Search

Summary: Climate and edaphic properties drive the biogeographic distribution of dominant soil microbial phylotypes in terrestrial ecosystems. However, the impact of plant species and their root nutritional traits on microbial distribution in coastal wetlands remains unclear.Here, we investigated the nutritional traits of 100 halophyte root samples and the bacterial communities in the corresponding soil samples from coastal wetlands across eastern China. This study spans 22° of latitude, covering over 2500 km from north to south.We found that 1% of soil bacterial phylotypes accounted for nearly 30% of the soil bacterial community abundance, suggesting that a few bacterial phylotypes dominated the coastal wetlands. These dominated phylotypes could be grouped into three ecological clusters as per their preference over climatic (temperature and precipitation), edaphic (soil carbon and nitrogen), and plant factors (halophyte vegetation, root carbon, and nitrogen). We further provide novel evidence that plant root nutritional traits, especially root C and N, can strongly influence the distribution of these ecological clusters.Taken together, our study provides solid evidence of revealing the dominance of specific bacterial phylotypes and the complex interactions with their environment, highlighting the importance of plant root nutritional traits on biogeographic distribution of soil microbiome in coastal wetland ecosystems. [ABSTRACT FROM AUTHOR]

Abstract Background Phylogeographic studies have gained prominence in linking past geological events to the distribution patterns of biodiversity, primarily in mountainous regions. However, such studies often focus on plant taxa, neglecting the intricate biogeographical patterns of microbes, particularly soil microbial communities. This article explores the spatial distribution of the nematode-trapping fungus Arthrobotrys oligospora, a widespread microorganism, in a tectonically active region at the southeastern edge of the Qinghai-Tibetan Plateau. By analysing the genetic variation of this fungus alongside the historical structure of major river watersheds, we sought to uncover potential connections between the two. Our study involved sampling 149 strains from 116 sites across six major watersheds in the region. Results The resulting haplotype network revealed five distinct clusters, each corresponding closely to a specific watershed. These clusters exhibited high haplotype diversity and low nucleotide diversity, supporting the notion of watershed-based segregation. Further analysis of haplotypes shared across watersheds provided evidence for three proposed past river connections. In particular, we found numerous shared haplotypes between the Yangtze and Mekong basins, as well as between the Yangtze and the Red basins. Evidence for a Irrawaddy-Salween-Red and a Yangtze-Pearl-Red river connections were also portrayed in our mapping exercise. Conclusions These findings emphasize the crucial role of historical geomorphological events in shaping the biogeography of microbial biodiversity, alongside contemporary biotic and abiotic factors. Watershed perimeters emerged as effective predictors of such patterns, suggesting their suitability as analytical units for regional-scale studies. Our study also demonstrates the potential of microorganisms and phylogeographic approaches to complement traditional geological analyses, providing a more comprehensive understanding of past landscape structure and its evolution.

Abstract Background Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53–2224 m) and geographic location (over 680 m) as well as the host coral’s genotype using RAD-sequencing. Results Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts’ ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. Conclusions Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.

Background: Phylogeographic studies have gained prominence in linking past geological events to the distribution patterns of biodiversity, primarily in mountainous regions. However, such studies often focus on plant taxa, neglecting the intricate biogeographical patterns of microbes, particularly soil microbial communities. This article explores the spatial distribution of the nematode-trapping fungus Arthrobotrys oligospora, a widespread microorganism, in a tectonically active region at the southeastern edge of the Qinghai-Tibetan Plateau. By analysing the genetic variation of this fungus alongside the historical structure of major river watersheds, we sought to uncover potential connections between the two. Our study involved sampling 149 strains from 116 sites across six major watersheds in the region. Results: The resulting haplotype network revealed five distinct clusters, each corresponding closely to a specific watershed. These clusters exhibited high haplotype diversity and low nucleotide diversity, supporting the notion of watershed-based segregation. Further analysis of haplotypes shared across watersheds provided evidence for three proposed past river connections. In particular, we found numerous shared haplotypes between the Yangtze and Mekong basins, as well as between the Yangtze and the Red basins. Evidence for a Irrawaddy-Salween-Red and a Yangtze-Pearl-Red river connections were also portrayed in our mapping exercise. Conclusions: These findings emphasize the crucial role of historical geomorphological events in shaping the biogeography of microbial biodiversity, alongside contemporary biotic and abiotic factors. Watershed perimeters emerged as effective predictors of such patterns, suggesting their suitability as analytical units for regional-scale studies. Our study also demonstrates the potential of microorganisms and phylogeographic approaches to complement traditional geological analyses, providing a more comprehensive understanding of past landscape structure and its evolution. [ABSTRACT FROM AUTHOR]

Introduction: Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang. Methods: Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed. Results: In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria, with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia. pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils. Discussion: These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau. [ABSTRACT FROM AUTHOR]

Background: Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53–2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing. Results: Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location. Conclusions: Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill. [ABSTRACT FROM AUTHOR]

