Microbial biogeography: putting microorganisms on the map

Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution

Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.

Warming effects on pelagic carbon metabolism is related to substrate composition and bacterioplankton community history

Investigating the critical role of carbon cycling feedback to warming is essential for understanding future biosphere development. One of the current challenges is that the warming effect on carbon cycling is inconsistent across various aquatic ecosystems. It was postulated that the composition of dissolved organic matter (DOM) and the microbial community influenced the response of carbon metabolism to warming. To test our hypothesis, we conducted a microcosm study in which three key factors were manipulated: initial DOM composition (adjusting the ratio of autochthonous and allochthonous substrates), bacterioplankton community history (characterized by two distinct sources of bacterioplankton community), and temperature (ambient and 4 °C warming). The results demonstrated that the initial composition of DOM exerted a dominant influence on carbon metabolism. In contrast, the history of bacterioplankton community influenced the active taxa and functional traits. The log-response ratio approach revealed that the warming treatment affected bacterial carbon demand (BCD) and bacterial growth efficiency (BGE). A piecewise structural equation model further validated the paths by which warming altered BCD, particularly by changing the consumption of fluorescent DOM, and altered BGE, by affecting the active bacterioplankton. Our study demonstrated that the impact of warming on carbon cycling was context-dependent, with particular relevance to the history and dynamics of bacterioplankton community in this process. Given ongoing changes in lacustrine environments, a more comprehensive understanding of the interactions between DOM and microbes is essential for the accurate prediction of future carbon cycling.

Recruiting high-efficiency denitrifying consortia using Pseudomonas aeruginosa

Synthesizing the microbial community with a high denitrifying capacity is the key for achieving efficient removal of nitrogen species in wastewater treatment plants. Here, we integrated the evolutionary top-down enrichment and bottom-up bioaugmentation to construct a high-efficiency Pseudomonas-recruited denitrifying consortium (PRDC). A PRDC with a high specific denitrification rate of 109.49 ± 10.58 mg N/(g MLVSS·h) was enriched after 181 days of microbiota construction with pre-inoculation of Pseudomonas strain onto carriers. The 16S rRNA gene sequencing analysis suggested that the pre-inoculated Pseudomonas was quickly washed out and replaced by dominant denitrifying genera, such as Halomonas and Thauera, under different hydraulic retention times (HRTs). The pre-inoculated Pseudomonas can facilitate PRDC by providing public goods, but compromising its nutrient requirements. The dominant community assembly processes switched from homogeneous selection to ecological drift and dispersal limitation under shortened HRT. Furthermore, a shortened HRT facilitated the colonization of new immigrants and intensified their competition with the pre-existing dominant denitrifiers. The PRDC carriers achieved a 1.65-fold enhancement in sludge denitrification and reduced the corresponding chemical oxygen demand consumption at a carrier filling ratio of 30%. Overall, our study developed a novel technique using Pseudomonas aeruginosa as a trigger to enrich high-efficiency denitrifying consortia for wastewater treatment.

Yearlong analysis of bacterial diversity in hospital sink drains: culturomics, antibiotic resistance and implications for infection control

Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI's) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.

Habitat preference drives the community composition, beta diversity and assembly processes of benthic diatoms: A case study of a wetland cluster in a cold region

The loss of biodiversity in urban wetlands has become increasingly severe due to urbanization. Based on their attachment patterns, benthic diatoms can be divided into several types according to habitat (i.e., epilithic, epiphytic, and epipelic). Diatoms are often used as ecological indicators due to their sensitivity to environmental changes. However, details concerning the composition, temporal dynamics, and assembly mechanisms of benthic diatom communities in urban wetland habitats remain unclear. In this study, we systematically evaluated the composition and seasonal dynamics of benthic diatoms among three different habitats and validated the applicability of eDNA for studies of diatoms. The relationship between the taxonomic and functional diversity of diatom communities was examined, and the assembly mechanisms of diatom communities were explored. An analysis of 249 benthic diatom samples and 27 water samples from nine sites over eight months revealed differences in the composition of diatom communities among epilithic, epiphytic, and epipelic habitats. In diatoms from different hydrological periods, the contribution of turnover to total taxonomic beta diversity was much larger than that of nestedness, while the nestedness components of functional diversity were comparatively large. Nutrients, total dissolved solids, and water temperature were the main variables that affected the taxonomic and functional beta diversity of the benthic diatom communities. The results suggested that benthic diatom community assembly in the three habitats and eDNA was primarily driven by deterministic processes. This study has demonstrated how habitat preference affects the composition, beta diversity and assembly processes of benthic diatom communities and provided novel insights into the conservation of biodiversity in urban wetlands.

Eukaryotic plankton community and assembly processes in a large-scale water diversion project in China

The Middle Route of the South to North Water Diversion Project (MRP) and its water source, the Danjiangkou Reservoir (DJK), play a pivotal role in mitigating the chronic water scarcity challenges faced by northern China. Eukaryotic plankton are widespread in aquatic ecosystems, which are crucial for the water quality stability of DJK and MRP, yet comparative studies on their contemporaneous dynamics and assembly processes are scarce. In this study, amplicon sequencing was used to investigate the eukaryotic plankton communities. The results revealed that the similarity in community composition of DJK is significantly higher than that of MRP, exhibiting distance-decay patterns. Environmental heterogeneity exhibits significant differences between DJK and MRP, and it significantly influences community composition and alpha diversity. Additionally, the assembly processes of eukaryotic plankton in both DJK and MRP are predominantly influenced by stochastic processes. However, in comparison to DJK, deterministic processes have a more pronounced impact on MRP, accounting for 39.29% and 1.82%, respectively. The variations in total nitrogen (TN), chlorophy IIa (Chl.a), and conductivity (Spc) have led to a transition in the assembly of eukaryotic phytoplankton communities in MRP from a stochastic process to a deterministic process. This study extends insights into the dynamics and assembly processes of eukaryotic plankton communities in the large, engineered drinking water diversion project and its water source, which is also useful for the management and regulation of the DJK and MRP.

