Community‐wide effects of below‐ground rhizobia on above‐ground arthropods

1. Plants take nutrients for their growth and reproduction from not only soil but also symbiotic microbes in the rhizosphere, and therefore below‐ground microbes may indirectly influence the above‐ground arthropod community through changes in the quality and quantity of plants. 2. Rhizobia are root‐nodulating bacteria that provide NH₄⁺ to legume plants. We examined bottom‐up effects of rhizobia on the community properties of the arthropods on host plants, using a root‐nodulating soybean strain (R+) and a non‐nodulating strain (R?) in a common garden. 3. R+ plants grew larger and produced a greater number of leaves than R? plants. We observed 28 species of herbivores and three taxonomic groups of predators on R+ and R? plants. The herbivorous species were classified into sap feeders (12 species) and chewers (16 species). 4. The species richness of overall herbivores, sap feeders, and chewers on R+ plants was greater than that on R? plants. Rhizobia positively affected the abundance of chewers. 5. The community composition of herbivores was significantly different between R? and R+ plants, although species diversity and evenness did not differ. 6. Rhizobia‐induced bottom‐up effects were transmitted to the third trophic level. The abundance, taxonomic richness, and diversity of the predators on R+ plants were greater but evenness was lower than those on R? plants. The community composition of predators was not affected by rhizobia. 7. These results indicate that the below‐ground microbes initiated bottom‐up effects on above‐ground herbivores and predators through trophic levels.     

Not all non‐natives are equally unequal: reductions in herbivore β‐diversity depend on phylogenetic similarity to native plant community

Effects of host plant α‐ and β‐diversity often confound studies of herbivore β‐diversity, hindering our ability to predict the full impact of non‐native plants on herbivores. Here, while controlling host plant diversity, we examined variation in herbivore communities between native and non‐native plants, focusing on how plant relatedness and spatial scale alter the result. We found lower absolute magnitudes of β‐diversity among tree species and among sites on non‐natives in all comparisons. However, lower relative β‐diversity only occurred for immature herbivores on phylogenetically distinct non‐natives vs. natives. Locally in that comparison, non‐native gardens had lower host specificity; while among sites, the herbivores supported were a redundant subset of species on natives. Therefore, when phylogenetically distinct non‐natives replace native plants, the community of immature herbivores is likely to be homogenised across landscapes. Differences in communities on closely related non‐natives were subtler, but displayed community shifts and increased generalisation on non‐natives within certain feeding guilds.     

Diversity in Mediterranean farm ponds: trade‐offs and synergies between irrigation modernisation and biodiversity conservation

1. Agricultural intensification has caused dramatic biodiversity loss in many agricultural landscapes over the last century. Here, we investigated whether new types of farm ponds (made of artificial substrata) in intensive systems and natural‐substratum ponds in traditional farming systems differ in their value for aquatic biodiversity conservation. 2. We analysed the main patterns of environmental variation, compared α‐, β‐ and γ‐diversity of macroinvertebrates between ponds types and evaluated the role of submerged aquatic vegetation (SAV). Generalised additive models (GAM) were used to analyse the relationships of α‐ and β‐diversity with environmental predictors, and variation partitioning to separate the effect of environmental and spatial characteristics on the variation in macroinvertebrate assemblages. Moran’s eigenvector maps (MEMs) were used to define spatial variables. 3. A principal coordinate analysis (PCoA) detected a primary environmental gradient that separated nutrient‐rich ponds from those dominated by SAV; a secondary morphometric gradient distinguished natural‐substratum ponds, with large surface area and structural complexity, from artificial‐substratum ponds with steeper slopes. Natural‐substratum ponds had almost twice the α‐ and γ‐diversity of artificial‐substratum ponds, and diversity significantly increased when SAV was present, particularly in artificial‐substratum ponds. Total phosphorus (TP) strongly contributed to explain the patterns in diversity, while SAV was a significant predictor of assemblage composition and diversity. GAMs revealed optima of both α‐diversity at intermediate SAV covers and β‐diversity at intermediate–high TP concentrations. 4. These findings have important implications for conservation planning. Adaptation of artificial‐substratum ponds by adding natural substratum and smoothing the gradient of pond margins would improve their conservation value. Development of SAV with occasional harvests and certain cautionary measures to control nutrient levels may also improve both the agronomical and environmental function of ponds.     

