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Bacterio- and Virioplankton in Water Bodies of a Raised Bog (Vologda Oblast, Russia)
Abstract
Stroynov Ya.V., Philippov D.A. 2017. Bacterio- and virioplankton in water bodies of a raised bog (Vologda oblast, Russia). Inland Water Biology, 10(1): 37–43. DOI: 10.1134/S1995082917010175
The abundance of virio-and bacterioplankton and the role of viruses in the mortality of heterotrophic bacteria have been studied in three different mire water bodies (lagg, hollow, and stream) in the Shichengskoe raised bog. The abundance of bacteria (up to 93 million cells/mL) and viruses (up to 152 million particles/mL) reached very high values. Considerable differences were found between the mire water bodies in seasonal dynamics and average values of the studied parameters. The ratio of the number of virioplankton to the number of bacterioplankton (median values from 1.3 in a hollow to 5.6 in a stream) is in low ranges of values which are available in literature sources. Viruses did not have a considerable direct effect on bacterioplankton while lysing ≤7.8% of the bacterial production.
Background:
The paper is based on the dataset whose purpose was to deliver, in the form of GBIF-mediated data, diverse materials on the biodiversity of a large mire, Shichengskoe mire (Vologda Region, north-western Russia), including its various mire sites and intra-mire water bodies. The dataset was based on our materials collected for two decades (from 2000 to 2021) in different parts and biotopes of the Shichengskoe mire and complemented by scarce data obtained previously by other researchers. The data contain materials on the diversity of Animalia (2886 occurrences), Bacteria (22), Chromista (256), Fungi (111), Plantae (2463) and Protozoa (131). Within the study period, the most detailed and long-term biodiversity studies were carried out for higher plants and invertebrates. On the other hand, the data on the composition of lichens, protozoa, algae, basidiomycetes, some groups of invertebrates and, to a lesser extent, lichens and vertebrates are far less comprehensive and require further substantial research efforts. The list includes occurrences from both the peatland (mire sites and mire margins different in typology) and the objects of the mire hydrographic network. In a standardised form, this article summarises both already published (mainly in Russian) and unpublished materials.
New information:
The paper summarises the results of long-term research on the biodiversity of a boreal mire, including its hydrographic network. A total of 5869 occurrences were included in the dataset published in the Global Biodiversity Information Facility (GBIF, gbif.org) for the first time. According to the GBIF taxonomic backbone, the dataset covers 1358 taxa, including 1250 lower-rank taxa (species, subspecies, varieties, forms) and 108 taxa identified to the genus level. Several species found in the Shichengskoe mire, mainly belonging to Bacteria, Chromista and Protozoa, have never been listed in GBIF for the territory of Russia before. The overwhelming majority of occurrences and identified species came from the territory of Shichengskiy Landscape Reserve. Due to our work, this Reserve is now the most studied regional reserve in the Vologda Region with respect to biodiversity. By the number of revealed species, it is close to two federal protected areas: Darwinskiy State Nature Biospheric Reserve and National Park "Russkiy Sever".
Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.
Philippov, D.A. (2017). Specific features of structural organization of hydrobiocenoses in different-type of mire water bodies and water courses. Transactions of Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, 79, 251-277 (in Russian).
The paper outlines and substantiates mire hydrobiology, a special area in hydrobiology, devoted to biological processes in different-type water objects of mires and the ways they are related to their environment. The main aim of mire hydrobiology is to study the regularities determining biodiversity, structural-functional organization, as well as seasonal, interannual, and long-term dynamics of communities in mire water bodies and water courses. All living organisms inhabiting mire water bodies and water courses may be considered as the object of study. The main issue is the structure and ecological role of aquatic communities in the functioning of ecosystems in mire water bodies and water courses. It is stated that the type of mire water object (including its genesis, location within the mire massif, morphometric features) determines the structural-functional organization of its ecosys- tem. The statement is verified and illustrated by the author's original data obtained in long-term studies of the Shichengskoe mire (Vologda Region). The distinguishing features of taxonomic and ecological composition and structural-functional organization of aquatic communities in different-type water objects of mires are described and analyzed, including such subsystems as the vegetation, bacterioplankton, phytoplankton, zooplankton and macrozoobenthos. The role of sphagnum mosses as a key taxonomic group and the coenogenetic traits of various components of mire aquatic communities are considered.