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats disturbed by Plateau pikas (Ochtona curzoniae). Pika disturbance had different impacts on bacterial and fungal communities. Fungal diversity generally increased with patch area, whereas bacterial diversity decreased. These strikingly different species–area relationships were closely associated with their community assembly mechanisms. The loss of bacterial diversity on larger patches was largely driven by deterministic processes, mainly due to the decline of nutrient supply (e.g., organic C, inorganic N). In contrast, fungal distribution was driven primarily by stochastic processes that dispersal limitation contributed to their higher fungal diversity on lager patches. A bacterial co-occurrence network exhibited a positive relationship of nodes and linkage numbers with patch area, and the fungal network presented a positive modularity–area relationship, suggesting that bacteria tended to form a closer association community under pika disturbance, while fungi tended to construct a higher modularity network. Our results suggest that pikas affects the microbial assembly process and co-occurrence patterns in alpine environments, thereby enhancing the current understanding of microbial biogeography under natural disturbances. [ABSTRACT FROM AUTHOR]

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine‐learning models, we generated high‐resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes. [ABSTRACT FROM AUTHOR]

Aim: The diversity and distribution of soil microorganisms and their potential for long‐distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba Apodera vas, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on‐going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land‐use changes (e.g. due to limited LDD). Location: Documented records: Southern Hemisphere and intertropical zone; modelling: Global. Methods: We first built an updated global distribution map of A. vas using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21 ± 3 ka BP; PMIP3 IPSL‐CM5A‐LR), present and future (IPSL‐CMP6A‐LR predictions for 2071–2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation). Results: Our models show that favourable climatic conditions for A. vas currently exist in the British Isles, an especially well‐studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of A. vas in isolated and geologically young peri‐Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL‐CM6A‐LR scenario for 2071–2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula. Main Conclusions: This study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for A. vas, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions. [ABSTRACT FROM AUTHOR]

Despite their enormous impact on the environment and humans, the distribution and variety of the biggest natural secondary metabolite producers, the genus Streptomyces, have not been adequately investigated. We developed representative maps from public EMP 16S rRNA amplicon sequences microbiomics data. Streptomyces ASVs were extracted from the EMP overall bacterial community, demonstrating Streptomyces diversity and identifying crucial diversity patterns. Our findings revealed that while the EMP primarily distinguished bacterial communities as host-associated or free-living (EMPO level 1), the Streptomyces community showed no significant difference but exhibited distinctions between categories in EMPO level 2 (animal, plant, non-saline, and saline). Multiple linear regression analysis demonstrated that pH, temperature, and salinity significantly predicted Streptomyces richness, with richness decreasing as these factors increased. However, latitude and longitude do not predict Streptomyces richness. Our Streptomyces maps revealed that additional samplings in Africa and Southeast Asia are needed. Additionally, our findings indicated that a greater number of samples did not always result in greater Streptomyces richness; future surveys may not necessitate extensive sampling from a single location. Broader sampling, rather than local/regional sampling, may be more critical in answering microbial biogeograph questions. Lastly, using 16S rRNA gene sequencing data has some limitations, which should be interpreted cautiously. [ABSTRACT FROM AUTHOR]

Purpose: Soil microbial communities and related key ecological processes play critical roles in timberline delineation and soil carbon balance in alpine ecosystems, which are highly vulnerable to climate change. Accordingly, understanding their geographical differentiation will facilitate recognition of ecosystem functions and improve soil carbon models. In this study, we explored the biogeographic patterns of soil bacterial communities and their mechanisms in maintaining soil carbon balance in an alpine timberline ecosystem of the Sygera Mountains, Southeast Tibet. Materials and methods: Soil samples were collected from typical forest belts above and below the timberline. The abundance and composition of bacterial communities, as well as functional genes, were assessed using the gene chip technology. The relationship of key microbial taxa, functional genes, and soil carbon maintenance was investigated using random forest analysis, multi-model inference, and structural equation modeling. Results and discussion: The shrubland soil bacterial community exhibited greater diversity compared with the coniferous forest community, with higher Shannon Index and more functional genes at the taxonomic and functional levels, respectively. Bacterial community composition differed between the two forest types, with copiotrophic bacteria more abundant in shrubland, and oligotrophic bacteria more abundant in coniferous forest. The shrubland community was also more efficient at utilizing labile organic carbon, while the coniferous forest community utilized recalcitrant organic carbon more efficiently. Genes related to labile carbon degradation were more intense in shrubland, while genes related to recalcitrant carbon degradation were more concentrated in the coniferous forest. Soil temperature and C:N ratio were dominant drivers of bacterial community composition and function. Besides key soil-environment and microbial properties, certain bacterial taxa and functional genes also exerted unique roles in soil carbon variation. Conclusions: Significant differences exist in soil bacterial community composition and functions between the two forest types above and below the timberline of the Sygera Mountains. These differences may be attributed to soil temperature and soil C:N ratio. Coupling these microbial variables into the earth system model can improve the predictive power of the carbon feedback process in terrestrial ecosystems. [ABSTRACT FROM AUTHOR]

Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions. [ABSTRACT FROM AUTHOR]

