Biogeography and ecological diversity patterns of rare and abundant bacteria in oil‐contaminated soils

Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long‐term oil‐contaminated soils at intervals of 46–360 km by performing high‐throughput sequencing of 16S rRNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples. Both rare and abundant subcommunities showed significant distance–decay relationships, and their assemblies were driven by different factors. The rare subcommunity primarily exhibited a spatially structured distribution (i.e., stochastic processes), while edaphic factors (i.e., deterministic processes) largely contributed to the structure of the abundant subcommunity. A network analysis revealed closer relationships between abundant bacteria and their heightened influence on other co‐occurrences in the community compared with rare species. In conclusion, rare microbial taxa may play potential roles in maintaining ecosystem diversity, although they do not appear to be central to microbial networks. Abundant microbes are vital for microbial co‐occurrences in oil‐contaminated soils, and high relative abundance and ubiquitous distribution suggest potential roles in the degradation of organic pollutants.     

Does shrub invasion indirectly limit grass establishment via seedling herbivory? A test at grassland‐shrubland ecotones

Question: Does shrub invasion at ecotones indirectly limit grass establishment by increasing mammalian seedling herbivory? Location: Chihuahuan Desert, New Mexico, USA. Methods: We tested the hypothesis that herbivore‐related mortality of seedlings of the dominant perennial grass Bouteloua eriopoda would be highest in shrub‐dominated portions of grassland‐shrubland ecotones. We tested the hypothesis in two Chihuahuan Desert sites featuring similar shrub encroachment patterns but different shrub species, grass cover, and different abundances of small mammals. Within each site we transplanted B. eriopoda seedlings to grass‐dominated, middle, and shrub‐dominated positions of replicate ecotones during the time of year (mid‐summer) when they would naturally appear and monitored seedling fates. We estimated population size/activity of putative small mammal herbivores. Results: Seedlings were killed by mammals in greater numbers in shrubland than in grassland or middle ecotone positions at the site with large herbivore numbers. At the site with low herbivore numbers, most seedlings were killed in middle ecotone positions. The abundance patterns of herbivores did not parallel patterns of seedling herbivory across the ecotones or between sites. Conclusions: Seedling herbivory is an important process and is related to vegetation composition, but the mechanisms underlying the relationship are not clear. We speculate that variation in small mammal foraging behavior may contribute to seedling herbivory patterns. Restoration strategies in the Chihuahuan Desert need to account for the abundance and/or behavior of native herbivores.     

Bird community composition across an Andean tree‐line ecotone

Few studies have found strong evidence to suggest that ecotones promote species richness and diversity. In this study we examine the responses of a high‐Andean bird community to changes in vegetation and topographical characteristics across an Andean tree‐line ecotone and adjacent cloud forest and puna grassland vegetation in southern Peru. Over a 6‐month period, birds and vegetation were surveyed using a 100 m fixed‐width Distance Sampling point count method. Vegetation analyses revealed that the tree‐line ecotone represented a distinctive high‐Andean vegetation community that was easily differentiated from the adjacent cloud forest and puna grassland based on changes in tree‐size characteristics and vegetation cover. Bird community composition was strongly seasonal and influenced by a pool of bird species from a wider elevational gradient. There were also clear differences in bird community measures between tree‐line vegetation, cloud forest and puna grassland with species turnover (β‐diversity) most pronounced at the tree‐line. Canonical Correspondence Analysis revealed that the majority of the 81 bird species were associated with tree‐line vegetation. Categorizing patterns of relative abundance of the 42 most common species revealed that the tree‐line ecotone was composed primarily of cloud forest specialists and habitat generalists, with very few species from the puna grassland. Only two species, Thlypopsis ruficeps and Anairetes parulus, both widespread Andean species more typical of montane woodland vegetation edges, were categorized as ecotone specialists. However, our findings were influenced by significant differences in species detectability between all three vegetation communities. Our study highlights the importance of examining ecotones at an appropriate spatial and temporal scale. Selecting a suitable distance between sampling points based on the detection probabilities of the target bird species is essential to obtain an unbiased picture of how ecotones influence avian richness and diversity.     