В работе обосновывается выделение особого направления гидробиологии - гидробиология болот, как науки о биологических процессах в разнотипных водных объектах болот и их связи со средой. Основной целью гидробиологии болот признается изучение закономерностей формирования биологического разнообразия, структурно-функциональной организации, сезонной, межгодовой и многолетней динамики биоценозов болотных водоёмов и водотоков. В качестве объекта исследования выступают все живые ор- ганизмы, обитающие в болотных водоёмах и водотоках, а предметом исследования является структура и экологическая роль сообществ гидробионтов в функционировании экосистем болотных водоёмов и водо- токов. Постулируется, что тип болотного водного объекта (включая его происхождение, положение в пределах болотного массива, морфометрию) определяет структурно-функциональную организацию его экосистемы. Данные утверждения проверяются и иллюстрируются авторскими данными, полученными в результате многолетних исследований Шиченгского болота (Вологодская область). Описываются особенности таксономического, экологического состава и структурно-функциональной организации гидробиоценозов разнотипных болотных водных объектов данного болота, включая такие подсистемы как растительность, бактерио-, фито-, зоопланктон, макрозообентос; роль сфагновых мхов как ключевого таксона, особенности ценогенеза различных компонентов гидробиоценозов болот.
A new nucleic acid stain, SYBR Green I, can be used for the rapid and accurate determi-nation of viral and bacterial abundances in diverse marine samples. We tested this stain with formalin-preserved samples of coastal water and also from depth profiles (to 800 m) from sites 19 and 190 km off-shore, by filtering a few m1 onto 0.02 pm pore-size filters and staining for 15 min. Comparison of bacterial counts to those made with acridine orange (AO) and virus counts with those made by trans-mission electron microscopy (TEM) showed very strong correlations. Bacterial counts with A 0 and SYBR Green 1 were indistinguishable and almost perfectly correlated (r2 = 0.99). Virus counts ranged widely, from 0.03 to 15 X 10' virus ml-l. Virus counts by SYBR Green 1 were on the average higher than those made by TEM, and a SYBR Green 1 versus TEM plot yielded a regression slope of 1.28. The cor-relation between the two was very high with an value of 0.98. The precision of the SYBR Green I method was the same as that for TEM, with coefficients of variation of 2.9%. SYBR Green I stained viruses and bacteria are intensely stained and easy to distinguish from other particles with both older and newer generation epifluorescence microscopes. Detritus is generally not stained, unlike when the alternative dye YoPro I is used, so this approach may be suitable for sediments. SYBR Green I stained samples need no desalting or heating, can be fixed with formalin prior to filtration, the optimal staining time is 15 min (resulting in a total preparation time of less than 25 min), and counts can be easily per-formed at sea immediately after sampling. This method may facilitate incorporation of viral research into most aquatic microbiology laboratories.
The frequency of virus infected bacterial cells (FIC) was estimated in surface waters of the Mediterranean Sea, the Baltic Sea and the North Sea using the frequency of visibly infected cells (FVIC) as determined by transmission electron microscopy (TEM) and published average conversion factors (average 5.42, range 3.7 to 7.14) to relate FVIC to FIC. A virus dilution approach was used to obtain an independent estimation of FIC in bacterioplankton, and we provide evidence for the relia- bility of this approach. Across all investigated environments, FIC ranged from 2.4 to 43.4%. FIC data using both approaches were well correlated; however, the values were higher using the virus dilu- tion approach. This indicates that the TEM approach has the potential to reveal spatiotemporal trends of viral infection; however, it may underestimate the significance of viral infection of bacteria when average conversion factors are used. Using data from the virus dilution approach and the TEM approach, we calculated new conversion factors for relating FVIC to FIC (average 7.11, range 4.34 to 10.78). Virally caused mortality of bacteria estimated from published FVIC data of marine and fresh- water systems and using the new conversion factors ranged from not detectable to 129%, thus con- firming that viral infection is a significant and spatiotemporally variable cause of bacterial cell death.