Distinct spatiotemporal patterns between fungal alpha and beta diversity of soil-plant continuum in rubber tree

Plant-associated microbial communities strongly relate to host health and productivity. Still, our knowledge of microbial community spatiotemporal patterns in soil-plant continuum is largely limited. Here, we explored the spatiotemporal dynamics of fungal communities across multiple compartments (phyllosphere, leaf endosphere, soil, rhizosphere, rhizoplane, and root endosphere) of rubber tree in two contrasting seasons collected from Hainan Island and Xishuangbanna. Our results demonstrate that the fungal alpha and beta diversity exhibited distinct pattern; the alpha diversity is highly dependent on seasonal changes, while beta diversity only showed a geographical variation pattern. The season-specific environmental factors (e.g., climatic factors) were the most important factors in shaping fungal alpha diversity across the soil-plant continuum. Physicochemical properties explained some of the microbial beta diversity spatiotemporal variation observed, with leaf phosphorus (P) and soil available potassium (AK) likely being the main factors that drove the geographical variation. We further identified the variation of edaphic (e.g., AK) and leaf physicochemical factors (e.g., P) were mainly caused by regional sites (P < 0.05). Taken together, our study provides an empirical evidence that the distinct spatiotemporal patterns of alpha and beta diversity of rubber tree fungal diversity and significantly expand our understanding of ecological drivers of plant-associated microbial communities.

IMPORTANCE

Plants harbor diverse microorganisms in both belowground and aboveground compartments, which play a vital role in plant nitrogen supply and growth promotion. Understanding the spatiotemporal patterns of microbial communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the alpha and beta diversity of soil-plant continuum in rubber tree exhibited distinct spatiotemporal pattern. Alpha diversity is highly dependent on seasonal changes, while beta diversity only showed a geographical variation pattern. Climatic factors were the most important factors in shaping fungal alpha diversity. Leaf phosphorus (P) and soil available potassium (AK) were major drivers to induce geographical variation.

Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures

Introduction

The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.

Methods

Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.

Results

Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.

Discussion

The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.

Ecology and Spatial Distribution of Magnetotactic Bacteria in Araguaia River Floodplain

Magnetotactic bacteria (MTB) are Gram-negative, ubiquitous, aquatic, flagellated, microaerophilic, or anaerobic microorganisms exhibiting magnetotactic behaviour based on magnetosomes, which are the structural signature of the group. Magnetosomes are ferrimagnetic nanocrystals surrounded by a lipid bilayer, usually aligned in chain(s) within the cell. Environmental abiotic conditions such as salinity, dissolved oxygen, pH, and oxidation-reduction potential may drive the diversity of MTB populations in environments. Our results reported the first evidence of MTB in sediments sampled from the Araguaia River floodplain in the Amazon-Cerrado biome. Light microscopy showed at least six morphotypes of South-seeking MTB. Transmission electron microscopy and energy-dispersive X-ray spectroscopy observations demonstrated magnetite cuboctahedral, prismatic, and anisotropic magnetosomes. PCA ordination demonstrated a more significant influence of depth, ORP (oxidation-reduction potential), and transparency in sampled data from the river main channel (MC). Non-metric multidimensional scaling (NMDS) ordination and correlation analysis demonstrated a difference between MTB populations inhabiting MC and lakes and affluent (LA). NGS and bioinformatic analysis revealed higher richness and diversity among magnetotactic cocci and the majority phylogenetic assignment of MTB affiliated to Pseudomonadota phylum. Hence, the complete acquisition of these results will provide further insight into magnetotaxis characterisation and the abiotic factors that impact MTB spatial distribution.

Bioclimatic zonation and spatial-scale dependence of lacustrine microbial assemblages

Bioclimatic zonation is critical for understanding how climate shapes biodiversity and biogeographic patterns. However, existing studies have primarily focused on macroorganisms, leaving microbial communities largely underexplored. This study seeks to address this gap through extensive sampling of bacterial communities from 931 sediment samples across 199 lakes in China. Based on the obtained data, we identified five distinct lacustrine microbial bioclimatic zones, each showing significant differences in multiple facets of bacterial diversity (i.e., alpha, beta, and gamma diversity) and clear bioclimatic zone-dependent microbial biogeographic patterns. Notably, the alpha and beta diversity of the bacterial communities showed opposing patterns across bioclimatic zones. Dominant environmental variables-specifically mean annual temperature, elevation, lake hydrological variables, and sediment pH-exerted contrasting effects on the alpha and beta diversity and played critical roles in shaping microbial community distribution at different spatial scales. At continental scales, predominant geographic and climatic variables dictated the patterns of bioclimatic zonation of lacustrine microbial communities. At regional scales, hydrological variables influenced the dispersal capacity of lake microbes, whereas sediment physicochemical variables were the most important selection factors shaping local microbial communities. Furthermore, our findings indicated that bioclimatic boundaries substantially enhanced the contribution of variable selection on bacterial community assembly and led to marked changes in distance-decay relationships in community dissimilarities. Overall, this study established a continental bioclimatic framework for lacustrine microbial communities, clarifying how environmental variables control microbial distributions across spatial scales, providing new insights into microbial biogeography, and advancing our knowledge about biodiversity under future climate change scenarios.

