Nutrient enrichment weakens the stabilizing effect of species richness

With global freshwater biodiversity declining at an even faster rate than in the most disturbed terrestrial ecosystems, understanding the effects of changing environmental conditions on relationships between biodiversity and the variability of community and population processes in aquatic ecosystems is of significant interest. Evidence is accumulating that biodiversity loss results in more variable communities; however, the mechanisms underlying this effect have been the subject of considerable debate. We manipulated species richness and nutrients in outdoor aquatic microcosms composed of naturally occurring assemblages of zooplankton and benthic invertebrates to determine how the relationship between species richness and variability might change under different nutrient conditions. Temporal variability of populations and communities decreased with increasing species richness in low nutrient microcosms. In contrast, we found no relationship between species richness and either population or community variability in nutrient enriched microcosms. Of the different mechanisms we investigated (e.g. overyielding, statistical averaging, insurance effects, and the stabilizing effect of species richness on populations) the only one that was consistent with our results was that increases in species richness led to more stable community abundances through the stabilizing effect of species richness on the component populations. While we cannot conclusively determine the mechanism(s) by which species richness stabilized populations, our results suggest that more complete resource-use in the more species-rich low nutrient communities may have dampened population fluctuations.     

Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977–2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a “region of common profile” approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.     

Principal factors controlling the species richness of European fens differ between habitat specialists and matrix‐derived species

Aim

We present the first continental‐scale study of factors controlling the species richness of groundwater‐fed fens, comparing land snails, vascular plants and bryophytes. We separately analyse two ecologically distinct groups differing in conservation value and colonization/extinction dynamics, that is habitat specialists, and matrix‐derived species. Considering the island‐like nature of fen habitats, we hypothesize larger differences in the species richness–environment relationships between habitat specialists and matrix‐derived species than among the taxonomic entities.

Location

Seven European regions

Methods

Richness was counted at 373 well‐preserved fens with undisturbed hydrology using the same protocols. Relationships between the species richness and water pH, waterlogging, climate and geography were explored by GLMs.

Results

Land snail richness responded mainly to water pH, regardless of habitat specialization. Richness of vascular plant and bryophyte specialists was strongly driven by geographical location of the sites, while that of matrix‐derived species was driven by waterlogging and water pH. The richness of matrix‐derived species of all taxa significantly increased with the decreasing waterlogging. Residual richness of specialists of all taxa decreased towards southern Europe.

Main conclusions

In island‐like terrestrial habitats, differences between specialists and matrix‐derived species may outweigh differences among taxa, unless there is one strong physiological determinant of species richness such as pH in land snails. The richness of specialists seems to be strongly related to difficult‐to‐measure regional factors such as historical frequency and connectivity of fen habitats. The richness of matrix‐derived species depends mainly on local conditions, such as pH and waterlogging, determining the degree of habitat contrast against the surrounding matrix. Sufficient waterlogging maintains a high representation of habitat specialists in fen communities, and disturbance of water regime may cause the increase in the number of matrix‐derived species and potentially trigger successional shifts towards non‐fen communities.

     

Mechanisms underpinning community stability along a latitudinal gradient: Insights from a niche-based approach

At large scales, the mechanisms underpinning stability in natural communities may vary in importance due to changes in species composition, mean abundance, and species richness. Here we link species characteristics (niche positions) and community characteristics (richness and abundance) to evaluate the importance of stability mechanisms in 156 butterfly communities monitored across three European countries and spanning five bioclimatic regions. We construct niche-based hierarchical structural Bayesian models to explain first differences in abundance, population stability, and species richness between the countries, and then explore how these factors impact community stability both directly and indirectly (via synchrony and population stability). Species richness was partially explained by the position of a site relative to the niches of the species pool, and species near the centre of their niche had higher average population stability. The differences in mean abundance, population stability, and species richness then influenced how much variation in community stability they explained across the countries. We found, using variance partitioning, that community stability in Finnish communities was most influenced by community abundance, whereas this aspect was unimportant in Spain with species synchrony explaining most variation; the UK was somewhat intermediate with both factors explaining variation. Across all countries, the diversity–stability relationship was indirect with species richness reducing synchrony which increased community stability, with no direct effects of species richness. Our results suggest that in natural communities, biogeographical variation observed in key drivers of stability, such as population abundance and species richness, leads to community stability being limited by different factors and that this can partially be explained due to the niche characteristics of the European butterfly assemblage.     