Although bacteria are often treated as one entity in ecological studies, bacterial assemblages are composed of individual species populations. Bacterial assemblages can have their own richness and structure, analogous to communities of plants and animals, although few studies have attempted to describe spatial or temporal patterns in their structure. In this study, we examined successional changes in the structure of bacterial assemblages using denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction amplified 16S rDNA fragments. Bacterial biofilm assemblages developing on glass slides in a mesocosm and a small lake showed an initial increase in richness over the first week, followed by a slight decrease and a subsequent increase after two to three months. Functional changes in the bacterial community were examined using most probable number estimates and revealed decreases in the abundance of glucose- and cellulose-degraders during biofilm development, whereas benzoate-degraders became more abundant in the lake biofilms. The banding patterns observed on DGGE gels were used to derive rank-abundance profiles for each stage of biofilm development. These pro-tiles resembled those observed for communities of macroorganisms and could usually be described by geometric series models. These models suggested greater equitability in bacterial community structure as the biofilms developed. A comparison of two successional series of biofilms separated by 30 d revealed that neither successional stage nor time of sampling was the major factor influencing bacterial assemblage structure. Our results allowed us to suggest a general model for the development of bacterial biofilm assemblages that emphasizes the interaction of species and resource diversity. This model suggests that, at least in biofilms, bacterial assemblages may not be structured by the resource competition or niche-driven patterns typical of communities of macroorganisms.
The waters of small lakes located in swampy catchment areas of upper Volga contain considerable amounts of ultrasmall microbial cells that pass through 0.22-μm-pore-size filters. As shown in our previous study [1], most of these cells represent the bacterial genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia of the class Betaproteobacteria, as well as euryarchaea of the uncharacterized clade LDS. The aim of the present study was to investigate the possible effect of the waters draining swampy areas on the composition of the filterable microbial fraction in lakes fed by swampy catchments. To address this question molecular identification was performed of prokaryotic ultramicroforms in the peat of the ombrotrophic Sphagnum bog Obukhovskoe, located, like the lakes studied previously [1], in the Mologa-Sheksna catchment area. The number of filterable microorganisms in 1 g wet peat was 3.8 × 106 cells, or 0.5% of total microbial cell number in the peat. From the DNA of the filterable cell fraction, 100 clones of bacterial and 77 clones of archaeal 16S rRNA genes were obtained. The bacterial clone library contained 16S rRNA gene sequences representing the classes Beta- and Gammaproteobacteria (the genera Janthinobacterium and Pseudomonas, respectively) and the phylum Bacteroidetes (the genera Chryseobacterium and Epilithonimonas) and differed significantly from the clone library of bacterial ultramicroforms of lake water. By contrast, the pools of filterable archaea in bogs and lakes were essentially similar. They were represented by the euryarchaeal clade LDS and methanogens of the orders Methanobacteriales and Methanosarcinales. Additionally, the pool of filterable archaea of the bog included methanogens of the order Methanomicrobiales and representatives of the uncharacterized euryarchaeal clade RC-V (Rice Cluster V) and of the phylum Thaumarchaeota.
