Pool Of Taxa Research Articles

Bridging ecological processes to diversity formation and functional profiles in belowground bacterial communities

Revealing the generation and maintenance of biodiversity is a central goal in ecology, but how dispersal, selection, and regional taxon pool size shape soil microbial communities is not well understood. Here, we examined how dispersal and environmental selection affected soil bacterial diversity and their related metabolic functions by leveraging large-scale cross-biome soil surveys of ∼1400 samples from diverse ecosystems across China, including agricultural, forest, grassland, and wetland soils. Our results showed that high dispersal increased α-diversity and decreased β-diversity, whereas strong selection generated the opposite pattern in various ecosystems. This is likely due to dispersal enabling species access to otherwise unreachable habitats, and environmental selection excluding non-adapted species from communities. The α-diversity increased with γ-diversity, whereas β-diversity did not covary. We also showed that bacterial phylotypes positively associated with dispersal and selection exhibited distinct metabolic diversity. Dispersal-induced phylotypes, which were abundant in agricultural soils, exhibited more metabolic diversity in fructose and mannose, starch and sucrose, and nitrogen metabolism. Conversely, selection-induced phylotypes, dominated in wetland soils, were primarily associated with sulfur and methane metabolism. In addition, the complexity of taxon associations increased when communities had higher selection increasing β-diversity. Our study establishes the predictive links of ecological processes to microbial diversity, metabolic functions, and taxon coexistence, thus facilitating a better understanding of the mechanisms underlying biodiversity generation and conservation.

Distribution of functionally distinct native and non‐indigenous species within marine urban habitats

AbstractAimTrait‐based approaches are powerful to examine the processes associated with biological invasions. Functional comparison among native and non‐indigenous species (NIS) can notably infer whether novel assemblages result from neutral or niche‐based assembly rules. Applying such a framework to biofouling communities, our study aimed to elucidate their distributions within two marine urban habitats (namely floating vs. nonfloating habitats).LocationSoutheast Pacific—Central Chilean coastline.MethodsHere, we examined the distribution of 12 functional traits in fouling communities established on settlement plates, after 3 and 13 months of deployment in the two habitats and across ports in Central Chile. Based upon previously described differences of assemblages and NIS contribution across habitats, we hypothesized that nonindigenous, cryptogenic and native taxon pools would be functionally distinct (and trait biased), and that functional diversity and structure would vary across habitats and successional stages.ResultsOur results show, as anticipated, that nonindigenous (13 taxa), cryptogenic (12) and native (18) taxon pools are functionally distinct, though overlapping in the trait space. Non‐indigenous species are rather related to colonizing traits, while native species are more related to competitive traits. Only one widespread NIS was functionally similar to the late successional and most competitive native species, including taxa elsewhere invasives. Despite differences in taxonomic composition between habitats, we did not observe functional differences between them. In contrast, temporal variations across colonization stages were detected along with an increased contribution in large and long‐lived taxa, together with site‐specific trajectories.Main ConclusionsWe conclude that the functional distinctness among nonindigenous, cryptogenic and native taxa occupying artificial habitats in ports reflects niche‐based processes. Site‐specific trajectories indicate that scale‐dependent assembly processes, such as dispersal and species interactions, are at play.

Arbuscular Mycorrhizal Fungal Communities in the Soils of Desert Habitats.

Deserts cover a significant proportion of the Earth’s surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.

Symbiont dynamics during ecosystem succession: co-occurring plant and arbuscular mycorrhizal fungal communities.

Although mycorrhizas are expected to play a key role in community assembly during ecological succession, little is known about the dynamics of the symbiotic partners in natural systems. For instance, it is unclear how efficiently plants and arbuscular mycorrhizal (AM) fungi disperse into early successional ecosystems, and which, if either, symbiotic partner drives successional dynamics. This study describes the dynamics of plant and AM fungal communities, assesses correlation in the composition of plant and AM fungal communities and compares dispersal limitation of plants and AM fungi during succession. We studied gravel pits 20 and 50 years post abandonment and undisturbed grasslands in Western Estonia. The composition of plant and AM fungal communities was strongly correlated, and the strength of the correlation remained unchanged as succession progressed, indicating a stable dependence among mycorrhizal plants and AM fungi. A relatively high proportion of the AM fungal taxon pool was present in early successional sites, in comparison with the respective fraction of plants. These results suggest that AM fungi arrived faster than plants and may thus drive vegetation dynamics along secondary vegetation succession.

