e.g. between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels.This article is protected by copyright. All rights reserved.
... In this section, Imfeld and Vuilleumier [5] give an overview of current research and critical issues on the responses of soil bacteria to pesticide exposure, and discuss the most useful techniques for quantifying the diversity and resilience of soil bacterial communities exposed to pesticides. Heger et al. [6] compare the impacts of organic and conventional farming practices on testate amoebae and diatoms in a long-term trial. In another study, Liu et al. [7] examine the dynamics of nematode communities and functions (decomposition) in soils subject to treatments with heavy metal (copper) or pest control chemical treatment (chloroform fumigation ), and/or heat and drying shocks. ...
Soils are home to a vast and still poorly known diversity of
organisms that perform essential ecosystem functions. Soil
communities also respond to and can reflect ecological gradients
and perturbations, including direct and indirect human impact
[1,2]. Soil quality indicators are physical, chemical, and biological
properties, processes, and characteristics that can be
measured and interpreted to monitor patterns and changes in
the soil.
Among the different soil quality indicators, bioindication, the
use of the information contained in the biological properties and
processes, represents a powerful approach for assessing and interpreting
the impact of natural or anthropogenic perturbations in
soil ecosystems. Living organisms provide information on the
cumulative effects of environmental stressors and as such bioindication
is complementary to direct physical and chemical
measurements. Bioindication is thus a highly valuable tool for
soil managers.
An important challenge for soil scientists and managers is to
distinguish “real” changes in soil quality from the background
generated by the “natural” soil heterogeneity and dynamics. Determining
the sensitivity and resolution of bioindicators requires in
depth descriptive and experimental studies, and of course knowing
the identity of the organisms, which, for soil organisms, is certainly
not trivial.
This special issue illustrates how soil organisms can provide
valuable information on the status and functioning of a soil, and
how this information can be used to assess the impact of environmental
stress and human activities on soils. The contributions in
this issue bring new insights into the development and application
of bioindication systems, in a multi-disciplinary perspective toward
improving our current understanding of bioindication in soil
ecosystems.
This special issue includes fifteen research studies and reviews i)
on the response of different taxonomic and functional groups of soil
organisms (Fig. 1) to natural ecological perturbations and anthropogenic
gradients, ii) on the selection of bioindicators across
different taxonomic groups, and iii) on the integration of biodiversity
indices and on methods and new approaches to characterize
organism diversity and community structure in soils. Several articles
highlight the usefulness of integrative approaches that
combine different methods and groups of organisms to assess the
status of soils. When measuring and interpreting the response of
soil organisms, these approaches often benefit from on-going
advances in molecular ecology, including high-throughput DNA
sequencing and metagenomics.
Microalgae have a great potential for enzyme synthesis for several applications in the industry; hence, they are referred to as biofactories. In comparison with other microbial cells, microalgae have the advantage of having a photoautotrophic attribute with minimal nutritional requirements. Enzymes are widely investigated in aquatic microalgae while some of them are studied to explore their abundance in soil and their role in the environment like laccases in green algae. The group of taxa that demonstrate Laccase enzyme activity includes taxa Tetracystis sp., Trebouxia sp., Scenedesmus sp., Chlamydomonas sp., Chlorococcum sp., Nostoc muscorum, and Chlorella vulgaris. Nostoc ellipsosporum are significantly responsible for phenolic/pesticide degradation. For example, enzymes for biodiesel production and for the production high-value-added lipids (acyl-CoA diacylglycerol acyltransferase in Chlorella ellipsoidea) and enzymes utilized in healthcare applications (polytone synthase, l-asparaginase, Lycopene β-cyclase, β-Carotene Oxygenase, found in Chlamydomonas reinhardtii, Chlorella vulgaris). Enzymes like glutathione reductase, dismutase, and laccases play significant role to removing toxic metals, pesticides, and phenolic pollutants. This environmental breakdown of phenolic pollutants contributes as a fundamental process of biodegradation. The source of these enzymes is the group of algal taxa includes Scenedesmus sp., Chlorella sp., Trebouxia sp. This chapter is an attempt to achieve the objective of “state-of-the-art” enzymes by illustrating the methods and enzymatic regulations and focusing on the microalgal enzymes in industrial, health, or environmental applications.
Since research began in diatom ecology, scientists have focussed more on diatoms from aquatic habitats as opposed to aerial habitats. In this paper, we present the first dataset on diatoms from aerial habitats in the Indo-Burma hot spot. We have chosen the Blue Mountain region to collect tree mosses, an aerial habitat where diatoms thrive. We have addressed diatom composition and diversity in relation to altitude. Twenty-two moss samples were collected and 53 diatom taxa belonging to 21 genera were discovered and enumerated using light microscopy. The diatom flora of tree mosses is dominated by acidophilous genera Eunotia and Luticola, with both of the most abundant species Orthoseira roeseana and Luticola acidoclinata being euaerial and oligotraphentic diatoms. The samples from 1902-m altitude had the highest species diversity. Species richness was 8–22 diatom per sample, with an average of 14. The species accumulation curve shows that more diatom species will be discovered with additional sampling of aerial habitats in the Blue Mountain region.
The productivist model implemented after the second world war has succeeded in improving production to meet growing demands for food, but it has also deeply affected soil physicochemical properties, as well as of aboveground and belowground biodiversity. Alternative farming systems such as organic farming, biodynamic farming and soil conservation farming are actually developing to enhance the sustainability of farming systems. Although the impact of agricultural practices on soil ecological quality is well known, there is little knowledge on the impact of the different farming systems as a whole. Here, we analysed the impact of the main farming systems on soil biodiversity and functioning, reported in about 100 scientific publications. We found that conventional, organic, and biodynamic systems are the most widely studied, whereas soil conservation farming is poorly documented. Soil biological indicators are improved by ca. 70% in organic farming and biodynamic farming relative to conventional farming. 43% of soil bioindicators are improved in biodynamic farming relatively to organic farming. Soil conservation farming scores better than conventional farming for 57% of the indicators. Therefore, biodynamic farming displays the highest soil ecological quality, followed by organic farming, soil conservation farming and, last, conventional farming. Organic fertilisation and longer crop rotations are the most favourable practices, whereas pesticides and soil tillage are the most deleterious ones. The review also evidences a lack of studies on soil conservation farming and on bioindicators of the soil fauna.
New Zealand (NZ) is a well-known hotspot of biodiversity and endemism for macroscopic organisms, but its microbial diversity is comparatively poorly documented. We assembled all records on NZ testate amoebae published since the early 20th century and present a comprehensive taxonomic checklist for NZ. Testate amoebae are reported from six major habitat types across both the North and South Islands of NZ, but the sampling effort is ecologically and geographically biased in favour of wetlands and the South Island. As a result, 93% of all 128 morphotypes recorded in NZ occur in wetlands, 28% are restricted to the South Island, and diversity is greater at higher latitudes. Around 50% of morphotypes have a broad latitudinal distribution across the NZ mainland, whereas 15% have narrow latitudinal ranges. Future research should aim to broaden the geographical and ecological ranges. We predict that our list of NZ testate amoebae will expand substantially with future work, and that the latitudinal diversity gradient will be inverted. We also introduce an interactive, fully illustrated, online Lucid key for the rapid identification of NZ testate amoebae. As many morphospecies are cosmopolitan, this key provides a useful tool for testate amoebae identification in other parts of the world.
This chapter provides identification keys to free-living ciliates, amebida, and flagellated protozoa. Special detail is included for Ciliophora and Amoebida. Also, information on preparation methods, definition of the most relevant morphological terms, and current limitations in our knowledge of the group are provided. Additional information on the “Ecology and General Biology” of Protozoa can be found in Volume I of this book series (Thorp and Rogers, 2015, Elsevier).