Constraining the spatial distribution of microorganisms and their ecological interactions is crucial for informing biogeochemistry. To that end, we explore horizontal and vertical patterns of microbial biogeography in the eastern Yucatán carbonate aquifer by examining the relative abundance of microbial taxa via 16S rRNA gene sequencing. As one of the largest anchialine groundwater systems on Earth, the density-stra tified Yucatán aquifer consists of a meteoric lens overlying saline groundwater. The myriad sinkholes (cenotes) of the eastern peninsula lead into a vast network of subsurface conduits. Several studies describe microbial communities within specific regions of the aquifer, yet fundamental questions remain regarding the ecology and distribution of biogeochemically relevant microbes. Our analysis demonstrates that this aquifer hosts a distinct microbiome from nearby seawater, with regionalism observed across cave systems and vertical water column zones. We apply novel software to construct taxonomic co-occurrence networks at different scales and categorize highly connected groups of taxa into potential niches. Our network analysis approach suggests that ubiquitous, metabolically flexible taxa such as the family Comamonadaceae act as ecological linchpins across several niches, often directly or indirectly co-occurring with taxa capable of anammox (e.g., Gemmataceae), methanotrophy (e.g., Methyloparacoccus), or organoheterotrophy. Furthermore, communities from a deep, pit-like cenote open to the surface show the strongest niche partitioning between water column zones, differing from those encountered throughout the mostly dark and oligotrophic aquifer system, including another deep pit cenote with no direct surface opening. Our results suggest that members of a core microbiome could modulate different biogeochemical regimes depending on location, acting as reservoirs of metabolic potential in disparate environments of this groundwater system. IMPORTANCE The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches. [ABSTRACT FROM AUTHOR]

Efforts to catalog global biodiversity have often focused on aboveground taxonomic diversity, with limited consideration of belowground communities. However, diversity aboveground may influence the diversity of belowground communities and vice versa. In addition to taxonomic diversity, the structural diversity of plant communities may be related to the diversity of soil bacterial and fungal communities, which drive important ecosystem processes but are difficult to characterize across broad spatial scales. In forests, canopy structural diversity may influence soil microorganisms through its effects on ecosystem productivity and root architecture, and via associations between canopy structure, stand age, and species richness. Given that structural diversity is one of the few types of diversity that can be readily measured remotely (e.g., using light detection and ranging—LiDAR), establishing links between structural and microbial diversity could facilitate the detection of belowground biodiversity hotspots. We investigated the potential for using remotely sensed information about forest structural diversity as a predictor of soil microbial community richness and composition. We calculated LiDAR‐derived metrics of structural diversity as well as a suite of stand and soil properties from 38 forested plots across the central hardwoods region of Indiana, USA, to test whether forest canopy structure is linked with the community richness and diversity of four key soil microbial groups: bacteria, fungi, arbuscular mycorrhizal (AM) fungi, and ectomycorrhizal (EM) fungi. We found that the density of canopy vegetation is positively associated with the taxonomic richness (alpha diversity) of EM fungi, independent of changes in plant taxonomic richness. Further, structural diversity metrics were significantly correlated with the overall community composition of bacteria, EM, and total fungal communities. However, soil properties were the strongest predictors of variation in the taxonomic richness and community composition of microbial communities in comparison with structural diversity and tree species diversity. As remote sensing tools and algorithms are rapidly advancing, these results may have important implications for the use of remote sensing of vegetation structural diversity for management and restoration practices aimed at preserving belowground biodiversity. [ABSTRACT FROM AUTHOR]

Bacterioplankton underpin biogeochemical cycles and an improved understanding of the patterns and drivers of variability in their distribution is needed to determine their wider functioning and importance. Sharp environmental gradients and dispersal barriers associated with ocean fronts are emerging as key determinants of bacterioplankton biodiversity patterns. We examined how the development of the Celtic Sea Front (CF), a tidal mixing front on the Northwest European Shelf affects bacterioplankton communities. We performed 16S‐rRNA metabarcoding on 60 seawater samples collected from three depths (surface, 20 m and seafloor), across two research cruises (May and September 2018), encompassing the intra‐annual range of the CF intensity. Communities above the thermocline of stratified frontal waters were clearly differentiated and less diverse than those below the thermocline and communities in the well‐mixed waters of the Irish Sea. This effect was much more pronounced in September, when the CF was at its peak intensity. The stratified zone likely represents a stressful environment for bacterioplankton due to a combination of high temperatures and low nutrients, which fewer taxa can tolerate. Much of the observed variation was driven by Synechococcus spp. (cyanobacteria), which were more abundant within the stratified zone and are known to thrive in warm oligotrophic waters. Synechococcus spp. are key contributors to global primary productivity and carbon cycling and, as such, variability driven by the CF is likely to influence regional biogeochemical processes. However, further studies are required to explicitly link shifts in community structure to function and quantify their wider importance to pelagic ecosystems. [ABSTRACT FROM AUTHOR]

Abstract Background Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. Results Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. Conclusion Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition. Video Abstract

Burrowing animals are a critical driver of terrestrial ecosystem functioning, but we know little about their effects on soil microbiomes. Here, we evaluated the effect of burrowing animals on microbial assembly processes and co-occurrence patterns using soil microbiota from a group of habitats disturbed by Plateau pikas (Ochtona curzoniae). Pika disturbance had different impacts on bacterial and fungal communities. Fungal diversity generally increased with patch area, whereas bacterial diversity decreased. These strikingly different species–area relationships were closely associated with their community assembly mechanisms. The loss of bacterial diversity on larger patches was largely driven by deterministic processes, mainly due to the decline of nutrient supply (e.g., organic C, inorganic N). In contrast, fungal distribution was driven primarily by stochastic processes that dispersal limitation contributed to their higher fungal diversity on lager patches. A bacterial co-occurrence network exhibited a positive relationship of nodes and linkage numbers with patch area, and the fungal network presented a positive modularity–area relationship, suggesting that bacteria tended to form a closer association community under pika disturbance, while fungi tended to construct a higher modularity network. Our results suggest that pikas affects the microbial assembly process and co-occurrence patterns in alpine environments, thereby enhancing the current understanding of microbial biogeography under natural disturbances.