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus

The microbiome associated with ornamental plants has largely been neglected, despite its potential for impacting plant health. This work characterized the composition, diversity, and microbial co‐associations in the soil microbiome associated with species and cultivars of plant in the genus Buxus (common name boxwood), a group of woody perennial shrubs commonly used in residential landscapes and found in native ecosystems. Soil was collected from 82 individual curated boxwood accessions at the U.S. National Arboretum National Boxwood Collection. Amplicon libraries targeting archaea, bacteria, and fungi were generated and sequenced using the Illumina MiSeq platform. Identification of individual sequence variants resulted in 275 archaeal, 15,580 bacterial, and 7,525 fungal taxa. Neither spatial distance among samples nor association with different types of boxwood were significant predictors of soil microbiome composition. However, archaeal and bacterial diversity was significantly different in soil from distinct types of boxwood. Co‐association networks indicated that archaea and bacteria show greater evidence of being keystone taxa than fungi. Overall, this work demonstrates the potential for targeting specific keystone taxa to shift the soil microbiome associated with these boxwood accessions and that planting different species or cultivars in the landscape may shift the diversity of prokaryotic microorganisms.     

Soil fungal composition changes with shrub encroachment in the northern Chihuahuan Desert

Woody species encroachment of grasslands globally causes many socioecological impacts, including loss of grazing pastures and decreased biodiversity. Soil microbial communities may partially regulate the pace of shrub encroachment, as plant-microbial interactions can strongly influence plant success. We measured fungal composition and activity under dominant plant species across a grassland to shrubland transition to determine if shrubs cultivate soil microbial communities as they invade. Specifically, soil microbial communities, abiotic soil properties, and extracellular enzyme activities were quantified for soils under four common Chihuahuan Desert plant species (three grasses, one shrub) in central New Mexico, U.S.A. Extracellular enzyme activity levels were fairly consistent under different plant species across the grassland to shrubland transition. Activity levels of two enzymes (alkaline phosphatase and beta-N-acetyl-glucosaminidase) were lower in the ecotone, presumably because soil organic matter content was also lower in ecotone soils. Community composition of soil fungi mirrored patterns in the plant community, with distinct plant and fungal communities in the shrubland and grassland, while grassland-shrubland ecotone soils hosted a mix of taxa from both habitats. We show that shrubs cultivate a distinct microbial community on the leading edge of the invasion, which may be necessary for shrub colonization, establishment, and persistence.     

A simulation test of the resource‐averaging hypothesis of ecotone formation

Abstract. The pattern at an ecotone may indicate the processes that created that ecotone. Such patterns may in turn affect the responses of ecotones to environmental change. The resource averaging hypothesis suggests a process for the development of tree lines that should produce patterns that are modifications of patterns in soil resources. A computer simulation model that embodies the resource averaging hypothesis is used to generate tree‐line patterns. Different spatial patterns in the variation of soil resources are represented in the model. The patterns of tree line computed by the simulation closely correspond to the patterns of soil resources that were input. These patterns are compared to patterns recorded in the field and by aerial photography. For the patterns of soil resources observed at some alpine tree lines, the model cannot produce the kinds of patterns of vegetation observed. Resource averaging alone cannot be an explanation of such tree lines.     

农牧交错带草地土壤剖面微生物总量、多样性和互作网络的垂直分布特征

【背景】草地土壤微生物是维持草地生态系统功能和稳定的关键要素之一,探寻微生物在土壤剖面的垂直分布特征和构建规律对于理解其在草地生态系统的作用至关重要。【目的】在80cm深的土壤剖面内,全面分析微生物的总量、多样性和物种间的相互作用网络表现出的垂直分布特征。【方法】基于内蒙古农牧交错带上典型草原土壤中原核微生物的定量和高通量测序数据,比较微生物的总量和多样性,使用分子生态网络方法(molecular ecological network approach,MENA)探究微生物相互作用网络的垂直变化。【结果】原核生物的总量和多样性随深度增加而逐渐降低,且群落结构变异沿土壤剖面逐渐增大。网络结构在表层最为复杂,微生物物种间联系紧密;随着深度的增加,微生物间紧密的关联会逐渐变稀疏,网络结构变得简单。此外,酸杆菌是当地土壤生态系统中的优势种群以及网络核心微生物物种,可能对土壤生态服务功能的稳定发挥具有重要的作用。【结论】原核微生物的总量、多样性和物种间的互作网络都表现出高度一致的垂直变化规律,即总量、多样性与深度成负相关,且其群落结构变异会逐渐扩大,同时微生物网络相关性会减弱。这些结果为我们提供了微生物动态变化的重要见解,对典型农牧交错带草地的生态保护具有一定的参考价值。     