Watersaturated soil and sediment ecosystems (i.e. wetlands) are ecologically as well as economically important systems due to their high productivity, their nutrient (re)cycling capacities and their prominent contribution to global greenhouse gas emissions. Being on the transition between terrestrial and – aquatic ecosystems, wetlands are buffers for terrestrial run off thereby preventing eutrophication of inland as well as coastal waters. The close proximity of oxic-anoxic conditions, often created by wetland plant roots, facilitates the simultaneous activity of aerobic as well as anaerobic microbial communities. Input of nutrients and fast recycling due to active aerobes and anaerobes makes these systems highly productive and therefore attractive for humans as well as many other organisms. Wetlands globally are under high pressure due to anthropogenic activities as well as climate change. Changes of land-use as well as altered hydrology due to climate change will lead to disturbance and loss of these habitats. However, the diversity and functioning of microbial communities in wetlands systems in highly underexplored in comparison to soils and aquatic ecosystems. Given the importance of wetlands and their immediate threats combined with the lack of knowledge on the microbiology of these systems is the basis for this special issue, focusing on the current microbiological knowledge and gaps therein to be assessed in future wetland research. Papers (research papers, reviews, perspectives, opinion papers) are welcomed that focus on all aspects that regulate the functioning and community composition of microbes (i.e. bacteria, archaea, protozoa, fungi) in wetland ecosystems (peat, coastal as well as freshwater marshes, flood plains, rice paddies, littoral zones of lakes etc) from all geographic regions. Welcomed topics are physiology, ecology, functioning, biodiversity, biogeography of microbes involved in nutrient cycling (C, N, P, Fe, Mn), green house gas emissions as well as plant-microbe interactions. These studies can be multidisciplinary and cover topics from the molecular to the community level.
1. We review studies of viruses in natural and constructed wetlands, focusing on the importance of surfaces as viral habitat, and differences in viral ecology between wetlands and other aquatic ecosystems.
2. Viruses in natural wetlands are predominantly associated with sediment, macrophytes and other submerged surfaces. In constructed wetlands, these surfaces are critical to the removal of viral pathogens and indicator organisms from wastewater.
3. Interactions between viruses and other ecosystem components have rarely been examined in wetlands, and the role of viruses in regulating wetland microbial communities is unclear. Environmental factors such as temperature and flooding regime are important abiotic controllers of viral abundances in wetlands but few studies have examined how abiotic or biotic factors affect community structure. Even basic information on wetland viral diversity is lacking.
4. Future research should include broad surveys of different types of wetlands, an emphasis on differences between microhabitats, and an increased use of molecular approaches to examine wetland viral diversity and its relationship to microbial community structure. Such studies should consider wetlands as part of the broader landscape, and emphasize interactions between wetlands and adjacent terrestrial and aquatic ecosystems.
The majority of studies on rhizospheric interactions focus on pathogens, mycorrhizal symbiosis, or carbon transformations. Although the biogeochemical transformations of N, S, and Fe have profound effects on vegetation, these effects have received far less attention. This review, meant for microbiologists, biogeochemists, and plant scientists includes a call for interdisciplinary research by providing a number of challenging topics for future ecosystem research. Firstly, all three elements are plant nutrients, and microbial activity significantly changes their availability. Secondly, microbial oxidation with oxygen supplied by radial oxygen loss from roots in wetlands causes acidification, while reduction using alternative electron acceptors leads to generation of alkalinity, affecting pH in the rhizosphere, and hence plant composition. Thirdly, reduced species of all three elements may become phytotoxic. In addition, Fe cycling is tightly linked to that of S and P. As water level fluctuations are very common in wetlands, rapid changes in the availability of oxygen and alternative terminal electron acceptors will result in strong changes in the prevalent microbial redox reactions, with significant effects on plant growth. Depending on geological and hydrological settings, these interacting microbial transformations change the conditions and resource availability for plants, which are both strong drivers of vegetation development and composition by changing relative competitive strengths. Conversely, microbial composition is strongly driven by vegetation composition. Therefore, the combination of microbiological and plant ecological knowledge is essential to understand the biogeochemical and biological key factors driving heterogeneity and total (i.e., microorganisms and vegetation) community composition at different spatial and temporal scales.