Abstract Efforts to catalog global biodiversity have often focused on aboveground taxonomic diversity, with limited consideration of belowground communities. However, diversity aboveground may influence the diversity of belowground communities and vice versa. In addition to taxonomic diversity, the structural diversity of plant communities may be related to the diversity of soil bacterial and fungal communities, which drive important ecosystem processes but are difficult to characterize across broad spatial scales. In forests, canopy structural diversity may influence soil microorganisms through its effects on ecosystem productivity and root architecture, and via associations between canopy structure, stand age, and species richness. Given that structural diversity is one of the few types of diversity that can be readily measured remotely (e.g., using light detection and ranging—LiDAR), establishing links between structural and microbial diversity could facilitate the detection of belowground biodiversity hotspots. We investigated the potential for using remotely sensed information about forest structural diversity as a predictor of soil microbial community richness and composition. We calculated LiDAR‐derived metrics of structural diversity as well as a suite of stand and soil properties from 38 forested plots across the central hardwoods region of Indiana, USA, to test whether forest canopy structure is linked with the community richness and diversity of four key soil microbial groups: bacteria, fungi, arbuscular mycorrhizal (AM) fungi, and ectomycorrhizal (EM) fungi. We found that the density of canopy vegetation is positively associated with the taxonomic richness (alpha diversity) of EM fungi, independent of changes in plant taxonomic richness. Further, structural diversity metrics were significantly correlated with the overall community composition of bacteria, EM, and total fungal communities. However, soil properties were the strongest predictors of variation in the taxonomic richness and community composition of microbial communities in comparison with structural diversity and tree species diversity. As remote sensing tools and algorithms are rapidly advancing, these results may have important implications for the use of remote sensing of vegetation structural diversity for management and restoration practices aimed at preserving belowground biodiversity.

Summary: The ecological and evolutionary processes shaping community structure and functions of microbial symbionts are known to be scale‐dependent. Nonetheless, understanding how the relative importance of these processes changes across spatial scales, and deciphering the hierarchical metacommunity structure of fungal endophytes has proven challenging.We investigated metacommunities of endophytic fungi within leaves of an invasive plant (Alternanthera philoxeroides) across wide latitudinal transects both in its native (Argentina) and introduced (China) ranges to test whether metacommunities of fungal endophytes were structured by different drivers at different spatial scales.We found Clementsian structures with seven discrete compartments (distinctive groups of fungal species with coincident distribution ranges), which coincided with the distribution of major watersheds. Metacommunity compartments were explicitly demarcated at three spatial scales, that is, the between‐continent, between‐compartment, and within‐compartment scales. At larger spatial scales, local environmental conditions (climate, soil, and host plant traits) were replaced by other geographical factors as principal determinants of metacommunity structure of fungal endophytes and community diversity–function relationships.Our results reveal novel insights into the scale dependency of diversity and functions of fungal endophytes, which are likely similar for plant symbionts. These findings can potentially improve our understanding of the global patterns of fungal diversity. [ABSTRACT FROM AUTHOR]

Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β‐diversity along vertical (0–240 cm of soil depth) and horizontal spatial dimensions (~500,000 km2) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray‐Curtis) and phylogenetic (weighted Unifrac) β‐diversity. Additionally, we assessed whether the distance‐decay (horizontal dimension) was greater in the topsoil (0–30 cm) or subsoil (in each 30 cm layer from 30–240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β‐diversity was impacted more by soil depth, while the taxonomic β‐diversity changed more between geographic locations. The distance‐decay was lower in the topsoil than in all subsoil layers analysed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche‐based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β‐diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems. [ABSTRACT FROM AUTHOR]

The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale‐dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N‐related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography. [ABSTRACT FROM AUTHOR]

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed. [ABSTRACT FROM AUTHOR]

Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.

