Microbial biogeography: putting microorganisms on the map

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.

Distance-decay equations of antibiotic resistance genes across freshwater reservoirs

Distance-decay (DD) equations can discern the biogeographical pattern of organisms and genes in a better way with advanced statistical methods. Here, we developed a data Compilation, Arrangement, and Statistics framework to advance quantile regression (QR) into the generation of DD equations for antibiotic resistance genes (ARGs) across various spatial scales using freshwater reservoirs as an illustration. We found that QR is superior at explaining dissemination potential of ARGs to the traditionally used least squares regression (LSR). This is because our model is based on the 'law of limiting factors', which reduces influence of unmeasured factors that reduce the efficacy of the LSR method. DD equations generated from the 99th QR model for ARGs were 'Sall = 90.03e-0.01Dall' in water and 'Sall = 92.31e-0.011Dall' in sediment. The 99th QR model was less impacted by uneven sample sizes, resulting in a better quantification of ARGs dissemination. Within an individual reservoir, the 99th QR model demonstrated that there is no dispersal limitation of ARGs at this smaller spatial scale. The QR method not only allows for construction of robust DD equations that better display dissemination of organisms and genes across ecosystems, but also provides new insights into the biogeography exhibited by key parameters, as well as the interactions between organisms and environment.

Biogeographic effects shape soil bacterial communities across intertidal zones on island beaches through regulating soil properties

Island coastal zones are often mistakenly perceived as "ecological desert". Actually, they harbour unique communities of organisms. The biodiversity on islands is primarily influenced by the effects of area and isolation (distance from the mainland), which mainly focused on plants and animals, encompassing studies of entire islands. However, the application of area and isolation effects to soil microorganisms on island beaches across the intertidal zones remains largely unexplored. We hypothesized that island area and isolation shape soil bacterial communities by regulating soil properties on island beaches, due to the fact that local soil properties might be strongly influenced by land-use, which may vary among islands of different sizes and isolations. To test this hypothesis, we conducted a study on 108 plots spanning 4 intertidal zones on 9 representative island beaches within Zhoushan Archipelago, eastern China. We employed one-way ANOVA and Tukey's honestly significant difference (HSD) test to assess the differences in diversity, composition of soil bacterial communities and soil properties among intertidal zones. Redundancy analysis and structural equation modelling (SEM) were used to examine the direct and indirect impacts of beach area and isolation on soil bacterial communities. Our findings revealed that the area and isolation did not significantly influence soil bacterial diversity and the relative abundance of dominant soil bacterial phyla. However, soil nitrogen (soil N), phosphorus (soil P), organic carbon (SOC), available potassium content (soil AK), and electrical conductivity (soil EC) showed significant increases with the area and isolation. As the tidal gradient increased on beaches, soil bacterial OTU richness, Chao 1, and relative abundance of Planctomycetota and Crenarchaeota decreased, while relative abundance of other soil bacterial phyla increased. We found that influences of island area and isolation shape soil bacterial communities on beaches by regulating soil properties, particularly soil moisture, salinity, and nutrients, all of which are also influenced by area and isolation. Island with larger areas and in lower intertidal zones, characterized by higher soil water content (SWC), soil EC, and soil AK, exhibited greater soil bacterial diversity and fewer dominant soil bacterial phyla. Conversely, in the higher intertidal zones with vegetation containing higher soil N and SOC, lower soil bacterial diversity and more dominant soil bacterial phyla were observed. These findings have the potential to enhance our new understanding of how island biogeography in interpreting island biome patterns.

Genomic fingerprints of the world's soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.

Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species

Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees.

