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Diversity, Taxonomic Versus Functional
Abstract
Taxonomic diversity refers to the number and the relative abundance of species in a community. Functional diversity refers to the different types of processes in a community that are important to its structure and dynamic stability. Taxonomic and functional diversity have been presented as being different and, as the title implies, competing approaches to the study of biodiversity. This article will provide specific examples of how taxonomic and functional diversity are interrelated and how information from both perspectives can be used to estimate biodiversity and propose mechanisms that govern biodiversity.
... Functional diversity has been evaluated by its importance to ecology and biological conservation studies since it is a component of biodiversity that contributes to the understanding of the structure and functioning of ecosystems, including information on the identity of species through the description of their functional traits (Moore, 2001;Tilman, 2001). A first approach to functional diversity is the formation of functional groups, which are defined as a set of species that have a similar life history, such that they use a resource similarly in a given space and time (Moore, 2001;Steneck, 2001;Tilman, 2001), or that are related to some activity in ecosystems (Naeem et al., 2009). ...
... Functional diversity has been evaluated by its importance to ecology and biological conservation studies since it is a component of biodiversity that contributes to the understanding of the structure and functioning of ecosystems, including information on the identity of species through the description of their functional traits (Moore, 2001;Tilman, 2001). A first approach to functional diversity is the formation of functional groups, which are defined as a set of species that have a similar life history, such that they use a resource similarly in a given space and time (Moore, 2001;Steneck, 2001;Tilman, 2001), or that are related to some activity in ecosystems (Naeem et al., 2009). Species with similar functional traits are commonly assigned to functional groups (Moore, 2001;Steneck, 2001;Tilman, 2001). ...
... A first approach to functional diversity is the formation of functional groups, which are defined as a set of species that have a similar life history, such that they use a resource similarly in a given space and time (Moore, 2001;Steneck, 2001;Tilman, 2001), or that are related to some activity in ecosystems (Naeem et al., 2009). Species with similar functional traits are commonly assigned to functional groups (Moore, 2001;Steneck, 2001;Tilman, 2001). In Neotropic grazing lands, we found that in the reviewed articles, both analyses of functional groups and functional traits are carried out. ...
Dung beetles are one of the most representative groups of insects associated with livestock, as they take advantage of the manure of livestock for food and reproduction. They have been widely used as a bio-indicator group to evaluate their responses to land-use change and other environmental disturbances by analyzing species diversity at different spatial and temporal scales. However, the impacts of livestock management practices, forms, and history on dung beetle diversity are still poorly understood. This paper is an exhaustive and systematic review of the existing peer-reviewed and indexed literature on the taxonomic diversity (species richness and composition), functional diversity, and ecological functions of dung beetles from different provinces and biogeographic domains in tropical grazing lands of the Neotropics. We analyzed the timeline of the studies conducted so far, and we detected increasing literature produced mainly in South America. We included the most frequent objectives, tendencies, software, and statistical analyses. Given the significant heterogeneity of livestock landscapes in the Neotropics, the reviewed studies have conceptualized broadly what a pasture is, and the authors have used different descriptions of other grazing lands. Additionally, management data and livestock practices vary widely among studies, and management history is poorly described. In future research, it is relevant to include as much information as possible and the consequences of different livestock management practices on additional ecological attributes of dung beetle assemblages at different landscape scales (spatial and temporal) to predict how ecological processes change in Neotropical landscapes. Considering the importance of the data to be included in future work, we propose a collection format to unify the information collected in the field when conducting ecological studies in grazing lands. Moreover, we define a classification system to homogenize the features that distinguish the multiple tropical grazing lands reported in the literature. Preserving dung beetle diversity and associated ecological functions is urgent for maintaining ecosystem services in grazing lands. The challenge for research institutions is to continue filling gaps in knowledge to help those who work in transferring knowledge, to help ranchers exercise better options for more sustainable livestock farming, and to publish results for conservation decision-making.
... According to Moore [31], the space, which a species occupies within Hutchinson's hypervolume is termed the fundamental niche and is defined by the species' basic resource requirements. The fundamental niche further shrinks to the level of realized niche, which can be determined using field data [31][32][33]. ...
... In addition, the PCA results in the current study show that obviously any single parameter cannot be responsible for the entire ecological niche formation, as shown earlier for the cyanobacteria [22]. The latter conclusion abides by the definition of an ecological niche, which involves the multiple habitat requirements of a certain species for survival and reproduction [29][30][31][32][33]. ...
Harmful algal blooms (HABs) and their consequences cause multiple devastating effects in various freshwater, brackish and marine ecosystems. However, HAB species at moderate population densities have positive ecological roles as primary producers of organic matter and food for zooplankton and fish. They also enhance benthic-pelagic coupling and participate in the biogeochemical cycles. The consequences of HABs are transported across the conventional environmental boundaries by numerous cascade effects in the food webs and beyond. Meanwhile, forecasts of bloom events are still limited, largely because of scarcity of reliable information on ecological niches of the bloom-forming algae. To fill up this knowledge gap, this study focused on dinoflagellates, a diverse group of mostly photosynthesizing protists (unicellular eukaryotes) capable of mixotrophy, since they play a key role in primary production and formation of blooms in marine and brackish waters worldwide. In this study, ecological niches of 17 abundant bloom-forming dinoflagellate species from coastal regions of the southern Baltic Sea were identified for the first time. It was hypothesized that wider ecological niches ensure more frequent dinoflagellate blooms compared to the species with narrower niches. This hypothesis was verified using the long-term (44 years) database on phytoplankton abundance and physical-chemical characteristics of the environment. It were analyzed 4534 datasets collected from 1972 to 2016. Fourteen abiotic parameters (water temperature, salinity, Secchi depth, pH, Chl a, and concentration of basic nutrients) were considered as ecological niche dimensions. The Principal Component Analysis presented the dissolved inorganic nitrogen, total nitrogen, Chl a, and temperature as principal niche dimensions of dinoflagellates. The algal bloom criteria were refined. It was for the first time proved statistically that HAB frequency of dinoflagellate species robustly correlated with the width of their ecological niches.
... The higher the species richness the greater the -diversity of a particular sample. -diversity occurs within a given area within a region that is smaller than the entire distribution of the species [68]. -diversity compares all the different kinds of microbes between two or more samples [69]. ...
... It gives an estimation of how similar or dissimilar the microbes of different communities are in different samples. -diversity is the rate of change in species richness that occurs with a change in spatial scale [68]. Both and diversities are determined from the Phylogenetic tree, which is a representation of the evolutionary relationships among various taxa [70]. ...
Fresh water is an increasingly scarce resource in both urban and rural developments. As a response to this challenge, non-potable water reuse is on the rise. This research explored a potential off-grid system for water purification, consisting of a staircase wetland with terracotta pot plants working as a filter for greywater. The study further investigated the physicochemical properties of the greywater and the soil before and after the wetland purification. Results showed that the filtered water satisfied all requirements for water reuse, e.g., pH, turbidity, and total coliforms. The research then uniquely investigated the effect of greywater on the soil biodiversity and soil biomass using soil DNA extraction and the tea bag index testing method. The filtered greywater absorbed by soil decomposed the soil faster and stabilized it better compared to tap water-absorbed soil or unfiltered greywater. The DNA generation sequencing revealed no significant differences in alpha diversity between control and treatment samples. The beta diversity differences were significant. This nature-based solution can lead to reduced load on the sewage system, resulting in less wastewater generation.
... It is discernible that Puerto Princesa City has a more uniformly distributed population than Bataraza. The results also showed a similarity in abundance among species in Puerto Princesa City than in Bataraza (Moore, 2013). This could be attributed to the fact that the area in Puerto Princesa City experienced rehabilitation through replanting by the local government units hence, several species thrive in the site. ...