Northern peatlands are a large repository of atmospheric carbon (C) due to an imbalance between primary production by plants and microbial decomposition. The James Bay Lowlands (JBL) of northern Ontario are a large peatland complex but remain largely unstudied. Climate change models predict the region will experience warmer and drier conditions, potentially altering plant community composition and shifting the region from a long-term carbon sink to a source. We collected a peat core from two geographically separated (ca. 200 km) ombrotrophic peatlands (Victor and Kinoje Bogs) and one minerotrophic peatland (Victor Fen) located near Victor Bog within the JBL. We characterized (i) archaeal, bacterial and fungal community structure with terminal restriction fragment length polymorphism of ribosomal DNA, (ii) estimated microbial activity using community level physiological profiling and extracellular enzymes activities, and (iii) temperature dependence of C mineralization at three depths (0-10, 50-60 and 100-110 cm) from each site. Similar dominant microbial taxa were observed at all three peatlands despite differences in nutrient content and organic matter quality. In contrast, we observed differences in basal respiration, enzyme activity and the magnitude of substrate utilization, which were all generally higher at Victor Fen and similar between the two bogs. However, there was no preferential mineralization of C substrates between the bogs and fens. Microbial community composition did not correlate with measures of microbial activity but pH was a strong predictor of activity across all sites and depths. Increased peat temperature and aeration stimulated CO2 production but this did not correlate with a change in enzyme activities. Potential microbial activity in the JBL appears to be influenced by the quality of the peat substrate and the presence of microbial inhibitors, which suggests the existing peat substrate will have a large influence on future JBL C dynamics.
Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circumneutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and qPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidizers (Ga-FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Ga-FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of Ga-FeOB was assessed using PCR-DGGE and the abundance of both Ga-FeOB and MOB by qPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of Ga-FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Ga-FeOB outnumbered the MOB subgroups suggesting their competitiveness or the prevalence of Fe(2+) over CH(4) oxidation in this floodplain.
Sphagnum mosses represent a main vegetation component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand the extend of host specificity and impact of environment, Sphagnum fallax and Sphagnum angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-single-strand conformation polymorphism of 16S rRNA and nitrogenase-encoding (nifH) genes were highly similar for both Sphagnum species. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH) coupled with confocal laser scanning microscopy (CLSM): Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila, and Phenylobacterium as major genera for both mosses. Nitrogen fixation is an important function of Sphagnum-associated bacteria, which is fulfilled by microbial communities of Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g., Cyanobacteria and Deltaproteobacteria. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological, and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.
Members of the bacterial phylum Planctomycetes inhabit various aquatic and terrestrial environments. In this study, fluorescence in situ hybridization (FISH) was applied to assess the abundance and depth distribution of these bacteria in nine different acidic wetlands of Northern Russia. Planctomycetes were most abundant in the oxic part of the wetland profiles. The respective cell numbers were in the range 1.1-6.7 × 10(7) cells g(-1) of wet peat, comprising 2-14% of total bacterial cells, and displaying linear correlation to the peat water pH. Most peatland sites showed a sharp decline of planctomycete abundance with depth, while in two particular sites this decline was followed by a second population maximum in an anoxic part of the bog profile. Oxic peat layers were dominated by representatives of the Isosphaera-Singulisphaera group, while anoxic peat was inhabited mostly by Zavarzinella- and Pirellula-like planctomycetes. Phylogenetically related bacteria of the candidate division OP3 were detected in both oxic and anoxic peat layers with cell densities of 0.6-4.6 × 10(6) cells g(-1) of wet peat.
The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.
The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.
The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of approximately 15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of approximately 5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments.