Undisclosed contribution of microbial assemblages selectively enriched by microplastics to the sulfur cycle in the large deep-water reservoir

The accumulation of microplastics in reservoirs due to river damming has drawn considerable attention due to their potential impacts on elemental biogeochemical cycling at the watershed scale. However, the effects of plastisphere communities on the sulfur cycle in the large deep-water reservoir remain poorly understood. Here, we collected microplastics and their surrounding environmental samples in the water and sediment ecosystems of Xiaowan Reservoir and found a significant spatiotemporal pattern of microplastics and sulfur distribution in this Reservoir. Based on the microbial analysis, plastic-degrading taxa (e.g., Ralstonia, Rhodococcus) involved in the sulfur cycle were enriched in the plastisphere of water and sediment, respectively. Typical thiosulfate oxidizing bacteria Limnobacter acted as keystone species in the plastisphere microbial network. Sulfate, oxidation reduction potential and organic matter drove the variations of the plastisphere. Environmental filtration significantly affected the plastisphere communities, and the deterministic process dominated the community assembly. Furthermore, predicted functional profiles related to sulfur cycling, compound degradation and membrane transport were significantly enriched in the plastisphere. Overall, our results suggest microplastics as a new microbial niche exert different effects in water and sediment environments, and provide insights into the potential impacts of the plastisphere on the sulfur biogeochemical cycle in the reservoir ecosystem.

Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

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 the biological soil crust regulates the fungal distribution and the stability of fungal networks

The heterogeneous composition of fungi plays an indispensable role in the foundation of the multifunctionalities of ecosystems within drylands. The precise mechanisms that govern fluctuations in soil fungal assemblages in dryland ecosystems remain incompletely elucidated. In this study, biological soil crusts (biocrusts) at different successional stages in the Gurbantunggut Desert were used as substrates to examine the characteristics and driving factors that influence fungal abundance and community dynamics during biocrust development using qPCR and high-throughput sequencing of the ITS2 region. The findings showed that the physicochemical properties changed significantly with the development of biocrusts. In particular, total nitrogen increased 4.8 times, along with notable increases in ammonium, total phosphorus (2.1 times) and soil organic carbon (6.5 times). Initially, there was a rise in fungal abundance, which was subsequently followed by a decline as the biocrust developed, with the highest abundance detected in lichen crust (2.66 × 107 copies/g soil) and the lowest in bare sand (7.98 × 106 copies/g soil). Ascomycetes and Basidiomycetes emerged as dominant phyla, collectively forming 85% of the fungal community. As the biocrust developed, noticeable alterations occurred in fungal community compositions, resulting from changes in the relative proportions of Dothideomycetes, Lecanoromycetes and unclassified ascomycetes. Nitrogen, phosphorus, organic carbon content, and pH of biocrusts were identified as direct or indirect regulators of fungal abundance and community structure. The complexity of fungal networks increased as biocrusts developed as revealed by network analysis, but reduced in the stability of fungal communities within algal and lichen crusts. Keystone species within the fungal community also underwent changes as biocrust developed. These results suggested that shifts in interspecies relationships among fungi could further contribute to the variation in fungal communities during the development of biocrusts.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing

The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.

Distinct Gastrointestinal and Reproductive Microbial Patterns in Female Holobiont of Infertility

The microbiota is in symbiosis with the human body as a holobiont. Infertility conditions affect the female reproductive tract (FRT) and its resident microbiota. However, a disturbance in homeostasis could influence the FRT and other distal body sites, such as the gastrointestinal tract (GIT). We included 21 patients with endometriosis and other infertility-associated diseases with clinical profiles and biological samples from the FRT (endometrium, endometrial fluid, and vagina), and GIT samples (oral and feces). We performed a 16S rRNA analysis of site-specific microbial communities and estimated diversity metrics. The study found body site-specific microbial patterns in the FRT-GIT. In both study groups, Lactobacillus was the most shared Amplicon Sequence Variant (ASV), a precise identifier of microbial sequences, between endometrial and vagina samples. However, shared Gardnerella and Enterobacteriaceae ASVs were linked to other conditions but not endometriosis. Remarkably, Haemophilus was a specific GIT-shared taxon in endometriosis cases. In conclusion, infertility influences distinctly the FRT and GIT microbiomes, with endometriosis showing unique microbial characteristics. We proposed the concept of 'female holobiont' as a community that comprises the host and microbes that must maintain overall homeostasis across all body sites to ensure a woman's health. Insights into these microbial patterns not only advance our understanding of the pathophysiology of infertility but also open new avenues for developing microbe-based therapeutic interventions aimed at restoring microbial balance, thereby enhancing fertility prospects.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.