Diatoms are remarkable organisms. They are present in almost all habitats containing water (e.g., lakes, streams, soils, bark) and rank among the most common algal groups in both freshwaters and marine ecosystems. The ubiquitous character of aquatic diatoms has triggered countless applications as environmental tracers for studies in water quality, paleoclimate reconstruction and sediment tracing. However, diatoms also occur in the terrestrial environment. It is this plethora of diatom life‐forms that has recently triggered interest in their use as tracers of hydrological processes. The use of diatoms in catchment hydrology has been very limited. Part of the reason is that until recently, the taxonomy and ecology of terrestrial diatom assemblages were largely unknown. However, in the past decade, much work has been done to quantify terrestrial diatom reservoir size, dynamics, and potential depletion following precipitation events. Therefore, such terrestrial diatoms now hold promise for use in catchment hydrology—for tracing runoff flow sources and pathways across a wide range of spatial scales. Here we review the literature on terrestrial diatoms and describe the various sampling protocols that have been designed and tested for specific applications in hydrological processes research. We review and summarize the work on terrestrial diatom reservoir characterization, transport mechanisms and pathways to show how such diatom‐based tracer work might be possible at the catchment scale for rainfall‐runoff studies. Finally, we present a vision for future work that might take advantage of terrestrial diatoms in catchment hydrology and discuss the main challenges going forward. WIREs Water 2017, 4:e1241. doi: 10.1002/wat2.1241
This article is categorized under: Science of Water > Hydrological Processes
Science of Water > Methods
A large amount of studies focuses on aquatic diatoms’ ecology and their use in the assessment of water quality. Little is known about terrestrial diatoms’ ecological behaviour and sensitivity to environmental factors. We hypothesise that terrestrial diatom communities can serve as a proxy of anthropic disturbance levels in terrestrial sites. To test our hypothesis, we apply an aquatic index to soil communities that is to deliver new information on the physiographic controls on soil diatoms. Diatom and soil samples were collected in the Attert River basin in Luxembourg during three seasons, in sites characterised by different combinations of geological, soil (schist, marl and sandstone) and land use (forest, grassland and agriculture) features. We found an effect of seasonality on soil diatom communities, reflected by different species dominance and abundances in samples during the three seasons. Soil pH and land use (which translates in a different amount of total carbon and nitrogen in soil) were identified as the variables having the largest impact in structuring the communities and as among the features with the highest importance in defining the ecological status of the sites (i.e. disturbed farmlands having higher pH and lower carbon and nitrogen content). However, the lack of information about the sensitivity of some of the most abundant terrestrial species in our study area caused some discrepancies between the expected (i.e. forested areas with low anthropic disturbance) and the obtained results, with several forested sites classified as having high anthropic disturbance. These results suggest that soil communities are likely to contain information about soil ecological status and highlight the importance of a better characterisation of terrestrial diatom species for developing a quality index based on soil communities.
Soil protists play fundamental roles in many earth system processes, yet we are only beginning to understand the true diversity of the organisms involved. In this study we used conventional (microscopy-based) methods to characterise the diversity and estimate protist population sizes in soils from a variety of distinct habitats within Mere Sands Wood nature reserve in NW England. We produced population size data for over ninety soil protists belonging to two major eukaryotic functional groups: testate amoebae (TA) and diatoms, adding substantial ‘cryptic diversity’ to the nature reserves recorded biota. From these population size data we estimated relative contributions of TA and diatoms to soil biogenic silicon (BSi) pools and found significant correlations between taxon richness and the TA and diatom Si pool. This could indicate that protist functional diversity can influence terrestrial BSi pools, especially in early successional plant communities where TA and diatoms can potentially increase Si mineralisation and/or create Si ‘hot spots’ and hence, the biological availability of this element for subsequent plant uptake. TA were particularly abundant in mor humus type soils further supporting the idea that they could be important players in nutrient cycling in such soils. Overall, we demonstrate this is a useful approach in order to start to attempt to estimate the role of protists in the Si cycle and other ecological processes.
To introduce the special issue this paper reviews the use of protists as bioindicators. Seven key advantages of protist bioindicators are highlighted, namely: environmental sensitivity, functional importance, distribution, size and numbers, response times, ease of analysis and preservation potential. Protist bioindicators have been used in a wide range of contexts from monitoring ecosystem restoration to fire history, and particularly environmental pollution. Most major protist groups have been used as bioindicators with diatoms, foraminifera and testate amoebae particularly widely studied. To increase uptake of protist bioindication methods in routine environmental monitoring technique development should consider the needs of stakeholders from an early stage. Papers in this special issue reflect the diversity of both protist life and possible bioindicator applications.
Soil microalgae live on small communities that change structure depending on many factors. Some of these factors include soil pH, agricultural practices as well as pesticide and herbicide treatments. The size and activity of these soil microbial communities is an indicator of health, quality and fertility necessary for sustainable agriculture. Methods: A commercial proprietary suspension of microalgae GOgreen® was applied at different concentrations through a center pivot irrigation system to a crop of cultivated corn (Zea mays) during six months. Experimental plots of 0.5 acres each were planted in four rows. Corn (34,000 plants/acre) was planted in May and harvested in November allowing each plot to be studied for 6 months. In addition, one plot was planted for a second year to study the effects of consecutive planting and harvesting on algae populations in the soil. Soil samples were collected at a depth of 6 inches. Microalgae species identification was based on morphological criteria. Soil analysis included organic matter content (OM), pH and cation exchange capacity (CEC). Results: Treatment with GOgreen® has significant and measurable positive effects on soil OM content, CEC, pH and microalgae species diversity. Conclusions: It was demonstrated through this study that GOgreen® increased diatom numbers and microalgae species diversity showing a restorative effect on soil quality after herbicide treatment in heavily farmed soil. Additionally, GOgreen® lowers the pH in soils with a pH higher than 7.0 emerging as an economical alternative that is safe for humans and the environment.
A total of 66 algal species representing 32 genera were recovered from soils of 10 sites in the Catavifia region of the Central Desert of Baja California, Mexico. The most common species encountered were the cyanophytes Nostoc commune and Schizothrix calcicola, the chlorophyte Myrmecia astigmatica, and the diatoms Hantzschia amphioxys, Hantzschia amphyoxys f. capitata, Luticola cohnii, Luticola mutica, and Pinnularia borealis var. Scalaris. Nine species not found in any previous studies of North American desert soils were present in our study sites, including 3 taxa new to science: Cylindrocystis brebissonii var. deserti, var. nov.; Elakatothrix obtusata, sp. nov.; and Fasciculochloris mexicana, sp. nov. Attempts to correlate species composition with soil chemical and physical parameters were unsuccessful apart from a pH effect on cyanobacterial distribution. Overall composition of the soil algal community in the Catavifia region is distinct from other desert sites we have studied, although some cosmopolitan desert soil taxa were present.
1. We studied vascular plant and soil‐dwelling testate amoeba communities in deglaciated sites across a range of substrate ages in Kenai Fjords, Alaska, USA to test four hypotheses. (i) Patterns of community assembly are similar for vascular plants and testate amoebae. (ii) Vascular plant and testate amoeba communities are more strongly correlated to abiotic variables than to each other, since these communities are not directly linked trophically. (iii) Plant community structure becomes less associated with abiotic condition in succession relative to testate amoebae, as species replacement is believed to be more common for plants than testate amoebae. (iv) Above‐ and below‐ground communities become more strongly linked over the succession, due a shift from predominantly allogenic to autogenic forces.
2. We assessed relationships among biotic communities and abiotic site variables across the chronosequence using multiple factor analysis, redundancy analysis (RDA) and a moving‐window analysis.
3. The diversity patterns and the communities’ response to site and soil variables differed between groups. The composition of both communities was significantly explained by bedrock type and moisture regime. The vascular plant community, however, was more influenced by distance from the glacier.
4. Testate amoeba and vascular plant community patterns were significantly linked to each other and to location and physical conditions. The moving‐window RDA indicates the variation explained by the physical and chemical environment tended to slightly decrease through the chronosequence for testate amoebae, while a bell‐shape response was evidenced for vascular plants. The variation of the microbial community explained by the plant community was very low in the early stages of the succession and became higher than the variation explained by the environmental variables later in the chronosequence.
5. Synthesis. These results suggest that vascular plants and testate amoebae are as linked or more in ecosystem development than either community is to changes in site condition. Furthermore, the strength of interactions varies along the succession. Thus, ecological links may be more important than macro‐scale abiotic site condition is to community development, even between communities without direct trophic interactions.
