Spatial scaling of microbial eukaryote diversity

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

BACKGROUND

High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.

RESULTS

Our broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals.

CONCLUSIONS

Currently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼ 15.64 m(2) and volume of ∼ 0.09 m(3), 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼ 2 m were significantly more similar than samples separated by ∼ 100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence-absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring.

Spatial structuring of arbuscular mycorrhizal communities in benchmark and modified temperate eucalypt woodlands

Arbuscular mycorrhizal fungi (AMF) are crucial to the functioning of the plant-soil system, but little is known about the spatial structuring of AMF communities across landscapes modified by agriculture. AMF community composition was characterized across four sites in the highly cleared south-western Australian wheatbelt that were originally dominated by forb-rich eucalypt woodlands. Environmentally induced spatial structuring in AMF composition was examined at four scales: the regional scale associated with location, the site scale associated with past management (benchmark woodlands with no agricultural management history, livestock grazing, recent revegetation), the patch scale associated with trees and canopy gaps, and the fine scale associated with the herbaceous plant species beneath which soils were sourced. Field-collected soils were cultured in trap pots; then, AMF composition was determined by identifying spores and through ITS1 sequencing. Structuring was strongest at site scales, where composition was strongly related to prior management and associated changes in soil phosphorus. The two fields were dominated by the genera Funneliformis and Paraglomus, with little convergence back to woodland composition after revegetation. The two benchmark woodlands were characterized by Ambispora gerdemannii and taxa from Gigasporaceae. Their AMF communities were strongly structured at patch scales associated with trees and gaps, in turn most strongly related to soil N. By contrast, there were few patterns at fine scales related to different herbaceous plant species, or at regional scales associated with the 175 km distance between benchmark woodlands. Important areas for future investigation are to identify the circumstances in which recolonization by woodland AMF may be limited by fungal propagule availability, reduced plant diversity and/or altered chemistry in agricultural soils.

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession

Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession. We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing. The EM fungal community consisted of 393 operational taxonomic units (OTUs), belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTUs showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series. This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession.

Marine bacterial communities are resistant to elevated carbon dioxide levels

It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification.

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km²): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes<Burgundy≤Brittany<<South-East) using the systematic grid of French Soil Quality Monitoring Network to evaluate the communities’ composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to 120 km radius) and/or medium (40 to 65 km radius) spatial scales, suggesting dispersal limitations at these scales.

Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.

Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding

The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.

The antimicrobial resistance crisis: causes, consequences, and management

The antimicrobial resistance (AMR) crisis is the increasing global incidence of infectious diseases affecting the human population, which are untreatable with any known antimicrobial agent. This crisis will have a devastating cost on human society as both debilitating and lethal diseases increase in frequency and scope. Three major factors determine this crisis: (1) the increasing frequency of AMR phenotypes among microbes is an evolutionary response to the widespread use of antimicrobials; (2) the large and globally connected human population allows pathogens in any environment access to all of humanity; and (3) the extensive and often unnecessary use of antimicrobials by humanity provides the strong selective pressure that is driving the evolutionary response in the microbial world. Of these factors, the size of the human population is least amenable to rapid change. In contrast, the remaining two factors may be affected, so offering a means of managing the crisis: the rate at which AMR, as well as virulence factors evolve in microbial world may be slowed by reducing the applied selective pressure. This may be accomplished by radically reducing the global use of current and prospective antimicrobials. Current management measures to legislate the use of antimicrobials and to educate the healthcare world in the issues, while useful, have not comprehensively addressed the problem of achieving an overall reduction in the human use of antimicrobials. We propose that in addition to current measures and increased research into new antimicrobials and diagnostics, a comprehensive education program will be required to change the public paradigm of antimicrobial usage from that of a first line treatment to that of a last resort when all other therapeutic options have failed.

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems

Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR--Stramenopiles, Alveolata, Rhizaria--Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep-branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade-10 Cercozoa, HAP-1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST-2 and MAST-12, already detected in freshwater, MAST-3 and possibly MAST-6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.

Spatial scaling effects on soil bacterial communities in Malaysian tropical forests

Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.