Hierarchical assembly rules in arbuscular mycorrhizal (AM) fungal communities

Processes controlling the assembly of microorganism communities are poorly understood. In taxonomic groups where many organisms are only described from environmental DNA, phylogenetic relationships may provide a proxy for functional attributes. We used a null model approach to compare the phylogenetic diversity of arbuscular mycorrhizal (AM) fungal communities coexisting within the roots of plant individuals sampled worldwide. Parallel null models were constructed using taxon pools that were filtered according to some or all of spatial scale, ecosystem type and host plant identity. This allowed us to assess the importance of individual ecological gradients in shaping phylogenetic diversity and to identify potential mechanisms. In general, coexisting fungi were more phylogenetically clustered than the random communities defined by null models. However, clustering increased when null models incorporated large spatial scales, indicating that communities are assembled according to the dispersal ability of fungal taxa. Clustering also increased when null models incorporated a variety of ecosystems or host plant species, indicating effects of habitat filtering and mutualist partner selection at wide and local scales, respectively. We did not record phylogenetic overdispersion among coexisting fungi, providing no support for a role of limiting similarity in structuring AM fungal communities. However, the existence of significant clustering even in comparison with the finest-scale null model indicates that, in addition to larger-scale deterministic and neutral processes, the symbiosis may be further influenced by genotypic selectivity or stochastic processes at very small scales.

The importance of biotic interactions for the prediction of macroinvertebrate communities under multiple stressors

Summary The community assembly of macroinvertebrates in streams depends on the regional taxon pool, dispersal limitations, local habitat conditions and biotic interactions. By integrating existing knowledge about these processes from theoretical ecology in a mechanistic model, we can test our mechanistic understanding and disentangle multiple stressor effects on community assembly. To assess to which degree we can predict the community composition of macroinvertebrates, we integrated these processes in the mechanistic food web model Streambugs and tested it on 36 sites in the Glatt catchment on the Swiss plateau. The model predicts the observation probability of taxa from a regional taxon pool at each site taking into account uncertain knowledge on parameters, environmental conditions at the sites and sampling errors. We use allometric scaling according to the metabolic theory of ecology, ecological stoichiometry and autecological data from trait databases that include the current knowledge on habitat requirements of the different taxa to parameterize their growth, respiration and death. Without any calibration, for the majority of taxa at the 36 sites, the difference between the observed and predicted relative frequency of occurrence is <50% when taking prior parameter uncertainty and the uncertainty of environmental conditions into account (79% compared to 61% for the random model). By calibrating taxon‐specific modification factors for the growth rate, we can increase the model compliance with data. Analysing the influence of different ecological traits and their corresponding environmental influence factors reveals that feeding types and sensitivity to organic toxicants contribute most to the predictive capabilities of the model in this catchment. The influence of temperature stress and oxygen depletion due to pollution with organic matter on the community composition is negligible. These results confirm our expectations regarding the most important water quality issues of streams on the Swiss plateau. Current velocity plays an intermediate role in this model application. The contribution of the feeding types to model performance highlights the importance of taking biotic interactions (competition for food sources and predator–prey interactions) into account to predict the coexistence of taxa. Better knowledge of the actual feeding links in the food web (e.g. from gut content or stable isotope data) that are currently inferred from feeding types, body size and food availability could further improve this approach.