Soils differ from aquatic sediments in environmental characteristics such as moisture availability and temperature fluctuations, and it is therefore believed that soil-inhabiting diatoms have a broader tolerance range to these stresses than aquatic diatoms. To test this hypothesis, we assessed the survival capacities of vegetative cells of 34 benthic diatom species from terrestrial and aquatic habitats in Belgium when exposed to desiccation and temperature stress. Six different stress conditions were studied: gradual heating up to +30 degrees C and +40 degrees C, abrupt heating to +40 degrees C, freezing. to -20 degrees C and desiccation with and without preconditioning at +30 degrees C. All six conditions resulted in a significantly decreased survival of cells compared to control conditions. Desiccation killed all tested strains, freezing was survived by only three species and abrupt heating was significantly more lethal than gradual heating, suggesting a generally high sensitivity of vegetative diatom cells to these three stress factors. While tolerance to temperature extremes (+40 degrees C and -20 degrees C) was to a large extent species-specific, habitat-specific differences in cell survival were also detected. Only terrestrial species survived freezing, and aquatic diatoms were less tolerant to gradual heating to +40 degrees C, both pointing at a higher tolerance of terrestrial diatoms to temperature extremes. Moreover, in two species with both aquatic and terrestrial isolates, only the terrestrial strains survived +40 degrees C. We conclude that vegetative cells of benthic diatoms (1) are very sensitive to desiccation, freezing and abrupt heating and (2) have a habitat-dependent tolerance to temperature extremes. The consequences of these observations for the dispersal capacities and the subsequent biogeographical patterns of diatoms are discussed.
Soil algae are photosynthetically active microorganisms showing changeable community structure, depending on the soil type, the agricultural practices and the application of pesticides. To characterise algal community structure, molecular approaches complementary to classical microbiological approaches based on the isolation and the culture of soil algae are required. Our study describes a polymerase chain reaction (PCR) approach targeting algal 18S rDNA sequences of desoxyribonucleic acid (DNA) samples extracted either from unialgal eukaryotic microalgae culture, complex assemblages of microalgae populations or natural soil communities. Our first results showed that microalgae rDNA can be amplified by PCR from soil DNA samples. They also indicated difficulties extracting DNA from diatoms directly from soils, probably because of the presence of robust silicate valves. An 18S rDNA library has been established and preliminary phylogenetic analysis showed the feasibility of applying molecular methods to studying edaphic algae community structure. This is promising for soil algae ecology and for developing soil biological indicators.
This paper examines how to obtain species biplots in unconstrained or constrained ordination without resorting to the Euclidean distance [used in principal-component analysis (PCA) and redundancy analysis (RDA)] or the chi-square distance [preserved in correspondence analysis (CA) and canonical correspondence analysis (CCA)] which are not always appropriate for the analysis of community composition data. To achieve this goal, transformations are proposed for species data tables. They allow ecologists to use ordination methods such as PCA and RDA, which are Euclidean-based, for the analysis of community data, while circumventing the problems associated with the Euclidean distance, and avoiding CA and CCA which present problems of their own in some cases. This allows the use of the original (transformed) species data in RDA carried out to test for relationships with explanatory variables (i.e. environmental variables, or factors of a multifactorial analysis-of-variance model); ecologists can then draw biplots displaying the relationships of the species to the explanatory variables. Another application allows the use of species data in other methods of multivariate data analysis which optimize a least-squares loss function; an example is K-means partitioning.
A index for monitoring the trophic status of rivers based on diatom composition (‚trophic diatom index’, TDI) has been developed,
in response to the National Rivers Authority (England & Wales)'s needs under the terms of the Urban Wastewater Treatment Directive
of the European Community. The index is based on a suite of 86 taxa selected both for their indicator value and ease of identification.
When tested on a dataset from 70 sites free of significant organic pollution, this index was more highly correlated with aqueous
P concentrations than previous diatom indices. However, where there was heavy organic pollution, it was difficult to separate
the effects of eutrophication from other effects. For this reason, the value of TDI is supplemented by an indication of the
proportion of the sample that is composed of taxa tolerant to organic pollution.
The index was tested on the R. Browney, N-E. England, above and below a major sewage discharge. TDI values indicated that
the effect of inorganic nutrients on the river downstream of the discharge was slight as the river was already nutrient-rich,
but there was a large increase in the proportion of organic pollution-tolerant taxa. This indicates that the river was already
so eutrophic upstream of the discharge that tertiary treatment to remove P would not be effective unless other aspects of
the discharge were also improved.
We investigated the species composition of testate amoebae at three altitudes (1000, 2000 and 3000 m) and two horizons (L and F/H/Ah) of a tropical mountain rain forest in southern Ecuador. A total of 135 species and intraspecific taxa of testate amoebae were found (36 samples). Rarefaction plots suggest that only few more species are to be expected. Species number in the L horizon was at a maximum at 2000 m (109 species) and similar at 1000 and 3000 m (75 and 71 species, respectively). Species numbers in the F/H/Ah horizon were 29, 67 and 48 at 1000, 2000 and 3000 m, respectively. The density of testate amoebae in the L horizon increased significantly in the order 1000<3000<2000 m with 3147±129, 9198±144 and 12,497±1317 ind. g−1 dry matter and in the F/H/Ah horizon with 176±25, 3118±97 and 4986±102 ind. g−1 dry matter, respectively. The significant Horizon×Elevation interaction reflects the exceptionally low abundance of testate amoebae in the Ah horizon at 1000 m. The results suggest that species richness of testate amoebae does not decrease continuously with elevation; rather, it peaks at an intermediate elevation. Further, the data suggest that diversity, but not density of testate amoebae in tropical forests exceeds that in temperate forests. Morphological features of testate amoebae reflected semiaquatic habitat conditions. The great majority of testate amoebae species of the studied tropical mountain rain forests are geographically widespread, including temperate regions; however 9 of the species (i.e. 6.7%) are considered tropical, some of these species likely represent Gondwana relicts.
Marine and freshwater ecosystems are fundamentally different regarding many biotic and abiotic factors. The physiological adaptations required for an organism to pass the salinity barrier are considerable. Many eukaryotic lineages are restricted to either freshwater or marine environments. Molecular phylogenetic analyses generally demonstrate that freshwater species and marine species segregate into different sub-clades, indicating that transitions between these two environments occur only rarely in the course of evolution. It is, however, unclear if the transitions between freshwater and environments characterized by highly variable salinities, such as the marine supralittoral zone, are also infrequent. Here, we use testate amoebae within the Euglyphida to assess the phylogenetic interrelationships between marine supralittoral and freshwater taxa. Euglyphid testate amoebae are mainly present in freshwater habitats but also occur in marine supralittoral environments. Accordingly, we generated and analyzed partial SSU rRNA gene sequences from 49 new marine/supralittoral and freshwater Cyphoderiidae sequences, 20 sequences of the Paulinellidae, Trinematidae, Assulinidae, and Euglyphidae families as well as 21 GenBank sequences of unidentified taxa derived from environmental PCR surveys. Both the molecular and morphological data suggest that the diversity of Cyphoderiidae is strongly underestimated. The results of our phylogenetic analyses demonstrated that marine supralittoral and freshwater euglyphid testate amoeba species are segregated into distinct sub-clades, suggesting that transitions between these two habitats occurred only infrequently.
Testate amoebae are an abundant and diverse polyphyletic group of shelled protozoa living in aquatic to moist habitats ranging from estuaries to lakes, rivers, wetlands, soils, litter, and moss habitats. Owing to the preservation of shells in sediments, testate amoebae are useful proxy indicators complementary to long-established indicators such as pollen and spores or macrofossils. Their primary use to date has been for inferring past moisture conditions and climate in ombrotrophic peatlands and, to a lesser extent, to infer pH in peatlands and the trophic or nutrient status of lakes. Recent research on these organisms suggests other possible uses in paleoecology and ecology such as sea-level reconstruction in estuarine environments, as indicators of soil or air pollution, and monitoring recovery of peatland. We review the past and present use of testate amoebae, the challenges in current research, and provide some ideas on future research directions.