Species richness–variability relationships in multi-trophic aquatic microcosms

While species loss may affect the temporal variability of populations and communities differently in multi- versus single-trophic level communities, the nature of these differences are poorly understood. Here, we report on an experiment where we manipulated species richness of multi-trophic rock pool invertebrate communities to determine the effects of species richness, S, on the temporal variability of communities, populations, and individual species. As in single-trophic level studies, temporal variability in community abundance decreased with increasing species richness. However, in contrast to most studies in single-trophic level systems, temporal variability of populations also decreased as species richness increased. Furthermore, the variability of the constituent populations strongly correlated with variability of community abundance suggesting that, in rock pools, S affects community variability through its stabilizing effect on component populations. Our results suggest that species loss may affect population and community variability differently in multi-trophic versus single trophic level communities. If this is so, then the mechanisms proposed to underlie the effects of S on community variability in single-trophic communities may have to be supplemented by those that describe contributions to population stability in order to fully describe the patterns observed in multi-trophic communities.     

Step Process for Selecting and Testing Surrogates and Indicators of Afrotemperate Forest Invertebrate Diversity

Background

The diversity and complexity of invertebrate communities usually result in their exclusion from conservation activities. Here we provide a step process for assessing predominantly ground-dwelling Afrotemperate forest invertebrates'' (earthworms, centipedes, millipedes, ants, molluscs) potential as surrogates for conservation and indicators for monitoring. We also evaluated sampling methods (soil and litter samples, pitfall traps, active searching quadrats and tree beating) and temporal (seasonal) effects.

Methodology/Principal Findings

Lack of congruence of species richness across taxa indicated poor surrogacy potential for any of the focus taxa. Based on abundance and richness, seasonal stability, and ease of sampling, molluscs were the most appropriate taxon for use in monitoring of disturbance impacts. Mollusc richness was highest in March (Antipodal late summer wet season). The most effective and efficient methods were active searching quadrats and searching litter samples. We tested the effectiveness of molluscs as indicators for monitoring by contrasting species richness and community structure in burned relative to unburned forests. Both species richness and community structure changed significantly with burning. Some mollusc species (e.g. Macroptychia africana) showed marked negative responses to burning, and these species have potential for use as indicators.

Conclusions/Significance

Despite habitat type (i.e., Afrotemperate forest) being constant, species richness and community structure varied across forest patches. Therefore, in conservation planning, setting targets for coarse filter features (e.g., habitat type) requires fine filter features (e.g., localities for individual species). This is especially true for limited mobility taxa such as those studied here. Molluscs have high potential for indicators for monitoring, and this requires broader study.     

How gradients of climate and soil determine Mediterranean annual-rich dryland vegetation

Questions

Dryland annual plant communities constitute the most species-rich small-scale vegetation in the Mediterranean. Nevertheless, the composition and diversity of these units and the factors controlling their variation are still insufficiently understood. Therefore, we investigated species composition and richness patterns in relation to important environmental gradients provided by climate and soil.

Location

Central Crete, Greece.

Methods

The study is based on 82 plots of 4 m² sampled at altitudes between 11 and 1400 m a.s.l. We conducted vegetation relevés and soil analyses. We used generalised additive models to model species richness and community characteristics along the studied gradients. We then performed distance-based redundancy analysis to determine the main environmental factors influencing species composition. To determine species of diagnostic value for bedrock types, we applied an indicator species analysis. Correlation tests were used to test the performance of the South Aegean Plant Indicator Values on our dataset.

Results

We recorded 347 taxa (species and subspecies) of 43 plant families, and mean species numbers of 47.2 ± 12.5 per plot. While overall species richness varied only slightly along the analysed environmental gradients, significant changes were observed for relative proportions of species from different life forms and families. Soil pH and elevation had the highest influence on the variation in species composition (23.3% explained). We found 22 species indicative of calcareous rock and 24 species indicative of lime-deficient rock types. The South Aegean Plant Indicator Values were relatively strongly correlated with environmental variables.