Vintage and terroir are the strongest determinants of grapevine carposphere microbiome in the viticultural zone of Drama, Greece

The role of microbial terroir for enhancing the geographical origin of wines is well appreciated. Still, we lack a good understanding of the assembly mechanisms driving carposphere grapevine microbiota. We investigated the role of cultivar, vintage, terroir units (TUs), and vineyard geographic location on the composition of the carpospheric microbiota of three important cultivars in the viticultural zone of Drama, Greece using amplicon sequencing. Our strategy to define TUs based on georeferencing analysis allowed us to disentangle the effects of TU and vineyards geographic location, considered as a lumped factor in most studies to date. We hypothesized that (i) these factors contribute differently on the assembly of the carposphere microbiome and that (ii) fungal and bacterial communities follow different assembly mechanisms. Vintage and TU were the stronger determinants of the carposphere fungal and bacterial communities, although the latter showed weaker response. The stronger effect of TU over vineyard geography and cultivar reinforces the role of microbial terroir in viticulture. We identified fungi (Cladosporium, Aureobasidium, Alternaria) and bacteria (Pseudomonas, Methylobacterium, Sphingomonadaceae) as main members of the core microbiome. These microorganisms were associated with specific cultivars and TUs, a feature that could be pursued towards a new microbiome-modulated paradigm of viticulture.

The Impact of Fluid Flow on Microbial Growth and Distribution in Food Processing Systems

This article examines the impact of fluid flow dynamics on microbial growth, distribution, and control within food processing systems. Fluid flows, specifically laminar and turbulent flows, significantly influence microbial behaviors, such as biofilm development and microbial adhesion. Laminar flow is highly conducive to biofilm formation and microbial attachment because the flow is smooth and steady. This smooth flow makes it much more difficult to sterilize the surface. Turbulent flow, however, due to its chaotic motion and the shear forces that are present, inhibits microbial growth because it disrupts attachment; however, it also has the potential to contaminate surfaces by dispersing microorganisms. Computational fluid dynamics (CFD) is highlighted as an essential component for food processors to predict fluid movement and enhance numerous fluid-dependent operations, including mixing, cooling, spray drying, and heat transfer. This analysis underscores the significance of fluid dynamics in controlling microbial hazards in food settings, and it discusses some interventions, such as antimicrobial surface treatments and properly designed equipment. Each process step from mixing to cooling, which influences heat transfer and microbial control by ensuring uniform heat distribution and optimizing heat removal, presents unique fluid flow requirements affecting microbial distribution, biofilm formation, and contamination control. Food processors can improve microbial management and enhance product safety by adjusting flow rates, types, and equipment configurations. This article helps provide an understanding of fluid-microbe interactions and offers actionable insights to advance food processing practices, ensuring higher standards of food safety and quality control.

Effects of temporal, spatial, and environmental factors on ciliates community in northeastern South China Sea, with notes on co-occurrence patterns of environment, phytoplankton, and ciliate

Little is known about temp-spatial variations and determining mechanism of microplankton community from continental shelf to deep basin. Here, the distribution and determinants of ciliates in the northeastern South China Sea were investigated in summer and winter. We found that the alpha diversity were generally similar, but community composition showed clear difference in summer and winter. For spatial dimension, the alpha diversity significantly decreased from neritic water to deep, and the variations of community composition were only detected between upper and deep water. The determinants of community varied depending on the research scale. For entire community, the variations were higher explained by environmental factors than by temp-spatial factors. Specially, physical factors were the main determinants, which may attribute to the effects of physical processes occurred in the research area. For the three spatial subareas, season showed more significant influences on communities than other factors. Network analyses revealed that the ciliate exhibited more relationships with phytoplankton than with environment factors. Diatom and physical factors accounted for most of the ciliate-phytoplankton-environment co-occurrence relationships, suggesting their significant influences to the community stability of the microbial food web. This study improves our understanding for the mechanisms of community structuring of microzooplankton in the open sea across both space and time.

IMPORTANCE

Ciliates are important components of microplanktons and play a crucial role in global nutrient cycling. There is still large knowledge gap on their structuring mechanisms from continental shelf to deep basin. We revealed the distribution patterns of ciliate community in neSCS and assessed the relative contribution of temporal, spatial, and environmental factors for their community structuring. Compared with temp-spatial factors, environmental factors take more responsibilities for the ciliate distribution. Among the environmental factors, physical factors showed the largest contribution to community variation. Moreover, the ciliate-environment co-occurrence pattern showed that physical factors contributed more for their relationships. These findings suggested that the physical processes play key roles in temp-spatial dynamics of ciliate community in open ocean.