An understanding of agroecosystems is key to determining effective farming systems. Here we report results from a 21-year study of agronomic and ecological performance of biodynamic, bioorganic, and conventional farming systems in Central Europe. We found crop yields to be 20% lower in the organic systems, although input of fertilizer and energy was reduced by 34 to 53% and pesticide input by 97%. Enhanced soil fertility and higher biodiversity found in organic plots may render these systems less dependent on external inputs.
Previous work has shown considerably enhanced soil fertility in agroecosystems managed by organic farming as compared to conventional farming. Arbuscular mycorrhizal fungi (AMF) play a crucial role in nutrient acquisition and soil fertility. The objective of this study was to investigate the diversity of AMF in the context of a long-term study in which replicated field plots, at a single site in Central Europe, had been cultivated for 22 years according to two "organic" and two "conventional" farming systems. In the 23rd year, the field plots, carrying an 18-month-old grass-clover stand, were examined in two ways with respect to AMF diversity. Firstly, AMF spores were isolated and morphologically identified from soil samples. The study revealed that the AMF spore abundance and species diversity was significantly higher in the organic than in the conventional systems. Furthermore, the AMF community differed in the conventional and organic systems: Glomus species were similarly abundant in all systems but spores of Acaulospora and Scutellospora species were more abundant in the organic systems. Secondly, the soils were used to establish AMF-trap cultures using a consortium of Plantago lanceolata, Trifolium pratense and Lolium perenne as host plants. The AMF spore community developing in the trap cultures differed: after 12 months, two species of the Acaulosporaceae (A. paulinae and A. longula) were consistently found to account for a large part of the spore community in the trap cultures from the organic systems but were found rarely in the ones from the conventional systems. The findings show that some AMF species present in natural ecosystems are maintained under organic farming but severely depressed under conventional farming, indicating a potentially severe loss of ecosystem function under conventional farming.
L'objet de ce guide méthodologique fournit à l'utilisateur l'ensemble des éléments nécessaires à la mise en oeuvre de l'Indice Biologique Diatomées ou IBD, conformément à la norme AFNOR homologuée T90-354. Ce guide se compose de deux parties : la première détaille les différentes étapes du calcul de l'IBD, depuis l'échantillonnage des diatomées jusqu'à l'exploitation des résultats. Le calcul de l'indice étant relativement complexe, une macro-commande Excel a été réalisée. Sont également fournies dans cette partie quelques adresses pour l'achat de matériel et d'ouvrages ainsi que des contacts utiles. La seconde est consacrée à la détermination des diatomées. Elle comprend une clé de détermination originale, spécifique à l'IBD, sous la forme de planches photographiques en couleurs. Elle donne pour un utilisateur plus exigeant une liste de nombreux ouvrages d'identification des diatomées des eaux continentales en langue française, anglaise et allemande. Par ailleurs, une version informatisée de la clé de détermination originale sous la forme d'un CDRom bilingue français-anglais utilisable sur Mac et PC est fournie. Intégrant la feuille de calcul Excel, ce cédérom permet outre la détermination des diatomées spécifiques à l'IBD, le calcul de l'indice.
Number of species, densities of living individuals and empty shells decreased with compression. Production and mortality were maintained at a low level. -from Author
Lenacil showed a higher and longer lasting toxicity than Pyrazon. Its lethal doses in aqueous culture amounted to 0.0148 mg dm- 3 of medium for the blue-green alga Anabaena variabilis, and to 0.023 mg dm-3 and 1.658 mg dm-3, respectively. Both herbicides impoverished the species composition and decreased the density of algal assemblages.-from Author
The native algal flora of an agricultural soil near Potsdam, Germany, was examined parallel to studies on herbicide influence on soil algae. Soil samples were taken every four to eight weeks from September 1994 to September 1995. Algal densities were determined from cultures on agar. Cell densities varied between 34,000 and 161,000 cells per g dry weight of soil, of which up to 15.7% were found to be diatoms. Five diatom taxa could be distinguished: Navicula atomus, N. lacunolaciniata, N. cf. mutica, Hantzschia amphioxys and Nitzschia palea. The most abundant taxon was Navicula lacunolaciniata, a very small and finely structured species known from highly organically polluted rivers, which has not been found in soils before. The other taxa are all known as typical soil algae with high tolerance towards nutritional enrichment, especially nitrogen and phosphorus.
The prokaryotic and eukaryotic algal components of soil were quantified and identified generically over a 17-mo period in 2 successional fields and a climax forest. A correlation of the quantitative and qualitative changes was sought with other biological components (bacteria, actinomycetes and fungi) and major chemical and physical parameters. The highest counts obtained for the eukaryotic algae were 3.3 x 10^7, 2.2 x 10^7, and 1.2 x 10^5 cells/g soil for a 1-yr old field, an 11-yr old field and the forest, respectively. The highest counts obtained for the prokaryotic (bluegreen) algae were 8.2 x 10^5, 2.3 x 10^5 and 1.6 x 10^4 cells/g soil for the same sites. The total number of algae in all 3 sites declined during the summer. There was no further decline in winter. The greatest number algal genera was found in the 1-yr old field, 28 of a total 35 isolated or 80%; fewer were observed in the 11-yr old field and the forest, 57% and 63%, respectively. A predictive model for numbers of soil algae was formed by multiple regression analysis. The significant factors that showed a relationship with the bluegreen algae were pH, time, Mg, precipitation and the eukaryotic algae, R^2 = 45%; significant factors with the eukaryotic algae were time, Mg and the bluegreen algae, R^2 = 37%. Prediction equations were tested against additional data with success.
Investigations were conducted in spruce stands (U1-southeast of the Schwäbische Alb nearby Ulm, Ux - Oberschwaben, Fg - Fichtelgebirge, Ed - Welzheimer Wald, Ks - Südschwarzwald), deciduous forests (V2 - Luzulo-Fagetum, EF - Melico-Fagetum, Au - meadow, Fraxino-Ulmetum) and an orchard (Ow), all sites nearby Ulm.
Soil testate amoebae are cosmopolitan and abundant protozoa, and accumulate silica for reproduction. Their effect on the terrestrial silica cycle, however, has not been quantitatively determined. We found that testate amoebae consumed 55% of silica absorbed by microbes in the incubation experiment. We estimated amoeban biosilica using our present data and published data. Although biosilica preserved by living testate amoebae was as small as 0.45–1.57 kg SiO2 ha−1, annual biosilicification in various forest soils was estimated to range from 10 to 227 kg SiO2 ha−1 yr−1. We concluded that testate amoebae have a high potential as silica consumers and suppliers, and play a role comparable to that of higher plants in the terrestrial silica cycle.
The process of colonization of Antarctic fellfield soils by micro- organisms has two phases: Firstly, the immigration, survival and establishment of microbial propagules thenlselves, and secondly the stabilization of the soil for subsequent colonization and establishment by mosses, lichens and invertebrates. Dominant amongst primary microbial colonizers are the phototrophic cyano- bacteria and algae. Not only do they introduce organic nutrients into the micro- habitat but they also have a structural function. Filaments of several dimensions frequently form a mesh over the surface of the soil. This mesh often has a canopy structure of fine filaments closely admixed with the mineral soil grains, overlain by a layer of broader, longer filaments. This structure may provide a rich grazing zone for micro-invertebrates such as protozoa and nematodes. Microbial filaments, clusters and unicells frequently have mucilaginous sheaths or capsules which may cement mineral grains together and improve soil crust stability. The combination of filaments and mucigel promotes the formation of microbial "rafts" which are dispersed by wind or water. The diverse microbiota of these compound propa- gules is likely to improve their chances of successful colonization of unpopulated soil surfaces. Phototrophic microbes can be distinguished in mixed natural com- munities of undisturbed soil crusts by selective filtration of their autofluorescence spectra. Heterotrophs can be distinguished after staining. The population can be selectively quantified by television image analysis (TVIA) using criteria of pig- mentation, size and morphology.