This unique textbook takes a broad look at the rapidly expanding field of freshwater microbiology. Concentrating on the interactions between viruses, bacteria, algae, fungi and micro-invertebrates, the book gives a wide biological appeal. Alongside conventional aspects such as phytoplankton characterisation, seasonal changes and nutrient cycles, the title focuses on the dynamic and applied aspects that are not covered within the current textbooks in the field. Complete coverage of all fresh water biota from viruses to invertebrates. Unique focus on microbial interactions including coverage of biofilms, important communities on all exposed rivers and lakes. New information on molecular and microscopical techniques including a study of gene exchange between bacteria in the freshwater environment. Unique emphasis on the applied aspects of freshwater microbiology with particular emphasis on biodegradation and the causes and remediation of eutrophication and algal blooms.
A new nucleic acid stain, SYBR Green I, can be used for the rapid and accurate determination of viral and bacterial abundances in diverse marine samples. We tested this stain with formalin-preserved samples of coastal water and also from depth profiles (to 800 m) from sites 19 and 190 km offshore, by filtering a few mi onto 0.02 mu m pore-size filters and staining for 15 min. Comparison of bacterial counts to those made with acridine orange (AO) and virus counts with those made by transmission electron microscopy (TEM) showed very strong correlations. Bacterial counts with AO and SYBR Green I were indistinguishable and almost perfectly correlated (r(2) = 0.99). Virus counts ranged widely, from 0.03 to 15 x 10(7) virus ml(-1). Virus counts by SYBR Green I were on the average higher than those made by TEM, and a SYBR Green I versus TEM plot yielded a regression slope of 1.28. The correlation between the two was very high with an r(2) value of 0.98. The precision of the SYBR Green I method was the same as that for TEM, with coefficients of variation of 2.9%. SYBR Green I stained viruses and bacteria are intensely stained and easy to distinguish from other particles with both older and newer generation epifluorescence microscopes. Detritus is generally not stained, unlike when the alternative dye YoPro I is used, so this approach may be suitable for sediments. SYBR Green I stained samples need no desalting or heating, can be fixed with formalin prior to filtration, the optimal staining time is 15 min (resulting in a total preparation time of less than 25 min), and counts can be easily performed at sea immediately after sampling. This method may facilitate incorporation of viral research into most aquatic microbiology laboratories.
The timing of lytic phage development and the relationship between host generation times and latent periods were investigated by electron microscopy of one-step growth experiments in two strains of marine Vibrio species. Results were used in a correction factor developed to interpret field studies of phage-infected marine bacteria. Both the number of mature phage per average cell section and the percentage of cells with mature phage increased exponentially by 73-86% into the latent periods. Assuming that bacterial infection and lysis take place continually in the ocean, conversion factors for relating the percentage of visibly infected bacteria to the total percentage of the bacterial community that are phage-infected were calculated as 3.70-7.14. When this range of factors was applied to previously-collected field data [Proctor LM, Fuhrman JA (1990) Nature (Lond) 343:60-62; Proctor LM, Fuhrman JA (1991) Mar Ecol Prog Ser 69:133-142] from 3 to 31% of the free-living bacteria and 3 to 26% of particulate-associated bacteria appeared to be phage-infected at any given time. Based upon a steady-state model in which half the daughter cells survive to divide again, the percent of total mortality would be twice the total percentage of phage-infected cells. From 6 to 62% and from 6 to 52% of mortality for the free-living and particulate-associated bacterial community, respectively, may be due to viruses.
Composition and seasonal dynamics of phytoplankton, bacteria, and zooplankton (including heterotrophic flagellates, ciliates, rotifers and crustaceans) were studied in 55 lakes in Northern Germany with different trophic status, ranging from mesotrophic to hypertrophic. Mean abundance and biomass of all groups increased significantly with trophic level of the lake, but bacteria and metazooplankton showed only a weak correlation and a slight increase with chlorophyll concentration. Composition of phytoplankton showed a dominance of cyanobacteria in hypertrophic lakes, whereas the importance of chrysophytes and dinophytes decreased with an increase in trophic status. Protozoans (heterotrophic flagellates and ciliates) made up 24% (mesotrophic lakes) to 42% (hypertrophic lakes) of total zooplankton biomass on average, and were dominated by ciliates (62‐80% of protozoan biomass). Seasonally, protozoans can build up to 60% of zooplankton biomass in spring, when heterotrophic flagellates can contribute � 50% to protozoan biomass. Correlation analyses revealed significant relationships between the planktonic groups and indicated that pelagic food webs are influenced by both bottom-up as well as top-down mechanisms. Comparing lakes along a trophic gradient, resource parameters seem to be of major importance, whereas seasonal changes within a lake were perhaps regulated by the presence of predators.