A floristic study was conducted in two ultramafic formations in Palawan Island, selected for their differing land uses, to assess the role of ultramafic forests as a carbon sink based on plant diversity and Soil Organic Carbon (SOC) content. A total of 17 tree species were identified inside an active mining area in Mt. Bulanjao, Rio Tuba, Bataraza, while only 15 tree species in Magarwak, Brgy. Sta. Lourdes, Puerto Princesa City. Palawan Mangkono (Xanthostemon speciosus Merr.), an island endemic species that thrives well in ultramafics, is the most dominant species in Rio Tuba, Bataraza, whereas Putian (Mastixia pentandra Blume) is the dominant species in Puerto Princesa City based on the Important Value Index (IVI). In terms of diversity, both sites exhibited low diversity index values, with Bataraza site having H'=2.232 while Magarwak, Puerto Princesa City had H'=2.286, respectively. Such data implied the alarming rate of species lost in ultramafic forest, primarily attributable to anthropogenic activities. Further analysis of SOC content indicated that Puerto Princesa City's ultramafic soils contained 99.05 t ha-1, while a much lower value of 85.68 t ha-1 at Bataraza was quantified. Considering the combined contribution of vegetation diversity and soil carbon, this study suggests that Puerto Princesa City's ultramafic formations have the potential to sequester atmospheric carbon and may act as a sink. Both the unusual characteristics of ultramafic soils and their existing vegetation contribute to the enhancement of the carbon storage potential of this forest type, although present land use serves as a crucial consideration. These findings underscore the importance of preserving and conserving native metallophytes in the area, making this research a pivotal basis for conservation efforts.
... To display the trajectories of the barcoded libraries, barcode frequencies of the respective samples were determined as previously described (24,25). The population evenness was calculated using the Shannon index (49). ...
Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote pathogen fitness in stationary phase. We discovered that the maintenance of lipid asymmetry (Mla) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type (WT) and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48 h stationary phase cultures. The mutant defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48 h. However, by 96 h the culturability of the WT and mutant strains were equivalent. By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for maintaining the culturability of V. cholerae because it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.
IMPORTANCE
Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction is limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high-energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis that emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.
... This complex structural heterogeneity provides a variety of microhabitats, each with its own unique microclimatic conditions, creating variations in temperature, humidity, light, and wind (Álvarez et al., 2024;Anhuf & Rollenbeck, 2001;Lindo & Winchester, 2013;Lowman & Rinker, 2004). The presence of different microhabitats and microclimates results in a greater diversity of resources, which in turn creates a wider range of ecological niches (De Frenne et al., 2021;Moore, 2013;Scheffers et al., 2014). The availability of niche spaces ultimately influences the distributions and interactions of species across vertical and horizontal spaces within forest ecosystems (MacArthur & Levins, 1964;Nakamura et al., 2017). ...
In tropical rainforests, trees and associated plants create vertically heterogeneous habitats mediated by seasonal changes in climate and plant phenology. Despite extensive studies on the spatiotemporal dynamics of tropical forest ecosystems, insect monitoring programs often neglect the vertical and seasonal dimensions because the relative importance of muti‐dimensional dynamics of insect diversity has not been well understood. In this study, we employed a spatially explicit sampling design to understand the distribution patterns of Coleoptera, Hymenoptera, and two families (Noctuidae and Nolidae) of Lepidoptera in the canopy and understory during the dry and wet seasons in two tropical rainforests located at lower and higher latitudes in Thailand. We compared the vertical stratification of gamma diversity, alpha diversity, total abundance, and beta turnover and nestedness. We also identified the insect species characteristic of certain vertical strata and/or seasons. Our samples resulted in a total of 4,452 insects (1,622 coleopterans, 1,763 hymenopterans, and 1,067 lepidopterans) representing 437 Coleoptera species, 694 Hymenoptera species, and 98 Lepidoptera species. All insect groups generally displayed moderately higher diversity in the canopy than in the understory, but the significance of this pattern varied among seasons, forests, and insect groups. Over 50% of significant habitat indicator species were restricted to certain vertical strata but were only found in certain seasons. Our findings demonstrate that spatiotemporal dynamics of insect diversity are highly context‐dependent and are not as clearly discernible as we hypothesized in three major insect groups, suggesting the importance of monitoring insects across vertical strata and seasons, even in low‐latitude tropical rainforests.
... (Moore, 2013), with higher values indicating higher biodiversity.Simpson's Index of Diversity (SID) were calculated as 1-D, proportion of observations accounted for by each species i, x i is the total number of each species recorded and N is the total number of individuals recorded.Objective Wild Animal Community Integrity Index (OWACII) was estimated by using the factoextra package to carry out a principal component analysis (PCA) of the values for all the various types of detections of all the wildlife species for each camp in the processed datasets provided in supplementary file 8. OWACII represents a synthetic statistical summary ...
Quantitative surveys of wild animal abundance or activity, and assessments of the integrity of the complex natural ecosystems they live in, are typically quite laborious and meaningful analysis of the data obtained may require considerable time and expertise. This study describes the development and evaluation of a practical procedure for semi-quantitative consensus-based synthesis of subjective impressions accumulated by a small team of investigators who visited 32 different locations distributed in or around a community-based Wildlife Management Area in southern Tanzania. The subjective natural ecosystem integrity index (SNEII) scores obtained represent a holistic indicator of all aspects of land use, wildlife and human activities, which correlated strongly with objective indicators of wild animal community or whole natural ecosystem integrity that were estimated directly from quantitative survey data by the same investigators at the same locations. Also, comparative regression analysis indicated that the SNEII was a far more sensitive to variations in observed human activities than any of the objective alternatives, correspondingly yielding far more detailed insights into ongoing conservation challenges. This simple procedure for summarizing the overall, multi-faceted subjective impressions of individuals traversing extensive conservation areas may well be applicable through participatory approaches to routine programmatic monitoring by community-based staff with minimal training, and may therefore be more practically useful to devolved conservation areas like WMAs than conventional objective statistical synthetic indices relying on laborious collection and expert analysis of quantitative survey data.
... web/ (Nparks, 2022). The orchid's diversity was assessed via species richness where the number of the taxa in UNIMAS-developed campus landscapes was enumerated accordingly (Moore, 2013). ...
For the past three decades, various biotic components in Universiti Malaysia Sarawak (UNIMAS) natural habitats have been studied but less attention given to the largest family of flowering plants, the Orchidaceae. A preliminary survey in the campus areas has resulted in the discovery of more than ten species of orchids. Therefore, in this study more field samplings were conducted throughout the UNIMAS campus focusing on the developed areas to unveil the potential of UNIMAS-developed areas as a growth ground for orchids. To date, 37 orchid species have been recorded from these areas; mainly found on the planted trees at the roadside and landscaped areas surrounding the academic buildings, while the terrestrial species were found to inhabit different types of disturbed habitat. Among them, Dendrobium pensile was identified as a new record to Sarawak while Dendrobium pseudostriatellum and Pinalia biglandulosa were endemic to Borneo. This study provides an insight into the orchid resiliency towards habitat alteration, landscape phorophytes species that can host orchids, and management of species in a developed landscape.
... Species Richness. Moore (2013) explains that species richness (S) refers to the number of species found in a given area or region. One can determine a region's species richness through sampling or a census. ...
This study was conducted to determine the taxonomy, ecology, and conservation of Aglaomorpha in common host trees in Olutanga, Zamboanga Sibugay, to develop potential conservation and management strategies, and help in the increase of awareness among people in the locality. Its primary target is to determine the species composition, richness, and relative abundance of Aglaomorpha and how common host trees affect its diversity. The study employed quadrat sampling and a non-random selective method to gather data. The descriptive taxonomic parameters were calculated using the Shannon index and Simpson index. These were quantified for each host tree using PAST software. Significant differences in the diversity indices were determined using One-way ANOVA. Findings revealed that only Cocos nucifera and Mangifera indica were common in all study areas and only two Aglaomorpha species were identified in the six barangays of Olutanga. A significant difference existed on the species composition, richness, and relative abundance of Kabkab among common host tree species. It was concluded that Olutanga is less diverse in ferns specifically Aglaomorpha species and local environmental activities like selective planting and logging greatly contributed to this. Further study is advised to directly pinpoint the cause of decreasing diversity of Aglaomorpha in Olutanga.
... Based on these results, the abundance and diversity of Chaetodontidae were classified as very good at both site locations. Every organism has its ecological niche (González et al., 2017;Moore, 2013). Chaetodontidae fish feed on corals in reefs with many crevices resembling small caves to hide, find food or a place to live . ...
Coral fish are one of the marine biotas that are highly sensitive to changes in coral reef ecosystems. Therefore, the presence or absence of specific reef fish species can describe the condition of coral reefs. The objective of the current study is to investigate the relationship between the biodiversity and abundance of Chaetodontidae fish and the live coral cover at 13 locations in the Spermonde area, Makassar City. Reef fish were counted using the Underwater Visual Census method. Coral cover percentages were determined using the Underwater Photo transects method. The results found 348 individuals of the Chaetodontidae family, comprising 21 species from four genera. The mean live coral cover categories in Spermonde were in pretty good condition (27.83%). Chaetodontidae in Spermonde Island was not diverse (mean H = 1.74) and not abundant (mean abundant = 721 ind./ha). There was a weak correlation between the diversity of Chaetodontidae and live coral cover, and also weak correlation between the abundance of Chaetodontidae and live coral cover in Spermonde Island, with R2 determination coefficient linear regression were 0.1697 and 0.0471, respectively.