Conclusions

Results indicate considerable species turnover both along climatic (elevation) and soil gradients, highlighting the special importance of soil pH. The data provided by our study are expected to supply relevant ecological background information for a pending classification of East Mediterranean annual-rich vegetation.     

Plant genetics affects arthropod community richness and composition: evidence from a synthetic eucalypt hybrid population

To examine how genetic variation in a plant population affects arthropod community richness and composition, we quantified the arthropod communities on a synthetic population of Eucalyptus amygdalina, E. risdonii, and their F1 and advanced-generation hybrids. Five major patterns emerged. First, the pure species and hybrid populations supported significantly different communities. Second, species richness was significantly greatest on hybrids (F1 > F2 > E. amygdalina > E. risdonii). These results are similar to those from a wild population of the same species and represent the first case in which both synthetic and wild population studies confirm a genetic component to community structure. Hybrids also acted as centers of biodiversity by accumulating both the common and specialist taxa of both parental species (100% in the wild and 80% in the synthetic population). Third, species richness was significantly greater on F1s than the single F2 family, suggesting that the increased insect abundance on hybrids may not be caused by the breakup of coadapted gene complexes. Fourth, specialist arthropod taxa were most likely to show a dominance response to F1 hybrids, whereas generalist taxa exhibited a susceptible response. Fifth, in an analysis of 31 leaf terpenoids that are thought to play a role in plant defense, hybrids were generally intermediate to the parental chemotypes. Within the single F2 family, we found significant associations between the communities of individual trees and five individual oil components, including oil yield, demonstrating that there is a genetic effect on plant defensive chemistry that, in turn, may affect community structure. These studies argue that hybridization has important community-level consequences and that the genetic variation present in hybrid zones can be used to explore the genetic-based mechanisms that structure communities.     

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large‐scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus''s time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic‐dry part that has a species rich grass‐dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%–40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.     

Fungi from the roots of the common terrestrial orchid Gymnadenia conopsea

The fungal community associated with the terrestrial photosynthetic orchid Gymnadenia conopsea was characterized through PCR-amplification directly from root extracted DNA and cloning of the PCR products. Six populations in two geographically distinct regions in Germany were investigated. New ITS-primers amplifying a wide taxonomic range including Basidiomycetes and Ascomycetes revealed a high taxonomic and ecological diversity of fungal associates, including typical orchid mycorrhizas of the Tulasnellaceae and Ceratobasidiaceae as well as several ectomycorrhizal taxa of the Pezizales. The wide spectrum of potential mycorrhizal partners may contribute to this orchid's ability to colonize different habitat types with their characteristic microbial communities. The fungal community of G. conopsea showed a clear spatial structure. With 43 % shared taxa the species composition of the two regions showed only little overlap. Regardless of regions, populations were highly variable concerning taxon richness, varying between 5 and 14 taxa per population. The spatial structure and the continuous presence of mycorrhizal taxa on the one hand and the low specificity towards certain fungal taxa on the other hand suggest that the fungal community associated with G. conopsea is determined by multiple factors. In this context, germination as well as pronounced morphological and genetic differentiation within G. conopsea deserve attention as potential factors affecting the composition of the fungal community.     

Composition and spatio-temporal changes of soil macroinvertebrates in the biodiversity hotspot of northern Hengduanshan Mountains, China

Aims

The aim of this study was to analyze the composition and spatio-temporal variation of soil macroinvertebrate communities in the northern Hengduanshan Mountains, Southwest China.

Methods

The soil macroinvertebrates were investigated in April, August and November of 2008 in two deciduous broad-leaved forests: secondary shrub forest (SSF) and Betula albosinensis forest (BSF), two coniferous forests: Picea asperata plantation (PAP) and Abies fabri and Larix kaempferi mixed forest (ALF), a coniferous (A. fabri) and broad leaf (B. albosinensis) mixed forest (ABF) and a subalpine meadow (SM) at elevations of 2659 to 3845 m.