Abstract Background In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks. Results Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (

Background: Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. Results: Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. Conclusion: Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition. 11R7XF31NC9oJy9jTm658c Video Abstract [ABSTRACT FROM AUTHOR]

Aim: Revealing the ecological mechanisms driving the diversity patterns of microbial communities across space and through time is an essential issue in microbial biogeography. This study links microbial spatial scaling with ecological mechanisms, aiming to provide novel mechanistic insights into the biogeographic patterns followed by different types of microbes. Location: Beibu Gulf, a semi‐enclosed oceanic bay located on the southern coast of China. Taxon: Bacteria, which were further classified as abundant and rare taxa. Methods: By employing high throughput sequencing, two typical spatial scaling models, diversity‐area (DAR) and distance‐decay relationships (DDR), were investigated for the abundant and rare microbial communities in a coastal sediment ecosystem. Both alpha‐ and beta‐diversity indices were extended to Hill numbers to verify the contribution of abundant and rare taxa to DAR and DDR. The iCAMP approach was used to quantify the contribution of different ecological processes in structuring microbial communities. Results: Strong spatial scaling patterns were observed for the whole communities and the rare subcommunities but only weak patterns for the abundant subcommunities. Rare subcommunities were mainly responsible for the observed spatial scaling patterns, as confirmed by extending spatial scaling diversity metrics to Hill numbers. Both environmental heterogeneity and local community assembly mechanisms drove the spatial scaling of microbial communities. Strong ecological drift and dispersal limitation underlay the spatial scaling of rare subcommunities, whereas high homogeneous selection weakened the spatial scaling of abundant subcommunities. Main Conclusions: Rare taxa were mainly responsible for the biogeographic patterns followed by sediment microbial communities in the Beibu Gulf. Distinct ecological mechanisms underlay the different biogeographic patterns followed by abundant and rare subcommunities. [ABSTRACT FROM AUTHOR]

Tropical montane ecosystems are the centers of biodiversity, and Janzen proposed that mountain climate variability plays a key role in sustaining this biodiversity. We test this hypothesis for soil bacteria and fungi along a 265-1,400 m elevational gradient on Hainan Island of tropical China, representing diverse vegetation types from deciduous monsoon forest to cloud forest. We found that bacterial and fungal diversity declined as elevation increased, and the dissimilarity of both groups increased with increasing separation in elevation, although changes in bacteria were larger than in fungi. Seasonal alterations and the range of soil moisture in the growing season were found to be the dominant drivers of fungal richness and Shannon diversity, whereas soil pH was the major driver of bacterial diversity. Dissimilarities of bacterial and fungal communities were best predicted by climate, particularly seasonal changes in soil temperature, with weaker influences of soil physicochemistry and vegetation. The dominant effect of seasonality in soil temperature was further detected in cloud forests, which harbored a higher proportion of unique bacterial species and dissimilarity of bacterial and fungal communities. Our findings suggest that local-climate variability plays a crucial role in structuring the distribution of soil microbial communities along a tropical montane gradient, which generally supports Janzen's hypothesis. Such a sensitivity to climatic variability suggests that soil microbial communities along tropical montane gradients may shift in response to future climate scenarios. [ABSTRACT FROM AUTHOR]

Despite their enormous impact on the environment and humans, the distribution and variety of the biggest natural secondary metabolite producers, the genus Streptomyces, have not been adequately investigated. We developed representative maps from public EMP 16S rRNA amplicon sequences microbiomics data. Streptomyces ASVs were extracted from the EMP overall bacterial community, demonstrating Streptomyces diversity and identifying crucial diversity patterns. Our findings revealed that while the EMP primarily distinguished bacterial communities as host-associated or free-living (EMPO level 1), the Streptomyces community showed no significant difference but exhibited distinctions between categories in EMPO level 2 (animal, plant, non-saline, and saline). Multiple linear regression analysis demonstrated that pH, temperature, and salinity significantly predicted Streptomyces richness, with richness decreasing as these factors increased. However, latitude and longitude do not predict Streptomyces richness. Our Streptomyces maps revealed that additional samplings in Africa and Southeast Asia are needed. Additionally, our findings indicated that a greater number of samples did not always result in greater Streptomyces richness; future surveys may not necessitate extensive sampling from a single location. Broader sampling, rather than local/regional sampling, may be more critical in answering microbial biogeograph questions. Lastly, using 16S rRNA gene sequencing data has some limitations, which should be interpreted cautiously.

Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60–70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.

Background: In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks. Results: Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances. Conclusions: We conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities. [ABSTRACT FROM AUTHOR]

Microbes carry out many critical biogeochemical transformations in the biosphere such as greenhouse gas production and consumption. Characterizing how microbial communities vary through space and time may hold insights into understanding ecosystem function, particularly as it responds to ongoing climate change. However, it remains unclear to what extent variability in the composition of microbial communities exerts long-term control over biogeochemistry independently of the physiochemical and macroorganismal context in which microbes reside. In this synthesis, we reviewed literature about the versatility and adaptability of microbial communities, and analogous research in medicine, agriculture, and bioremediation. We synthesized data from microbial diversity experiments to determine thresholds at which loss of microbial richness impairs function and compared it to actual microbial richness in nature. The evidence suggests that, in environments such as surface soils, sediments, rivers, lakes, oceans, and the atmosphere, which are open to microbial inoculum and which dominate biogeochemical processes in the biosphere, microbial function equilibrates to environmental conditions over a much shorter interval (days to years) than the time scale on which anthropogenic climate change influences ecosystems (decades to centuries). We conclude that the degree of microbial control over ecosystem processes has been overstated because the correlation of taxonomic information with ecosystem function has obscured the understanding of causality in natural ecosystems. We recommend experiments in which microbial communities are manipulated in ways that allow us to disentangle the influence of microbial community structure from confounding environmental covariates. [ABSTRACT FROM AUTHOR]