... In this sense, collecting, sorting, and identifying morphospecies of those generalist ant species may represent a valuable tool for indicating soil properties in these croplands. Species richness is a biodiversity measure commonly used to estimate the variety of species in a community, dependent on the recorded number of species (Moore, 2013). In our results, this measure only significantly predicted three soil properties (i.e., organic matter content, total P, and total N) in the third sampling, composed of three sampling weeks. ...
Ants respond fast to changes in soil conditions in agricultural fields, thus they represent a practical, cheap, clean, and accurate tool to diagnose soil fertility before planting a crop. This study assesses the capacity of richness, occurrence, and activity of ant assemblages to indicate soil physicochemical properties in chayote monoculture in Veracruz, Mexico. Sampling was performed in 15 1-ha-plots and was replicated three times before planting chayote from August to October. Ants were collected using pit-fall traps and determined soil properties were texture, density, contents of organic matter (OM), nitrogen (N), and phosphorous (P), pH, and electrical conductivity (EC). In total, 20,385 ant workers belonging to 51 species, 28 genera, 9 tribes and 6 subfamilies were collected. Species richness significantly explained contents of OM, N, and P in a three-weeks sampling. Species occurrence explained clay percentage in the one-week sampling, N, and P contents in the two-weeks sampling and the aforementioned and percentages of sand and silt in the three-weeks sampling. Ant activity predicted more soil properties in the one-week sampling than in those that lasted two and three weeks.Richness, occurrence, and activity of ant assemblages are valuable tools for diagnosing texture, contents of OM, N, and P, and pH of soil before planting chayote monoculture. It contributes to the understanding of the role that ants play in agricultural fields. Therefore, soil management practices should consider indication capacity of ant assemblages to ensure growth and development of morphological structures such roots, stems, leaves, shoots, and fruits of cultivated plants.
... Where, S is the total number of species and N is the total number of individuals of all species; it represents the total number of species within a defined region (Moore, 2013). ...
Adoption of silvicultural system aims to enhance the regeneration of desired species. Irregular shelterwood system was initiated in Shorea robusta dominated forest under different forest management regimes including community forest in lowland forest of Nepal. The present study was conducted in 2023 to compare the regeneration status and species diversity between the two different management practices (scientific forest management and conventional forest management) in Patela Community Forest in far-western lowland of Nepal. A total of 27 quadrat sample plots (each with 4 m2) were established at a spacing of 50 m x 50 m across the three scientifically managed blocks, each with an area of 2.14 ha. An equal number of sample plots (27) were established within the conventionally managed blocks. Important Value Index, Sorenson’s Similarity Indices, and the distribution patterns of each species were calculated in both the management blocks to compare the species diversity. Shapiro-Wilk test was performed to check the normality of regeneration count, and a two-sample t-test was employed to examine the significant differences in the mean count of the plant species. The present study revealed that the conventionally managed forest block has higher species diversity; however, the number of seedlings was significantly high in the scientifically managed forest blocks. The Important Value Index Analysis indicated that S. robusta was dominant tree species in both the management blocks followed by Terminalia tomentosa; however, there was higher number of S. robusta regeneration under the scientifically managed blocks. The study concludes that irregular shelter-wood system is effective for regulating S. robusta forests in the western lowlands of Nepal.
... Phytosociological analysis of plant communities is essential for comprehending the critical ecological characteristics of the forests considering it provides insightful information on species interactions, diversity in community structure, and species turnover in a forest ecosystem (Mandal & Joshi, 2014). Additionally, autecological studies, which concentrate on the ecology of individual species, are also crucial for comprehending a species' range, abundance, and interactions with other plant communities in an ecosystem (Moore, 2013). ...
Podocarpus neriifolius is a rare species in the Himalayan region with a restricted distribution in small, dispersed areas. This study aims to understand the floristic composition and influence of environmental factors on the distribution of P. neriifolius in Athang block in Wangdue Phodrang district. Additionally, it also investigates its regeneration status and the habitat suitability of P. neriifolius in Bhutan. Fifteen quadrats (size 400 m2) were established following a purposive sampling method between 1000 and 2000 m elevation to gather tree data. Quadrats of size 25 m2 and 400 cm2 were nested within each tree quadrat to enumerate the regeneration of tree species and collect soil samples. Thirty herb plots (size 4 m2), two plots at the corner of each tree plot were established to investigate ground cover. A total of 105 plant species belonging to 93 genera and 58 families were recorded from the study area. P. neriifolius was the most dominant species with an Important Value Index (IVI) value of 41.65% and a Log(SumAbund) value of 2.52. The regeneration status of P. neriifolius was good which consisted of 46.58% , but, the Kruskal Wallis test revealed that there were no significant differences between the regeneration groups, H(2) = 1.387, p = 0.500. Based on DBH and Height class analysis, P. neriifolius showed inverse-J and sporadic type of regeneration where
regeneration occurred continuously or intermittently. The CCA ordination depicted that temperature (r = .924) was an important environmental factor followed by precipitation (r = .541) for the growth and distribution of P. neriifolius. This study found that the tree is found in forests with good canopy cover ranging from 50% to 90% and in acidic soil with pH values ranging from 4.35 to 6.10. A total area of 1,630.09 km2 was predicted to be highly suitable for the growth and distribution of the species in Bhutan. Therefore, in pursuit of conserving the species, those projected areas can be managed to ensure the stability of its population in the natural habitat.
... We also considered the concept of Hutchinson (1959), who expanded the latter definition by disaggregating the habitat ('n-dimensional hypervolume') into a number of resources ('niche dimensions') embodied by the species' niche. The space, which each species occupies within Hutchinson's hypervolume, is defined by its basic resource requirements (i.e., the fundamental niche) and is winnowed down by antagonistic interactions with other organisms, thus forming the realized niche (Moore, 2013). In other words, the environmental conditions where the organisms of a certain species are able to exist based on their physiological capabilities constitute the fundamental ecological niche, which largely corresponds to the organism's range of tolerance of different environmental parameters . ...
... Additionally, a quantitative closed-question survey was administered to record the gardeners' demographic profile (age, occupation, formal education, and gender). The species richness (S), defined as the number of species within a plot, was obtained through sampling or via a census of individual frequencies and recorded (Moore, 2013). Once the agrobiodiversity of the urban gardens was plotted, we used an extrapolation tool to describe and report its evidence across the city. ...
Small-scale agroecological practices in the urban areas of Querétaro, México, as in other mid-sized cities, could maintain agrobiodiversity pools and sufficient productivity for a food sovereignty baseline. The application of agroecological principles fosters agrobiodiversity and socio-ecological resilience in urban food production. Emerging urban gardens result from an immediate necessity for food that does not appear in local statistics, nor is there any account of them in any cadastral source or land register of Querétaro City. Based on studies of 28 urban gardens, we survey and analyze farming practices using socio-ecological resilience methodologies and the Diagnostic Survey of Agroecological Practices. We find that the agroecological management of urban gardens results in significantly more species richness than in conventionally managed plots, likely due to the multifunctional purposes associated with biocultural memory. The number of social actors participating in agroecological management is increasing. It represents an urban strategy of resilience that contributes to enhancing the microclimate and nutrient cycling, as well as to improving water management and biodiversity. Results also indicate that gardens of approximately 200 m 2 harbor the highest levels of agrobiodiversity. This area size for home vegetable production appears optimal for user-friendly management practices in urban settings and could represent the minimum benchmark for a family and a goal for urban planning and policy recommendations. Urban gardens contribute to the adaptive capacities of city dwellers to enhance their food security and sovereignty. Therefore, given that 70% of the national population face some level of food insecurity, we argue that, along with the protection of land-use rights, the promotion of a diverse urban landscape could improve long-term socio-ecological and food supply resilience. Additionally, urban gardens promote neighborhood social inclusion and affordable access to food. The empirical results and insights from this study in Querétaro can inform land-use policies for urban agriculture more broadly, especially in Latin American metropolitan areas.
... The alpha diversity was inferred based on the Shannon Diversity Index, Simpson Diversity Index, and Pielou's Evenness Index. The Shannon index is sensitive to species richness, whilst Simpson and Pielou's evenness indices are more sensitive to species evenness (20). Mann Whitney U test was performed to test if there was a significant difference between the smokers and the non-smokers by comparing the medians of the two groups. ...