Effects of habitat types and within lake environmental gradients on the diversity of chironomid assemblages

Understanding the distribution of biotic diversity across various spatial scales and environmental gradients is important from fundamental, practical and conservation biological aspects. We applied a hierarchical diversity partitioning framework to quantify the variability of sample level α- and β 1 -diversity, and environment related β 2 -diversity of benthic chironomid assemblages within and among a priori defined habitat types, and along the gradients of individual environmental factors in a large and shallow lake (Lake Balaton, Hungary). Taxon richness (both additive and multiplicative) and Shannon index based diversity approaches yielded highly concordant results. The α-diversity was much lower and β 1 -diversity higher than predicted by null model and both measures varied substantially among habitat types and along most individual environmental gradients. The β 2 -diversity indicated a marked variability of taxon (identified at species to genus level) pool among habitat types and higher than predicted taxon turnover along all examined environmental gradients. Moreover, the observed β 2 -diversity varied greatly among individual environmental gradients. The difference between the expected and observed β 2 -diversity values suggests that taxon turnover was most influential (in decreasing order) along the algae coverage gradient, the lake bed substratum gradient and the macrophyte coverage gradient among others. We argue that within-lake environmental heterogeneity and its effect on the taxon richness should receive more attention in biodiversity assessment and conservation. Management could benefit from the identification of within lake gradients along which taxonomic turnover maximizes.

The composition of arbuscular mycorrhizal fungal communities in the roots of a ruderal forb is not related to the forest fragmentation process.

Land-use changes and forest fragmentation have strong impact on biodiversity. However, little is known about the influence of new landscape configurations on arbuscular mycorrhizal fungal (AMF) community composition. We used 454 pyrosequencing to assess AMF diversity in plant roots from a fragmented forest. We detected 59 virtual taxa (VT; phylogenetically defined operational taxonomic units) of AMF - including 10 new VT - in the roots of Euphorbia acerensis. AMF communities were mainly composed of members of family Glomeraceae and were similar throughout the fragmented landscape, despite variation in forest fragment size (i.e. small, medium and large) and isolation (i.e. varying pairwise distances). AMF communities in forest fragments were phylogenetically clustered compared with the global, but not regional and local AMF taxon pools. This indicates that non-random community assembly processes possibly related to dispersal limitation at a large scale, rather than habitat filtering or biotic interactions, may be important in structuring the AMF communities. In this system, forest fragmentation did not appear to influence AMF community composition in the roots of the ruderal plant. Whether this is true for AMF communities in soil and the roots of other ecological groups of host plants or in other habitats deserves further study.

How stressor specific are trait-based ecological indices for ecosystem management?

Using macroinvertebrates as ecological indicators for different stressors has a long tradition. However, when applied to field data, one often observes correlations between different macroinvertebrate indices that can be attributed to both correlations of stressors and inherent correlations due to the sensitivity of taxa to different stressors. Ignoring the source of any given correlation leads to ambiguous conclusions about the impact of different stressors.Here, we demonstrate how to distinguish the causes of correlation by means of Monte Carlo simulations. We assessed to which degree trait-based indices are stressor-specific and whether this depends on the pool of taxa and its taxonomic resolution. Therefore, we (1) analysed the frequencies of “sensitive” and “insensitive” taxa for pairwise combinations of different indices, (2) analysed the inherent correlation of indices with random samples from different taxon pools derived from field samples and from a complete species list of a whole ecoregion, and (3) compared this inherent correlation with the actual correlation of the field samples. We exemplified this approach by analysing two existing indices (SPEARpesticides, Saprobic Index) and new indices for temperature, flow and pH stress. We used these new indices to illustrate our approach while in-depth testing of their applicability was not the focus of our study.We found strong correlations between several indices in our study area at the Swiss Plateau. The probability that this correlation is only due to inherent correlation in the taxa sensitivities was low (maximum of 0.34). The problem of inherent correlation between indices is more severe for the smaller taxon pool with lower taxonomic resolution.Correlation in the sensitivity of different taxa to different stressors leads to an inherent correlation in trait-based indices, which weakens their explanatory power. Our results highlight the importance of correlation analyses when using trait-based indices to guide ecosystem-management, especially in regions with reduced biodiversity.