The contribution of microbial necromass to soil organic carbon and influencing factors along a variation of habitats in alpine ecosystems

A growing consensus is reached that microbes contributes to regulating the formation and accumulation of soil organic carbon (SOC). Nevertheless, less is known about the role of soil microbes (necromass, biomass) in SOC accumulation in different habitat conditions in alpine ecosystems. To address this knowledge gap, the composition and distribution of amino sugars (ASs) and phospholipid fatty acids (PLFAs) as biomarkers of microbial necromass and biomass were investigated in forest, meadow and wetland soil profile (0-40 cm) of Mount Segrila, Tibet, China, as well the contribution of bacterial and fungal necromass to SOC. The results revealed that microbial necromass carbon contributed 45.15 %, 72.51 % and 78.08 % on average to SOC in 0-40 cm forest, meadow and wetland soils, respectively, and decreased with microbial biomass. Fungal necromass contributed more to SOC in these habitats than bacterial necromass. Microbial necromass increased with microbial biomass and both of them decreased with soil depth in all habitats. The necromass accumulation coefficient was significantly correlated with microbial necromass and biomass, affected by habitat and soil moisture. Structural equation model indicated that soil abiotic factors indirectly mediated the accumulation of SOC through microbial necromass and biomass. This study revealed that different habitats and soil depths control considerably soil physicochemical properties and microbial community, finally influencing SOC accumulation in alpine ecosystems, which emphasized the influence of abiotic factors on microbial necromass and biomass for SOC accumulation in alpine ecosystems.

Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding

Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.

Labile dissolved organic matter (DOM) and nitrogen inputs modified greenhouse gas dynamics: A source-to-estuary study of the Yangtze River

Although rivers are increasingly recognized as essential sources of greenhouse gases (GHG) to the atmosphere, few systematic efforts have been made to reveal the drivers of spatiotemporal variations of dissolved GHG (dGHG) in large rivers under increasing anthropogenic stress and intensified hydrological cycling. Here, through a source-to-estuary survey of the Yangtze River in March (spring) and October (autumn) of 2018, we revealed that labile dissolved organic matter (DOM) and nitrogen inputs remarkably modified the spatiotemporal distribution of dGHG. The average partial pressure of CO2 (pCO2), CH4 and N2O concentrations of all sampling sites in the Yangtze River were 1015 ± 225 μatm, and 87.5± 36.5 nmol L-1, and 20.3 ± 6.6 nmol L-1, respectively, significantly lower than the global average. In terms of longitudinal and seasonal variations, higher GHG concentrations were observed in the middle-lower reach in spring. The dominant drivers of spatiotemporal variations in dGHG were labile, protein-like DOM components and nitrogen level. Compared with the historical data of dGHG from published literature, we found a significant increase in N2O concentrations in the Yangtze River during 2004-2018, and the increasing trend was consistent with the rising riverine nitrogen concentrations. Our study emphasized the critical roles of labile DOM and nitrogen inputs in driving the spatial hotspots, seasonal variations and annual trends of dGHG. These findings can contribute to constraining the global GHG budget estimations and controls of GHG emission in large rivers in response to global change.

The defensome of complex bacterial communities

Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (defensome) encompasses a growing number of defense lines that include well-studied innate and adaptive systems such as restriction-modification, CRISPR-Cas and abortive infection, but also newly found ones whose mechanisms are still poorly understood. While the abundance and distribution of defense systems is well-known in complete and culturable genomes, there is a void in our understanding of their diversity and richness in complex microbial communities. Here we performed a large-scale in-depth analysis of the defensomes of 7759 high-quality bacterial population genomes reconstructed from soil, marine, and human gut environments. We observed a wide variation in the frequency and nature of the defensome among large phyla, which correlated with lifestyle, genome size, habitat, and geographic background. The defensome's genetic mobility, its clustering in defense islands, and genetic variability was found to be system-specific and shaped by the bacterial environment. Hence, our results provide a detailed picture of the multiple immune barriers present in environmentally distinct bacterial communities and set the stage for subsequent identification of novel and ingenious strategies of diversification among uncultivated microbes.

Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance

BACKGROUND AND AIMS

Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation.

METHODS

In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment.

KEY RESULTS

We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome.

CONCLUSIONS

Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.

Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities

In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.

Seasonal variation and human impacts of the river biofilm bacterial communities in the Shiting River in southeastern China

Bacterial communities in epilithic biofilm plays an important role in biogeochemistry processes in freshwater ecosystems. Nevertheless, our understanding of the geographical and seasonal variations of the composition of bacterial communities in the biofilm of gravels on river bed is still limited. Various anthropogenic activities also influence the biofilm bacteria in gravel rivers. By taking the Shiting River in the upper Yangtze River basin in Sichuan Province as an example, we studied the geographical and seasonal variations of epilithic bacteria and the impacts of weirs and other human activities (e.g., sewage pollution). The river has experienced severe degradation since the Ms 8.0 Wenchuan Earthquake, and weirs were constructed to prevent bed erosion. We collected epilithic biofilms samples at 17 sites along ~ 30 km river reach of the Shiting River in the autumn of 2021 and the summer of 2022, respectively. We applied 16S rRNA gene high-throughput sequencing technology and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to analyze the seasonal and biogeographic patterns and potential functions of the biofilm bacterial communities. The results showed that epilithic bacteria from the two surveys exhibited variation in community composition, bacterial diversity and potential functions. The bacteria samples collected in the autumn have much higher alpha diversity and richness than those collected in the summer. Bacterial richness and diversity were lower downstream of the weirs than upstream. Low diversity was observed at a sampling site influenced by sewage inflow, which contains high level of nitrogen-related chemicals.

Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.

Spatial variations of fungal community assembly and soil enzyme activity in rhizosphere of zonal Stipa species in inner Mongolia grassland

Rhizosphere soil fungal and enzyme activities affect the nutrient cycling of terrestrial ecosystems, and rhizosphere fungi are also important participants in the ecological process of vegetation succession, responding to changes in plant communities. Stipa is an excellent forage grass with important ecological and economic value, and has the spatial distribution pattern of floristic geographical substitution. In order to systematically investigate the synergistic response strategies of fungal communities and enzyme activities in the rhizosphere under the vegetation succession. Here we explored the turnover and assembly mechanisms of Stipa rhizosphere fungal communities and the spatial variation of metabolic activity under the succession of seven Stipa communities in northern China grassland under large scale gradients. The results indicated that the composition, abundance and diversity of fungal communities and microbial enzyme activities in rhizosphere soil differed among different Stipa species and were strikingly varied along the Stipa community changes over the geographic gradient. As the geographical distribution of Stipa community changed from east to west in grassland transect, Mortierellomycetes tended to be gradually replaced by Dothideomycetes. The null models showed that the rhizosphere fungal communities were governed primarily by the dispersal limitation of stochastic assembly processes, which showed decreased relative importance from S. grandis to S. gobica. Moreover, the MAT and MAP were the most important factors influencing the changes in the fungal community (richness, β-diversity and composition) and fungal community assembly, while SC and NP also mediated fungal community assembly processes. These findings deepen our understanding of the responses of the microbial functions and fungal community assembly processes in the rhizosphere to vegetation succession.