Background
While oral mirobial dysbiosis due to tobacco smoking has been studied thoroughly, there is limited data on the effect of waterpipe smoking on the oral microbiome. This study aims to compare the salivary microbiome between waterpipe smokers and non-smokers.
Materials and methods
Unstimulated saliva samples were collected from 60 participants, 30 smokers and 30 non-smokers in Kuala Lumpur and Klang Valley, Malaysia. DNA extraction was performed using the Qiagen DNA mini kit, and the 16S rRNA bacterial gene was amplified and sequenced using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and the alpha and beta diversity of the bacterial community was assessed. Significantly differentiated taxa were identified using LEfSe analysis, while differentially expressed pathways were identified using MaAsLin2.
Results
A significant compositional change (beta diversity) was detected between the two groups (PERMANOVA P < 0.05). Specifically, the levels of phylum Firmicutes and genus Streptococcus were elevated in smokers, whereas phylum Proteobacteria and genus Haemophilus were depleted compared to non-smokers. At the species level, Streptococcus oralis, Streptococcus salivarius, and Streptococcus gingivalis were enriched in smokers. We observed significant differences in the abundance of thirty-seven microbial metabolic pathways between waterpipe smokers and non-smokers. The microbial pathways enriched in smokers were those implicated in polymer degradation and amino acid metabolism.
Conclusion
The taxonomic and metabolic profile of the salivary microbiome in waterpipe smokers compared to healthy controls exhibited a paradigm shift, thus, implying an alteration in the homeostatic balance of the oral cavity posing unique challenges for oral health.
... Species richness represents the number of different species occupying a particular ecological niche, or region (Moore, 2013). In our case, we analyzed four rodent species-great gerbil, yellow ground squirrel, Libyan jird, and midday jird-presenting the main plague risk in the Zhambyl region, and created the combined SDMs (Figures 2-7). ...
One of the most extensive natural plague centers, or foci, is located in Central Asia, in particular, the Zhambyl region in Southern Kazakhstan. Here, we conducted plague surveillance from 2000 to 2020 in the Zhambyl region in Kazakhstan and confirmed 3,072 cases of infected wild animals. We used Species Distribution Modeling by employing MaxEnt, and identified that the natural plague foci are primarily located in the Moiynqum, Betpaqdala, and Tauqum Deserts. The Zhambyl region's central part, including the Moiynqum and Sarysu districts, has a high potential risk of plague outbreak for the rural towns and villages. Since the phenomenon of climate change has been identified as a determinant that affects the rodent populations, thereby elevating the likelihood of an outbreak of plague, we investigated the potential dissemination routes of the disease under the changing climate conditions, thus creating Species Distribution Forecasts for the rodent species in southern part of Kazakhstan for the year 2100. By 2100, in case of increasing temperatures, the range of host species is likely to expand, leading to a higher risk of plague outbreaks. The highest risk of disease transmission can be expected at the outer limits of the modeled total distribution range, where infection rates are high, but antibody presence is low, making many species susceptible to the pathogen. To mitigate the risk of a potential plague outbreak, it is necessary to implement appropriate sanitary‐epidemiological measures and climate mitigation policies.
... Therefore, the use of traits and functional diversity indices alongside with taxonomic diversity provide a more holistic understanding about biodiversity (Hulme and Bernard-Verdier 2018). Both types of diversity metrics are important when evaluating the biodiversity of a given ecosystem (Villéger et al. 2010;Moore 2013;Teittinen and Virta 2021). In fact, due to the importance of functional diversity to biodiversity assessments, the number of scientific manuscripts integrating functional diversity into the ecological assessments has been increasing exponentially in recent years (Palacio et al. 2022). ...
As the effects of climate change continue to intensify, non-native species are becoming more prevalent in estuarine ecosystems. This has implications for the taxonomic and functional diversity of fish communities. Historically, biodiversity has been a synonym of taxonomic diversity, however this approach often fails to provide accurate insights on ecosystem functioning and resilience. To better understand how climate change is impacting fishes and their traits’ composition, a long-term dataset from Minho Estuary (NW Iberian Peninsula) fish assemblage was analyzed. The results suggest that climate change and extreme weather events altered the prevailing trait modalities of fishes, which led to the overall decrease in functional diversity of the fish assemblage over the course of a decade. This decrease is associated to the loss of some trait modalities that are exclusively found in native species. On the other hand, the invasive species added novel traits associated with the conditions of high temperatures and low precipitation regime currently observed in the studied area. Our results highlight that the shift in the presence and dominance of some traits is directly influenced by climatic changes. Also, despite the addition of novel modalities by the invasive species, the fish assemblage is now less functional and taxonomically diverse than previously.
Graphical abstract
... Among the estuaries of Portugal, the Minho Estuary has relatively low levels of pollution, but has a significant history of biological invasions (Sousa et al. 2008, 2013, Reis et al. 2009, Ilarri et al. 2014). The Minho Estuary is described as mesotidal, with an average depth of 2.6 meters and a maximum depth of 26 meters (Alves 1997). ...
As the effects of climate change continue to intensify, non-native species are becoming more prevalent in estuarine ecosystems. This has implications for the taxonomic and functional diversity of fish communities. Historically, biodiversity has been a synonym of taxonomic diversity, however this approach often fails to provide accurate insights on ecosystem functioning and resilience. To better understand how climate change is impacting fishes and their traits composition, a long-term dataset from Minho Estuary (NW Iberian Peninsula) fish assemblage was analyzed. The results suggest that climate change and extreme weather events are altering the prevailing trait modalities of fishes, which led to the overall decrease in functional diversity of the fish assemblage over the course of a decade. This decrease is associated to the loss of some trait modalities that are exclusively found in native species. On the other hand, the invasive species added novel traits associated to the conditions of high temperatures and low precipitation regime currently observed in the studied area. Our results highlight that the shift in the presence and dominance of some functional traits is directly influenced by climatic changes. Also, despite the addition of novel modalities by the invasive species, the fish assemblage is now less functional and taxonomic diverse than previously.
... Populations near the range edge may be more sensitive to environmental changes because these areas are associated with the limits of species' ecological niches (Hargreaves et al., 2015;Lee-Yaw et al., 2016;Orme et al., 2019). These populations are likely to be under higher stress from pressures such as extreme temperature, moisture (Moore, 2013), and less suitable vegetation and soil conditions (Cumming et al., 2014) than populations further from the range edge. In addition, populations near the range edge might have a higher probability of local extinction because they have fewer populations surrounding them which facilitates source-sink dynamics (Angert, 2009;Torrenta et al., 2022). ...
The relative effects of habitat loss and fragmentation on biodiversity have been a topic of discussion for decades. While it is acknowledged that habitat amount can mediate the effects of habitat fragmentation, it is unclear what other factors may drive inter- and intraspecific variation in fragmentation effects and their implications for conservation. We tested whether the effects of forest fragmentation on 362 bird species' occurrence in the Atlantic Forest of Brazil are mediated by distance to geographic range edge and habitat amount, and whether these effects explain intraspecific variation across populations. Using a single binomial linear mixed effects model, we found that fragmentation had mostly negative effects on occurrence probability up to 1080 km from the species' range edge, independent of habitat amount. We also show that above this distance, fragmentation has predominantly positive effects, more accentuated in deforested landscapes. We demonstrate that fragmentation effects can be both positive and negative, indicating that different populations of the same species can respond differently depending on distance to range edge and local forest cover. Our results help clarify one of the drivers of contradictory results found in the fragmentation literature and highlight the importance of preventing habitat fragmentation for the conservation of endangered populations. Conservation initiatives should focus on minimising fragmentation closer to range edges of target species and in regions where species range edges overlap.
... This index returns scores between 0 and 1, with a high score indicating high diversity and a low score indicating low diversity. Thus, as diversity increases and approaches 1, the distribution of species becomes more even -i.e., the dominance of a few species decreases (Moore, 2013). ...