The knowledge about the microbial diversity of different olives varieties from diverse regions in the Mediterranean basin is limited. This work aimed to determine the microbial diversity of three different fermented olive varieties, collected from different regions in Cyprus, via Next Generation Sequencing (NGS) analysis. Olives were spontaneously fermented for 120days, microbial DNA was extracted from the final products, and subjected to 16S rRNA gene and ITS1 loci metabarcoding analysis for the determination of bacterial and fungal communities, respectively. Results revealed that the bacterial profile of the studied varieties was similar, while no noteworthy differences were observed in olives from different regions. The bacterial profile was dominated by the co-existence of Lactobacillus and Streptococcus, while the genera Lactococcus and Salinivibrio and the family Leuconostocaceae were also present in increased relative abundances. Regarding fungal communities, the analysis indicated discrimination among the different varieties, especially in Kalamata ones. The most abundant fungi were mainly the genera Aspergillus, Botryosphaeria, Meyerozyma, and Zygosaccharomyces for Cypriot olives, the genera Botryosphaeria, Saccharomyces, Geosmithia, and Wickeromyces for Kalamata variety, while the dominant fungi in the Picual variety were mainly members of the genera Candida, Penicillium, Saccharomyces, Hanseniospora and Botryosphaeria. Potential microbial biomarkers that distinguish the three varieties are also proposed. Moreover, interaction networks analysis identified interactions among the key taxa of the communities. Overall, the present work provides useful information and sheds light on an understudied field, such as the comparison of microbiota profiles of different varieties from several regions in Cyprus. The study enriches our knowledge and highlights the similarities and the main differences between those aspects, booming in parallel the need for further works on this frontier, in the attempt to determine potentially olives’ microbial terroir in Cyprus. Our work should be used as a benchmark for future works in this direction. [ABSTRACT FROM AUTHOR]

Most eukaryotic microbial biodiversity is undescribed, and most species might be morphologically indistinguishable. Notable exceptions are so-called flagship species which are highly conspicuous and can therefore be used to address biogeographical questions. Here we describe Hyalosphenia papilio subsp. paynei, an arcellinid testate amoeba (Amoebozoa; Arcellinida; Hyalospheniidae) from wet hollows in two Sphagnum peatlands, one in Wales and one in Ireland. Phylogenetic analysis based on Cytochrome C oxidase subunit I (COI) sequencing places it within the lineage A of the H. papilio complex, but it differs from all 13 known H. papilio genetic lineages by its very distinctive, wider than long, morphology. The fact that such a conspicuous taxon was never reported in hundreds of studies published on Holarctic Sphagnum peatlands since Leidy's description of H. papilio in 1874 suggests that this subspecies has not dispersed and survived beyond Britain and Ireland. Furthermore its genetic similarity to H. papilio s. str. suggests that it has recently evolved. The discovery of this new taxon calls for a more detailed analysis of the morphological, ecological and molecular diversity of the H. papilio species complex. [ABSTRACT FROM AUTHOR]

Biotic interactions are known as a major control on microbial diversity. However, biotic interactions have rarely been quantified in an adequate manner, often leaving much residual variation unexplained in microbial biogeographic studies. Herein, we propose a holistic approach to disentangle the relative importance of inter-domain interactions in shaping microbial diversity by incorporating community-level characteristics. Taking coastal bacterioplankton on a regional scale as an example, we designated a range of community characteristics of pico- and nanoeukaryotes derived from metabarcoding and flow cytometric data as inter-domain interacting proxies, which were then considered in statistical modeling. We found that the bacterial diversity indices and community structure were much more accurately explained by a number of eukaryotic characteristics than by the measured environmental variables and/or spatial variables alone, as were the richness, relative abundances, and assemblage structures of major bacterial taxa. In co-occurrence networks, the nodes of characteristics that had more edges (links) were frequently the best explanatory variables for bacterial diversity indices. Over 70% of total variation in bacterial community structure could be explained by three categories of biotic interactions: parasitism (27%), fungi-bacterial competition (32%), and trophic structure and bacterivory (13%). This study showcases a methodological framework to infer different types of inter-domain interactions at play, and stresses the importance of non-grazing interacting processes in shaping bacterial diversity and community assembly.

Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (∼75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ∼50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings illuminate the widespread potential of climate change to influence belowground diversity and the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems. IMPORTANCE There have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the contrary in Tibet and North America. These findings could significantly improve understanding of climate impacts on soil microbial communities.