土壤微生物多样性海拔格局研究进展

生物多样性的海拔分布格局与维持机制是生物多样性与生态系统功能研究的热点领域。相比动植物多样性海拔分布格局,土壤微生物多样性海拔分布格局的研究还处在起步阶段。近年来,随着以罗氏454、Illumina Mi Seq等为代表的高通量测序平台的发展,土壤微生物海拔梯度分布格局的研究进展较快。对土壤微生物多样性海拔分布格局最新研究综述发现,土壤微生物海拔分布模式并不明确,表现为无趋势、下降、单峰或者下凹型等多种海拔分布模式。这与大型动植物并不相同,暗示其驱动机制可能存在一定的差异。微生物由于其个体微小、扩散能力强以及较高的多样性和个体丰度而在局域尺度上可能更易受到气候环境因素的影响。土壤pH、碳、氮等因子是影响微生物多样性和群落组成在海拔梯度上变异的重要因素。此外,温度和降水也具有重要作用。另外,除微生物自身属性以及取样限制外,测序深度可能是影响土壤微生物物种丰富度海拔分布格局的重要因素。目前,对土壤微生物群落的研究在功能基因、群落构建机制以及生态学理论的验证方面还存在着不足。未来的研究应进一步加大测序深度,增加取样密度,着重关注全球气候变化及生物多样性丧失背景下土壤微生物群落的构建和维持机制及其生态系统功能等方面。     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

Differential biodiversity responses between kingdoms (plants,fungi, bacteria and metazoa) along an Alpine succession gradient

Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across‐habitat β‐diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil β‐diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below‐ground biodiversity responses.     

Agriculture erases climate‐driven β‐diversity in Neotropical bird communities

Earth is experiencing multiple global changes that will, together, determine the fate of many species. Yet, how biological communities respond to concurrent stressors at local‐to‐regional scales remains largely unknown. In particular, understanding how local habitat conversion interacts with regional climate change to shape patterns in β‐diversity—differences among sites in their species compositions—is critical to forecast communities in the Anthropocene. Here, we study patterns in bird β‐diversity across land‐use and precipitation gradients in Costa Rica. We mapped forest cover, modeled regional precipitation, and collected data on bird community composition, vegetation structure, and tree diversity across 120 sites on 20 farms to answer three questions. First, do bird communities respond more strongly to changes in land use or climate in northwest Costa Rica? Second, does habitat conversion eliminate β‐diversity across climate gradients? Third, does regional climate control how communities respond to habitat conversion and, if so, how? After correcting for imperfect detection, we found that local land‐use determined community shifts along the climate gradient. In forests, bird communities were distinct between sites that differed in vegetation structure or precipitation. In agriculture, however, vegetation structure was more uniform, contributing to 7%–11% less bird turnover than in forests. In addition, bird responses to agriculture and climate were linked: agricultural communities across the precipitation gradient shared more species with dry than wet forest communities. These findings suggest that habitat conversion and anticipated climate drying will act together to exacerbate biotic homogenization.     

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils

Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.     

Partitioning beta‐diversity through different pond hydroperiod lengths reveals predominance of nestedness in assemblages of immature odonates

Patterns of freshwater invertebrate assemblage structure in the transition from permanent to non‐permanent lentic habitats are well described in the literature. However, the effects of small changes in the hydroperiod of non‐permanent ponds on invertebrate assemblage structure remain less studied, especially on β‐diversity. Thus, we tested the effects of different pond hydroperiod lengths on the assemblage structure of immature odonates, in terms of both α‐ and β‐diversity. Small high‐altitude ponds with different hydroperiod lengths (assigned to ‘short’, ‘medium’ and ‘long’ hydroperiods) were sampled in southern Brazil between 2013 and 2014. Based on the hypothesis that shorter hydroperiods filter constituents of lentic fauna, i.e. that long‐living species cannot inhabit shorter‐hydroperiod ponds, we expected to find higher α‐ and β‐diversity in longer hydroperiods, as well as predominance of the nestedness component in β‐diversity. Restricted occurrence of some genera and higher α‐diversity of immature odonate assemblages was detected in long‐hydroperiod ponds. Within‐hydroperiod β‐diversity values did not vary among hydroperiods, because the occasional occurrence of some genera with high dispersal ability of adults in short‐hydroperiod ponds yielded similar values of the β‐diversity among hydroperiods. Partitioning of β‐diversity among hydroperiods revealed a significant higher contribution of the nestedness component rather than turnover. This pattern is explained by the occurrence of some generalist genera across the whole gradient of hydroperiod, as a subset of fauna in longer‐hydroperiod ponds. Thus, our results suggest that reduction in hydroperiod length, if occurring in the future climate change, would favor habitat‐generalist taxa in lentic ecosystems.     