Fire use in protected savannas of Africa is a common practice. Fires in these savannas create many environmental benefits, such as reducing grass, brush and trees that can fuel large and severe wildfires and improving wildlife habitat. However, wrong timing of fire can threaten plants, animals and habitats. This study investigated the effects of time of burning on woody plant composition, diversity and density in the Mole National Park, Ghana. A total of twelve 300 m 2 plots were systematically sampled in a 200 m × 200 m treatment plot established by Park Management each for early burn, late burn and no-burn plots. Twenty-seven different woody species belonging to fourteen families were recorded in all the treatments. Most of the species identified belonged to the families Fabaceae and Combretaceae. Vitellaria paradoxa (Shea), Terminalia avicennioides, Combretum adenogonium and Combretum molle were the most common and abundant in all treatments. A TWINSPAN on sites and species revealed four species groups based on affinity to burning time. A follow-up DCA showed a strong association between burning time and species composition, with the first two axes explaining 65% of variation. The late burn and no-burn treatments recorded the lowest diversity amongst the three treatments. Stem density was highest in no-burn treatment which had lowest species richness and diversity compared to early and late burn treatments. Early burn treatment had the highest diversity and the lowest density of woody species. The study revealed that the different times of prescribed burning influenced vegetation differently. Prescribed early dry season burning could contribute to the management of indigenous woody species in protected fire-prone savannas, because it can promote the diversity of species, as found in the Mole National Park in the Guinea savanna of Ghana.
... Species richness (S) [38], taxonomic diversity (Simpson's diversity index-D [35,39]) and functional diversity (Rao index [35,40]), calculated per decade, were used as biodiversity estimates. To calculate D, both S and the number of occurrences of each species in each ecosystem were considered [35,41]. ...
Mangroves and seagrasses present with high marine macroinvertebrate biodiversity that contributes to their structure and functioning. Macroinvertebrates possess a broad range of functional traits, making them excellent models for biodiversity and available-trait-based studies. This study aimed to characterize the biodiversity of marine macroinvertebrates as two different ecosystems situated along the coastline of Maputo Bay by compiling dispersed data from online databases. Specifically, this study addressed species richness, taxonomic and functional diversity based on two traits (habitat occupation and trophic guild), and the community structure of these traits. Mangroves presented with a higher species richness and taxonomic diversity than seagrasses. The functional diversity of mangroves was mostly explained by the trophic guild trait. In the case of seagrasses, functional diversity was mostly due to differences in habitat occupation in the 20th century, but the trophic guild accounted for this functional diversity from 2000 onwards. The comparison of community compositions between the two ecosystems showed low or no similarity. The use of digital databases revealed some limitations, mostly regarding the sampling methods and individual counts. The trends and data gaps presented in this study can be further used to inform subsequent systematic data acquisition and support the development of future research. A further step that may be taken to improve the use of digital data in future biodiversity studies is to fully incorporate functional traits, abundance and sampling methods into online databases.
... The Simpson evenness index (E) was used to assess the evenness of livelihood strategies in the study area. Evenness of a livelihood strategies considers the number of livelihood strategies and their relative abundance in the study area (Moore, 2013). According to Krebs et al. (1999) Simpson's index of evenness is calculated as shown below ...
Rural households in Ethiopia are characterized by subsistence agriculture, while empirical evidence reveals that rural livelihoods are limited. The aim of this study was to assess the rural livelihoods diversification with evidence of households surrounding Lake Tana. Data was collected using a survey from 413 households. The results of the study revealed that the mean overall asset score of the households was 0.313. Crop production, livestock rearing and employment were the major livelihood strategies. The households practiced a mean of three livelihood strategies, and the evenness score of the households was 0.18 referring to the dominance of small livelihood strategies. The mean annual income of the households was 26,696 ETB which was found to have a strong positive correlation with the asset possession of the households (r = 0.56). In addition, the Simpson diversification index result showed that 46.3%, 43.8% and 9.9% of households were low, medium and high-income diversifiers, respectively. Diversification groups have shown a significant difference in asset holdings but not in the income of the households. Moreover, significant variations were observed between Tana Zuria Rice and Tana Zuria livelihood zone households in asset, number of strategies, income and diversification status. The study concludes that the asset ownership of the households is limited. Development of rural livelihood assets is recommended to improve rural livelihoods and, as a result, household income.
... where N and P i are the same as in the Simpson index calculation (Moore, 2013). ...
The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs) in the larger particles along the water depths, might be due to the fast sinking and major contribution of carbon flux of the larger particles from the euphotic layer. In addition to polymers as the major carbon source, carbohydrates and amino acids were preferentially used by microbial community at the upper and lower boundary, respectively. This could potentially be attributed to the metabolic capabilities of attached microbial groups in different particles, and reflected the initial preference of the carbon source by the natural microbes in the twilight zone as well. The microbial structure and carbon metabolic profiles could be complemented with metatranscriptomic analysis in future studies to augment the understanding of the complex carbon cycling pathways in the twilight zone.
... Other studies have been successful at modelling different aspects of functional diversity (Pacheco-Labrador et al., 2022;Rossi et al., 2020), rather than taxonomic diversity, since it provides information on the functional value of each community. Combining information at landscape scale on biomass productivity, and taxonomic and functional diversity can be used to propose more insightful mechanisms to manage ecosystems (Moore, 2013). ...
Spatial predictions of biomass production and biodiversity at regional scale in grasslands are critical to evaluate the effects of management practices across environmental gradients. New generations of remote sensing sensors and machine learning approaches can predict these grassland characteristics with varying accuracy. However, such studies frequently fail to cover a sufficiently broad range of environmental conditions, and their prediction models are often case-specific. To address this gap, we have modelled above-ground biomass and species richness in 150 spatially independent grassland plots of three geographical regions in Germany. These regions follow a North-South climate gradient and differ in soil types, topography, elevation, climatic conditions, historical contexts, and management intensities. The predictors tested in this study are Sentinel-1 backscatter, Sentinel-2 time series of surface reflectance along with derived vegetation indices and Rao's Q, and a set of topoedaphic variables. We compared the performance of a feed-forward deep neural network (DNN) with a random forest (RF) regression algorithm. The DNN achieved the best estimations of biomass (r² = 0.45) when trained with Sentinel-2 surface reflectance only. Moreover, the DNN showed a higher generalizability than RF during spatial cross-validations (i.e., calibrating and validating in different regions, r² = 0.38 vs. 0.26). Species richness predictions by both algorithms improved when the full time series of Sentinel-2 surface reflectance values were used (highest r² = 0.42 achieved by the DNN), but both performed poorly during spatial cross-validations. Overall, the DNN-based models were more robust than RF models, showed a lower bias and lower systematic error, and required fewer inputs. Explainability analysis indicated that red-edge and near infrared information from May and October was the most relevant to predict species richness. This study presents an important step forward in generating robust spatially explicit predictions of grassland attributes and biodiversity variables across large areas, environmental gradients, and phenological stages.
... (Kwon et al., 2018;Luo et al., 2020;Vila-Viçosa et al., 2020). Species richness is the number of species within a defined region (Moore, 2013). In this study, species richness index was computed by compiling species distribution maps then summing species presences at pixel scale (250 m × 250 m). ...
Around the world, SDMs have been widely used to support forest management planning and biodiversity conservation. Beyond the prediction of species distribution provided by the SDMs, this study aimed to analyze the spatial distribution of tree species diversity using SDMs. The study area is a Faidherbia albida parkland in Central Senegal. It is characterized by a tree-based farming system dominated by Faidherbia albida.
Using a robust and representative dataset of 9258 tree species occurrence, we first determined by an SDM the current potential spatial distribution of the 16 main tree species forming the parkland. Specifically, using 6 SDM algorithms and applying several modeling techniques with different categories of predictor variables (e.g., climate, topography, soil properties and human impact) we benchmarked 576 SDMs to achieve best model predictions for tree species. Then, tree species diversity maps were created on the basis of the resulting SDM predictions. Finally, the spatial dynamics of tree species diversity were discussed in relation to landscape characteristics, including heterogeneity, composition and human impact.
The results showed that there is no single ‘best’ SDM algorithm (among the 6 algorithms tested) or modeling approach for all species. Benchmarking several modeling techniques allowed strengthening SDM performance, achieving AUC values that ranged from 0.64 (intermediate accuracy) to 0.87 (very good accuracy). The spatial dynamics of tree species diversity is related to the landscape heterogeneity and composition. In the Sahelian agroforestry systems (AFS), tree diversity is sustained by anthropization. A significant negative correlation with the distance to the village was found, i.e. the closer you get to the village, the greater the diversity of trees.
This study could be crucial for analyzing tree species diversity when abundance information is not available.