Immigration reduces selection in water microbial community assembly

To investigate the influence of immigration on the selection in structuring local water bacterial communities, we conducted a new community assembly experiment using microcosms filled with sterile original water medium under outdoor conditions. We collected air particulate matter from dust pooled from samples collected at 10 locations across ~20 km in a warm temperate region in Linfen City (northern China). The immigration rates were increased by introducing air particulate matter into the microcosms. The diversity, structure, and composition of the bacterial community in the water were assessed using 16S rRNA gene amplicon sequencing on the 13th and 60th days after the start of the experiment. Our results showed that increasing immigration did not lead to significant changes in the overall diversity of the total bacterial community on the 13th day. However, on the 60th day, diversity significantly increased. The variation explained by the environment substantially decreased from the 13th to the 60th day. The amount decreased from the control to the high immigration treatments, with a range of 65.0 to 29.8% on the 13th day and 34.0 to 15.4% on the 60th day. The dominant phyla differed significantly. In the early stage, Proteobacteria (69.6%) accounted for a higher relative average abundance, while Firmicutes (4.6%), Cyanobacteria (6.0%), Planctomycetota (8.1%), Verrucomicrobiota (2.0%), and Halobacterota (0.9%) were more abundant in the late stage. Additionally, the late stage had an average of 33 phyla, compared to 15 phyla in the early stage. All the results suggested a minimal role of dispersal limitation in structuring water bacterial communities in the early stage, whereas, in the late stage, the bacterial communities might experience dispersal swamping in our study area. Variance partitioning indicated that throughout the experiment, increasing immigration weakened the signal of environmental selection in the water microbial community assembly. These results expand our understanding of the impact of immigration on environmental selection and provide insights into the varying importance of dispersal and selection on microbial community assembly at different stages of succession.

Water Quality and Land Use Shape Bacterial Communities Across 621 Canadian Lakes

Human activities such as agriculture and urban development are linked to water quality degradation. Canada represents a large and heterogeneous landscape of freshwater lakes, where variations in climate, geography and geology interact with land cover alteration to influence water quality differently across regions. In this study, we investigated the influence of water quality and land use on bacterial communities across 12 ecozones. At the pan-Canadian scale, total phosphorus (TP) was the most significant water quality variable influencing community structure, and the most pronounced shift was observed at 110 μg/L of TP, corresponding to the transition from eutrophic to hypereutrophic conditions. At the regional scale, water quality significantly explained bacterial community structure in all ecozones. In terms of land use effect, at the pan-Canadian scale, agriculture and, to a lesser extent, urbanisation were significant land use variables influencing community structure. Regionally, in ecozones characterised by extensive agriculture, this land cover variable was consistently significant in explaining community structure. Likewise, in extensively urbanised ecozones, urbanisation was consistently significant in explaining community structure. Overall, these results demonstrate that bacterial richness and community structure are influenced by water quality and shaped by agriculture and urban development in different ways.

The Role of Local and Upstream Colonisation in Determining Stream Periphyton Metacommunity Assemblages

Stream periphyton is an ideal study system for explaining how dispersal shapes community patterns. Few studies have tried to investigate periphyton metacommunities at the reach scale, and studies comparing local versus upstream periphyton propagule sources are lacking. We aimed to address these knowledge gaps by disentangling environmental constraints and dispersal sources, including dispersal hypotheses related to periphyton functional guilds. We covered 25-m sections of streambed with plastic silage cover sheets in three streams in Southern New Zealand, allowing river water to flow over the sheets. Samples on top of these sheets allowed periphyton colonisation only by drifting upstream propagules, while 'control' samples placed directly upstream of the plastic sheets were colonised by local and upstream propagules. We collected samples after 7, 14, and 25 days of colonisation. Response variables included periphyton biomass, community structure, and relative abundances of functional guilds. Control samples showed 1.5-6 times higher cell densities than plastic-cover samples, suggesting that local colonisation is very important for biomass accrual. Periphyton communities on both tile types became more similar to each other with time, indicating that environmental filters overcame effects of colonisation sources. While motile and flagellated taxa showed the ability to reach their preferred microhabitats in all streams, the responses of the remaining functional guilds did not follow the expected patterns. We conclude that periphyton community assembly strongly depends on reach-scale connectivity, which results in higher biomass accrual and community structure. These findings suggest that the mass effect paradigm is likely to be the principal metacommunity process shaping stream periphyton communities at the reach scale.

Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale

Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.

Diversity and biogeography of the bacterial microbiome in glacier-fed streams

The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

The diversity and biogeography of bacterial communities in lake sediments across different climate zones

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.

Local Scale Biogeographic Variation in the Magnolia (Magnolia grandiflora) Phyllosphere

The phyllosphere (aerial plant surfaces colonized by microorganisms) remains an understudied ecosystem in terms of bacterial biogeography, particularly at intermediate or local spatial scales. This study characterized the phyllosphere bacterial community on the leaves of 87 Magnolia grandiflora trees sampled throughout a small town, encompassing an area of approximately 60 km2. Sequencing of the 16S ribosomal RNA gene revealed the dominant bacterial phyla to be Alphaproteobacteria, Bacteroidetes, and Acidobacteria, consistent with other studies of the phyllosphere. There was a small but significant relationship between the phyllosphere community similarity and the distance between the trees (i.e., trees further apart were more likely to have dissimilar bacterial communities). There was also a relationship between the assigned categories of tree height (low, medium, high) and the phyllosphere bacterial community composition, with the trees in the high category having more diverse bacterial communities on their leaves than the shorter trees. This study provides insight into the relationship between phyllosphere community composition and host tree characteristics and shows that the distance between M. grandiflora trees has a significant, albeit low, influence on bacterial composition. These findings contribute to a deeper understanding of phyllosphere microbiome biogeography, highlighting how individual tree characteristics and spatial proximity shape phyllosphere bacterial communities.