Dispersal distance and the pool of taxa, but not barriers, determine the colonisation of restored river reaches by benthic invertebrates

Summary Restoration is an increasingly central theme in river ecology. Recent studies have highlighted the importance of the species pool in the surrounding river network for determining colonisation of restored river reaches by both invertebrates and fish. Using a comprehensive data set of 21 river restoration sites and 292 sites in the immediate surroundings, we tested the influence of distance to nearest colonist source on invertebrate colonisation based on a comparison of river network distances and Euclidean distances, expecting river network distances would better align with colonisation rates. We then assessed the importance of dispersal distance in relation to several other parameters, such as the number and intensity of barriers along the river network, surrounding taxon pool occupancy rate, physical characteristics of the restored sites and restoration techniques used in determining colonisation of commonly occurring benthic invertebrates. We hypothesised that (i) distance would be critical, with colonisation of restored sites declining with increasing distance; (ii) barriers between these sites would be a minor, but taxon‐specific, influence on the colonisation; and (iii) the higher the regional pool occupancy rate of a certain taxon, the higher its probability of presence at a restored site. Overall, taxon pool occupancy rate was the most important driver of colonisation likelihood, followed by distance to nearest source, with the first kilometre particularly important. The effect of barriers was minor but significant, and taxon identity had no effect on the predictive ability of the model. Factors associated with the restoration projects such as techniques used and physical characteristics had minor influences, being completely outweighed by taxon pool and dispersal‐related factors. To gauge the likelihood of successful outcomes of habitat restoration projects, we suggest it is important to assess regional taxon pools and ensure distances between healthy populations are minimised. These results clearly emphasise the importance of spatial planning for restoration projects.

Root-colonizing and soil-borne communities of arbuscular mycorrhizal fungi in a temperate forest understorey

We analyzed arbuscular mycorrhizal fungal (AMF) communities in plant root samples from a natural forest ecosystem — a primeval forest in Järvselja, Estonia. AMF small-subunit (SSU) ribosomal RNA genes were subjected to 454-pyrosequencing and BLAST-based taxonomic identification. Seventy-six AMF sequence groups (virtual taxa, VT) were identified from plant roots. Taken together with seven additional VT recorded in an earlier investigation of soil AMF communities at the site, this represents the highest number of AMF reported from a single ecosystem to date. The six study plant species hosted similar AMF communities. However, AMF community composition in plant roots was significantly different from that in soil and considerably more VT were retrieved from roots than from soil. AMF VT identified from plant roots as a whole and from individual plant species were frequently phylogenetically clustered compared with local and global taxon pools, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped fungal assemblages. In contrast, the phylogenetic dispersion of AMF communities in soil did not differ from random subsets of the local or global taxon pools.

Declines in littoral species richness across both spatial and temporal nutrient gradients: a palaeolimnological study of two taxonomic groups

Summary1. Using a palaeolimnological approach in shallow lakes, we quantified the species richness responses of diatoms and Cladocera to phosphorus enrichment. We also examined differences in species richness responses between littoral and pelagic assemblages of our focal communities. To address both spatial and temporal relationships, our study includes an analysis of both surface sediments from 40 lakes and of a lake sediment record spanning c. 120 years. The objective of our study was to determine whether similar species richness patterns occurred across trophic levels, as well as along spatial and temporal gradients.2. We found that both diatom and Cladocera species richness estimates significantly declined with increasing phosphorus across space and through time. When the assemblages were subdivided according to known habitat preferences, littoral biodiversity maintained a negative trend, whereas pelagic species richness tended to show no relationship with phosphorus.3. Negative productivity–diversity patterns have been observed across almost all palaeolimnological studies that span large productivity gradients. This congruence in patterns is most likely due to the similarity in data collection methods and in focal communities studied. The contrasting responses between littoral and pelagic assemblages may be explained by the differences in physical habitat and the pool of taxa in each of these environments. Consistent with the literature, we found statistical support for the idea that littoral diversity declines could be explained by an interaction between macrophytes and nutrients along strong trophic gradients. The general lack of a diversity response in our pelagic assemblages could be attributable to the limited pool of subfossil taxa. The response of the pelagic diatom could also be related to their broad range of nutrient tolerances.4. The observed negative response of species richness to phosphorus enrichment, particularly in the littoral assemblages, has implications for ecosystems functioning because communities with reduced biodiversity often are less resilient to anthropogenic change.