Assembly processes of rhizosphere and phyllosphere bacterial communities in constructed wetlands created via transformation of rice paddies

Constructed wetlands are an efficient and cost-effective method of restoring degraded wetlands, in which the microorganisms present make a significant contribution to the ecosystem. In this study, we comprehensively investigated the patterns of diversity and assembly processes of 7 types of constructed wetlands at the rhizosphere and phyllosphere levels. The results showed that the rhizosphere communities of the constructed wetlands exhibited a more balanced structure than that of paddy fields, and 5 types of constructed wetland demonstrated higher potential diversity than that of paddy fields. However, the opposite trend was observed for the phyllosphere communities. Analysis of mean nearest taxon difference indicated that both deterministic and stochastic processes affected the establishment of the rhizosphere and phyllosphere communities, and stochastic processes may have had a larger effect. An iCAMP model showed that dispersal limitation was the most important factor (67% relative contribution) in the rhizosphere community, while drift was the most important (47% relative contribution) in the phyllosphere community. Mantel tests suggested that sucrase, average height, top height, total biomass, belowground biomass, maximum water-holding capacity, and capillary porosity were significantly correlated with processes in the rhizosphere community, whereas factors such as the deterministic process, average height, top height, and SOC were significantly correlated with deterministic processes in the phyllosphere community. Our results can assist in the evaluation of artificial restorations, and can provide understanding of the ecological processes of microbial communities, as well as new insights into the manipulation of microorganisms in polluted wetland ecosystems.

Spatiotemporal assembly and functional composition of planktonic microeukaryotic communities along productivity gradients in a subtropical lake

Microeukaryotes play crucial roles in the microbial loop of freshwater ecosystems, functioning both as primary producers and bacterivorous consumers. However, understanding the assembly of microeukaryotic communities and their functional composition in freshwater lake ecosystems across diverse environmental gradients remains limited. Here, we utilized amplicon sequencing of 18S rRNA gene and multivariate statistical analyses to examine the spatiotemporal and biogeographical patterns of microeukaryotes in water columns (at depths of 0.5, 5, and 10 m) within a subtropical lake in eastern China, covering a 40 km distance during spring and autumn of 2022. Our results revealed that complex and diverse microeukaryotic communities were dominated by Chlorophyta (mainly Chlorophyceae), Fungi, Alveolata, Stramenopiles, and Cryptophyta lineages. Species richness was higher in autumn than in spring, forming significant hump-shaped relationships with chlorophyll a concentration (Chl-a, an indicator of phytoplankton biomass). Microeukaryotic communities exhibited significant seasonality and distance-decay patterns. By contrast, the effect of vertical depth was negligible. Stochastic processes mainly influenced the assembly of microeukaryotic communities, explaining 63, 67, and 55% of community variation for spring, autumn, and both seasons combined, respectively. Trait-based functional analysis revealed the prevalence of heterotrophic and phototrophic microeukaryotic plankton with a trade-off along N:P ratio, Chl-a, and dissolved oxygen (DO) gradients. Similarly, the mixotrophic proportions were significantly and positively correlated with Chl-a and DO concentrations. Overall, our findings may provide useful insights into the assembly patterns of microeukaryotes in lake ecosystem and how their functions respond to environmental changes.

Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater

Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones.

Bacterioplankton diversity and potential health risks in volcanic lakes: A study from Arxan Geopark, China

Bacterioplankton play a vital role in maintaining the functions and services of lake ecosystems. Understanding the diversity and distribution patterns of bacterioplankton, particularly the presence of potential pathogenic bacterial communities, is crucial for safeguarding human health. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the diversity and geographic patterns of bacterioplankton communities, as well as potential pathogens, in eight volcanic lakes located in the Arxan UNESCO Global Geopark (in the Greater Khingan Mountains of China). Our results revealed that the bacterial communities primarily comprised Bacteroidota (45.3%), Proteobacteria (33.1%), and Actinobacteria (9.0%) at the phylum level. At the genus level, prominent taxa included Flavobacterium (31.5%), Acinetobacter (11.0%), Chryseobacterium (7.9%), and CL500-29 marine group (5.6%). Among the bacterioplankton, we identified 34 pathogen genera (165 amplicon sequence variants [ASVs]), with Acinetobacter (59.8%), Rahnella (18.3%), Brevundimonas (9.6%), and Pseudomonas (5.8%) being the most dominant. Our findings demonstrated distinct biogeographic patterns in the bacterial communities at the local scale, driven by a combination of dispersal limitation and environmental factors influenced by human activities. Notably, approximately 15.3% of the bacterioplankton reads in the Arxan lakes were identified as potential pathogens, underscoring the potential risks to public health in these popular tourist destinations. This study provides the first comprehensive insight into the diversity of bacterioplankton in mountain lake ecosystems affected by high tourist activity, laying the groundwork for effective control measures against bacterial pathogens.