Results

The soil macroinvertebrate community showed typical zonal characteristics compared with other localities in China. It comprised at least 113 taxa and was dominated by Insects (43.33%, mainly Coleoptera and Diptera), followed by Diplopoda (16.37%), Malacostraca (14.31%), Oligochaeta (12.71%) and Chilopoda (6.67%). Abundances of each taxa showed clear differences among habitats. Community abundance ranged from 71.56 individuals/m² in the PAP to 148.00 individuals/m² in the SM. The composition and structure of the soil macroinvertebrate communities varied among the six habitats and changed with the sampling periods. The richness, abundance and Shannon index of soil macroinvertebrate communities were significantly different among habitats, but not between sampling periods. Significant temporal responses in abundance were recorded in the SSF and BSF and the Shannon index for the SM. Further analysis showed that the abundance of the seven taxonomic groups also differed significantly among habitats, but that sampling period only had significant effects on a few taxonomic groups. Patterns of temporal variation in abundance differed among the seven taxonomic groups, even when the same taxa also differed markedly among habitat types. On the whole, these temporal variations in abundance on community and taxa group levels were greater in the SSF and BSF than in the PAP, ABF, ALF and the SM. However, the habitat had a stronger effect on soil macroinvertebrates than the sampling period. Moreover, a significant correlation was found between the abundance, richness and Shannon index of soil macroinvertebrate community and plant species richness, but not with soil properties or elevation. Additionally, more taxonomic groups were significantly influenced by the litter mass and plant coverage, but few with soil properties.

Conclusions

Plant community was the main environmental determinant influencing macroinvertebrate distribution in ecosystem of the northern Hengduanshan Mountains and presented a greater effect on the soil macroinvertebrates than soil properties or elevation. The temporal effects on soil macroinvertebrates were stronger in the deciduous broad-leaved forests than in the coniferous forests.     

Potential effects of future climate change on global reptile distributions and diversity

Aim

Until recently, complete information on global reptile distributions has not been widely available. Here, we provide the first comprehensive climate impact assessment for reptiles on a global scale.

Location

Global, excluding Antarctica.

Time period

1995, 2050 and 2080.

Major taxa studied

Reptiles.

Methods

We modelled the distribution of 6296 reptile species and assessed potential global and realm-specific changes in species richness, the change in global species richness across climate space, and species-specific changes in range extent, overlap and position under future climate change. To assess the future climatic impact on 3768 range-restricted species, which could not be modelled, we compared the future change in climatic conditions between both modelled and non-modelled species.

Results

Reptile richness was projected to decline significantly over time, globally but also for most zoogeographical realms, with the greatest decreases in Brazil, Australia and South Africa. Species richness was highest in warm and moist regions, with these regions being projected to shift further towards climate extremes in the future. Range extents were projected to decline considerably in the future, with a low overlap between current and future ranges. Shifts in range centroids differed among realms and taxa, with a dominant global poleward shift. Non-modelled species were significantly stronger affected by projected climatic changes than modelled species.

Main conclusions

With ongoing future climate change, reptile richness is likely to decrease significantly across most parts of the world. This effect, in addition to considerable impacts on species range extent, overlap and position, was visible across lizards, snakes and turtles alike. Together with other anthropogenic impacts, such as habitat loss and harvesting of species, this is a cause for concern. Given the historical lack of global reptile distributions, this calls for a re-assessment of global reptile conservation efforts, with a specific focus on anticipated future climate change.     

Influence of Habitat and Climate Variables on Arbuscular Mycorrhizal Fungus Community Distribution,as Revealed by a Case Study of Facultative Plant Epiphytism under Semiarid Conditions