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long‐term biodiversity experiment

Soil microbes are known to be key drivers of several essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition in the rhizosphere is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this time frame plants with a monoculture or mixture history changed in the bacterial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same field monocultures or mixtures (plant history in monoculture vs. mixture) in pots inoculated with microbes extracted from the field monoculture and mixture soils attached to the roots of the host plants (soil legacy). After 5 months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Bacterial community structure in the plant rhizosphere was primarily determined by soil legacy and by plant species identity, but not by plant history. In seven of the eight plant species the number of individual operational taxonomic units with increased abundance was larger when inoculated with microbes from mixture soil. We conclude that plant species richness can affect below‐ground community composition and diversity, feeding back to the assemblage of rhizosphere bacterial communities in newly establishing plants via the legacy in soil.     

Primary productivity is weakly related to floristic alpha and beta diversity across Australia

Aim Ecosystem functions such as productivity may be influenced not only by the biological diversity at each location (α‐diversity) but also by the biological turnover between locations (β‐diversity). We perform a continental‐scale test of the strength and direction of relationships between gross primary productivity (GPP) and both α‐ and β‐diversity. Location Continental Australia. Methods Species occurrence records were used to quantify the taxonomic α‐diversity of vascular plants in approximately 11,000 1 km × 1 km grid cells across Australia, and to calculate the average β‐diversity within a 10‐km radius around each cell. The magnitude and variability of monthly, MODIS‐derived remotely sensed GPP (2001–12) were summarized for continental Australia, as were rainfall and temperature over the same period. Generalized additive models were then used to test whether the magnitude or variability of GPP were distinctly influenced by either biodiversity measure, over and above the influence of environmental conditions. Results Precipitation and temperature explained large proportions of deviance in the magnitude (75.6%) and variability (38.3%) of GPP across the Australian continent. GPP was marginally more strongly related to species richness than it was to species turnover. However, neither diversity measure provided substantial increases in the explanatory power of GPP models over and above that of environment‐only models (always < 1%). Main conclusions The relationship between primary productivity and taxonomic α‐ and β‐diversity was weak for the Australian flora. Our findings question the generality of key assumptions, predictions and results in the literature regarding the strength of empirical relationships between productivity and biodiversity across multiple biological levels (α‐, β‐ and γ‐diversity) at macroecological scales.     

Identifying qualitative effects of different grazing types on below‐ground communities and function in a long‐term field experiment

Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore‐induced changes on below‐ground processes and communities is limited. Using a long‐term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit and invertebrate grazing impacted soil functions and microbial community structure. All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits. Furthermore, our results suggest that exclusion of invertebrate grazers decreases both microbial biomass and abundance of genes associated with key biogeochemical cycles, and could thus have long‐term consequences for ecosystem functions. The mechanism behind these impacts are likely to be driven by both direct effects of grazing altering the pattern of nutrient inputs and by indirect effects through changes in plant species composition. However, we could not entirely discount that the pesticide used to exclude invertebrates may have affected some microbial community measures. Nevertheless, our work illustrates that human activity that affects grazing intensity may affect ecosystem functioning and sustainability, as regulated by multi‐trophic interactions between above‐ and below‐ground communities.     

The shift from plant–plant facilitation to competition under severe water deficit is spatially explicit

The stress‐gradient hypothesis predicts a higher frequency of facilitative interactions as resource limitation increases. Under severe resource limitation, it has been suggested that facilitation may revert to competition, and identifying the presence as well as determining the magnitude of this shift is important for predicting the effect of climate change on biodiversity and plant community dynamics. In this study, we perform a meta‐analysis to compare temporal differences of species diversity and productivity under a nurse plant (Retama sphaerocarpa) with varying annual rainfall quantity to test the effect of water limitation on facilitation. Furthermore, we assess spatial differences in the herbaceous community under nurse plants in situ during a year with below‐average rainfall. We found evidence that severe rainfall deficit reduced species diversity and plant productivity under nurse plants relative to open areas. Our results indicate that the switch from facilitation to competition in response to rainfall quantity is nonlinear. The magnitude of this switch depended on the aspect around the nurse plant. Hotter south aspects under nurse plants resulted in negative effects on beneficiary species, while the north aspect still showed facilitation. Combined, these results emphasize the importance of spatial heterogeneity under nurse plants for mediating species loss under reduced precipitation, as predicted by future climate change scenarios. However, the decreased water availability expected under climate change will likely reduce overall facilitation and limit the role of nurse plants as refugia, amplifying biodiversity loss.     

Dispersal and neutral sampling mediate contingent effects of disturbance on plant beta‐diversity: a meta‐analysis

A major challenge in ecology, conservation and global‐change biology is to understand why biodiversity responds differently to similar environmental changes. Contingent biodiversity responses may depend on how disturbance and dispersal interact to alter variation in community composition (β‐diversity) and assembly mechanisms. However, quantitative syntheses of these patterns and processes across studies are lacking. Using null‐models and meta‐analyses of 22 factorial experiments in herbaceous plant communities across Europe and North America, we show that disturbance diversifies communities when dispersal is limited, but homogenises communities when combined with increased immigration from the species pool. In contrast to the hypothesis that disturbance and dispersal mediate the strength of niche assembly, both processes altered β‐diversity through neutral‐sampling effects on numbers of individuals and species in communities. Our synthesis suggests that stochastic effects of disturbance and dispersal on community assembly play an important, but underappreciated, role in mediating biotic homogenisation and biodiversity responses to environmental change.     