The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys

Contrary to earlier assumptions, molecular evidence has demonstrated the presence of diverse and localized soil bacterial communities in the McMurdo Dry Valleys of Antarctica. Meanwhile, it remains unclear whether fungal signals so far detected in Dry Valley soils using both culture-based and molecular techniques represent adapted and ecologically active biomass or spores transported by wind. Through a systematic and quantitative molecular survey, we identified significant heterogeneities in soil fungal communities across the Dry Valleys that robustly correlate with heterogeneities in soil physicochemical properties. Community fingerprinting analysis and 454 pyrosequencing of the fungal ribosomal intergenic spacer region revealed different levels of heterogeneity in fungal diversity within individual Dry Valleys and a surprising abundance of Chytridiomycota species, whereas previous studies suggested that Dry Valley soils were dominated by Ascomycota and Basidiomycota. Critically, we identified significant differences in fungal community composition and structure of adjacent sites with no obvious barrier to aeolian transport between them. These findings suggest that edaphic fungi of the Antarctic Dry Valleys are adapted to local environments and represent an ecologically relevant (and possibly important) heterotrophic component of the ecosystem.

Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns

The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e. elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon∶nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment.

Integrating niche-based process and spatial process in biogeography of magnetotactic bacteria

Microorganisms play key roles in biogeochemical and nutrient cycling in all ecosystems on Earth, yet little is known about the processes controlling their biogeographic distributions. Here we report an investigation of magnetotactic bacteria (MTB) designed to evaluate the roles of niche-based process and spatial process in explaining variation in bacterial communities across large spatial scales. Our results show that both environmental heterogeneity and geographic distance play significant roles in shaping dominant populations of MTB community composition. At the spatial scale in this study, the biogeography of MTB is relatively more influenced by environmental factors than geographic distance, suggesting that local conditions override the effects of dispersal history on structuring MTB community. Of note, we found that the strength of geomagnetic field may influence the biogeography of MTB. We argue that MTB have the potential to serve as a model group to uncover the underlying processes that influence microbial biogeography.

Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography

Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species and the geographical scale of comparisons. In this study, we asked whether these factors also predict diversity and turnover in parasite communities. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked whether parasite prevalence and community structure varied with host population, host phylogeography or geographical distance. We used PCR to screen birds for infections and then used Bayesian methods to determine phylogenetic relationships among malaria strains. Metrics of both community and phylogenetic beta diversity were used to examine patterns of malaria strain turnover between host populations, and partial Mantel tests were used determine the correlation between malaria beta diversity and geographical distance. Finally, we developed microsatellite markers to describe the genetic structure of host populations and assess the relationship between host phylogeography and parasite beta diversity. We found that different genera of malaria parasites infect the two hosts at different rates. Within hosts, parasite communities in one population were phylogenetically clustered, but there was otherwise no correlation between metrics of parasite beta diversity and geographical or genetic distance between host populations. Patterns of parasite turnover among host populations are consistent with malaria transmission occurring in the winter rather than on the breeding grounds. Our results indicate greater turnover in parasite communities between different hosts than between different study sites. Differences in host species, as well as transmission location and vector ecology, seem to be more important in structuring malaria communities than the distance-decay relationships frequently found in macroorganisms. Determining the factors affecting parasite community diversity and turnover has wide-ranging implications for understanding the selective pressures shaping host ecology and ecosystem structure. This study shows that metrics of community and phylogenetic beta diversity can be useful tools for disentangling the ecological and evolutionary processes that underlie geographical variation in parasite communities.