Geographic Distribution Pattern Determines Soil Microbial Community Assembly Process in Acanthopanax senticosus Rhizosphere Soil

The geographic distribution patterns of soil microbial communities associated with cultivated Acanthopanax senticosus plants in Northeast China were investigated. High-throughput sequencing revealed that the diversity and community assembly of bacterial and fungal communities in the inter-root soil varied significantly with geographic location. The study found that bacterial communities were predominantly assembled through stochastic processes at most sites, while fungal communities showed greater variation, with both stochastic and deterministic processes involved. The complexity of bacterial-fungal co-occurrence networks also varied with longitude and latitude, demonstrating both positive and negative interactions. PICRUSt 2.0 and FUNGuild were used to predict the potential functions of soil bacterial and fungal microbiota, respectively, during different land use patterns. The average taxonomic distinctness (AVD) index indicated varying degrees of community stability across sites. Key microbial taxa contributing to community variability were identified through Random Forest modeling, with Bacteriap25 and Sutterellaceae standing out among bacteria, and Archaeorhizomyces and Clavaria among fungi. Soil chemical properties, including pH, TN, TP, EC, and SOC, significantly correlated with microbial diversity, composition, and co-occurrence networks. Structural equation modeling revealed that geographic distribution patterns directly and indirectly influenced soil chemical properties and microbial communities. Overall, the study provides insights into the geographic distribution patterns of soil microbial communities associated with A. senticosus and highlights the need for further research into the underlying mechanisms shaping these patterns.

Environmental DNA metabarcoding reveals the influence of environmental heterogeneity on microeukaryotic plankton in the offshore waters of East China Sea

Microeukaryotic plankton are essential to marine food webs and biogeochemical cycles, with coastal seas playing a critical role in aquatic ecosystems. Understanding the diversity of microeukaryotic plankton, deciphering their community structure and succession patterns, and identifying the key factors influencing these dynamics remain central challenges in coastal ecology. In this study, we examine patterns of biodiversity, community structure, and co-occurrence using environmental DNA (eDNA)-based methods. Our results show a linear correlation between α-diversity and distance from the shore, with nutrient-related factors, especially inorganic nitrogen, being the primary determinants of the spatial distribution of plankton communities. Alternation of coastal habitat have shifted the succession patterns of coastal eukaryotic plankton communities from stochastic to deterministic processes. Additionally, our observations indicate that the topology and structure of eukaryotic plankton symbiotic patterns and networks are significantly influenced by environmental heterogeneity such as nutrients, which increase the vulnerability and decrease the stability of offshore ecological networks. Overall, our study demonstrates that the distribution of microeukaryotic plankton communities is influenced by factors related to environmental heterogeneity.

Response of particle-attached and free-living bacterial communities to Microcystis blooms

The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.

Microbial necromass contribution to soil carbon storage via community assembly processes

Soil organic matter has been well acknowledged as a natural solution to mitigate climate change and to maintain agricultural productivity. Microbial necromass is an important contributor to soil organic carbon (SOC) storage, and serves as a resource pool for microbial utilization. The trade-off between microbial births/deaths and resource acquisition might influence the fate of microbial necromass in the SOC pool, which remains poorly understood. We coupled soil microbial assembly with microbial necromass contribution to SOC on a long-term, no-till (NT) farm that received maize (Zea mays L.) stover mulching in amounts of 0 %, 33 %, 67 %, and 100 % for 8 y. We characterized soil microbial assembly using the Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP), and microbial necromass using its biomarker amino sugars. We found that 100 % maize stover mulching (NT100) was associated with significantly lower amino sugars (66.4 mg g-1 SOC) than the other treatments (>70 mg g-1 SOC). Bacterial and fungal communities responded divergently to maize stover mulching: bacterial communities were positive for phylogenetic diversity, while fungal communities were positive for taxonomic richness. Soil bacterial communities influenced microbial necromass contribution to SOC through determinism on certain phylogenetic groups and bacterial bin composition, while fungal communities impacted SOC accumulation through taxonomic richness, which is enhanced by the positive contribution of dispersal limitation-dominated saprotrophic guilds. The prevalence of homogeneous selection and dispersal limitation on microbial cell wall-degrading bacteria, specifically Chitinophagaceae, along with increased soil fungal richness and interactions, might induce the decreased microbial necromass contribution to SOC under NT100. Our findings shed new light on the role of microbial assembly in shaping the dynamics of microbial necromass and SOC storage. This advances our understanding of the biological mechanisms that underpin microbial necromass associated with SOC storage, with implications for sustainable agriculture and mitigation of climate change.

Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts

The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.

Bacterial diversity along the geothermal gradients: insights from the high-altitude Himalayan hot spring habitats of Sikkim

Geothermal habitats present a unique opportunity to study microbial adaptation to varying temperature conditions. In such environments, distinct temperature gradients foster diverse microbial communities, each adapted to its optimal niche. However, the complex dynamics of bacterial populations in across these gradients high-altitude hot springs remain largely unexplored. We hypothesize that temperature is a primary driver of microbial diversity, and bacterial richness peaks at intermediate temperatures. To investigate this, we analysed bacterial diversity using 16S rRNA amplicon sequencing across three temperature regions: hot region of 56-65 °C (hot spring), warm region of 35-37 °C (path carrying hot spring water to the river), and cold region of 4-7 °C (river basin). Our findings showed that Bacillota was the most abundant phylum (45.51 %), followed by Pseudomonadota (32.81 %) and Actinomycetota (7.2 %). Bacillota and Chloroflexota flourished in the hot and warm regions, while Pseudomonadota thrived in cooler areas. Core microbiome analysis indicated that species richness was highest in the warm region, declining in both cold and hot regions. Interestingly, an anomaly was observed with Staphylococcus, which was more abundant in cases where ponds were used for bathing and recreation. In contrast, Clostridium was mostly found in cold regions, likely due to its viability in soil and ability to remain dormant as a spore-forming bacterium. The warm region showed the highest bacterial diversity, while richness decreased in both cold and hot regions. This highlights the temperature-dependent nature of microbial communities, with optimal diversity in moderate thermal conditions. The study offers new insights into microbial dynamics in high-altitude geothermal systems.