Biodiversity assessment underpins our understanding of ecosystems and determines environmental management decisions on resource use and conservation priorities. Recently, a new discipline - environmental or ecological genomics (ecogenomics) - has emerged from major advances in sequencing technologies, such as pyrosequencing (a technique based on the detection of pyrophosphate during nucleotide incorporation), and enabled extraordinary progress in the way biodiversity can be assessed. Since 2008, numerous high-impact microbial metagenomic sequencing studies, which have relied on both classical and next-generation sequencing, have been published. As a result, many previously unrecognized taxa and biota have been identified, but none of these studies explored eukaryote diversity. Here, we illustrate the power of applying next-generation pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems.
The number and abundance of algal species were not significantly different between non-topsoiled areas and top-soiled areas. Successional trends were evident at both sites, since the number of species and their abundance increased over time. Soil-algal interactions were determined by regression analysis. A conceptual model was developed that illustrated the influence of soil chemical properties on algal abundance. Important factors affecting the soil algae were sodium, calcium, potassium, magnesium and certain trace elements. The possible influence of these factors on algal growth is discussed.
Forty-eight soil samples were collected from Ile de la Possession, Crozet Archipelago. One hundred sixty-five taxa belonging to 32 genera were recorded. The cluster analysis revealed four assemblages, separated by a moisture and a possible pH-gradient. The Eunotia paludosa var. paludosa assemblage was found on relative wet acid soils, mostly bound to the valleys on the island. The less diverse Diadesmis contenta assemblage is typical for drier soils, occurring on the entire island. Two assemblages, i.e. the Fragilaria maillardii and the Achnanthes confusa assemblage, were found on wetter, non-acid soils. They are separated from each other by the degree of influence of salinity caused by animal transport and/or sea-spray with the F. maillardii assemblage occurring closer to the coastline and the penguin rookeries of the island.RésuméLa flore diatomique des sols de l'île de la Possession (archipel de Crozet) a été examinée dans 48 échantillons. Au total, 165 taxons de diatomées appartenant à 32 genres ont été observés. Une analyse de classification révèle l'existance de quatre communautés, distinguées par un gradient d'humidité et probablement aussi de pH. La communauté de Eunotia paludosa var. paludosa a été trouvée dans des sols acides et relativement humides, comme on en trouve dans les grandes vallées de l'île. La communauté de Diadesmis contenta, moins divers que les autres, est caractéristique des sols secs, présents dans toutes l'île. Les communautés de Fragilaria maillardii et Achnanthes confusa sont retrouvées dans des sols humides et non-acides. Elles se sont séparées sous l'influence de la salinité, due au transport animalier et/ou les embruns et le vent. La communauté de Fragilaria maillardii est plutôt retrouvée près de la zone côtière.
We adapted a direct count method for obtaining counts of active protozoa that was not overly time consuming. Soil samples from an agricultural field were examined at 1- to 3-day intervals three times through the year. The three sampling periods represented different weather conditions. At each sampling event, fresh soil samples were extracted upon return to the laboratory for protozoa. These were enumerated at the microscope without prior culture, in soil–water suspension dilutions. We describe a procedure that allowed all samples to be processed in a few hours. Our results suggest there is good reproducibility and agreement between samples collected on the same day. Our data resolve differences between days as soil conditions changed slowly with drying or wetting. This procedure is suitable for describing species active at the time of sampling. Unlike the ‘most probable number’ procedure that relies on cultivable species, it is less prone to enumerating excysting individuals, and it provides better resolution between sampling dates, with a relatively low number of samples.
Testacea were observed ingesting nematodes in the litter horizons of native forests in New Zealand. Nematodes were most commonly attacked from the tail end but some specimens were attacked at mid-body. Nematodes with damaged tails were recovered in greatest numbers from the highest, wettest site sampled. Nebela (Apodera) vas (Certes, 1989) and Difflugia sp. (possibly lanceolata Penard, 1890) were the predators; both species were redescribed using light and scanning electron microscopy and morphometry. Most damaged nematodes were Ironus sp. but Clarkus, Tobrilus, Iotonchus, Cobbonchus, Dorylaimus and Plectus were also attacked. Literature on testacean feeding strategies was reviewed briefly.
Four herbicides (2,4-D, trifluralin, MCPA and TCA) were applied at two concentration levels to isolated cores of a grassland loam soil. After herbicide contact times of 1, 5, and 20 days, samples were taken and the algal population estimated both quantitatively and qualitatively using two selective mineral salts media. Thirty one genera of algae were identified as occurring in the soil. Of these, Chlamydomonas, Chlorococcum, Hormidium, Palmella, and Ulothrix proved to be so sensitive to the four herbicides that they were rarely isolated from the cores after treatment. Other algal genera were found to be less sensitive, and the theoretical percentile sensitivity of fifteen genera was calculated. Chlorella, Lyngbya, Nostoc, and Hantzschia were found to be the most resistant algae, having percentile sensitivity to all four herbicides of less than 50%. Some algal genera varied in their sensitivity to each of the herbicides. Scytonema was sensitive to all of the herbicides except 2,4-D, while Tolypothrix showed a greater tolerance to MCPA. In the top cm of the soil, the reduction in cell numbers experienced by many algal genera after herbicide treatment was offset by an increase in the population of Chlorella. Stichococcus, Oscillatoria, and Spongiochloris all exhibited the ability to recover rapidly after a reduction in cell numbers resulting from the application of one of the herbicides. An overall reduction in cell numbers was noted for the algae growing preferentially on a nitrogen-free medium (i.e. potential nitrogen-fixers). re]19760511
Algae occur in nearly all terrestrial environments on earth and are invariably encountered both on and beneath soil surfaces.
The algal flora of the soil includes members of the Cyanochloronta, Chlorophycophyta, Euglenophycophyta, Chrysophycophyta,
and Rhodophycophyta. Thirty-eight genera of prokaryotic and 147 genera of eukaryotic algae include terrestrial species, the
majority of which are edaphic. Whereas systematic nomenclature of blue-green algae adheres to traditional classification based
upon morphological features, proper taxonomic treatment of eukaryotic soil algae is predicated on standard methods of culture
and interpretation of physiological attributes, plant mass characteristics, and morphological properties of axenic clones.
While knowledge of the physiological ecology of soil algae is primarily based on laboratory evidence, it is well established
that solar radiation, water, and temperature are the most important abiotic factors governing their distribution, metabolism,
and life history strategies. Biotic interactions are often as important, whereas ionic factors (including pH), oxidation-reduction
potential, and soil texture are less important, if only because their influences are less well understood.
Algae play an important role in primary and secondary plant community succession by acting as an integral part of the colonial
synusium. The principal functional attributes of algal communities in soil include primary production, dinitrogen fixation,
and stabilization of aggregates. Although as many as 108 algae per gram have been documented, soils commonly support between 103 and 104 per gram. As an avenue for the incorporation of carbon and nitrogen and for minimizing erosion through stabilization of aggregates,
algae are valuable in agriculture. Although manipulation of edaphic algal populations in temperate countries is of novel occurence,
their successful use in India as a means for reclaiming saline soils and as a source of fertilizer nitrogen is well documented.
Soil algae are affected by synthetic pesticides and pollutants. In general, most herbicides, fungicides, and soil fumigants
are detrimental to soil algae while most insecticides are not. Algae have been utilized as biological assay organisms for
anticipating crop response to both fertilizers and pesticides because of their biochemical similarity to higher plants and
their quick generation time.
As future research with soil algae leads to a greater awareness of their importance in soil, it might be anticipated that
manipulation of populations in agricultural systems of temperate regions will become more widespread with consideration of
the potential benefits of soil algae made by scientists in other disciplines.
Unter fast allen terrestrischen Bedingungen können Algen vorkommen, ganz besonders auf oder direkt unter den Bodenoberflächen.
Die Algenflora auf den Böden umfaßt unter anderem Vertreter der Cyanochloronta, Chlorophycophyta, Euglenophycophyta, Chrysophycophyta
und Rhodophycophyta. Acht und dreissig Gattungen prokaryotischer und 147 eukaryotischer Algen zeichnen sich durch terrestrische
Arten aus, die meist edaphisch vorkommen.