Environmental harshness and global richness patterns in glacier‐fed streams

ABSTRACTAim To test for a possible effect of environmental harshness on large‐scale latitudinal and elevational patterns in taxon richness of macrofauna in arctic and alpine glacier‐fed streams.Location Svalbard (79° N), Iceland (65° N), Norway (62° N), Switzerland and Italy (46° N), France (43° N), New Zealand (43° S) and Ecuador (0°), covering an elevational gradient from sea level to 4800 m a.s.l.Methods We gathered data from 63 sites along 13 streams and created an index of glacial influence (the glacial index, GI) as an integrative proxy for environmental harshness. The explicative power of the GI, environmental variables, latitude and elevation on taxon richness was tested in generalized linear models. Taxon richness along geographical gradients was analysed at standardized levels of GI in contour plots. Beta diversity and assemblage similarity was calculated at different GI intervals and compared with a null‐model.Results Overall, taxon richness decreased exponentially with increased GI (r2= 0.64), and of all included factors, GI had the highest explicative power. At low values of GI we found that local taxon richness varied along the coupled gradients of latitude and elevation in a hump‐shaped manner. However, this pattern disappeared at high values of GI, i.e. when environmental harshness increased. Beta diversity increased, while similarity among assemblages decreased towards high GI values.Main conclusions In our study system, the number of taxa able to cope with the harshest conditions was largely independent of the regional taxon pool, and environmental harshness constituted a ‘fixed’ constraint for local richness, irrespective of latitude and elevation. Contrary to expectations, we found that beta diversity was highest and similarity lowest among the harshest sites, suggesting that taxon richness was not solely driven by niche selection based on environmental tolerances, but also stochastic ecological drift, leading to dispersal‐limited communities.

Arbuscular mycorrhizal fungal communities in plant roots are not random assemblages

We investigated whether arbuscular mycorrhizal fungal (AMF) communities in plant roots are random subsets of the local taxon pool or whether they reflect the action of certain community assembly rules. We studied AMF small subunit rRNA gene sequence groups in the roots of plant individuals belonging to 11 temperate forest understorey species. Empirical data were compared with null models assuming random association. Distinct fungal species pools were present in young and old successional forest. In both forest types, the richness of plant-AMF associations was lower than expected by chance, indicating a degree of partner selectivity. AMF communities were generally not characteristic of individual plant species, but those associated with ecological groups of plant species - habitat generalists and forest specialists - were nonrandom subsets of the available pool of fungal taxa and differed significantly from each other. Moreover, these AMF communities were the least distinctive in spring, but developed later in the season. Comparison with a global database showed that generalist plants tend to associate with generalist AMF. Thus, the habitat range of the host and a possible interaction with season played a role in the assembly of AMF communities in individual plant root systems.

Anthropogenic disturbance and landscape patterns affect diversity patterns of aquatic benthic macroinvertebrates

Measures of species diversity are valuable tools for assessing ecosystem health. However, most assessments have addressed individual sites or regional taxon pools, with few comparisons of differences in assemblage composition within or among regions. We examined the effects of anthropogenic disturbance on local richness (a diversity) and species turnover (b diversity) of benthic macroinvertebrates in small streams within and between 2 ecoregions (Northern Piedmont vs Southeastern Plains ecoregions) of the Patuxent River basin (Maryland, USA). Regional species pools did not differ between ecoregions (Piedmont = 166 taxa, Plains = 162 taxa); however, local richness was lower in the Plains (mean = 17.4 taxa/stream) compared to the Piedmont (mean = 22.2 taxa/stream). When streams were categorized into disturbance classes (low, medium, high), local richness did not differ among categories for either region. However, at the entire Patuxent scale, local richness tended to decrease with % impervious cover in a watershed. Variation in species composition, analyzed with nonmetric multidimensional scaling (nMDS), differed significantly between Piedmont and Plains streams, and Plains streams had higher b diversity than Piedmont streams. When partitioned by disturbance category and region, b diversity differed only between the low-disturbance sites (Plains . Piedmont). Relationships between b diversity and environmental variables varied by region. b diversity was weakly negatively related to % row-crop cover in a watershed at the entire Patuxent scale. For the Piedmont region, b diversity tended to decrease with % forest, % pasture, and % row-crop cover in a watershed. Such negative relationships between b diversity and landuse variables indicate a possible homogenization of the assemblage. The incongruence between diversity measures and composition measures, together with differing effects of anthropogenic land use on b diversity in the 2 regions, emphasizes the need to incorporate both a and b diversity and regional environmental factors in conservation/land management studies.