Environmental selection and advective transport shape the distribution of two cyst-forming Acantharia clades in the Canadian Arctic

Anthropogenic induced climate perturbations are seen in changes in oceanic circulation patterns, and Arctic water masses defined by salinity are vulnerable to change. Biogeography of marine microbial eukaryotes is expected to be impacted by changes in local environmental conditions and advective processes, but tracking the extent of plankton distribution requires understanding routes for both active and passive tracers. To identify such tracers, we focused on samples collected in the western (Canada Basin) and eastern (Nares Strait); extremes of the Canadian High Arctic that are connected by an east flowing current north of Canada. Sequencing of the V4 region of 18S rRNA revealed that Acantharia, a taxonomically and functionally diverse group of large planktonic protists, were particularly common. Arctic acantharians in our study were dominated by two clades belonging to cyst-forming groups. The distribution of one clade suggested successful advective transport from the Pacific sourced water in the Beaufort Gyre to southern Nares Strait, with cells transported along the northern shelf of the Canadian Arctic. A second clade appeared to be a resident taxon of the Canada Basin whose distribution correlated to local environmental conditions, and detection in deeper samples would be consistent with swarmer formation enabling reestablishment the following year.

Community structure and assembly of myxomycetes in northern Chinese forests under geographic barriers

The study of myxomycete biogeography has a long-standing history and has consistently drawn scholarly interest. Nevertheless, studies focusing specifically on the spatial and temporal distribution patterns of myxomycete diversity are relatively limited, with even fewer investigating the mechanisms driving the generation and maintenance of myxomycete diversity. Therefore, this study selected two geographically distant sampling sites within northern Chinese forests to investigate myxomycete species composition, community structure, environmental drivers, and assembly patterns under geographic barriers. We established plots in the Altai Mountains (ALE) and the Greater Khingan Mountains (GKM), gathered bark and litter, and conducted 80-day moist chamber cultures of myxomycetes. Additionally, myxomycete specimens were collected in the field simultaneously to supplement the data set. This study collected 541 myxomycete specimens belonging to 73 species from 28 genera, spanning 12 families and eight orders. The ALE and the GKM had 20 identical species, accounting for 27% of the total species. Myxomycetes from both regions exhibited abundant occurrence 18 days after cultivation, with the quantity on bark substrates notably higher than on litter. Arcyria pomiformis and Comatricha elegans were the most common species in moist chamber cultures. Mantel test outcomes revealed that environmental factors had no significant impact on myxomycete community similarity between the two areas, aligning with findings from the neutral community model analysis, indicating a predominant influence of stochastic processes on myxomycete community structure in moist chamber cultures. This study represents the first application of a quantitative framework to analyze myxomycete community assembly cultivated in moist chambers.

Habitat specificity modulates the bacterial biogeographic patterns in the Southern Ocean

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.

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Persistent tissue-specific resident microbiota in oysters across a broad geographical range

Marine animals often harbour complex microbial communities that influence their physiology. However, strong evidence for resident microbiomes in marine bivalves is lacking, despite their contribution to estuarine habitats and coastal economies. We investigated whether marine bivalves harbour stable, resident microorganisms in specific tissues or if their microbiomes primarily consist of transient members reflecting the environmental microbial pool. Conducting a latitudinal study of wild eastern oysters (Crassostrea virginica) along the East Coast of the United States, we aimed to identify resident microorganisms that persist across a wide geographical range. Our results revealed that microbial communities in seawater and sediment samples followed latitudinal diversity patterns driven by geographic location. In contrast, oyster-associated microbiomes were distinct from their surrounding environments and exhibited tissue-specific compositions. Notably, oyster microbiomes showed greater similarity within the same tissue type across different geographic locations than among different tissue types within the same location. This indicates the presence of tissue-specific resident microbes that persist across large geographical ranges. We identified a persistent set of resident microbiome members for each tissue type, with key microbial members consistent across all locations. These findings underscore the oyster host's role in selecting its microbiome and highlight the importance of tissue-specific microbial communities in understanding bivalve-associated microbiomes.

Spatial and environmental drivers of temperate estuarine archaeal communities

Archaea play a crucial role in the global biogeochemical cycling of elements and nutrients, helping to maintain the functional stability of estuarine systems. This study characterised the abundance and diversity of archaeal communities and identified the environmental conditions shaping these microbial communities within six temperate estuaries along approximately 500 km of the New South Wales coastline, Australia. Estuarine sediments were found to exhibit significantly higher species richness than planktonic communities, with representative sequences from the Crenarchaeota phylum characterising each environment. Ordinate analyses revealed catchment characteristics as the strongest drivers of community variability. Our results also provide evidence supporting distance-decay patterns of archaeal biogeography across intermediate scales within and between temperate estuaries, contributing to a growing body of evidence revealing the extent spatial scales play in shaping microbial communities. This study expands our understanding of microbial diversity in temperate estuaries, with a specific focus on archaeal community structure and their role in maintaining ecosystem stability.

Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance

Introduction

In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

Methods

Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

Results and discussion

This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.

Endemic, cosmopolitan, and generalist taxa and their habitat affinities within a coastal marine microbiome

The relative prevalence of endemic and cosmopolitan biogeographic ranges in marine microbes, and the factors that shape these patterns, are not well known. Using prokaryotic and eukaryotic amplicon sequence data spanning 445 near-surface samples in the Southern California Current region from 2014 to 2020, we quantified the proportion of taxa exhibiting endemic, cosmopolitan, and generalist distributions in this region. Using in-situ data on temperature, salinity, and nitrogen, we categorized oceanic habitats that were internally consistent but whose location varied over time. In this context, we defined cosmopolitan taxa as those that appeared in all regional habitats and endemics as taxa that only appeared in one habitat. Generalists were defined as taxa occupying more than one but not all habitats. We also quantified each taxon's habitat affinity, defined as habitats where taxa were significantly more abundant than expected. Approximately 20% of taxa exhibited endemic ranges, while around 30% exhibited cosmopolitan ranges. Most microbial taxa (50.3%) were generalists. Many of these taxa had no habitat affinity (> 70%) and were relatively rare. Our results for this region show that, like terrestrial systems and for metazoans, cosmopolitan and endemic biogeographies are common, but with the addition of a large number of taxa that are rare and randomly distributed.

Community organization and network complexity and stability: contrasting strategies of prokaryotic versus eukaryotic microbiomes in the Bohai Sea and Yellow Sea

Unraveling the effects of spatial gradients on microbiome assembly and association is a challenging topic that remains understudied in the coastal ecosystem. Here, we aimed to investigate the effects of spatial variation on the network complexity and stability of plankton microbiomes in the Bohai Sea and Yellow Sea. These seas serve as spawning and nursery grounds for economically important fisheries valued at billions of dollars annually. Environmental heterogeneity structures microbial communities into distinct spatial patterns, leading to complex direct/indirect relationships and broader ecological niches of bacterioplankton compared to microeukaryotic communities. Interestingly, salinity gradients positively influenced the richness of rare subgroups of bacterioplankton, while the rare microeukaryotic subgroups showed an opposite trend. Abundant subgroups of prokaryotic/eukaryotic microbiomes exhibited greater environmental niche breadth and lower phylogenetic distance compared to the rare subgroups. Stochastic processes contributed greatly to microbiome dynamics, and deterministic processes governed the bacterioplankton organization with a lower phylogenetic turnover rate. Compared to microeukaryotes, bacterioplankton exhibit higher network modularity, complexity, and robustness and lower fragmentation, and vulnerability. These observations offer vital insights into the anti-interference ability and resistance of plankton microbiomes in response to environmental gradients in terms of organization and survival strategy as well as their adaptability to environmental disturbances.IMPORTANCEAn in-depth understanding of community organization and stability of coastal microbiomes is crucial to determining the sustainability of marine ecosystems, such as the Bohai Sea and Yellow Sea. Distinct responses between prokaryotic and eukaryotic microbiomes to spatial heterogeneity were observed in terms of geographical distribution, phylogenetic distance, niche breadth, and community assembly process. Environmental variations are significantly correlated with the dynamics of rare eukaryotic plankton subcommunities compared to prokaryotic plankton subcommunities. Deterministic processes shaped prokaryotic plankton community organization with a lower phylogenic turnover rate. Rare subgroups had noticeably higher phylogenetic distance and lower niche breadth than the corresponding abundant subgroups. Prokaryotic microbiomes had higher molecular network complexity and stability compared to microeukaryotes. Results presented here show how environmental gradients alter both the geographical characteristics of the microbial organization in coastal seas and also their co-occurrence network complexity and stability and thus have critical implications for nutrient and energy cycling.

Modern microbiology: Embracing complexity through integration across scales

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.

Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers

The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.

Terrestrialization of sediment bacterial assemblages when temporary rivers run dry

Bacterial communities in river sediments are shaped by a trade-off between dispersal from upstream or nearby land and selection by the local environmental conditions. In temporary rivers (i.e. those characterized by long drying periods and subsequent rewetting) seasonal hydrological dynamics shape bacterial communities by connecting or disconnecting different river habitats. In this study, we tracked and compared the temporal and spatial changes in the composition of bacterial communities in streambed sediments and floodplain habitats across both permanent and intermittent river segments. Our findings revealed that environmental selection played a key role in assembling bacterial communities in both segments. We argue that distinct environmental features act as filters at the local scale, favoring specific bacterial taxa in isolated pools and promoting some typically terrestrial taxa in dry areas. Considering the prospective extension of drying intervals due to climate change, our results suggest an emerging trend wherein bacterial assemblages in temporary streams progressively incorporate microorganisms of terrestrial origin, well-adapted to tolerate desiccation phases. This phenomenon may constitute an integral facet of the broader adaptive dynamics of temporary river ecosystems in response to the impacts of climate change.