A simulation‐based approach to understand how metacommunity characteristics influence emergent biodiversity patterns

To understand controls over biodiversity, it is necessary to take a multi‐scale approach to understand how local and regional factors affect the community assembly processes that drive emergent patterns. This need is reflected in the growing use of the metacommunity concept to interpret multi‐scale measures of biodiversity, including metrics derived from diversity partitioning (e.g. α, β and γ diversity) and variation partitioning (e.g. spatial and environmental components of compositional turnover) techniques. However, studies have shown limited success using these metrics to characterize underlying community assembly dynamics. Here we demonstrate how a metacommunity simulation package (MCSim) can be used to evaluate when and how biodiversity metrics can be used to make inferences about metacommunity characteristics. We examined a wide range of parameter settings representing ecologically relevant scenarios. We used artificial neural networks (ANNs) to assess the sensitivity of diversity and variation partitioning metrics (calculated from simulation outcomes) to metacommunity parameter settings. In the scenarios examined in this study, the niche‐neutral gradient strongly influenced most biodiversity metrics, metacommunity size exhibited a marginal influence over some metrics, and dispersal dynamics only affected a subset of variation partitioning outcomes. Variation partitioning response curves along the niche‐neutral gradient were not monotonic; however, simulation outcomes suggest other biodiversity metrics (e.g. dissimilarity saturation) can be used in combination with variation partitioning metrics to make inferences about metacommunity properties. With the growing availability of archived ecological data, we expect future work will apply simulation‐based techniques to better understand links between biodiversity and the metacommunity characteristics that are presumed to control the underlying community assembly processes.     

A phylogenetic perspective on species diversity, β‐diversity and biogeography for the microbial world

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high‐altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β‐diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High‐altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β‐diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β‐diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter‐ and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.     

Differentiating between niche and neutral assembly in metacommunities using null models of β‐diversity

The β‐null deviation measure, developed as a null model for β‐diversity, is increasingly used in empirical studies to detect the underlying structuring mechanisms in communities (e.g. niche versus neutral and stochastic versus deterministic). Despite growing use, the ecological interpretation of the presence/absence and abundance‐based versions of the β‐null diversity measure have not been tested against communities with known assembly mechanisms, and thus have not been validated as an appropriate tool for inferring assembly mechanisms. Using a mechanistic model with known assembly mechanisms, we simulated replicate metacommunities and examined β‐null deviation values 1) across a gradient of niche (species‐sorting) to neutrally structured metacommunities, 2) through time, and 3) we compared the effect of changes in assembly mechanism on the performance of the β‐null deviation measures. The impact of stochasticity on assembly outcomes was also considered. β‐null deviation measures proved to be interpretable as a measure of niche or neutral assembly. However, the presence/absence version of the β‐null deviation measure could not differentiate between niche and neutral metacommunities if demographic stochasticity were present. The abundance‐based β‐null deviation measure was successful in distinguishing between niche and neutral metacommunities and was robust to the presence of stochasticity, changes through time, and changing assembly mechanisms. However, we suggest that it is not robust to changing abundance evenness distributions or sampling of communities, and so its interpretation still requires some care. We encourage the testing of the assumptions behind null models for ecology and care in their application.     

Phylogenetic alpha and beta diversities of butterfly communities correlate with climate in the western Swiss Alps

The observation of non‐random phylogenetic distribution of traits in communities provides evidence for niche‐based community assembly. Environment may influence the phylogenetic structure of communities because traits determining how species respond to prevailing conditions can be phylogenetically conserved. In this study, we investigate the variation of butterfly species richness and of phylogenetic α‐ and β‐diversities along temperature and plant species richness gradients. Our study indicates that butterfly richness is independently positively correlated to temperature and plant species richness in the study area. However, the variation of phylogenetic α‐ and β‐diversities is only correlated to temperature. The significant phylogenetic clustering at high elevation suggests that cold temperature filters butterfly lineages, leading to communities mostly composed of closely related species adapted to those climatic conditions. These results suggest that in colder and more severe conditions at high elevations deterministic processes and not purely stochastic events drive the assemblage of butterfly communities.     

Aquatic insect β‐diversity is not dependent on elevation in Southern Rocky Mountain streams

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