... Macroinvertebrates were identified to the genus level and enumerated using a dissecting microscope (× 6 magnification) according to the standard keys (Edmondson, 1959;Pennak, 1978;McCafferty and Provonsha, 1998;Borror et al., 1989;Ward, 1992;Engblom & Lingdell, 1999;Dar et al., 2002, Bouchard Jr, 2004Merritt & Cummins, 2006;Subramanian & Sivaramakrishnan, 2007;Bhagat, 2013;APHA, 2012). Several ecological characteristics of macroinvertebrate assemblages were calculated including Shannon diversity (H) (Shannon and Weiner, 1949), Simpson diversity (1_D) (-Simpson, 1949), richness (Duan et al., 2008;Moore, 2013), Equitability_J (Magurran, 2003), and dominance (D) (Camargo, 1992). Macroinvertebrate samples were collected in four replicas, and the average values were used in the final claculations. ...
Dachigam-Dara catchment feeding the world-famous Dal Lake was assessed and evaluated for water quality and anthropogenic impacts using physico-chemical and biological data from 2016 to 2018. Seven sites belonging to Dachigam (DACZ) and Dara zone (DARZ) catchment, three sites from the confluence zone (WANZ), and two sites at the downstream end (TELZ) were selected characterized by varying degrees of anthropogenic pressures. Biological Monitoring Working Program, and Average Score Per Taxon at the upstream zones (DACZ, DARZ, and WANZ) recorded significantly higher scores with water quality indices falling within the good category than the downstream zone (TELZ). Taxa richness, and diversity indices of benthic macroinvertebrates recorded higher values at the upstream zones (DACZ, and DARZ), and confluence zone (WANZ), compared to the downstream zone (TELZ). Results revealed that phylum Arthropoda was most dominant contributing 37 invertebrate families (constituting 90% of the total macroinvertebrate community, including Crustacea and Arachnida) while phylum Mollusca and Annelida constitute 5% each. Macroinvertebrate families Baetidae, Erpobdellidae, Gammaridae, Chironomidae, and Heptagenidae contributed significantly to the similarity and dissimilarity between the sampling zones. The best subset of environmental variables (BIOENV) test revealed that the distribution of benthic macroinvertebrate assemblage in the Dachigam-Dara catchment is driven by pH, electrical conductivity, dissolved oxygen, and phosphate phosphorous. The upstream zones (DACZ, and DARZ) and confluence zone (WANZ), compared to the downstream zone (TELZ) suggest progressive shift of pollution sensitive macroinvertebrate taxa to pollution tolerant taxa in response to anthropogenic activities in the stream ecosystem over time.
... Taxonomic as well as functional diversity are two ways to assess an organism's biodiversity patterns (Sanders, 2003;Reymond et al., 2013). 'Taxonomic diversity' denotes the number and the relative abundance of species in a community and the 'functional diversity' refers to the various processes that are crucial to the community's structure and dynamic stability (Moore, 2013). The study of biodiversity has been addressed by using these two distinct methods i.e., taxonomic diversity and functional diversity. ...
Ants play a crucial role as ecosystem engineers and natural enemies of insect pests in different forests and agroecosystems. Bangladesh’s varied agroecosystem harbors a diverse ant community, it can be utilized to track recent changes to the agricultural environment. However, it’s utilization is deemed due to insufficient taxonomic checklist of ant fauna and their diversity pattern in various ecosystems in Bangladesh. This research aimed to measure the taxonomic and functional diversity of ants in an agroecosystem. Sampling was done by time-unit sampling (TUS) during March- April 2021 in different cropland habitats in Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) campus. A total of 172 individuals of 20 genera under 5 subfamilies were identified, of which Myrmicinae was the richest subfamily with 9 genera, while Camponotus is the most dominant genus in the ecosystem. Four habitats from BSMRAU campus significantly contributed on ant species richness and diversity matrix as revealed through Principal component analysis (PCA). The functional diversity of identified ant genera was explained using the results retrieved from Shannon Diversity Index, Species Evenness index and Effective number of species (ENS). The Shannon-Wiener diversity index of Field pathway (2.5202) is highest, followed by Entomology field (2.38086), agroforestry field (1.37315) and lowest in rice field (0.16794). Field pathway had the highest value due to comprising several types of vegetation alongside and non-ploughed soil. Rice field has only rice crops that were grown in a wetland; hence, water causes the lowest value. The evenness index (>0.75) implies the probability of stable communities in all the tested habitats except in rice field (0.242), which indicates a depressed community structure and is strengthened by the ENS value as 12.4, 10.8, 3.9, and 1.18 in the field pathway, in entomology field, agroforestry field, and rice field, respectively. The findings generated a comprehensive ant checklist and diversity indices with indicator species to measure the land type transformation and restoration in the agroecosystem of Bangladesh for future research.
... Taxonomic as well as functional diversity are two ways to assess an organism's biodiversity patterns (Sanders, 2003;Reymond et al., 2013). 'Taxonomic diversity' denotes the number and the relative abundance of species in a community and the 'functional diversity' refers to the various processes that are crucial to the community's structure and dynamic stability (Moore, 2013). The study of biodiversity has been addressed by using these two distinct methods i.e., taxonomic diversity and functional diversity. ...
... Species richness (S) is the number of species within a defined region (Moore 2013). According to (Colwell et al., 2016), community ecologists and conservation biologists regarded measuring species richness as a fundamental objective where the number of species in a local aggregation is an instinctive and natural index of a community structure. ...
Data visualisation is essential for communicating and interpreting biodiversity data effectively. When compared to numerical values, visualising information with images is easier. Citizen Science has facilitated the collection of biodiversity data that can be used to conserve and preserve biodiversity sites. Google Earth provides a visualisation platform that can be used for biodiversity site monitoring. The latter has frequently been expressed in terms of biodiversity indices. The use of biodiversity indices for sites can be improved by incorporating visualisation elements. Previous studies that attempted to incorporate the calculation of biodiversity indices into biodiversity monitoring systems lacked the visualisation feature. This novel study aims to create an online module that combines biodiversity data from citizen science with a visualisation component. The observation data is imported from iNaturalist (https://www.inaturalist.org/) using the REST API method, which includes the species name and location. Species richness, Shannon-Wiener index, and Simpson index, as well as Hill Numbers, are automatically calculated and displayed on the Google Map alongside the green space area. The University of Malaya, which is located in an urban area, will be used as the study site for the demonstration of the developed prototype. The online biodiversity module prototype is available at http://www.umlivinglabsystem.com/Map/multipoly.
Quantitative surveys of wild animal abundance or activity, and assessments of the integrity of the complex natural ecosystems they live in, are typically quite laborious and meaningful analysis of the data obtained may require considerable time and expertise. This study describes the development and evaluation of a practical procedure for semi‐quantitative consensus‐based synthesis of subjective impressions accumulated by a small team of investigators who visited 32 different locations distributed in or around a community‐based Wildlife Management Area in southern Tanzania. The subjective natural ecosystem integrity index (SNEII) scores obtained represent a holistic indicator of all aspects of land use, wildlife and human activities, which correlated strongly with objective indicators of wild animal community or whole natural ecosystem integrity that were estimated directly from quantitative survey data by the same investigators at the same locations. Also, comparative regression analysis indicated that the SNEII was a far more sensitive to variations in observed human activities than any of the objective alternatives, correspondingly yielding far more detailed insights into ongoing conservation challenges. This simple procedure for summarizing the overall, multi‐faceted subjective impressions of individuals traversing extensive conservation areas may well be applicable through participatory approaches to routine programmatic monitoring by community‐based staff with minimal training, and may therefore be more practically useful to devolved conservation areas like WMAs than conventional objective statistical synthetic indices relying on laborious collection and expert analysis of quantitative survey data.
Plant colonization patterns on deglaciated terrain give insight into the factors influencing alpine ecosystem development. Our objectives were to use a chronosequence, extending from the Little Ice Age (~1850) terminal moraine to the present glacier terminus, and biophysical predictors to characterize vegetation across Sperry Glacier’s foreland—a mid-latitude cirque glacier in Glacier National Park, Montana, USA. We measured diversity metrics (i.e., richness, evenness, and Shannon’s diversity index), percent cover, and community composition in 61 plots. Field observations characterized drainage, concavity, landform features, rock fragments, and geomorphic process domains in each plot. GIS-derived variables contextualized the plots’ aspect, terrain roughness, topographic position, solar radiation, and curvature. Overall, vegetation cover and species richness increased with terrain age, but with colonization gaps compared to other forelands, likely due to extensive bedrock and slow soil development, potentially putting this community at risk of being outpaced by climate change. Generalized linear models revealed the importance of local site factors (e.g., drainage, concavity, and process domain) in explaining species richness and Shannon’s diversity patterns. The relevance of field-measured variables over GIS-derived variables demonstrated the importance of fieldwork in understanding alpine successional patterns and the need for higher-resolution remote sensing analyses to expand these landscape-scale studies.