Natural selection and recombination at host-interacting lipoprotein loci drive genome diversification of Lyme disease and related bacteria

Lyme disease, caused by spirochetes in the Borrelia burgdorferi sensu lato clade within the Borrelia genus, is transmitted by Ixodes ticks and is currently the most prevalent and rapidly expanding tick-borne disease in Europe and North America. We report complete genome sequences of 47 isolates that encompass all established species in this clade while highlighting the diversity of the widespread human pathogenic species B. burgdorferi. A similar set of plasmids has been maintained throughout Borrelia divergence, indicating that they are a key adaptive feature of this genus. Phylogenetic reconstruction of all sequenced Borrelia genomes revealed the original divergence of Eurasian and North American lineages and subsequent dispersals that introduced B. garinii, B. bavariensis, B. lusitaniae, B. valaisiana, and B. afzelii from East Asia to Europe and B. burgdorferi and B. finlandensis from North America to Europe. Molecular phylogenies of the universally present core replicons (chromosome and cp26 and lp54 plasmids) are highly consistent, revealing a strong clonal structure. Nonetheless, numerous inconsistencies between the genome and gene phylogenies indicate species dispersal, genetic exchanges, and rapid sequence evolution at plasmid-borne loci, including key host-interacting lipoprotein genes. While localized recombination occurs uniformly on the main chromosome at a rate comparable to mutation, lipoprotein-encoding loci are recombination hotspots on the plasmids, suggesting adaptive maintenance of recombinant alleles at loci directly interacting with the host. We conclude that within- and between-species recombination facilitates adaptive sequence evolution of host-interacting lipoprotein loci and contributes to human virulence despite a genome-wide clonal structure of its natural populations.

IMPORTANCE

Lyme disease (also called Lyme borreliosis in Europe), a condition caused by spirochete bacteria of the genus Borrelia, transmitted by hard-bodied Ixodes ticks, is currently the most prevalent and rapidly expanding tick-borne disease in the United States and Europe. Borrelia interspecies and intraspecies genome comparisons of Lyme disease-related bacteria are essential to reconstruct their evolutionary origins, track epidemiological spread, identify molecular mechanisms of human pathogenicity, and design molecular and ecological approaches to disease prevention, diagnosis, and treatment. These Lyme disease-associated bacteria harbor complex genomes that encode many genes that do not have homologs in other organisms and are distributed across multiple linear and circular plasmids. The functional significance of most of the plasmid-borne genes and the multipartite genome organization itself remains unknown. Here we sequenced, assembled, and analyzed whole genomes of 47 Borrelia isolates from around the world, including multiple isolates of the human pathogenic species. Our analysis elucidates the evolutionary origins, historical migration, and sources of genomic variability of these clinically important pathogens. We have developed web-based software tools (BorreliaBase.org) to facilitate dissemination and continued comparative analysis of Borrelia genomes to identify determinants of human pathogenicity.

New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica

The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.

Assembling bacterial puzzles: piecing together functions into microbial pathways

Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in the KEGG database. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.

Disentangling the factors defining Bacillus subtilis group species abundance in natural soils

Bacillus subtilis is ubiquitously and broadly distributed in various environments but is mostly isolated from soil. Given that B. subtilis is known as a plant growth-promoting rhizobacterium in agriculture, we aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered that B. subtilis group species are most abundant in grasslands but can rarely be isolated from forest soil, even if the soil sample sites are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certain Bacillus species in grassland environments. Network analysis further revealed that Bacillus and other Bacillota established a densely interconnected hub module in the grassland, characterised by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we combined amplicon sequencing with physico-chemical analysis of soil samples and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influence B. subtilis abundance in natural soils and, therefore, offers insights for designing B. subtilis-based biocontrol products in agricultural settings.

Microbial core communities in activated sludge plants are strongly affected by immigration and geography

BACKGROUND

The microbiota in wastewater treatment plants (WWTPs) and incoming wastewater is critical for the treatment process, the preservation of natural ecosystems and human health, and for the recovery of resources and achievement of sustainability goals. Both core species and conditionally rare and abundant taxa (CRAT) are considered process-critical but little is known about identity as well as true functional and ecological importance. Here, we present a comprehensive investigation of the microbiota of 84 municipal activated sludge (AS) plants with nutrient removal treating ~ 70% of all wastewater within a confined geographical area, Denmark (43,000 km2). With the use of an ecosystem-specific database (MiDAS 5.2), species-level classification allowed us to investigate the core and CRAT species, whether they were active, and important factors determining their presence.

RESULTS

We established a comprehensive catalog of species with names or placeholder names showing each plant contained approx. 2,500 different species. Core and CRAT represented in total 258 species, constituting around 50% of all reads in every plant. However, not all core and CRAT could be regarded as process-critical as growth rate calculations revealed that 43% did not grow in the AS plants and were present only because of continuous immigration from the influent. Analyses of regional microbiota differences and distance decay patterns revealed a stronger effect for species than genera, demonstrating that geography had a clear effect on the AS microbiota, even across a limited geographical area such as Denmark (43,000 km2).

CONCLUSIONS

The study is the first comprehensive investigation of WWTPs in a confined geographical area providing new insights in our understanding of activated sludge microbiology by introducing a concept of combining immigration and growth calculation with identifying core and CRAT to reveal the true ecosystem-critical organisms. Additionally, the clear biogeographical pattern on this scale highlights the need for more region-level studies to find regional process-critical taxa (core and CRAT), especially at species and amplicon sequence variant (ASV) level.

Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards

Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3--N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.

Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California

Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.

Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China

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.

The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment

The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.

Surface currents shape protist community structure across the Indo-Pacific

Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.

The development of terrestrial ecosystems emerging after glacier retreat

The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.