Effects of Forest Management on Amphibians and Reptiles: Generalist Species Obscure Trends Among Native Forest Associates

In the future, land stewards are expected to increase their use of fire surrogates to manage longleaf pine forests. Varying land management strategies may have disparate effects on wildlife and the strength of these effects may depend upon the degree to which each target species is associated with the longleaf pine forest. To determine how amphibian and reptile assemblages respond to prescribed burns and fire surrogates, we sampled these animals within plots of land managed under four common management practices (burning, thinning, thinning and burning, and application of herbicide) and on unmanaged reference plots. We analyzed these data first by examining the entire herpetofauna and then by repeating all analyses for only taxa exhibiting some evidence of an evolutionary association with longleaf pine forests. We found that estimates of species richness of all amphibians did not differ significantly among treatments. These trends were altered when the pool of taxa was restricted to amphibian species known to be associated with longleaf pine forests. For associated amphibians, species richness was elevated on plots that were exposed to herbicide and burn, hardwood thinning, and hardwood thinning plus prescribed fire, relative to reference plots. No significant trends were identified for squamates in general or those squamate species known to be associated with longleaf forests. Fire surrogates may facilitate conservation for individual species of the ancestral biota of longleaf pine forests, but these trends may be obscured when entire assemblages are considered.

The Effect of Paralogous Lineages on the Application of Reconciliation Analysis by Cophylogeny Mapping

Paralogy defines similarity caused by duplication rather than common descent and is well known in the case of paralogous gene copies within a single genome. The term is here extended to paralogous lineages of associates within a single host. The phylogenies of four genera within the Herpesviridae were reconciled with host phylogenies using cophylogenetic mapping. The observed correspondence for each pair of phylogenies was evaluated through randomization of the viral phylogeny and demonstrated to be greater than expected by chance. A simulation study was then carried out to assess the influence of paralogous lineages on the efficacy of reconciliation analysis. Combining viral taxa from different genera that infected common hosts introduced incongruence into the cophylogenies and reduced both the minimum and maximum observed number of codivergence events relative to the initial analysis of orthologous clades. However, at an average sample size this did not alter the fundamental significance of observed correspondence. With smaller sample sizes, the number of orthologous taxa selected at random from the pool of taxa was reduced. False-negative results then increased in proportion from 0.02 to 0.33. These results demonstrated that reconciliation analysis is robust under conditions of paralogy at "normal" sample sizes but is adversely affected by a combination of paralogy and low sample size. Consideration of phylogenies for Papillomavirus, Atadenovirus, and Mastadenovirus suggest that paralogous lineages may be a widespread phenomenon among DNA viruses and that duplication irrespective of host speciation is an important cause of viral diversification.

Bioassessment without reference sites: use of environmental filters to predict natural assemblages of river macroinvertebrates

Abstract Sets of reference sites often are used to create a benchmark for biological assessment of river condition. Unfortunately, human modification of river systems is now so widespread and complex that this practice can result in comparisons against a reference condition that embodies an appreciable and poorly defined degree of human impact. Our paper describes an alternative means of deriving reference conditions that does not require the use of reference sites. Instead, the tolerances and preferences of each taxon in the regional taxon pool are established for various environmental factors. These factors can be regarded as filters that exclude members of the regional pool from sites where environmental conditions are incompatible with their tolerances and preferences. The suite of taxa that can occupy an assessment site under natural conditions can be estimated if the natural values of the environmental filters at that site can be determined. A comparison between this suite of potential taxa and the ...