When conducting sequence-based analysis of microbiome samples, it is important to accurately represent the bacterial communities present. The aim of this study was to compare two commercially available DNA isolation and PCR amplification approaches to determine their impact on the taxonomic composition of microbiome samples following 16S rRNA gene sequencing. A well-established 16S rRNA gene profiling approach, which was widely used in the Human Microbiome Project (HMP), was compared with a novel alkaline degenerative technique that utilizes alkaline cell lysis in combination with a degenerate pool of primers for nucleic acid extraction and PCR amplification. When comparing these different approaches for the microbiome profiling of human and mouse fecal samples, we found that the alkaline-based method was able to detect greater taxonomic diversity. An in silico analysis of predicted primer binding against a curated 16S rRNA gene reference database further suggested that this novel approach had the potential to reduce population bias found with traditional methods, thereby offering opportunities for improved microbial community profiling.
Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote the pathogen’s fitness in stationary phase. We discovered that the Mla ( m aintenance of lipid a symmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutant’s defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and Δ mlaE strains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the mlaE mutant’s defect. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance of V. cholerae’s culturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.
Importance
Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction are limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis which emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.
Despite the ecological importance of mesozooplankton, little is known about their global distribution and diversity in the mesopelagic realm. This study examines the spatial distribution and diversity of 861 mesozooplankton species using species distribution models. The highest species richness and range-size rarity were found in the offshore North Atlantic and coastal areas across both hemispheres, while the Pacific and Indian ocean basins had low rarity and species richness. Latitudinal species richness peaks around 30° N and 30° S, with hotspots mainly within 40°S and 40°N, absent in polar areas. However, mean species richness per area is higher and more evenly distributed in polar regions compared to equatorial or tropical areas. The study also found a correlation between water temperature and species richness, with the highest richness at around 25°C, decreasing sharply below ~10°C.
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single‐cell T‐cell receptor and B‐cell receptor sequencing. We also discuss two case studies where single‐cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
This research paper investigates the potential of repurposing abandoned bauxite pits in the Adriatic karst region as key contributors to biodiversity conservation and restoration efforts. Emphasizing the importance of innovative approaches, the study proposes strategic rehabilitation measures for these unrehabilitated pits, focusing on the creation of rainwater-sustained water surfaces and fostering vegetation succession. The research underscores the significance of environmental compensation for new mining projects, advocating for the remediation of previously mined areas to support indigenous flora and fauna, particularly bird habitats. Despite slow natural succession, the unrehabilitated bauxite pits in Dalmatia, Croatia, exhibit biodiversity interest, hosting several bird species, including endangered ones. The petrology of bauxite deposits facilitates habitat engineering, with limestone providing structural support and marl contributing to biotope creation. Furthermore, the unique properties of bauxite help sustain water ponds and shield pits from strong winds, aiding in flora and fauna restoration. The study underscores the importance of multidisciplinary research, field trials, and continuous monitoring for effective habitat engineering in decommissioned mining sites. It recommends a step-by-step procedure for biodiversity restoration in mining regions, encompassing assessment, data collection, technical rehabilitation, planting and ongoing maintenance. By implementing these recommendations, mining regions can contribute significantly to biodiversity conservation and align with national and European Union (EU)-level objectives. The results of this study can be applied to similar contexts in broader area of Adriatic karst/external Dinaric Alps.
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A complimentary shared article can be viewed at Springer Nature Sharedit https://rdcu.be/dEX92.
Mangrove forests play a vital role in the environment. They provide a number of ecosystem services for supporting marine biodiversity, humans, and other living organisms inhabiting the area. This study aimed to determine the community structure and regeneration capacity of mangrove forests in Lebak, Sultan Kudarat, Philippines. Community structure was determined through relative density, relative frequency, relative dominance, and importance value. Using the center point circular plot method, 13 plots with 40 m diameter were established in two sampling sites: natural stand and reforested. Shannon-Weiner diversity and evenness indexes were used to determine species diversity and distribution, respectively. This study recorded a total of 14 462 individuals within the 1256 m² sampling plots, having Rhizophoraceae as the most abundant family with seven species that cover about 71% of both mangrove ecosystems. The vegetation analysis revealed that Ceriops tagal (70.35%) and Rhizophora mucronata (96.51%) had the highest importance value in the natural stand and reforested mangrove forests, respectively. Furthermore, these two species were also accounted for having the highest regeneration contribution among all species in each site. Shannon-Weiner diversity index revealed that the natural stand was more diverse compared to the reforested mangrove forest. However, the Shannon-Weiner evenness index showed that species in the reforested mangrove forest are more evenly distributed than species in the natural stand. Natural mangrove stands in Lebak have complex community structure and have higher regeneration capacity than the reforested mangrove forest. With this, the study suggested continuing the best practices employed for mangrove conservation in the area and crafting a strategic plan for sustainable mangrove resource utilization.
Understory vegetation is one of the most important links for improving forest biodiversity, and its restoration is conducive to sustainable forest development, energy flow, and nutrient cycling. However, little is known about the developmental dynamics and main driving factors of the long-time series coverage, biomass, diversity, and species composition of plantation understory vegetation. In a case study of three typical plantations, with a natural secondary forest as reference in the Loess Plateau of China, we collected understory vegetation from a Robinia pseudoacacia Linn. deciduous broad-leaved plantation, Pinus tabulaeformis Carr. evergreen coniferous plantation, and mixed plantation with an age span of 10 to 50 years. (1) The understory plantation coverage and biomass results of stands with different ages showed the R. pseudoacacia plantation to be significantly higher than the P. tabulaeformis plantation, and the species diversity of the P. tabulaeformis plantation changed the most with the stand age. However, the growth resource imbalance, and drastic changes in the stands’ environment caused by excessive intraspecific competition in the early stage of the P. tabulaeformis plantation vegetation restoration, are the main reasons that make the species diversity of undergrowth vegetation of P. tabulaeformis plantation lower than that of other stand types. (2) The understory species composition of the plantations revealed their degree of community stability. Compared to the R. pseudoacacia plantation and P. tabulaeformis plantation, the mixed plantation had higher stability, and its species composition closely resembled a natural secondary forest. The community stability of the P. tabulaeformis plantation was the lowest because it had the lowest coverage, biomass, and species diversity of understory vegetation. However, the understory species composition of the three plantation types converged, which was due to atypical species contribution. (3) The dynamic changes of canopy and soil nutrients were the main driving factors affecting the R. pseudoacacia plantation understory vegetation species composition. Stand density and elevation limited the understory vegetation communities of P. tabulaeformis plantation restoration. Soil bulk density is the key factor affecting understory vegetation in mixed plantations, and this effect weakens with the stand age. In future studies, the focus should be on the converged action and further development trend of atypical species, choosing an appropriate recovery strategy (active or passive), and providing more possibilities for the intensive management of vegetation under different plantations.
Environmental biomonitoring techniques have been widely applied to assess the quality states of toxic chemical compounds in surface freshwater quality. The methods based on macrophytes are generally recruited to present trustworthy assessments of ecological status for surface water bodies. The chief goal of the present investigation was to improve robust machine learning models (MLMs) to establish relationships among macrophyte indices and the simultaneous effects of water quality parameters (WQPs) and hydromorphological factors. In the present research, the dataset included monthly WQPs, which have been accumulated from 200 sample points located in the bottomland of studied rivers, placed in Poland. This research utilized three ecological indices, namely the macrophyte index for rivers (MIR), the macrophyte biological index for rivers (IBMR), and river macrophyte nutrient index (RMNI) whereas species richness (N) and Simpson index (D) were considered as diversity indices. 12 WQPs and two hydromorphological indices have been considered as input variables for the MLMs namely gene-expression programming (GEP), evolutionary polynomial regression (EPR), multivariate adaptive regression spline (MARS), and model tree (MT). In terms of the best performance of MLMs’ results, RMNI predictions were obtained by EPR (correlation coefficient [R] = 0.6061 and root mean square error [RMSE] = 0.5355) whereas MIR, IBMR, species richness, and Simpson index were predicted by MARS (R = 0.4333 and RMSE = 11.5046), EPR (R = 0.6020 and RMSE = 1.6923), GEP (R = 0.6089 and RMSE = 7.7229), and MARS (R = 0.5066 and RMSE = 0.2217), respectively. The great impact of these indexes was evaluated by the statistical parameters. This study showed that the biological assessment of rivers through macrophyte indexes not only helps to broaden knowledge related to the ecological status of the river but also aids in managing natural and anthropogenic activities’ impacts on the water body.