In semiarid Mediterranean ecosystems, epiphytic plant species are practically absent, and only some species of palm trees can support epiphytes growing in their lower crown area, such as Phoenix dactylifera L. (date palm). In this study, we focused on Sonchus tenerrimus L. plants growing as facultative epiphytes in P. dactylifera and its terrestrial forms growing in adjacent soils. Our aim was to determine the possible presence of arbuscular mycorrhizal fungi (AMF) in these peculiar habitats and to relate AMF communities with climatic variations. We investigated the AMF community composition of epiphytic and terrestrial S. tenerrimus plants along a temperature and precipitation gradient across 12 localities. Epiphytic roots were colonized by AMF, as determined by microscopic observation; all of the epiphytic and terrestrial samples analyzed showed AMF sequences from taxa belonging to the phylum Glomeromycota, which were grouped in 30 AMF operational taxonomic units. The AMF community composition was clearly different between epiphytic and terrestrial root samples, and this could be attributable to dispersal constraints and/or the contrasting environmental and ecophysiological conditions prevailing in each habitat. Across sites, the richness and diversity of terrestrial AMF communities was positively correlated with rainfall amount during the most recent growing season. In contrast, there was no significant correlation between climate variables and AMF richness and diversity for epiphytic AMF communities, which suggests that the composition of AMF communities in epiphytic habitats appears to be largely determined by the availability and dispersion of fungal propagules from adjacent terrestrial habitats.     

Ecological realism and mechanisms by which diversity begets stability

We investigated how ecological realism might impact the outcome of three experimental manipulations of species richness to determine whether the patterns and the mechanisms underlying richness–variability relationships differ as ecological communities are increasingly exposed to external forces that may drive richness–variability patterns in nature. To test for such an effect, we conducted experiments using rock pool meio‐invertebrate communities housed in three experimental venues: controlled laboratory microcosms, artificially constructed rock pools in the field, and naturally occurring rock pools in the field. Our results showed that experimental venue can have a strong effect on the outcome of richness manipulation experiments. As ecological realism increased, the strength of the relationship between species richness and community variability declined from 32.9% in the laboratory microcosms to 16.8% in the artificial pools to no effect of species richness on community variability in the natural rock pools. The determinants of community variability also differed as ecological realism increased. In laboratory microcosms, community variability was driven solely by mechanisms related to increasing species richness. In artificial rock pools, community variability was driven by a combination of direct and indirect environmental factors as well as mechanisms related to increasing species richness. In the natural rock pools community variability was independent of species richness and was only related to environmental factors. In summary, we found that stabilizing mechanisms associated with species interactions were influential in establishing species richness–variability relations only in the less realistic experimental venues (the laboratory microcosms and the artificial rock pools in the field), and that these mechanisms diminished in importance as ecological realism and complexity of the experimental venue increased. Our results suggest that the effects of diversity might be more difficult to detect in natural systems due to the combined effects of biotic and abiotic forcing, which can mask our ability to detect richness effects.     

Effects of nonnative species on the stability of riverine fish communities

Despite the increasing ubiquity of biological invasions worldwide, little is known about the scale-dependent effects of nonnative species on real-world ecological dynamics. Here, using an extensive time series dataset of riverine fish communities across different biogeographic regions of the world, we assessed the effects of nonnative species on the temporal variability and synchrony in abundance at different organizational levels (population, metapopulation, community and metacommunity) and spatial scales (stream reach and river basin). At the reach scale, we found that populations of nonnative species were more variable over time than native species, and that this effect scaled up to the community level – significantly destabilizing the dynamics of riverine fish communities. Nonnative species not only contributed to reduced community stability, but also increased variability of native populations. By contrast, we found no effect of nonnative species dominance on local interspecific synchrony among native species. At the basin scale, nonnative metapopulations were again more variable than the native ones. However, neither native metapopulations nor metacommunities showed differences in temporal variability or synchrony as nonnative species dominance increased basin-wide. This suggests a ‘dilution effect’ where the contribution to regional stability of local native populations from sites displaying low levels of invasion reduced the destabilizing effects of nonnative species. Overall, our results indicate that accounting for the destabilizing effect of nonnative species is critical to understanding native species persistence and community stability.     

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity

Background

“The enigma of soil animal species diversity” was the title of a popular article by J. M. Anderson published in 1975. In that paper, Anderson provided insights on the great richness of species found in soils, but emphasized that the mechanisms contributing to the high species richness belowground were largely unknown. Yet, exploration of the mechanisms driving species richness has focused, almost exclusively, on above-ground plant and animal communities, and nearly 35 years later we have several new hypotheses but are not much closer to revealing why soils are so rich in species. One persistent but untested hypothesis is that species richness is promoted by small-scale environmental heterogeneity.