The species-area relationship (SAR) and its mechanisms regarding microbes are not as clear as those of plants and animals; this may result from the impact of sampling effects and the confusion between SAR and distance attenuation. We hypothesize that we can find more accurate microbial SAR curve, after removing these two factors. In this study, 27 leaves of three horticultural plants were selected as island models, and microbial biodiversity assessment was done with HTS (high-throughput sequencing). The separate and small systems using leaves as islands allow us to conduct a comprehensive survey of the microbial biodiversity of the leaves, without disturbance from sampling effects and distance attenuation effects. Interestingly, we did not find microbial SAR in those 27 leaves (also not found in evergreen trees Magnolia grandiflora and Eriobotrya japonica), but we did find significant microbial SAR in deciduous tree Ficus altissima. No significant differences were found between the different trees at the alpha diversity level of microbial biodiversity, but quite different on beta diversity. The results of beta diversity partition showed that F. altissima had the highest similarity of the microbial community among the leaves compared to those of M. grandiflora and E. japonica. Since leaf genesis in deciduous plants is more simultaneous than in evergreen plants; the result suggested that inconsistent historical background of leaf islands may mask microbial SAR. Thus, intensive sampling and consistent historical background are important for understanding microbial SAR. [ABSTRACT FROM AUTHOR]

Environmental conditions change rapidly along elevational gradients and have been found to affect community composition in macroscopic taxa, with lower diversity typically observed at higher elevations. In contrast, microbial community responses to elevation are still poorly understood. Specifically, the effects of elevation on vector-associated microbiota have not been studied to date, even though the within-vector microbial community is known to influence vector competence for a range of zoonotic pathogens. Here we characterize the structure and diversity of the bacterial microbiota in an important zoonotic disease vector, the sheep tick Ixodes ricinus, along replicated elevational gradient (630–1673 m) in the Swiss Alps. 16S rRNA sequencing of the whole within-tick bacterial microbiota of questing nymphs and adults revealed a decrease in Faith's phylogenetic microbial alpha diversity with increasing elevation, while beta diversity analyses revealed a lower variation in microbial community composition at higher elevations. We also found a higher microbial diversity later in the season and significant differences in microbial diversity among tick life stages and sexes, with lowest microbial alpha diversity observed in adult females. No associations between tick genetic diversity and bacterial diversity were observed. Our study demonstrates systematic changes in tick bacterial microbiota diversity along elevational gradients. The observed patterns mirror diversity changes along elevational gradients typically observed in macroscopic taxa, and they highlight the key role of environmental factors in shaping within-host microbial communities in ectotherms. [ABSTRACT FROM AUTHOR]

Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Theory and experiments support that plant invasions largely impact aboveground biodiversity and function. Yet, much less is known on the influence of plant invasions on the structure and function of the soil microbiome of coastal wetlands, one of the largest major reservoirs of biodiversity and carbon on Earth. We studied the continental-scale invasion of Spartina alterniflora across 2451 km of Chinese coastlines as our model-system and found that S. alterniflora invasion can largely influence the soil microbiome (across six depths from 0 to 100 cm), compared with the most common microhabitat found before invasion (mudflats, Mud). In detail, S. alterniflora invasion was not only positively associated with bacterial richness but also resulted in important biotic homogenization of bacterial communities, suggesting that plant invasion can lead to important continental scale trade-offs in the soil microbiome. We found that plant invasion changed the community composition of soil bacterial communities across the soil profile. Moreover, the bacterial communities associated with S. alterniflora invasions where less responsive to climatic changes than those in native Mud microhabitats, suggesting that these new microbial communities might become more dominant under climate change. Plant invasion also resulted in important reductions in the complexity and stability of microbial networks, decoupling the associations between microbes and carbon pools. Taken together, our results indicated that plant invasions can largely influence the microbiome of coastal wetlands at the scale of China, representing the first continental-scale example on how plant invasions can reshuffle the soil microbiome, with consequences for the myriad of functions that they support. [ABSTRACT FROM AUTHOR]

The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed. [ABSTRACT FROM AUTHOR]

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe. [ABSTRACT FROM AUTHOR]

Aim: Deterministic and neutral processes shape the biogeography of fungi. Arbuscular mycorrhizal fungi (AMF), an important group of plant root symbionts, remains poorly studied in the Neotropics. Here, we provided the first molecular survey of AMF diversity and tested whether the environment or space shapes AMF biogeography along a 12° latitudinal transect in the Brazilian Caatinga, a unique tropical dry forest ecoregion. Location: Caatinga, Brazil. Taxon: Arbuscular mycorrhizal fungi (Glomeromycotina). Methods: Soil and root samples were collected across a latitudinal transect of 1500 km within the Brazilian Caatinga. AMF communities were characterized using Illumina LSU amplicon sequencing. Operational taxonomic unit (OTU) richness, composition and phylogenetic niche conservatism were assessed using univariate and multivariate analyses, and the potential for new taxa discovery was assessed with BLAST analysis against reference and environmental sequences sets. Result: Glomeraceae was the most abundant and diverse family, resembling more dry Saharo‐Arabian and Australian realms or European croplands than other tropical forests from South America, but 10% of the OTUs could be taxa new to science, especially within Archaeospora, Claroideoglomus, Acaulospora, Gigaspora, Dentiscutata and Redeckera. AMF communities showed strong biogeographical structure inconsistent with a classical latitudinal diversity gradient, which further differed between soil and roots. Soil AMF biogeography best correlated with precipitation; community composition converged and richness increased towards both ends of the latitudinal transect where precipitation increased. Root AMF biogeography correlated to temperature, with decreasing diversity at higher temperatures. We found no evidence of phylogenetic niche conservatism. Main conclusions: Niche‐based processes driven by regional climate, most importantly precipitation and temperature, shape AMF biogeography across the Caatinga, with niche divergence among closely related AMF taxa. Given the expected future decrease in precipitation and increase in temperature, climate change may strongly affect the unique and yet unknown AMF biodiversity in neotropical dry forests. [ABSTRACT FROM AUTHOR]