Context
Macrochloa tenacissima (L.) Kunth (= Stipa tenacissima L.), also defined as Alpha grass steppes, form the main dryland ecosystems throughout the Mediterranean region. Recent studies suggest that ongoing climate change will lead to a sequence of changes in them, including modifications in the composition of vegetation and reduction in vegetation cover and biomass, which will diminish plant-derived organic inputs into the soil. These changes are expected to affect the spatial arrangement of vegetation and the ecosystem’s water-nutrient balance, as well as the microbial populations in the underlying soil. In addition, the lithological legacy affecting soil hydrological properties might modulate the effects of aridity.
Objectives
With this study, we wanted to evaluate the interactive effects of the lithological legacy on soil water availability and aridification on vegetation cover, spatial structure, and composition, and on soil microbial biomass.
Methods
We combined field data, including plant composition and soil physicochemical and biological properties, with unmanned aerial vehicle (UAV) images collected at eight study sites along two different altitudinal-aridity gradients with contrasting lithologies in a space-for-time substitution approach to explain the role of lithological legacies on soil properties in aridification. High-resolution UAV images were used to determine the vegetation cover and three spatial metrics related with the hydrological connectivity within the study areas. Soil microbial biomass was estimated using the substrate-induced respiration method.
Results
Aridification was critical to explaining changes in vegetation coverage, diversity, richness, and spatial distribution, reducing plant cover, and promoting dominance of small round isolated vegetation patches. By modulating soil physicochemical properties, lithology interacted with aridity controlling the variations in plant composition and the changes in soil microbial biomass along the altitudinal aridity gradients. This may have also affected nutrient cycling, thus determining the response of the ecosystem to aridification.
Conclusion
According to our results, the effect of the lithology legacy on soil properties interacts with aridity, determining the response of M. tenacissima steppes to aridification, as it modifies water availability on soil and plant composition, leading to differences in microbial biomass. Thus, both factors should be considered in the development of management strategies aimed for reducing and mitigating the negative impacts of climate change and aridification in drylands.
Maternal milk supports offspring development by providing microbiota, macronutrients, micronutrients, immune factors, and hormones. The hormone prolactin (PRL) is an important milk component with protective effects against metabolic diseases. Because maternal milk regulates microbiota composition and adequate microbiota protect against the development of metabolic diseases, we aimed to investigate whether PRL/PRL receptor signaling regulates gut microbiota composition in newborn mice at weaning. 16SrRNA sequencing of feces and bioinformatics analysis was performed to evaluate gut microbiota in PRL receptor-null mice (Prlr-KO) at weaning (postnatal day 21). The normalized colon and cecal weights were higher and lower, respectively, in the Prlr-KO mice relative to the wild-type mice (Prlr-WT). Relative abundances (Simpson Evenness Index), phylogenetic diversity, and bacterial concentrations were lower in the Prlr-KO mice. Eleven bacteria species out of 470 differed between the Prlr-KO and Prlr-WT mice, with two genera (Anaerotruncus and Lachnospiraceae) related to metabolic disease development being the most common in the Prlr-KO mice. A higher metabolism of terpenoids and polyketides was predicted in the Prlr-KO mice compared to the Prlr-WT mice, and these metabolites had antimicrobial properties and were present in microbe-associated pathogenicity. We concluded that the absence of the PRL receptor altered gut microbiota, resulting in lower abundance and richness, which could contribute to metabolic disease development.
The Commons have been recognised throughout history as an inalienable right to access whatever is necessary to ensure life and a livelihood. The commons are free and allow citizens to generate food and income. The tragedy of the commons was described over a century ago, pointing to the loss of clean air, freshwater, and green pastures. Worse, the liberal economic model permits each player to increase its benefit from the commons, ultimately leading to its irreparable destruction. Once the commons are affected by human interventions, then the community will have less resilience. When a crisis hits, then the toll will be high. The article studies the framework conditions that permit a reversal of these trends leading to the definition of the framework conditions that will permit the design of a production and consumption model where happiness has a chance. These conditions include the zero-waste concept, no one is producing something no one else desires; the full employment, meaning that the community permits everyone to contribute to the best of their abilities; and no cheating, or everyone plays according to the rules of Nature and operates within the tradition and culture while embracing innovations.KeywordsThe commonsLiberal economic modelIrreparable destructionZero-wasteNon-linear logicResilience through diversity
Aquatic community dynamics are closely dominated by flow regime and water quality conditions, which are increasingly threatened by dam regulation, water diversion, and nutrition pollution. However, further understanding of the ecological impacts of flow regime and water quality conditions on aquatic multi-population dynamics has rarely been integrated into existing ecological models. To address this issue, a new niche-based metacommunity dynamics model (MDM) is proposed. The MDM aims to simulate the coevolution processes of multiple populations under changing abiotic environments, pioneeringly applied to the mid-lower Han River, China. The quantile regression method was used for the first time to derive ecological niches and competition coefficients of the MDM, which are demonstrated to be reasonable by comparing them with the empirical evidence. Simulation results show that the Nash efficiency coefficients for fish, zooplankton, zoobenthos, and macrophytes are more than 0.64, while the Pearson correlation coefficients for them are no less than 0.71. Overall, the MDM performs effectively in simulating metacommunity dynamics. For all river stations, the average contributions of biological interaction, flow regime effects, and water quality effects to multi-population dynamics are 64%, 21%, and 15%, respectively, suggesting that the population dynamics are dominated by biological interaction. For upstream stations, the fish population is 8%-22% more responsive to flow regime alteration than other populations, while other populations are 9%-26% more responsive to changes in water quality conditions than fish. For downstream stations, flow regime effects on each population account for less than 1% due to more stable hydrological conditions. The innovative contribution of this study lies in proposing a multi-population model to quantify the effects of flow regime and water quality on aquatic community dynamics by incorporating multiple indicators of water quantity, water quality, and biomass. This work has potential for the ecological restoration of rivers at the ecosystem level. This study also highlights the importance of considering threshold and tipping point issues when analyzing the "water quantity-water quality-aquatic ecology" nexus in future works.
The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al3+ ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.
The excessive proliferation of cyanobacteria in surface waters is a widespread problem worldwide, leading to the contamination of drinking water sources. Short- and long-term solutions for managing cyanobacterial blooms are needed for drinking water supplies. The goal of this research was to investigate the cyanobacteria community composition using shotgun metagenomics in a short term, in situ mesocosm experiment of two lakes following their coagulation with ferric sulfate (Fe2(SO4)3) as an option for source water treatment. Among the nutrient paramenters, dissolved nitrogen was related to Microcystis in both Missisquoi Bay and Petit Lac St. François, while the presence of Synechococcus was related to total nitrogen, dissolved nitrogen, dissolved organic carbon, and dissolved phosphorus. Results from the shotgun metagenomic sequencing showed that Dolichospermum and Microcystis were the dominant genera in all of the mesocosms in the beginning of the sampling period in Missisquoi Bay and Petit Lac St. François, respectively. Potentially toxigenic genera such as Microcystis were correlated with intracellular microcystin concentrations. A principal component analysis showed that there was a change of the cyanobacterial composition at the genus level in the mesocosms after two days, which varied across the studied sites and sampling time. The cyanobacterial community richness and diversity did not change significantly after its coagulation by Fe2(SO4)3 in all of the mesocosms at either site. The use of Fe2(SO4)3 for an onsite source water treatment should consider its impact on cyanobacterial community structure and the reduction of toxin concentrations.
Explicit consideration of timescales and dynamics is required for an understanding of fundamental issues in ecology. Endogenous dynamics can lead to transient states where asymptotic behavior is very different from dynamics on short timescales. The causes of these kinds of transients can be placed in one of three classes: linear systems with different timescales embedded or exhibiting reactive behavior, the potentially long times to reach synchrony across space for oscillating systems, and the complex dynamics of systems with strong density-dependent (nonlinear) interactions. It is also important to include the potentially disparate timescales inherent in ecological systems when determining the endogenous dynamics. I argue that the dynamics of ecological systems can best be understood as the response, which may include transient dynamics, to exogenous influences leading to the observed dynamics on ecologically relevant timescales. This view of ecosystem behavior as responses of ecological systems governed by endogenous dynamics to exogenous influences provides a synthetic way to unify different approaches to population dynamics, to understand mechanisms that determine the distribution and abundance of species, and to manage ecosystems on appropriate timescales. There are implications for theoretical approaches, empirical approaches, and the statistical approaches that bridge theory and observation.