Changes within a single land-use category alter microbial diversity and community structure: molecular evidence from wood-inhabiting fungi in forest ecosystems

The impact of changes within a single land-use category or land-use intensity on microbial communities is poorly understood, especially with respect to fungi. Here we assessed how forest management regimes and a change in forest type affect the richness and community structure of wood-inhabiting fungi across Germany. We used molecular methods based on the length polymorphism of the internal transcribed spacers and the 5.8S rRNA gene to assess fungal operational taxonomic units (OTUs). A cloning/sequencing approach was used to identify taxonomic affinities of the fungal OTUs. Overall, 20-24% and 25-27% of native fungal OTUs from forest reserves and semi-natural forests became undetectable or were lost in managed and converted forests, respectively. Fungal richness was significantly reduced during a regeneration phase in age-class beech forests with a high level of wood extraction (P = 0.017), whereas fungal community structures were not significantly affected. Conversion of forests from native, deciduous to coniferous species caused significant changes in the fungal community structure (R = 0.64-0.66, P = 0.0001) and could reduce fungal richness (P < 0.05) which may depend on which coniferous species was introduced. Our results showed that Ascocoryne cylichnium, Armillaria sp., Exophiala moniliae, Hyphodontia subalutacea and Fomes fomentarius, all known for wood-decaying abilities were strongly reduced in their abundances when forests were converted from beech to coniferous. We conclude that changes within a single land-use category can be regarded as a major threat to fungal diversity in temperate forest ecosystems.

Pyrosequencing reveals regional differences in fruit-associated fungal communities

We know relatively little of the distribution of microbial communities generally. Significant work has examined a range of bacterial communities, but the distribution of microbial eukaryotes is less well characterized. Humans have an ancient association with grape vines (Vitis vinifera) and have been making wine since the dawn of civilization, and fungi drive this natural process. While the molecular biology of certain fungi naturally associated with vines and wines is well characterized, complementary investigations into the ecology of fungi associated with fruiting plants is largely lacking. DNA sequencing technologies allow the direct estimation of microbial diversity from a given sample, avoiding culture-based biases. Here, we use deep community pyrosequencing approaches, targeted at the 26S rRNA gene, to examine the richness and composition of fungal communities associated with grapevines and test for geographical community structure among four major regions in New Zealand (NZ). We find over 200 taxa using this approach, which is 10-fold more than previously recovered using culture-based methods. Our analyses allow us to reject the null hypothesis of homogeneity in fungal species richness and community composition across NZ and reveal significant differences between major areas.

Patterns and processes of microbial community assembly

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure

The spatial patterns of microbial communities are largely determined by the combined effects of historical contingencies and contemporary environmental disturbances, but their relative importance remains poorly understood. Empirical biogeographic data currently available are mostly based on the traditional method of observational survey, which typically involves comparing indigenous microbial communities across spatial scales. Here, we report a long-term soil transplantation experiment, whereby the same two soils (red Acrisol and purple Cambisol from Yingtan) were placed into two geographic locations of ∼1000 km apart (i.e., Yingtan in the mid-subtropical region and Fengqiu in warm-temperate region; both located in China). Twenty years after the transplantation, the resulting soil microbial communities were subject to high-throughput 454 pyrosequencing analysis of 16S and 18S rRNA genes. Additionally, bacteria and archaea involved in nitrogen cycling were estimated using clone library analysis of four genes: archaeal amoA, bacterial amoA,nirK, and nifH. Data of subsequent phylogenetic analysis show that bacteria, fungi, and other microbial eukaryotes, as well as the nitrogen cycling genes, are grouped primarily by the factor of geographic location rather than soil type. Moreover, a shift of microbial communities toward those in local soil (i.e., Chao soil in Fengqiu) has been observed. The results thus suggest that the historical effects persistent in the soil microbial communities can be largely erased by contemporary disturbance within a short period of 20 years, implicating weak effects of historical contingencies on the structure and composition of microbial communities in the soil.

The temporal scaling of bacterioplankton composition: high turnover and predictability during shrimp cultivation

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance-similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity-time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P = 0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w = 0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO4 (3-), and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance-similarity decay model.

Rapid extraction of PCR-competent DNA from recalcitrant environmental samples

Advances in sequencing technologies have made the investigation of microbial ecology and community dynamics more tractable. The critical first step in such analyses is the efficient and representative recovery of PCR-competent DNA from complex environmental samples. All extraction protocols contain inherent biases, meaning that choice of method involves compromise between various factors, including efficiency, yield, universality, and representative extraction. Here, details are given for a routine method used in our laboratory to extract DNA from soils, sediments, biofilms, roots, and fungi.

Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

Microbial biogeography is influenced by the combined effects of passive dispersal and environmental selection, but the contribution of either factor can be difficult to discern. As thermophilic bacteria cannot grow in the cold seabed, their inactive spores are not subject to environmental selection. We therefore conducted a global experimental survey using thermophilic endospores that are passively deposited by sedimentation to the cold seafloor as tracers to study the effect of dispersal by ocean currents on the biogeography of marine microorganisms. Our analysis of 81 different marine sediments from around the world identified 146 species-level 16S rRNA phylotypes of endospore-forming, thermophilic Firmicutes. Phylotypes showed various patterns of spatial distribution in the world oceans and were dispersal-limited to different degrees. Co-occurrence of several phylotypes in locations separated by great distances (west of Svalbard, the Baltic Sea and the Gulf of California) demonstrated a widespread but not ubiquitous distribution. In contrast, Arctic regions with water masses that are relatively isolated from global ocean circulation (Baffin Bay and east of Svalbard) were characterized by low phylotype richness and different compositions of phylotypes. The observed distribution pattern of thermophilic endospores in marine sediments suggests that the impact of passive dispersal on marine microbial biogeography is controlled by the connectivity of local water masses to ocean circulation.

Influence of spatio-temporal resource availability on mushroom mite diversity

Although biodiversity in nature is of fundamental importance because it improves the sustainability of ecosystems, communities of microscopic organisms are generally excluded from conservation targets for biodiversity. Here, I hypothesize that mushroom mite species richness is correlated with both spatial (i.e., mushroom size) and temporal (i.e., longevity of fruiting bodies) resource availability. I collected fruiting bodies in an old-growth forest over 4 years to collect mites and insects inhabiting the mushrooms. Mites were collected from 47 % of the fruiting bodies and approximately 60 % of the mite species were collected only once. Mite species richness was significantly correlated with the availability of long-lasting fruiting bodies. For example, bracket fungi contained more mite species than ephemeral fruiting bodies. Insect presence was also correlated with mushroom mite richness, probably as phoretic hosts and food resources for predacious mites. On the other hand, mushroom size seemed to be less important; small fruiting bodies sometimes harbored several mite species. Although mite species richness was correlated with mushroom species richness, mushroom specificity by mites was not clear except for a preference for long-lasting fruiting bodies. Therefore, I suggest that a constant supply of coarse woody debris is crucial for maintaining preferred resources for mushroom mites (e.g., bracket fungi) and their associated insects (mycophilous and possibly saproxylic insects).

Biogeography of the uncultured marine picoeukaryote MAST-4: temperature-driven distribution patterns

The MAST-4 (marine stramenopile group 4) is a widespread uncultured picoeukaryote that makes up an important fraction of marine heterotrophic flagellates. This group has low genetic divergence and is composed of a small number of putative species. We combined ARISA (automated ribosomal intergenic spacer analysis) and ITS (Internal Transcribed Spacer) clone libraries to study the biogeography of this marine protist, examining both spatial and temporal trends in MAST-4 assemblages and associated environmental factors. The most represented MAST-4 clades appeared adapted to different temperature ranges, and their distributions did not suggest clear geographical barriers for dispersal. Distant samples sharing the same temperature had very similar assemblages, especially in cold temperatures, where only one clade, E1, dominated. The most highly represented clades, A and E1, showed very little differentiation between populations from distant geographical regions. Within a single site, temporal variation also followed patterns governed by temperature. Our results contribute to the general discussion on microbial biogeography by showing strong environmental selection for some picoeukaryotes in the marine environment.

Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.

Digging the New York City Skyline: soil fungal communities in green roofs and city parks

In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.