Variation Among Japanese Miso Breweries in Indoor Microbiomes is Mainly Ascribed to Variation in Type of Indoor Surface

Miso is a microbially-fermented soybean food. The miso brewery indoor microbiome contributes to miso fermentation. Japanese breweries are not climate-controlled, so indoor spaces are strongly affected by the prevailing climate. Because climate influences microorganism distribution, our first hypothesis is that latitude, as a proxy for climate, is a major determinant of brewery indoor microbiome structure. Breweries vary in interior surface materials and in the way operations (steaming, processing, fermenting) are apportioned among rooms. Therefore, our second hypothesis is that more variability in indoor microbiomes exists among breweries than can be ascribed to a latitudinal gradient. Most miso produced today is inoculated with commercial microbial strains to standardize fermentation. If commercial strains outcompete indigenous microbes for membership in the indoor microbiome, this practice may homogenize indoor microbiomes among regions or breweries. Therefore, our third hypothesis is that inoculant fungal species dominate indoor fungal communities and make it impossible to distinguish communities among breweries or across their latitudinal gradient. We tested these hypotheses by sampling indoor surfaces in several breweries across a latitudinal gradient in Japan. We found that latitude had a significant but relatively small impact on indoor fungal and bacterial communities, that the effect of brewery was large relative to latitude, and that inoculant fungi made such small contributions to the indoor microbiome that distinctions among breweries and along the latitudinal gradient remained apparent. Recently, the Japanese Ministry of Agriculture, Forestry and Fisheries specified fungal inoculants to standardize miso production. However, this may not be possible so long as the indoor microbiome remains uncontrolled.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents

The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.

Different Microeukaryotic Trophic Groups Show Different Latitudinal Spatial Scale Dependences in Assembly Processes across the Continental Shelves of China

The relative role of stochasticity versus determinism is critically dependent on the spatial scale over which communities are studied. However, only a few studies have attempted to reveal how spatial scales influence the balance of different assembly processes. In this study, we investigated the latitudinal spatial scale dependences in assembly processes of microeukaryotic communities in surface water and sediment along the continental shelves of China. It was hypothesized that different microeukaryotic trophic groups (i.e., autotroph, heterotroph, mixotroph, and parasite) showed different latitudinal scale dependences in their assembly processes. Our results disclosed that the relative importance of different assembly processes depended on a latitudinal space scale for planktonic microeukaryotes. In surface water, as latitudinal difference increased, the relative contributions of homogenous selection and homogenizing dispersal decreased for the entire community, while those of heterogeneous selection and drift increased. The planktonic autotrophic and heterotrophic groups shifted from stochasticity-dominated processes to heterogeneous selection as latitudinal differences surpassed thresholds of 8° and 16°, respectively. For mixotrophic and parasitic groups, however, the assembly processes were always dominated by drift across different spatial scales. The balance of different assembly processes for the autotrophic group was mainly driven by temperature, whereas that of the heterotrophic group was driven by salinity and geographical distance. In sediment, neither the entire microeukaryotic community nor the four trophic groups showed remarkable spatial scale dependences in assembly processes; they were always overwhelmingly dominated by the drift. This work provides a deeper understanding of the distribution mechanisms of microeukaryotes along the continental shelves of China from the perspective of trophic groups.

Direct observations of microbial community succession on sinking marine particles

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group

Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.

Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Assembly mechanisms of microbial communities in plastisphere related to species taxonomic types and habitat niches

A lot of plastic floats are presented in the kelp cultivation zone, enabling us to effectively evaluate the differences between surface water (SW) and plastic-attached (PA) microbial communities. In this study, we explored the microbial communities (both bacteria and protists) in SW and PA niches during the kelp cultivation activities. Effects of habitat niches on the diversity and composition of microbial communities were found. Beta partitioning and core taxa analyses showed species turnover and local species pool governed the microbial community assembly, and they contributed more to bacteria and protists, respectively. Based on the results of null model, bacterial communities presented a more deterministic and homogeneous assembly compared to protistan communities. Moreover, microbial communities in PA niche had higher species turnover and homogenizing assembly compared to the SW niche. The results of this study supplemented the theory of microbial community assembly and expanded our understanding of protists in plastisphere.

Forecasting the dynamics of a complex microbial community using integrated meta-omics

Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community. We forecast the signals over the subsequent five years and use 21 extra samples collected at defined time intervals for testing and validation. Our forecasts are correct for six signals and hint on phenomena such as predation cycles. Using all the 17 forecasts and the environmental variables, we predict gene abundance and expression, with a coefficient of determination ≥0.87 for the subsequent three years. Our study demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.

Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers

Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.

Molecular characterization of Listeria monocytogenes strains isolated from imported food in China from 14 countries/regions, 2003-2018

Listeria monocytogenes (Lm) is associated with severe foodborne infections and ubiquitous in the nature. Identification of characteristics of Lm transmission through trading of food products is essential for rapidly tracking Lm sources and controlling dissemination of listeriosis. In this study, a total of 44 Lm strains were isolated from food products originating from 14 countries/regions during 2003-2018 at the Shanghai port. The genomes of these Lm strains were sequenced by high-throughput sequencing. Multilocus sequence typing (MLST) analysis showed that 43 isolates were divided into 17 sequence types (STs). The distribution of STs was decentralized, with the dominant ST2 accounting for only 18.18% of the strains. The LM63 strain did not match with any of the existing STs. Core-genome MLST (cgMLST) analysis based on 1748 core genes categorized the 44 strains into 30 cgMLST types (CTs), with CT10153 and CT7892 as the most predominant CTs. Notably, LM63 and LM67 shared the same CT in the cgMLST analysis. The phylogenetic analysis based on single-copy homologous genes revealed that the 44 Lm strains were primarily classified into two lineages. The SNP analysis also indicated that these strains were roughly divided into two clades, with strains in the first clade mainly collected earlier than those in the second clade, which were predominantly collected from 2010 onwards. The analysis using the virulence factor database (VFDB) indicated that the virulence gene inlJ was the most prevalent among these 44 strains. Notably, ddrA, msbA, and sugC were enriched in this dataset, requiring further clarification of their roles in Listeria through future studies. These results might provide a clue for understanding of the global epidemiology and surveillance of Lm and present insights for implementing effective measures to reduce or prevent Listeria contamination outbreaks in imported food products.

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort

Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Fertilization Weakens the Ecological Succession of Dissolved Organic Matter in Paddy Rice Rhizosphere Soil at the Molecular Level

Dissolved organic matter (DOM) is involved in numerous biogeochemical processes, and understanding the ecological succession of DOM is crucial for predicting its response to farming (e.g., fertilization) practices. Although plentiful studies have examined how fertilization practice affects the content of soil DOM, it remains unknown how long-term fertilization drives the succession of soil DOM over temporal scales. Here, we investigated the succession of DOM in paddy rice rhizosphere soils subjected to different long-term fertilization treatments (CK: no fertilization; NPK: inorganic fertilization; OM: organic fertilization) along with plant growth. Our results demonstrated that long-term fertilization significantly promoted the molecular chemodiversity of DOM, but it weakened the correlation between DOM composition and plant development. Time-decay analysis indicated that the DOM composition had a shorter halving time under CK treatment (94.7 days), compared to NPK (337.4 days) and OM (223.8 days) treatments, reflecting a lower molecular turnover rate of DOM under fertilization. Moreover, plant development significantly affected the assembly process of DOM only under CK, not under NPK and OM treatments. Taken together, our results demonstrated that long-term fertilization, especially inorganic fertilization, greatly weakens the ecological succession of DOM in the plant rhizosphere, which has a profound implication for understanding the complex plant-DOM interactions.

Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.

The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean

Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean, despite the limitations of detecting de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating the epipelagic zones from the mesopelagic layers. Functional genes related to B12 biosynthesis were relatively stably distributed across different oceans, but the taxa harboring them varied considerably, showing clear functional redundancy among microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen, and nitrate. However, the composition of functional genes was only weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the variations in B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between the chlorophyll a concentration and B12 biosynthesis, confirming its importance in primary production in the global ocean. The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature: the environment selects for function rather than taxonomy; functional redundancy underlies stochastic community assembly.

Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient

The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.

Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient

Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Microbial ecological clusters structured by environments drive maize residue decomposition at the continental scale

Environmental factors (e.g., climate and edaphic factors) indirectly regulate residue decomposition via microbial communities. Microbial ecological clusters (eco-clusters) structured by specific environmental factors have consequences for ecosystem functions. However, less is known about how microbial eco-clusters affect residue decomposition, especially over broad geographic scales. We collected agricultural soils from adjacent pairs of upland and paddy fields along a latitudinal gradient from the cold-temperature zone to the tropical zone, and conducted a microcosm experiment with 13C-labelled maize residue to explore the continental pattern of maize residue-derived 13CO2 (RDC), and whether and how microbial eco-clusters drive and predict RDC. Results showed that RDC decreased with latitude in both upland and paddy fields. Further, we identified 21 well-defined eco-clusters according to microbial environmental preferences, which explained 51.15 % of the spatial variations in RDC. The eco-clusters of high-total annual precipitation (TAP), high-mean annual temperature (MAT), low-pH, and some low-nutrient-associated exerted a positive effect on RDC. These eco-clusters contained many taxa belonging to the Actinobacteriota, Firmicutes, and Sordariomycetes, and their relative abundance decreased with latitude. Upland soils displayed 2.40-fold of RDC over paddy soils. Low-pH and high-organic matter (OM) eco-clusters were found to be the most prominent predictors of RDC in upland and paddy fields, respectively. Finally, we constructed a continental atlas of RDC in both upland and paddy fields based on eco-clusters and high-resolution climate and soil data. Overall, our study provides important evidence that historical environment-shaped microbial eco-clusters can drive and predict residue decomposition, providing new insights into how environmental factors indirectly regulate residue decomposition.

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.

Microbial biogeography of the eastern Yucatán carbonate aquifer

IMPORTANCE

The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches.

Differences in Soil Fungal Communities between Forested Reclamation and Forestry Sites in the Alberta Oil Sands Region

Fungi play key roles in forest soils and provide benefits to trees via mycorrhizal symbioses. After severe disturbance, forest regrowth can be impeded because of changes in fungal communities. In 2013-2014, soil fungi in forest floor and mineral soil were examined by Roche 454 pyrosequencing in undisturbed, harvested, and burned jack pine stands in a forested area near Fort Chipewyan, Alberta. These fungal communities were compared with jack pine, white spruce, and larch stands in Gateway Hill, a nearby certified reclaimed area. In 2014, a more detailed sampling of forestry and reclamation jack pine sites examined fungi in soil fractions using two high-throughput sequencing platforms and a sporocarp survey. The significances of compositional and functional differences in fungal communities between the forested and reclamation sites were assessed using permutation tests of partially constrained ordinations, accounting for confounding factors by variance partitioning. Taxa associated with the forestry area were primarily ectomycorrhizal. Fungal richness and diversity were greater in soils from the reclamation sites and included significantly more pathogenic taxa and taxa with unknown functional properties. Fungal community dissimilarities may have been artefacts of historical legacies or, alternatively, may have resulted from contrasting niche differentiation between forestry and reclamation sites.