Tall shrub and tree expansion in Siberian tundra ecotones since the 1960s

Circumpolar expansion of tall shrubs and trees into Arctic tundra is widely thought to be occurring as a result of recent climate warming, but little quantitative evidence exists for northern Siberia, which encompasses the world's largest forest‐tundra ecotonal belt. We quantified changes in tall shrub and tree canopy cover in 11, widely distributed Siberian ecotonal landscapes by comparing very high‐resolution photography from the Cold War‐era ‘Gambit’ and ‘Corona’ satellite surveillance systems (1965–1969) with modern imagery. We also analyzed within‐landscape patterns of vegetation change to evaluate the susceptibility of different landscape components to tall shrub and tree increase. The total cover of tall shrubs and trees increased in nine of 11 ecotones. In northwest Siberia, alder (Alnus) shrubland cover increased 5.3–25.9% in five ecotones. In Taymyr and Yakutia, larch (Larix) cover increased 3.0–6.7% within three ecotones, but declined 16.8% at a fourth ecotone due to thaw of ice‐rich permafrost. In Chukotka, the total cover of alder and dwarf pine (Pinus) increased 6.1% within one ecotone and was little changed at a second ecotone. Within most landscapes, shrub and tree increase was linked to specific geomorphic settings, especially those with active disturbance regimes such as permafrost patterned‐ground, floodplains, and colluvial hillslopes. Mean summer temperatures increased at most ecotones since the mid‐1960s, but rates of shrub and tree canopy cover expansion were not strongly correlated with temperature trends and were better correlated with mean annual precipitation. We conclude that shrub and tree cover is increasing in tundra ecotones across most of northern Siberia, but rates of increase vary widely regionally and at the landscape scale. Our results indicate that extensive changes can occur within decades in moist, shrub‐dominated ecotones, as in northwest Siberia, while changes are likely to occur much more slowly in the highly continental, larch‐dominated ecotones of central and eastern Siberia.     

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.     

Border and ecotone detection by vegetation composition along forest‐savanna transects in Ivory Coast

Abstract. Question: How do properties of different vegetation components vary along ecotones of semi‐deciduous forest islands, and can the depth of edge influence (DEI) of the components be detected using a novel combination of analyses? Location: Comoé National Park (CNP), NE Ivory Coast. Methods: Along eight transects at semi‐deciduous forest islands tree individuals > 20 cm DBH were mapped. At one transect, tree and shrub individuals down to 1 cm DBH were measured and cover of species was estimated. Split moving window dissimilarity analysis (SMWDA) and moving window regression analysis (MWRA) were combined to detect statistical significance of borders in multivariate vegetation data along continuous transects, to determine the width of associated ecotones, and, thus, the DEI towards the forest interior. Results: For trees > 20 cm DBH, a distinct boundary formation was detected, dominated by the semi‐fire resistant tree species Anogeissus leiocarpus. The median of DEI towards the forest interior was 55 m. Ecotone detection with all species present revealed an interlocked sequence of ecotones for grasses, herbs, woody climbers, shrubs and trees, with each of these ecotones being narrower than the overall ecotone. DEI ranged from 10 m for grasses up to 120 m for trees and shrubs. Conclusions: The coherent set of analyses applied proved to be an objective method for detecting borders and the width of associated ecotones. The patterns found may be explained by successional processes at the forest‐savanna border. The DEI measured for the forest islands in the nearly undisturbed semi‐natural system of the CNP is of relevance to concepts of core‐area analysis and the protection of forest interior species in semi‐deciduous forests in tropical West Africa.     

Land‐use influences phosphatase gene microdiversity in soils

Phosphorus cycling exerts significant influence upon soil fertility and productivity – processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared with arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH‐EDTA extractable orthophosphate. Beta‐propeller phytase genes were most abundant in bare fallowed soil. Phylogenetic analysis of metagenome sequences indicated the phenotypic shift observed in the capacity to mineralise phytate in bare fallow soil was accompanied by an increase in phoD, phoX and beta‐propeller phytase genes coding for exoenzymes. However, there was a remarkable degree of genetic similarity across the soils despite the differences in land‐use. Predicted extracellular ecotypes were distributed across a greater range of soil structure than predicted intracellular ecotypes, suggesting that microbial communities subject to the dual stresses of low nutrient availability and reduced access to organic material in bare fallowed soils rely upon the action of exoenzymes.     

From rags to enriched: metagenomic insights into ammonia-oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem

Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia-oxidizing archaea (AOA) can be considered one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.     

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.     