The role of local environment and geographical distance in determining community composition of arbuscular mycorrhizal fungi at the landscape scale

Arbuscular fungi have a major role in directing the functioning of terrestrial ecosystems yet little is known about their biogeographical distribution. The Baas-Becking hypothesis ('everything is everywhere, but, the environment selects') was tested by investigating the distribution of arbuscular mycorrhizal fungi (AMF) at the landscape scale and the influence of environmental factors and geographical distance in determining community composition. AMF communities in Trifolium repens and Lolium perenne roots were assessed in 40 geographically dispersed sites in Ireland representing different land uses and soil types. Field sampling and laboratory bioassays were used, with AMF communities characterised using 18S rRNA terminal-restriction fragment length polymorphism. Landscape-scale distribution of AMF was driven by the local environment. AMF community composition was influenced by abiotic variables (pH, rainfall and soil type), but not land use or geographical distance. Trifolium repens and L. perenne supported contrasting communities of AMF, and the communities colonising each plant species were consistent across pasture habitats and over distance. Furthermore, L. perenne AMF communities grouped by soil type within pasture habitats. This is the largest and most comprehensive study that has investigated the landscape-scale distribution of AMF. Our findings support the Baas-Becking hypothesis at the landscape scale and demonstrate the strong influence the local environment has on determining AMF community composition.

The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China

Whether fungal community structure depends more on historical factors or on contemporary factors is controversial. This study used culture-dependent and -independent (polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)) methods to assess the influence of historical and contemporary factors on the distributions of fungi in the wetland sediments at 10 locations along the Changjiang River and at 10 other locations in China. The culture-dependent approach detected greater species diversity (177 operational taxonomic units (OTUs)) than PCR-DGGE analysis (145 OTUs), and the species in the genera of Penicillium (relative frequency=16.8%), Fusarium (15.4%), Aspergillus (7.6%), Trichoderma (5.8%) and Talaromyces (4.2%) were dominant. On the basis of DGGE data, fungal diversity along the Changjiang River increased from upstream to downstream; altitude explained 44.8% of this variation in diversity. And based on the data from all 20 locations, the fungal communities were geographically clustered into three groups: Southern China, Northern China and the Qinghai-Tibetan Plateau. Multivariate regression tree analysis for data from the 20 locations indicated that the fungal community was influenced primarily by location (which explained 61.8% of the variation at a large scale), followed by total potassium (9.4%) and total nitrogen (3.5%) at a local scale. These results are consistent with the concept that geographic distance is the dominant factor driving variation in fungal diversity at a regional scale (1000-4000 km), whereas environmental factors (total potassium and total nitrogen) explain variation in fungal diversity at a local scale (<1000 km).

Environmental selection of protistan plankton communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea

High salt concentrations, absence of light, anoxia, and high hydrostatic pressure make deep hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea one of the most polyextreme habitats on Earth. Taking advantage of the unique chemical characteristics of these basins, we tested the effect of environmental selection and geographic distance on the structure of protistan communities. Terminal restriction fragment length polymorphism (T-RFLP) analyses were performed on water samples from the brines and seawater/brine interfaces of five basins: Discovery, Urania, Thetis, Tyro, and Medee. Using statistical analyses, we calculated the partitioning of diversity among the ten individual terminal restriction fragment (T-RF) profiles, based on peak abundance and peak incidence. While a significant distance effect on spatial protistan patterns was not detected, hydrochemical gradients emerged as strong dispersal barriers that likely lead to environmental selection in the DHAB protistan plankton communities. We identified sodium, magnesium, sulfate, and oxygen playing in concerto as dominant environmental drivers for the structuring of protistan plankton communities in the Eastern Mediterranean DHABs.

Global biogeography of highly diverse protistan communities in soil

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.

Different distribution patterns between putative ercoid mycorrhizal and other fungal assemblages in roots of Rhododendron decorum in the Southwest of China

Fungal diversity within plant roots is affected by several factors such as dispersal limitation, habitat filtering, and plant host preference. Given the differences in life style between symbiotic and non-symbiotic fungi, the main factors affecting these two groups of fungi may be different. We assessed the diversity of root associated fungi of Rhododendron decorum using internal transcribed spacer (ITS) sequencing and terminal restriction fragment length polymorphism (T-RFLP) analysis, and our aim was to evaluate the role of different factors in structuring ericoid mycorrhizal (ERM) and non-ericoid mycorrhizal (NEM) fungal communities. Thirty-five fungal operational taxonomic units (OTUs) were found in roots of R. decorum, of which 25 were putative ERM fungal species. Of the two main groups of known ERM, helotialean fungi were more abundant and common than sebacinalean species. Geographic and host patterning of the fungal assemblages were different for ERM and NEM. The distribution of putative ERM fungal terminal restriction fragments (TRFs) showed that there were more common species within ERM than in the NEM fungal assemblages. Results of Mantel tests indicated that the composition of NEM fungal assemblages correlated with geographic parameters while ERM fungal assemblages lacked a significant geographic pattern and instead were correlated with host genotype. Redundancy analysis (RDA) showed that the NEM fungal assemblages were significantly correlated with latitude, longitude, elevation, mean annual precipitation (MAP), and axis 2 of a host-genetic principle component analysis (PCA), while ERM fungal assemblages correlated only with latitude and axis 1 of the host-genetic PCA. We conclude that ERM and NEM assemblages are affected by different factors, with the host genetic composition more important for ERM and geographic factors more important for NEM assemblages. Our results contribute to understanding the roles of dispersal limitation, abiotic factors and biotic interactions in structuring fungal communities in plant roots.

Differences in soil fungal communities between European beech (Fagus sylvatica L.) dominated forests are related to soil and understory vegetation

Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwäbische Alb in Southwestern, the Hainich-Dün in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p≤0.001) among the three regions and was characterized by non-random fungal OTUs co-occurrence. Soil parameters, herbaceous understory vegetation, and litter cover affected fungal community structure. However, within each study region we found no difference in fungal community structure between management types. Our results also showed region specific significant correlation patterns between the dominant ectomycorrhizal fungal genera. This suggests that soil fungal communities are region-specific but nevertheless composed of functionally diverse and complementary taxa.

Distance decay of similarity in neotropical diatom communities

Background

The regression of similarity against distance unites several ecological phenomena, and thus provides a highly useful approach for illustrating the spatial turnover across sites. Our aim was to test whether the rates of decay in community similarity differ between diatom growth forms suggested to show different dispersal ability. We hypothesized that the diatom group with lower dispersal ability (i.e. periphyton) would show higher distance decay rates than a group with higher dispersal ability (i.e. plankton).

Methods/Principal findings

Periphyton and phytoplankton samples were gathered at sites distributed over an area of approximately 800 km length in the Negro River, Amazon basin, Brazil, South America (3°08′00″S; 59°54′30″W). Distance decay relationships were then estimated using distance-based regressions, and the coefficients of these regressions were compared among the groups with different dispersal abilities to assess our predictions. We found evidence that different tributaries and reaches of the Negro River harbor different diatom communities. As expected, the rates of distance decay in community similarity were higher for periphyton than for phytoplankton indicating the lower dispersal ability of periphytic taxa.

Conclusions/Significance

Our study demonstrates that the comparison of distance decay relationships among taxa with similar ecological requirements, but with different growth form and thus dispersal ability provides a sound approach to evaluate the effects of dispersal ability on beta diversity patterns. Our results are also in line with the growing body of evidence indicating that microorganisms exhibit biogeographic patterns. Finally, we underscore that clumbing all microbial taxa into one group may be a flawed approach to test whether microbes exhibit biogeographic patterns.

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4-1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r=0.443, P=0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.

Spatial and temporal scales of aquatic bacterial beta diversity

Understanding characteristic variation in aquatic bacterial community composition (BCC) across space and time can inform us about processes driving community assembly and the ability of bacterial communities to respond to perturbations. In this study, we synthesize BCC data from north temperate lakes to evaluate our current understanding of how BCC varies across multiple scales in time and space. A hierarchy of average similarity emerged with the highest similarity found among samples collected within the same lake, especially within the same basin, followed by similarity among samples collected through time within the same lake, and finally similarity among samples collected from different lakes. Using decay of similarity across time and space, we identified equivalent temporal (1 day) and spatial (10 m) scales of BCC variation. Finally, we identify an intriguing pattern of contrasting patterns of intra- and inter-annual BCC variation in two lakes. We argue our synthesis of spatio-temporal variation of aquatic BCC informs expectations for the response of aquatic bacterial communities to perturbation and environmental change. However, further long-term temporal observations will be needed to develop a general understanding of inter-annual BCC variation and our ability to use aquatic BCC as a sensitive metric of environmental change.

Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that 'everything is not everywhere'

BACKGROUND

The study of soil biota in the context of exotic plant invasions has led to an explosion in our understanding of the ecological roles of many different groups of microbes that function in roots or at the root-soil interface. Part of this progress has been the emergence of two biogeographic patterns involving invasive plants and soil microbes. First, in their non-native ranges invasive plants commonly interact differently with the same soil microbes than native plants. Second, in their native ranges, plants that are invasive elsewhere commonly interact functionally with soil microbes differently in their home ranges than they do in their non-native ranges. These studies pose a challenge to a long-held paradigm about microbial biogeography - the idea that microbes are not limited by dispersal and are thus free from the basic taxonomic, biogeographical and evolutionary framework that characterizes all other life on Earth. As an analogy, the global distribution of animals that function as carnivores does not negate the fascinating evolutionary biogeographic patterns of carnivores. Other challenges to this notion come from new measurements of genetic differences among microbes across geographic boundaries, which also suggest that meaningful biogeographic patterns exist for microorganisms.

SCOPE AND CONCLUSIONS

We expand this discussion of whether or not 'everything is everywhere' by using the inherently biogeographic context of plant invasions by reviewing the literature on interactions among invasive plants and the microorganisms in the rhizosphere. We find that these interactions can be delineated at multiple scales: from individual plants to continents. Thus the microbes that regulate major aspects of plant biology do not appear to be exempt from the fundamental evolutionary processes of geographical isolation and natural selection. At the important scales of taxonomy, ecotype and ecosystem functions, the fundamental ecology of invaders and soil microbes indicates that everything might not be everywhere.

Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules

Dispersal plays a prominent role in most conceptual models of community assembly. However, direct measurement of dispersal across a whole community is difficult at ecologically relevant spatial scales. For cryptic organisms, such as fungi and bacteria, the scale and importance of dispersal limitation has become a major point of debate. We use an experimental island biogeographic approach to measure the effects of dispersal limitation on the ecological dynamics of an important group of plant symbionts, ectomycorrhizal fungi. We manipulated the isolation of uncolonized host seedlings across a natural landscape and used a range of molecular techniques to measure the dispersal rates of ectomycorrhizal propagules and host colonization. Some species were prolific dispersers, producing annual spore loads on the order of trillions of spores per km(2). However, fungal propagules reaching host seedlings decreased rapidly with increasing distance from potential spore sources, causing a concomitant reduction in ectomycorrhizal species richness, host colonization and host biomass. There were also strong differences in dispersal ability across species, which correlated well with the predictable composition of ectomycorrhizal communities associated with establishing pine forest. The use of molecular tools to measure whole community dispersal provides a direct confirmation for a key mechanism underlying island biogeography theory and has the potential to make microbial systems a model for understanding the role of dispersal in ecological theory.

Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms

Microbial biogeography studies expend much effort in determining whether environmental selection or stochastic processes related to dispersal are more important in shaping community composition. While both types of factors are possibly influential, it is tacitly assumed that protists, or microbial eukaryotes in general, behave biogeographically as prokaryotes because of their small physical size. However, direct evidence for this in exactly the same environment and at the same phylogenetic depth is lacking. In this study, we compared the structure of both prokaryotic and eukaryotic components of microbial communities forming biofilms on mineral substrates in different geographic locations at the level of small-subunit (SSU) rRNA-based operational taxonomic units (OTUs). These microbial communities are subjected to strong environmental selection and contain significant proportions of extremophilic microorganisms adapted to desiccation and UV radiation. We find that the nature of the substrate as well as climatic variables and geography influences microbial community structure. However, constrained correspondence analyses and distance-decay curves showed that, whereas the substrate type was the most significant factor structuring bacterial communities, geographic location was the most influential factor for microbial eukaryote communities. Biological explanations implying a higher dispersal success for bacteria combined with more mobile lifestyles for predatory protists may underlie these different prokaryote versus microbial eukaryote biogeographic patterns.