Viruses are typically viewed as microorganisms responsible for diseases in other, larger organisms. During the last one-and-a-half decades, it has become increasingly clear that they are (together with bacteria) the most abundant microorganisms and life forms, and that only a relatively small number are pathogenic to humans; the vast majority play a critical role in aquatic ecosystems. Ample research, plenty of it being conducted in marine systems, has revealed that viruses are involved in the cycling of nutrients and carbon; however, the impact on their hosts’ distribution and on the genetic information harbored in aquatic organisms is still at the dawn of comprehensive scientific understanding. Therefore, this field has a tremendous potential for further development and is already widely accepted as an integral and promising discipline in the inland water sciences as well. This chapter will not cover the survival and distribution of human, animal, and plant pathogenic viruses, since topics related to such disease-causing viruses have been reviewed extensively elsewhere. Rather, this chapter will provide a basic insight into aquatic virus ecology, presenting a short overview on current knowledge. It also provides suggestions about important and excellent sources for further reading.
The relative contribution of viral lysis to overall mortality in aquatic bacterial populations is often estimated as twice the frequency of infected cells (FIC). The 'factor-of-two rule' upon which this estimate is based assumes (l) steady-state conditions, (2) that latent period is equivalent to generation time, a n d (3) that infected cells are not grazed. FIC values for this calculation are themselves derived from measurements of the frequency of vlsibly infected cells (FVIC) by the use of a slmple conversion factor. A steady-state model was developed to more ngorously define the relationships between FIC, FVIC, and the fraction of mortality from viral lysis (FMVL). This model shows that even under the restrictive assumptions listed above, the factor-of-two rule systematically overestimates FMVL for typ-ically reported values of FVIC. The model also shows that although grazing on infected cells further reduces FMVL for a given estimate of FIC, at the same time such grazing increases FIC for a given mea-surement of FVIC. In combination, these 2 effects mnimize the influence of grazing on the calculation of FMVL from FVIC. Overall, the relationship between FMVL and FVIC is well approxin~ated as fol-lows: FMVL S FVIC/[y ln(2) (1 -E -FVIC)], where y = the ratio between the latent period and genera-tion time, and E = the fraction of the latent period during which viral particles are not yet visible. Using typically observed values of FVIC, and assuming that y = 1 (per assumption 2, above) and E = 0 186 (per literature estimates), the model suggests that, on average, viral lysis accounts for approximately 22% (range: 4.5 to 45' ::) of total bacterial mortality in a range of aquatic environments, corresponding to a mean overestimate of 24 % (range: 4 to 44'%) by the factor-of-two rule. Perhaps most importantly, the model shows that calculations of FMVL from FIC or FVIC are very sensitive to changes in the relative length of the latent period (y) and in the assumed proportion of the latent period during which viral par-ticles are not recognizable (E). Constraining these 2 factors would greatly improve the reliability of FMVL calculations.
1. Viruses are the most abundant biological entities on the planet, and sediments provide a highly suitable environment for them. This review presents the first comparative synthesis of information on the fresh water and marine viriobenthos and explores differences and similarities to the better known virioplankton. We present methods for studying life cycles of the viriobenthos, data on viral distribution and diversity, interactions with host microbes, and information on the role of viruses in benthic food webs and biogeochemical cycles.
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