生态交错带及其研究进展

生态交错带研究对探索自然生态规律和保护环境有重要意义。近30a来,有关生态交错带的论文数平均年增57%,显示其得到了愈来愈广泛的关注。回顾了生态交错带概念的产生与发展,区分了它与边缘、生态边界层与生态过渡带等概念的异同;简述了其7个基本属性,即高生物多样性、丰富的特有种、大量外来种、频繁的物质流动、敏感的时空动态性、结构的异质性和脆弱性;总结提炼了生态交错带的基本原理和假说;综述了生态交错带的生物多样性产生机制、对全球变化的响应与反馈、生态设计与管理以及生态交错带模型发展和整合的研究进展。提出今后需要大力发展理论研究、多尺度模型转化和多因子综合分析,以完善生态交错带理论并支持生态学机理的探索。     

No general edge effects for invertebrates at Afromontane forest/grassland ecotones

The Afromontane region of South Africa is characterised by numerous small, remnant forests in a grassland matrix. The edges, or ecotones between forests and grasslands are usually sharp (typically just over a few metres) and are mainly maintained by both natural and, more recently, anthropogenic fires. We investigated epigaeic amphipod, carabid and ant distribution patterns across Afromontane forest/grassland ecotones and found little evidence to support the biological edge effect. Five of the fifty-two sampled species however, did increase significantly in abundance at the ecotone. Among these was a very distinct edge species, the amphipod Talistroides africana. Overall, carabids were more abundant and species rich in forests while for ants it was in the grasslands. Ants and carabids were both more abundant and species rich in spring and summer than in autumn and winter. More interestingly, the abundance and species richness patterns across the ecotone did not change with the passing of the seasons. We argue that a conservation strategy for the Afromontane forest patches must also incorporate the surrounding grassland. The grassland habitat is often perceived as less valuable than forest and, as a consequence, is subject to many anthropogenic disturbances such as fragmentation, cattle grazing and afforestation. Protecting grasslands around forest patches not only conserves the rich ant diversity, but also conserves the biota in the forests and at the edges, and would therefore be more meaningful in terms of the overall conservation of Afromontane biodiversity.     

Novel model‐based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient

A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome‐based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate‐associated ecotypes in populations of nitrogen‐fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate‐associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.     

Tropical montane forest ecotones: climate gradients, natural disturbance, and vegetation zonation in the Cordillera Central, Dominican Republic

Aim We examined relationships between climate–disturbance gradients and patterns of vegetation zonation and ecotones on a subtropical mountain range. Location The study was conducted on the windward slopes of the Cordillera Central, Dominican Republic, where cloud forest appears to shift in a narrow ecotone to monodominant forest of Pinus occidentalis. Methods Climate, disturbance and vegetation data were collected over the elevation range 1100–3100 m and in 50 paired plots along the ecotone. Aerial photographs were georeferenced to a high‐resolution digital elevation model in order to enable the analysis of landscape‐scale patterns of the ecotone. Results A Shipley–Keddy test detected discrete compositional ecotones at 2200 and 2500 m; the distributions of tree species at lower elevations were continuous. The elevation of the ecotone determined with aerial photographs was fairly consistent, namely ± 164 m (SD) over its 124‐km length, but it exhibited significant landscape variation, occurring at a lower elevation in a partially leeward, western zone. The ecotone also occurred significantly lower on ridges than it did in drainage gullies. Ecotone forest structure and composition differed markedly between paired plots. In pine paired plots, the canopy height was 1.7 times higher and the basal area of non‐pine species was 6 times lower than in the cloud forest directly below. Fire evidence was ubiquitous in the pine forest but rare in the abutting cloud forest. Mesoclimate changed discontinuously around the elevation of the ecotone: humidity and cloud formation decreased markedly, and frost frequency increased exponentially. Main conclusions The discreteness of the ecotone was produced primarily by fire. The elevational consistency of the ecotone, however, resulted from the overarching influence of mesoclimate on the elevational patterns of fire occurrence. Declining temperature and precipitation combine with the trade‐wind inversion to create a narrow zone where high‐elevation fires extinguish, enabling fire‐sensitive and fire‐tolerant taxa to abut. Once established, mesotopography and contrasting vegetation physiognomy probably reinforce this boundary through feedbacks on microenvironment and fire likelihood. The prominence of the pine in this study – and of temperate and fire‐tolerant taxa in subtropical montane forests in general – highlights the importance of climate‐disturbance–biogeography interactions in ecotone formation, particularly where fire mediates a dynamic between climate and vegetation.     

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.     

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.