Methodology/Principal Findings

To test this hypothesis we manipulated small-scale heterogeneity in soil properties in a one-year field experiment and investigated the impacts on the richness of soil fauna and evenness of the microbial communities. We found that heterogeneity substantially increased the species richness of oribatid mites, collembolans and nematodes, whereas heterogeneity had no direct influence on the evenness of either the fungal, bacterial or archaeal communities or on species richness of the large and mobile mesostigmatid mites. These results suggest that the heterogeneity-species richness relationship is scale dependent.

Conclusions

Our results provide direct evidence for the hypothesis that small-scale heterogeneity in soils increase species richness of intermediate-sized soil fauna. The concordance of mechanisms between above and belowground communities suggests that the relationship between environmental heterogeneity and species richness may be a general property of ecological communities.     

Global distribution and richness of terrestrial mammals in tidal marshes

Aim

Understanding the determinants of species distribution and richness is key to explaining global ecological patterns. We examined the current knowledge about terrestrial mammals in tidal marshes and evaluated whether species richness increased with the marsh surface area and/or with their proximity to the equator and whether species distribution ranges decreased with latitude.

Location

Global.

Methods

We reviewed the existing literature on terrestrial mammals in tidal marshes. We examined their ecological characteristics (e.g. habitat specialists, native or alien), predicted their variation in species richness and range size along latitude, and explored factors, such as surface area, underlying the global patterns found.

Results

We found 962 records, describing 125 mammalian species using tidal marshes worldwide, also including several alien species. Most species (95%) were not marsh specialized, and some (18%) were of conservation concern. There were information gaps in South America, Africa, Australia and Asia, and a lack of information about mammalian ecological roles worldwide. We found that species richness increased with surface area, and showed a bimodal pattern peaked between 40° and 50° latitude in each hemisphere. We found no relationship between latitude and species range size.

Main conclusions

Our worldwide findings revealed a broader range of tidal marshes inhabited by terrestrial mammals, and higher values of species richness than previously reported. The bimodal pattern of species richness was consistent with the species–area hypothesis, but it also suggested that further studies of species distribution in relation to historical and environmental factors will yield significant insights about variables driving richness in tidal marshes. Despite terrestrial mammal ubiquitous distribution in these ecosystems, there are considerable geographic gaps as regards knowledge about their functional importance and the impact of alien species on tidal marsh functioning. Consequently, extending our research efforts is key to planning the conservation of these coastal ecosystems.     

BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

Motivation

We have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present-day to millions of years ago.

Main Types of Variables Included

BioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series.

Spatial Location and Grain

The database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm² to grid cells of ~100 km².

Time Period and Grain

BioDeepTime in aggregate currently spans the last 451 million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7 years and for fossil series is 54,872 years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years.

Major Taxa and Level of Measurement

The database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime.

Software Format

SQLite, Comma-separated values.     

Changes in the dominant assembly mechanism drive species loss caused by declining resources

The species–energy hypothesis predicts that more productive areas support higher species richness. Conversely, when resources are reduced, species richness is reduced. Empirical tests of whether extinctions are predominantly caused by environmental constraints or competitive exclusion are lacking. We experimentally reduced dead wood to c. 15% of the initial amount after a major windstorm and examined changes in assembly mechanisms by combining trait‐based and evolutionary species dissimilarities of eight taxonomic groups, differing in their dependence on dead wood (saproxylic/non‐saproxylic). Species richness and assembly mechanisms of non‐saproxylic taxa remained largely unaffected by removal of dead wood. By contrast, extinctions of saproxylic species were caused by reversing the predominant assembly mechanisms (e.g. increasing importance of competitive exclusion for communities assembled through environmental filtering or vice versa). We found no evidence for an intensification of the predominant assembly mechanism (e.g. competitive exclusion becoming stronger in a competitively structured community).     

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing

Background

The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes’ phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities.

Results

We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community.

Conclusions

The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing.