Transitivity and intransitivity in soil bacterial networks.

Competition can lead to the exclusion of bacterial taxa when there is a transitive relationship among competitors with a hierarchy of competitive success. However, competition may not prevent bacterial coexistence if competitors form intransitive loops, in which none is able to outcompete all the rest. Both transitive and intransitive competition have been demonstrated in bacterial model systems. However, in natural soil microbial assemblages competition is typically understood as a dominance relationship leading to the exclusion of weak competitors. Here, we argue that transitive and intransitive interactions concurrently determine the structure of soil microbial communities. We explain why pairwise interactions cannot depict competition correctly in complex communities, and propose an alternative through the detection of strongly connected components (SCCs) in microbial networks. We finally analyse the existence of SCCs in soil bacterial communities in two Mediterranean ecosystems, for illustrative purposes only (rather than with the aim of providing a methodological tool) due to current limitations, and discuss future avenues to experimentally test the existence of SCCs in nature.

How harmful are exotic plantations for soils and its microbiome? A case study in an arid island.

The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.

RecruitNet: A global database of plant recruitment networks.

Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country, locality, responsible author, sampling dates, sampling method, and life habits of both canopy and recruit species are provided. This database will allow researchers to test ecological, biogeographical, and evolutionary hypotheses related to plant recruitment interactions. There are no copyright restrictions on the data set; please cite this data paper when using these data in publications.

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods.

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

The functional structure of plant communities drives soil functioning via changes in soil abiotic properties.

While biodiversity is expected to enhance multiple ecosystem functions (EFs), the different roles of multiple biodiversity dimensions remain difficult to disentangle without carefully designed experiments. We sowed plant communities with independent levels of functional (FD) and phylogenetic diversities (PD), combined with different levels of fertilization, to investigate their direct and indirect roles on multiple EFs, including plant-related EFs (plant biomass productivity, litter decomposability), soil fertility (organic carbon and nutrient pool variables), soil microbial activity (respiration and nutrient cycling), and an overall multifunctionality. We expected an increase in most EFs in communities with higher values of FD and/or PD via complementarity effects, but also the dominant plant types (using community weighted mean, CWM, independent of FD and PD) via selection effects on several EFs. The results showed strong direct effects of different dimensions of plant functional structure parameters on plant-related EFs, through either CWM or FD, with weak effects of PD. Fertilization had significant effects on one soil microbial activity and indirect effects on the other variables via changes in soil abiotic properties. Dominant plant types and FD showed only indirect effects on soil microbial activity, through litter decomposition and soil abiotic properties, highlighting the importance of cascading effects. This study shows the relevance of complementary dimensions of biodiversity for assessing both direct and cascading effects on multiple EFs.

Functional trait effects on ecosystem stability: assembling the jigsaw puzzle.

Under global change, how biological diversity and ecosystem services are maintained in time is a fundamental question. Ecologists have long argued about multiple mechanisms by which local biodiversity might control the temporal stability of ecosystem properties. Accumulating theories and empirical evidence suggest that, together with different population and community parameters, these mechanisms largely operate through differences in functional traits among organisms. We review potential trait-stability mechanisms together with underlying tests and associated metrics. We identify various trait-based components, each accounting for different stability mechanisms, that contribute to buffering, or propagating, the effect of environmental fluctuations on ecosystem functioning. This comprehensive picture, obtained by combining different puzzle pieces of trait-stability effects, will guide future empirical and modeling investigations.

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis.

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.

nir gene-based co-occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire.

Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co-existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co-existence of denitrifiers across multiple assemblages by using nir gene-based co-occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co-occurrence patterns. Bacteria with the same nir co-occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co-occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.

Phenotypic structure of plant facilitation networks.

Identifying the plant traits that determine the outcome of facilitation interactions is essential to understand how communities are assembled and can be restored. Plant facilitation networks are phylogenetically structured but which traits are behind such a pattern is unknown. We sampled plant interactions in stressful ecosystems from south-eastern Spain to build seedling and adult facilitation networks. We collected 20 morphological and ecophysiological traits for 151 species involved in interactions between 879 nurse individuals benefiting 24 584 seedlings and adults. We detected a significant phenotypic signal in the seedling facilitation network that was maintained in the adult network, whereby functionally similar nurses tended to facilitate functionally similar species whose traits differ from those of their nurses. We provide empirical evidence to support a long-lasting theoretical postulate stating that facilitation networks are phenotypically structured. Trait matching through which nurse and facilitated species avoid phenotypic overlap, and consequently competition, is the main linkage rule shaping plant facilitation networks.

Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes.

Co-occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co-existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co-occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co-occurrence networks to identify pairs of significantly associated taxa, either co-existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%-4%) or habitat filtering (55%-77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat-filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co-occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.

Native soil microorganisms hinder the soil enrichment with antibiotic resistance genes following manure applications.

Bacterial genes responsible for resistance to antibiotic agents (ARG) are spread from livestock to soil through application of manure, threatening environmental and human health. We investigated the mechanisms of ARG dissemination and persistence to disentangle i) the influence of nutrients and microorganisms on the soil tetracycline (TET) resistome, and ii) the role of indigenous soil microbiota in preventing ARG spread. We analysed short-term (7 days) and persistent (84 days) effects of manure on the resistome of three antibiotic-free pasture soils. Four microcosm treatments were evaluated: control, mineral nutrient fertilization, and deposition of a layer of fresh manure onto soil or γ-irradiated soil. We quantified five TET-resistance genes, isolated 135 TET-resistant bacteria and sequenced both culturable TET-resistant and whole bacterial communities. Manure amendments, but not nutrient addition, increased the abundance of TET-r genes such as tet(Y). Such changes persisted with time, in contrast with the TET-resistant bacterial composition, which partially recovered after manure amendments. Manured γ-irradiated soils showed significantly lower nutrient content and higher TET-r gene abundance than non-irradiated soils, suggesting that native soil bacteria are essential for the fertilization effect of manure on soil as well as control the dissemination of potentially risky TET-r genes.

Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits.

Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands.

Poor plant performance under simulated climate change is linked to mycorrhizal responses in a semiarid shrubland.

Warmer and drier conditions associated with ongoing climate change will increase abiotic stress for plants and mycorrhizal fungi in drylands worldwide, thereby potentially reducing vegetation cover and productivity and increasing the risk of land degradation and desertification. Rhizosphere microbial interactions and feedbacks are critical processes that could either mitigate or aggravate the vulnerability of dryland vegetation to forecasted climate change.We conducted a four-year manipulative study in a semiarid shrubland in the Iberian Peninsula to assess the effects of warming (~2.5ºC; W), rainfall reduction (~30%; RR) and their combination (W+RR) on the performance of native shrubs (Helianthemum squamatum) and their associated mycorrhizal fungi.Warming (W and W+RR) decreased the net photosynthetic rates of H. squamatum shrubs by ~31% despite concurrent increases in stomatal conductance (~33%), leading to sharp decreases (~50%) in water use efficiency. Warming also advanced growth phenology, decreased leaf nitrogen and phosphorus contents per unit area, reduced shoot biomass production by ~36% and decreased survival during a dry year in both W and W+RR plants. Plants under RR showed more moderate decreases (~10-20%) in photosynthesis, stomatal conductance and shoot growth.Warming, RR and W+RR altered ectomycorrhizal fungal (EMF) community structure and drastically reduced the relative abundance of EMF sequences obtained by high-throughput sequencing, a response associated with decreases in the leaf nitrogen, phosphorus and dry matter contents of their host plants. In contrast to EMF, the community structure and relative sequence abundances of other non-mycorrhizal fungal guilds were not significantly affected by the climate manipulation treatments.Synthesis: Our findings highlight the vulnerability of both native plants and their symbiotic mycorrhizal fungi to climate warming and drying in semiarid shrublands, and point to the importance of a deeper understanding of plant-soil feedbacks to predict dryland vegetation responses to forecasted aridification. The interdependent responses of plants and ectomycorrhizal fungi to warming and rainfall reduction may lead to a detrimental feedback loop on vegetation productivity and nutrient pool size, which could amplify the adverse impacts of forecasted climate change on ecosystem functioning in EMF-dominated drylands.

Phylogenetic-scale disparities in the soil microbial diversity-ecosystem functioning relationship.

The historical conditions under which bacterial lineages evolve determine their functional traits, and consequently their contribution to ecosystem functions (EFs). Under significant trait conservatism, which is common in prokaryotes, phylogeny may track the evolutionary history of species and predict their functionality. Productive communities can arise from: (i) the coexistence of functional, and therefore phylogenetically distant lineages, producing high EF rates at large phylogenetic diversity (PD); (ii) the dominance of productive lineages that outcompete other clades, generating high EF at low PD. Community composition will modulate the PD-EF relationship: The effects of anciently divergent lineages, whose deeply conserved functions determine the occupancy of major niches, may differ from that of recently divergent lineages showing adaptations to current conditions. We hypothesized that, in our model Mediterranean ecosystem, EF can be explained both by competitive superiority of ancient lineages and functional complementarity of recent lineages. To test this hypothesis, we sequenced a phylogenetic marker targeting bacteria across 28 soil plots and quantified EF related to microbial productivity, decomposition and nutrient cycling. Plots accumulating recently divergent lineages consistently showed higher EF levels that were slightly modified by the accumulation of ancient lineages. We discuss the assembly processes behind these phylogenetic-scale disparities and the final outcome in terms of ecosystem functioning.

Resilience to fire of phylogenetic diversity across biological domains.

Fire alters the structure and composition of above- and belowground communities with concurrent shifts in phylogenetic diversity. The inspection of postfire trends in the diversity of ecological communities incorporating phylogenetic information allows to better understand the mechanisms driving fire resilience. While fire reduces plant phylogenetic diversity based on the recruitment of evolutionarily related species with postfire seed persistence, it increases that of soil microbes by limiting soil resources and changing the dominance of competing microbes. Thus, during postfire community reassembly, plant and soil microbes might experience opposing temporal trends in their phylogenetic diversity that are linked through changes in the soil conditions. We tested this hypothesis by investigating the postfire evolution of plant and soil microbial (fungi, bacteria and archaea) communities across three 20-year chronosequences. Plant phylogenetic diversity increased with time since fire as pioneer seeders facilitate the establishment of distantly related late-successional shrubs. The postfire increase in plant phylogenetic diversity fostered plant productivity, eventually recovering soil organic matter. These shifts over time in the soil conditions explained the postfire restoration of fungal and bacterial phylogenetic diversity, which decreased to prefire levels, suggesting that evolutionarily related taxa with high relative fitness recover their competitive superiority during community reassembly. The resilience to fire of phylogenetic diversity across biological domains helps preserve the evolutionary history stored in our ecosystems.

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients.

The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.

Prokaryotic communities and potential pathogens in sewage sludge: Response to wastewaster origin, loading rate and treatment technology.

Sewage sludge features high nitrogen and phosphorous contents encouraging its use as a biosolid in agriculture, but it bears potential chemical and microbiological risks. To tease apart the relative contribution of main factors determining the sludge chemical and microbial features, we analysed 28 treatment plants differing in the wastewater origin (municipal residues, agro-food or chemical industries), organic loading rate and treatment technology (extended aeration, activated sludge or activated sludge followed by anaerobic digestion). We found that the treatment technology and the organic loading rate are main determinants of the sludge chemical properties, including its organic load, nutrient and metal contents, and override the effect of the wastewater origin. Sludge bacterial and archaeal community structure and diversity, characterized through massive sequencing of the 16S rRNA gene, were also mostly determined by the treatment technology partly through shifts in the sludge nutrient load. The same factor conditioned the relative abundance of sequenced bacteria most closely related to potential pathogens, but not that of cultivable Escherichia coli or Salmonella spp. We did not find an effect of the geographic location of the plant on any of the variables at the regional scale of our study. Operational parameters appear as major determinants of the sludge chemical and microbial properties, irrespective of the source of wastewaters, thus leaving a broad management window for improving the agronomic value of sewage sludge.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

Fire alters ecosystems by changing the composition and community structure of soil microbes. The phylogenetic structure of a community provides clues about its main assembling mechanisms. While environmental filtering tends to reduce the community phylogenetic diversity by selecting for functionally (and hence phylogenetically) similar species, processes like competitive exclusion by limiting similarity tend to increase it by preventing the coexistence of functionally (and phylogenetically) similar species. We used co-occurrence networks to detect co-presence (bacteria that co-occur) or exclusion (bacteria that do not co-occur) links indicative of the ecological interactions structuring the community. We propose that inspecting the phylogenetic structure of co-presence or exclusion links allows to detect the main processes simultaneously assembling the community. We monitored a soil bacterial community after an experimental fire and found that fire altered its composition, richness and phylogenetic diversity. Both co-presence and exclusion links were more phylogenetically related than expected by chance. We interpret such a phylogenetic clustering in co-presence links as a result of environmental filtering, while that in exclusion links reflects competitive exclusion by limiting similarity. This suggests that environmental filtering and limiting similarity operate simultaneously to assemble soil bacterial communities, widening the traditional view that only environmental filtering structures bacterial communities.

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Opposing phylogenetic diversity gradients of plant and soil bacterial communities.

Plants and soil microbes show parallel patterns of species-level diversity. Diverse plant communities release a wider range of organics that are consumed by more microbial species. We speculated, however, that diversity metrics accounting for the evolutionary distance across community members would reveal opposing patterns between plant and soil bacterial phylogenetic diversity. Plant phylogenetic diversity enhances plant productivity and thus expectedly soil fertility. This, in turn, might reduce bacterial phylogenetic diversity by favouring one (or a few) competitive bacterial clade. We collected topsoils in 15 semi-arid plant patches and adjacent low-cover areas configuring a plant phylodiversity gradient, pyrosequenced the 16S rRNA gene to identify bacterial taxa and analysed soil fertility parameters. Structural equation modelling showed positive effects of both plant richness and phylogenetic diversity on soil fertility. Fertility increased bacterial richness but reduced bacterial phylogenetic diversity. This might be attributed to the competitive dominance of a lineage based on its high relative fitness. This suggests biotic interactions as determinants of the soil bacterial community assembly, while emphasizing the need to use phylogeny-informed metrics to tease apart the processes underlying the patterns of diversity.