Während die taxonomische Nomenklatur der Cyanochloronta noch an der auf morphologischen Kriterien beruhenden traditionellen
Klassifikation festhält, basiert die beste taxonomische Behandlung der eukaryotischen Bodenalgen auf Standardmethoden der
Kultur sowie der Auswertung physiologischer Kennzeichen. Morphologische Eigenschaften sollten nur von axenisch kultivierten
Klonen herangezogen werden.
Obwohl unsere Kenntnis der physiologischen Ökologie der Bodenalgen weitgehend durch Laborbefunde erreicht wurde, ist doch
gut belegt, daß die wichtigsten abiotischen Faktoren, die Verbreitung, Stoffwechsel und Lebensstrategie regulieren, Sonnenstrahlung,
Wasser und Temperatur sind. Biotische Interaktionen sind oft von gleicher Bedeutung; Ionen-Bedingungen (einschließlich pH),
Redox-Potentiale und Bodentextur erscheinen vielleicht nur deshalb weniger bedeutungsvoll, weil ihr Einfluß weniger gut verstanden
wird.
Algen spielen eine entscheidende Rolle bei den primären und sekundären Pflanzensukzessionen, da sie ein integraler Teil der
beginnenden Besiedlung darstellen (Kleinlebensgemeinschaften). Die wichtigsten funktionellen Beiträge der Algengesellschaften
umfassen u.a. Primärproduktion, N2-Fixierung und Stabilisierung des Bodens. Bis zu 108 Algen pro Gramm wurden nachgewiesen, doch enthalten Böden pro Gramm meist zwischen 103-104 Individuen.
Für die Agrikultur sind die Algen wegen des Einbaus von Kohlenstoff und Stickstoff wertvoll, ebenso wegen ihrer erosionsmindernden
Eigenschaften. Obwohl die Manipulation von Populationen edaphischer Algen in temperierten Gebieten noch ganz neuartig ist,
wird sie erfolgreich in Indien bei der Wiederbesiedlung saliner Böden und als Quelle gebundenen (Dünger-) Stickstoffs angewendet.
Bodenalgen werden von synthetischen Pestiziden und Verschmutzungen beeinflußt. Im allgemeinen gilt, daß die meisten Herbizide,
Fungizide und Bodenräuchermittel starke Wirkungen haben, viele Insektizide jedoch heine. Algen werden auch als Testorganismen
zur Abschätzung der Effekte von Düngemitteln und Pestiziden auf die Kulturpflanzen verwendet, da sie biochemisch sehr ähnlich
wie die Höheren Pflanzen reagieren und zudem eine kurze Generationszeit haben.
Weitere Forschung an Bodenalgen wird zur verbesserten Kenntnis ihrer Bedeutung führen und es kann erwartet werden, daß ihre
Nutzung sich auch in der Landwirtschaft temperierter Zonen ausbreitet, insbesondere wenn man auch ihre mögliche Verwendung
berücksichtigt, die durch Forschungen anderer Disziplinen angeregt wird.
Organic farming may contribute substantially to future agricultural production worldwide by improving soil quality and pest control, thereby reducing environmental impacts of conventional farming. We investigated in a comprehensive way soil chemical, as well as below and aboveground biological parameters of two organic and two conventional wheat farming systems that primarily differed in fertilization and weed management strategies. Contrast analyses identified management related differences between "herbicide-free" bioorganic (BIOORG) and biodynamic (BIODYN) systems and conventional systems with (CONFYM) or without manure (CONMIN) and herbicide application within a long-term agricultural experiment (DOK trial, Switzerland). Soil carbon content was significantly higher in systems receiving farmyard manure and concomitantly microbial biomass (fungi and bacteria) was increased. Microbial activity parameters, such as microbial basal respiration and nitrogen mineralization, showed an opposite pattern, suggesting that soil carbon in the conventional system (CONFYM) was more easily accessible to microorganisms than in organic systems. Bacterivorous nematodes and earthworms were most abundant in systems that received farmyard manure, which is in line with the responses of their potential food sources (microbes and organic matter). Mineral fertilizer application detrimentally affected enchytraeids and Diptera larvae, whereas aphids benefited. Spider abundance was favoured by organic management, most likely a response to increased prey availability from the belowground subsystem or increased weed coverage. In contrast to most soil-based, bottom-up controlled interactions, the twofold higher abundance of this generalist predator group in organic systems likely contributed to the significantly lower abundance of aboveground herbivore pests (aphids) in these systems. Long-term organic farming and the application of farmyard manure promoted soil quality, microbial biomass and fostered natural enemies and ecosystem engineers, suggesting enhanced nutrient cycling and pest control. Mineral fertilizers and herbicide application, in contrast, affected the potential for top-down control of aboveground pests negatively and reduced the organic carbon levels. Our study indicates that the use of synthetic fertilizers and herbicide application changes interactions within and between below and aboveground components, ultimately promoting negative environmental impacts of agriculture by reducing internal biological cycles and pest control. On the contrary, organic farming fosters microbial and faunal decomposers and this propagates into the aboveground system via generalist predators thereby increasing conservation biological control. However, grain and straw yields were 23% higher in systems receiving mineral fertilizers and herbicides reflecting the trade-off between productivity and environmental responsibility. © 2008 Elsevier Ltd. All rights reserved.
Aim To review published evidence regarding the factors that influence the geographic variation in diversity of soil organisms at different spatial scales.
Location Global.
Methods A search of the relevant literature was conducted using the Web of Science and the author's personal scientific database as the major sources. Special attention was paid to include seminal studies, highly cited papers and/or studies highlighting novel results.
Results Despite their significant contribution to global biodiversity, our taxonomic knowledge of soil biota is still poor compared with that of most above-ground organisms. This is particularly evident for small-bodied taxa. Global patterns of soil biodiversity distribution have been poorly documented and are thought to differ significantly from what is reported above-ground. Based on existing data, it appears that microorganisms do not respond to large-scale environmental gradients in the same way as metazoans. Whereas soil microflora seem to be mainly represented by cosmopolitan species, soil animals respond to altitudinal, latitudinal or area gradients in the same way as described for above-ground organisms. At local scales, there is less evidence that local factors regulate above- and below-ground communities in the same way. Except for a few taxa, the humpbacked response to stress and disturbance gradients doesn't seem to apply underground. Soil communities thus appear weakly structured by competition, although competitive constraints may account for assembly rules within specific taxa. The main factor constraining local soil biodiversity is the compact and heterogeneous nature of soils, which provides unrivalled potential for niche partitioning, thus allowing high levels of local biodiversity. This heterogeneity is increased by the impact of ecosystem engineers that generate resource patchiness at a range of spatio-temporal scales.
This paper emphasizes some aspects of soil protozoology related to agriculture, viz. farming systems, biocides, and biodiversity. Ecofarming slightly increases abundances and biomasses of soil protozoa and stimulates soil life in general. Agroecosystems are more sensitive to conventional farming practices than grasslands, especially under severe climatic conditions, e.g. water stress. The increased soil life under ecofarming is not associated with an increased crop yield. In contrast, yield decreases more or less distinctly. However, the yield loss is usually partially or completely compensated by the reduced operating expenses (energy input) per crop unit. Thus, ecofarming appears to be a useful practice, especially for sustaining biodiversity.
The soil fauna of ecofarmed and conventionally farmed fields and grasslands was investigated in various regions of Austria. The results obtained from the evaluation of a total of 13 paired sites are reviewed in this contribution: (1) many of the investigated soil zoological parameters do not differ statistically in ecofarmed and conventionally farmed fields and grasslands; (2) there are no striking differences in species composition and dominance structure of the protozoa, an important group of indicator organisms due to their delicate external membranes, their short generation time and their high contribution to energy flow and nutrient cycling; (3) all differences which can be guaranteed with an error probability of α = 10% or less invariably show higher biological activity in the ecofarmed plots. The soil physical and chemical investigations which accompanied the zoological studies on some sites indicate that the higher biological activity is caused by the higher humus content and the lower soil compaction. The organic matter content is significantly higher in the ecofarmed plots, whereas soil compaction is more pronounced under conventional cultivation; (4) conventional agriculture has a more detrimental effect on soil fauna in semi-arid regions without stockfarming than in atlantic regions with mixed husbandry. A short review of the literature shows our results to be consistent with those of other studies. It is increasingly evident that generalizations like ‘Conventional farming destroys life in the soil’ or ‘Ecofarming stimulates soil life’ are only partially supported by the available data. A far more comprehensive view taking into account especially climate, soil type and farm management is necessary. However, the discernible detrimental effects on the soil organisms caused by conventional farming call for serious consideration and ought to stimulate the development of soft agricultural technology and intensified soil biological research. Future research should include studies on productivity of soil animals under various management systems, the analysis of single factors (e.g. the special admixtures used in biodynamic farming) to elucidate causative mechanisms, and studies on the relationship between soil animals, crop production and sustained yield.
The population studies of Testacea in an aspen woodland soil revealed 28 taxa of living Testacea, 14 of which were considered constant. The 14 species, while comprising 98 and 96% of the mean annual density and total annual production numbers respectively, accounted for only 80% of the mean annual biomass and 86% of the total annual production biomass. All 14 species had a peak in abundance in autumn, immediately or soon after leaf litter fall. While most species maintained small, active and reproducing populations over the winter period, some maintained higher than normal densities, had seasonal peaks in abundance and biomass, or higher than normal rates of production and turnover. All species had an increase in reproduction and usually in abundance also during the late winter-early spring period before spring thaw. The annual mean weekly density and biomass and the annual production totals tor numbers and biomass were highest in the H layer and lowest in the L. The F layer produced the highest numbers of generations per year and the highest annual mean weekly biomass turnover rate for most of the species. The majority of the periods of high intrinsic rate of natural increase, biomass production and turnover occurred during or after an increase, a decrease or a stabilization in soil moisture content. Mean annual biomass and total annual production were estimated as 0.72 and 206 g wet weight m⁻² respectively. The aspen woodland soil Testacea (in a mor humus) had a much higher production and number of generations per year than Testacea from mull and moder humus forms.
This paper emphasizes some general aspects of soil protozoa as indicators of environmental quality—pros and cons, methods, and diversity. Protozoa are at the base of the heterotrophic eukaryotic food web and an essential component in marine, freshwater, and soil ecosystems because they consume a significant portion (usually >50%) of the bacterial productivity, enhancing nutrient cycles and energy flows to the benefit of microorganisms, plants and animals. Accordingly, studies of their dynamics and community structures provide a powerful means for assessing and monitoring changes in the biotic and abiotic environment. This is exemplified by some representative studies focusing on soil oxygen regime, differentiation of humus types, pesticides, global warming, forest decline, movement of protozoan pathogens in soil, and soil protozoan bioassays. Usually, protozoa are not replaceable by higher animals (meso- and macrofauna) as indicator organisms because they have unique physiological properties: they consume more food and have a higher respiration rate per mass unit, have shorter generation and life times, and reproduce much faster. Direct counting methods should be given preference over dilution culture techniques, which are beset with uncontrollable deficiencies. Thus, ciliates and, especially, testate amoebae, whose abundance and diversity can be reliably estimated in simple soil suspensions, should be preferred in environmental studies. About 1600 protozoan species are known to live in terrestrial habitats. However, data from studies of ciliates suggest that this is only a minor portion (20–30%) of the species actually present, most of which are still undescribed. Overcoming the methodological and taxonomic problems are urgent needs which, at present, limit the use of protozoa as bioindicators in terrestrial environments. Furthermore, species monographs are required to compile the taxonomic, faunistic, and ecological information available.
Species lists and relative species composition of soil diatom assemblages are difficult to obtain because soil diatoms are often sparse and hard to detect among soil particles. Because soil diatoms are usually within the silt size range (5–50 μm), assemblages can be made more observable using soil sieving and sedimentation procedures to remove sand and clay. Diatomaceous silica (opal) can be further concentrated by using heavy liquid centrifugation, but this procedure is expensive, time consuming and involves handling potentially dangerous chemicals. Three fractionation procedures (5–50 μm silt, 5–50 μm opal and 20–50 μm opal) were compared using surface soils from five contrasting desert sites. The 20–50 μm opal method selected against some of the smaller diatom species. The 5–50 μm opal method gave slightly better results than the 5–50 μm silt method. But because results obtained through use of these two methods were highly correlated, the 5–50 μm silt procedure is preferred as a simple, inexpensive alternative to conventional examination methods. We favor sedimentation and concentration methods over culturing techniques because the latter may modify the relative proportions of observed species.
Herbivore damage is generally detrimental to plant fitness, and the evolu- tionary response of plant populations to damage can involve either increased resistance or increased tolerance. While characters that contribute to resistance, such as secondary chem- icals and trichomes, are relatively well understood, characters that contribute to a plant's ability to tolerate damage have received much less attention. Using Helianthus annuus (wild sunflower) and simulated damage of Haplorhynchites aeneus (head-clipping weevil) as a model system, we examined morphological characters and developmental processes that contribute to compensatory ability. We performed a factorial experiment that included three levels of damage (none, the first two, or the first four inflorescences were clipped with scissors) and eight sires each mated to four dams. We found that plants compensated fully for simulated head-clipper damage and that there was no variation among plant families in compensatory ability: seed production and mean seed mass did not vary among treat- ments, and sire X treatment interactions were not significant. Plants used four mechanisms to compensate for damage: (1) Clipped plants produced significantly more inflorescences than unclipped plants. Plants produced these additional inflorescences on higher order branches at the end of the flowering season. (2) Clipped plants filled significantly more seeds in their remaining heads than did unclipped plants. (3) Clipped plants, because they effectively flowered later than unclipped plants, were less susceptible to damage by seed- feeding herbivores other than Haplorhynchites. (4) In later heads, seed size was greater on clipped plants, which allowed mean seed size to be maintained in clipped plants. Although there was genetic variation among the families used in this experiment for most of the characters associated with compensation for damage (seed number, mean seed size, mean flowering date, length of the flowering period, and branching morphology), in analyses of these characters, no sire X treatment interactions were significant indicating that all of the families relied on similar mechanisms to compensate for damage.
Five water samples from three sources, two municipal reservoirs in central North Carolina and Toolik Lake in Alaska, were processed to conduct a comparative survey of microbial small subunit rDNA sequences. Genomic DNA was extracted and amplified by PCR using universal SSU rDNA primers to generate 16S and 18S rDNA clone libraries and 50 clones from each library were sequenced and placed in operational taxonomic units (OTUs). Through this recovery and analysis of SSU rRNA genes, a metagenomic profile of the microbial community emerged for each environmental sample. Analyses of these profiles, including species diversity estimates and rank-abundance curves, revealed that approximately 64% of prokaryotic OTUs and 80% of eukaryotic OTUs were novel. Diversity estimates were consistent with predicted ecosystem characteristics: they were greater for the mesotrophic to eutrophic temperate lakes, than for the oligotrophic arctic lake. Sample comparisons showed that community similarity declined as geographic distance between sites increased. Real-time quantitative PCR results showed that OTUs which had been recovered from only one library were actually present in other samples, but at much lower frequencies, suggesting that many, if not most, microorganisms are cosmopolitan. Together, these results support the potential value of using the microbial community as an indicator of local environmental conditions. In other words, it may be realistic to monitor water quality using a single, comprehensive suite of microorganisms by analyzing patterns of relative abundance.
Soil algae can perform important services for agro-ecosystems and functions as a bioindicator for soil quality. Communities of topsoil algae were studied (species composition and counts) in four different agro-ecosystems in relation to different land uses, including tillage. The chosen agro-ecosystems were an intensively-cultivated corn (Zea mays L.) field, a vineyard, a pasture and a field abandoned for 12 years. In all, 92 algal species were identified in the different ecosystems, which were sampled twice (March and May). In 2001 the main algal species were Cyanophyceae, Chlamydophyceae, and Chlorophyceae. The greatest species richness of algal species was recorded in the pasture, followed by the abandoned field, the corn field and the vineyard. Using a dilution method on solid media to count the algae enabled the distinction and separate quantification of cyanophytes, diatoms and greenish algae (cholorophytes (CH) + xanthophytes (X) + eustigmatophytes (E)). This last group of greenish algae dominated at all four sites, together with cyanophytes in the pasture and the abandoned field, whereas cyanophytes were almost absent in the vineyard. The highest mean abundance of algal cells in the 0–2 cm soil layer was found in the abandoned field and in the pasture, while it was lower in the corn field and in the vineyard. The undisturbed sites (abandoned field and, to some extent, pasture) were also characterised by a greater diversity of algae. Disturbance (tillage and use of pesticides) seemed to have a strong effect on both the composition and the density of the algal communities. Cyanophytes (Calothrix sp., Cylindrospermum sp., Pseudoanabaena sp., Scytonema sp. and Thricormus sp.) seemed to be particularly sensitive to disturbance. Heavy metals residues in the soil, especially Cu (linked to fungicide sprays, used particularly in vineyards), may be a factor affecting the abundance of cyanobacteria. It would be reasonable to conclude that the structure of soil algal communities is affected more by soil use rather than by physico-chemical soil parameters. Cyanobacteria showed the most evident response in the different agro-ecosystems, and therefore seem to be the most suitable group to consider as a soil bioindicator of land use.
Initial environmental pyrosequencing studies suggested highly complex protistan communities with phylotype richness decisively higher than previously estimated. However, recent studies on individual bacteria or artificial bacterial communities evidenced that pyrosequencing errors may skew our view of the true complexity of microbial communities. We pyrosequenced two diversity markers (hypervariable regions V4 and V9 of the small-subunit rDNA) of an intertidal protistan model community, using the Roche GS-FLX and the most recent GS-FLX Titanium sequencing systems. After pyrosequencing 24 reference sequences we obtained up to 2039 unique tags (from 3879 V4 GS-FLX Titanium reads), 77% of which were singletons. Even binning sequences that share 97% similarity still emulated a pseudodiversity exceeding the true complexity of the model community up to three times (V9 GS-FLX). Pyrosequencing error rates were higher for V4 fragments compared with the V9 domain and for the GS-FLX Titanium compared with the GS-FLX system. Furthermore, this experiment revealed that error rates are taxon-specific. As an outcome of this study we suggest a fast and efficient strategy to discriminate pyrosequencing signals from noise in order to more realistically depict the structure of protistan communities using simple tools that are implemented in standard tag data-processing pipelines.
Belowground processes are essential for the overall carbon and nitrogen fluxes in forests. Neither the functioning of the soil food web mediating these fluxes, nor its modulation by environmental factors is sufficiently understood. In this study the belowground carbon and nitrogen mineralisation of four European coniferous forest sites (northern Sweden to north‐east France) with different climate and N depositional inputs was analysed by investigating the soil food webs using field observations and modelling. The soil fauna directly contributed 7–13% to C mineralisation, among which the testate amoebae (Protozoa) made the largest contribution. Microbial grazing was suggested to have an important indirect effect by stimulating bacterial turnover. Due to relatively high C:N ratios of their substrate, bacteria immobilized N, while the fauna i.e. testate amoebae, nematodes, microarthropods and enchytraeids, counteracted this N immobilisation.
Despite similar food web biomass, the sites differed with respect to food web structure and C and N flows. Model calculations suggested a significant influence of food web structure on soil ecosystem processes in addition to environmental factors and resource quality. Mineralisation rates were lowest at the low N input boreal site with a food web dominated by fungal pathways. Further south, as N availability increased, bacterial pathways became more important and the cycling of C and N was faster. The bioavailability of degradable C sources is suggested to be a limiting factor for microbial activity and overall mineralisation rates. In this respect, above‐ and belowground interactions e.g. transfers of labile C sources from the vegetation to the decomposer system deserve further attention.
Our study revealed the combined effects of climate and nutrient inputs to ecosystems and the subsequent changes in the structure and functioning of the systems. If decomposition, and therefore carbon loss, is stimulated as a consequence of structural and/or nutritional changes, resulting for example from continuous industrial N emission, the storage capacity of forest ecosystems could be altered.
Despite the significance of diatoms in biomonitoring, many aspects of their biodiversity and geographical distribution are poorly understood. Recent evidence from molecular data has shown that traditional cosmopolitan and euryvalent morphospecies are often heterogeneous, containing cryptic or pseudo-cryptic species. It is important to establish whether these more finely differentiated species are also cosmopolitan or show restricted distributions. According to the standard freshwater diatom floras, Navicula cryptocephala and morphologically similar species (N. veneta, N. trivialis, N. gregaria and N. cryptotenella) are common, cosmopolitan freshwater pennate diatoms. Although allopatric and even sympatric populations of N. cryptocephala are extremely similar morphologically, they have previously been found to be highly polymorphic with respect to reproductive and nuclear characteristics; however, molecular data supporting the existence of cryptic diversity were lacking. Phylogenetic analyses (LSU rDNA, ITS of the rRNA operon) of 52 strains of N. cryptocephala-like diatoms confirmed the existence of genetically distinct lineages within N. cryptocephala, and revealed a close relationship between N. trivialis and N. cryptocephala. Cytological, reproductive and morphological variation, investigated by means of landmark-based geometric morphometrics, were in congruence with molecular data. Two pseudo-cryptic species within N. cryptocephala coexist sympatrically and are widely distributed, occurring in both European and Australian lakes.
Aim A current debate in microbial biogeography contrasts two views concerning the distribution of free-living microorganisms. The first view assumes a ubiquitous distribution, while the second assumes that at least some species have limited geographical distributions. We tested for limited geographical distributions by identifying testate amoebae morphospecies from an extremely remote oceanic island where the potential for endemism is high.
Location Amsterdam Island, Indian Ocean.
Methods Sixty moss and water samples collected from the top of the volcano to the lowland were investigated for their testate amoeba content. Due to taxonomic uncertainties among the Argynnia (Nebela) dentistoma species complex (including A. antarctica), we also performed light and scanning electron microscopy investigations on the shell ultrastructure and biometric analyses on several specimens of this taxon.
Results We identified a total of 43 testate amoeba taxa belonging to 15 genera. Only four testate amoeba taxa had previously been recorded on this island. Testate amoeba communities of Amsterdam Island are dominated by cosmopolitan ubiquitous euglyphid taxa such as Trinema lineare, Assulina muscorum and Corythion dubium. The length and width ranges for Argynnia dentistoma on Amsterdam Island overlap with other records of this species and of A. antarctica, suggesting that A. antarctica is not a distinct taxon.
Main conclusions Although Amsterdam Island is among the most remote islands in the world, an extensive inventory of testate amoeba morphospecies provided no clear evidence for endemism. On the one hand, our detailed morphometric analysis of the A. dentistoma complex revealed that A. antarctica, a morphospecies previously suggested to display endemism, cannot be confidently distinguished from the cosmopolitan morphospecies A. dentistoma. On the other hand, five morphotaxa could not be identified with certainty and might represent new species, potentially with limited distribution. These examples illustrate how taxonomic uncertainties undermine biogeographical studies of testate amoebae. In order to allow better interpretation of morphology-based testate amoeba distribution data, an assessment of genetic diversity among and within morphotaxa in relation to geographical distance for some common testate amoebae should be given high priority.
We have developed a method for determining the potential abundance of free-living protozoa in soil. The method permits enumeration of four major functional groups (flagellates, naked amoebae, testate amoebae, and ciliates) and it overcomes some limitations and problems of the usual 'direct' and 'most probable number' methods. Potential abundance is determined using light microscopy, at specific time intervals, after quantitative re-wetting of air-dried soil with rain water. No exogenous carbon substrates or mineral nutrients are employed, so the protozoan community that develops is a function of the resources and inhibitors present in the original field sample. The method was applied to 100 soil samples (25 plots x 4 seasons) from an upland grassland (Sourhope, Southern Scotland) in the UK. Median abundances for all four functional groups lie close to those derived from the literature on protozoa living in diverse soil types. Flagellates are the most abundant group in soil, followed by the naked amoebae, then the testate amoebae and ciliates. This order is inversely related to typical organism size in each group. Moreover, preliminary evidence indicates that each functional group contains roughly the same number of species. All of these observations would be consistent with soil having fractal structure across the size-scale perceived by protozoa. The method described will be useful for comparing the effects on the soil protozoan community of different soil treatments (e.g. liming and biocides).