One of the major goals in microbial ecology is to understand whether the empirical biogeographic patterns of macroorganisms also apply to microorganisms. Here, we used morphological data from live organisms, along with molecular data, to investigate the importance of spatial factors and environmental variables in influencing ciliate composition from floodplain lakes. Our main goal was to use 2 different approaches (morphological and molecular) to compare ciliate diversity and distribution patterns as well as to compare how these methods differ in their ability to detect distribution patterns and the roles of spatial and environmental factors that shape ciliate assemblages in the 4 largest floodplains in Brazil. Planktonic water samples were gathered from 33 lakes associated with 4 different river floodplain systems in Brazil. We analyzed ciliates in vivo and sequenced surface water DNA using a metabarcoding approach with general eukaryotic primers. We showed that the diversity of operational taxonomic units was much higher than that of morphospecies. Regardless of the method of identification, we found a consistent spatial assembly pattern of ciliate assemblages across the 4 floodplain systems. We also found that environmental filters had a stronger association with the morphological than with the molecular site-by-site dissimilarities. Meanwhile, biogeographic factors and the distance among sites limited the distribution of molecular-based composition, resulting in strong differences among the floodplain lakes analyzed. This finding suggests that ecological research and biomonitoring activities should find an equilibrium between morphological and molecular approaches because each approach provides unique insights. [ABSTRACT FROM AUTHOR]

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27-10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95-10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes. • Microbial distribution patterns differed significantly in the tripolar ice-covered lakes. • Microbial diversity and metabolism were greatly limited by nutrients in ice-covered lakes. • Salinity and nutrients were deterministic factors that shaped microbial assembly. • Stochastic processes predominated over deterministic processes in shaping the biogeographic distribution. [ABSTRACT FROM AUTHOR]

Microbial communities display biogeographical patterns that are driven by local environmental conditions and dispersal limitation, but the relative importance of underlying dispersal mechanisms and their consequences on community structure are not well described. High dispersal rates can cause soil microbial communities to become more homogenous across space and therefore it is important to identify factors that promote dispersal. This study experimentally manipulated microbial dispersal within different land management treatments at a native tallgrass prairie site, by changing the relative openness of soil to dispersal and by simulating vector dispersal via bison dung addition. We deployed experimental soil bags with mesh open or closed to dispersal, and placed bison dung over a subset of these bags, to areas with three different land managements: active bison grazing and annual fire, annual fire but no bison grazing, and no bison grazing with infrequent fire. We expected microbial dispersal to be highest in grazed and burned environments, and that the addition of dung would consistently increase overall microbial richness and lead to homogenization of communities over time. Results show that dispersal rates, as the accumulation of taxa over the course of the 3-month experiment, increase taxonomic richness similarly in all land management treatments. Additionally, bison dung seems to be serving as a dispersal and homogenization vector, based on the consistently higher taxon richness and increased community similarity across contrasting grazing and fire treatments when dung is added. This finding also points to microbial dispersal as an important function that herbivores perform in grassland ecosystems, and in turn, as a function that was lost at a continental scale following bison extermination across the Great Plains of North America in the nineteenth century. This study is the first to detect that dispersal and vector dispersal by grazing mammals promote grassland soil microbial diversity and affect microbial community composition. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly — in particular the roles of dispersal limitation and historical drivers — remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small‐subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities — occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil. [ABSTRACT FROM AUTHOR]

Microbial communities display biogeographical patterns that are driven by local environmental conditions and dispersal limitation, but the relative importance of underlying dispersal mechanisms and their consequences on community structure are not well described. High dispersal rates can cause soil microbial communities to become more homogenous across space and therefore it is important to identify factors that promote dispersal. This study experimentally manipulated microbial dispersal within different land management treatments at a native tallgrass prairie site, by changing the relative openness of soil to dispersal and by simulating vector dispersal via bison dung addition. We deployed experimental soil bags with mesh open or closed to dispersal, and placed bison dung over a subset of these bags, to areas with three different land managements: active bison grazing and annual fire, annual fire but no bison grazing, and no bison grazing with infrequent fire. We expected microbial dispersal to be highest in grazed and burned environments, and that the addition of dung would consistently increase overall microbial richness and lead to homogenization of communities over time. Results show that dispersal rates, as the accumulation of taxa over the course of the 3-month experiment, increase taxonomic richness similarly in all land management treatments. Additionally, bison dung seems to be serving as a dispersal and homogenization vector, based on the consistently higher taxon richness and increased community similarity across contrasting grazing and fire treatments when dung is added. This finding also points to microbial dispersal as an important function that herbivores perform in grassland ecosystems, and in turn, as a function that was lost at a continental scale following bison extermination across the Great Plains of North America in the nineteenth century. This study is the first to detect that dispersal and vector dispersal by grazing mammals promote grassland soil microbial diversity and affect microbial community composition.

BackgroundThe study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building.ResultsIndoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air.ConclusionsIndoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics.