Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Soil-sediment connectivity through Bayesian source tracking in an urban naturalised waterway via microbial and isotopic markers

Riverine sediments are important habitats for microbial activity in naturalised waterways to provide potential ecosystem services that improve stormwater quality. Yet, little is known about the sources of these sediment microbes, and the factors shaping them. This study investigated the dominant source of sediments in a tropical naturalised urban waterway, using two Bayesian methods for microbial and isotopic 13C/15N markers concurrently. Additionally, key factors shaping microbial communities from the surrounding landscape were evaluated. A comprehensive two-year field survey identified source land covers of interest based on topology and soil context. Among these land covers, riverbanks were the dominant source of sediments contribution for both edaphic and microbial components. The physico-chemical environment explains most of the variation in sediment communities compared to inter-location distances and microbial source contribution. As microbes provide ecosystem services important for rewilding waterways, management strategies that establish diverse sediment microbial communities are encouraged. Since riverbanks play a disproportionately important role in material contribution to sediment beds, management practices aimed at controlling soil erosion from riverbanks can improve overall functioning of waterway systems.

Distinct structure, assembly, and gene expression of microplankton in two Arctic estuaries with varied terrestrial inputs

The Laptev Sea is a major Marginal Sea in the Western Arctic Ocean. The Arctic amplification brought by global warming influences the hydrological properties of rivers passing through the permafrost zone, which would alter the biological community structure at continental margin. In this study, the structure, assembly, and gene expression of planktonic microbial communities in two estuaries (Protoka Ularovskaya River Estuary, PURE; Lena River Estuary, LRE) of Laptev Sea were examined to investigate the environmental effects of polar rivers. PURE and LRE exhibited distinct environmental characteristics: low temperature and high salinity for PURE, and high temperature and low salinity for LRE, influenced by runoff size. Salinity more closely influenced microbial communities in LRE, with freshwater species playing a significant role in community composition. The findings revealed differences between two estuaries in community composition and diversity. Prokaryotes and microeukaryotes had shown different assembly patterns in response to habitat changes caused by terrestrial freshwater input. Furthermore, compared with the PURE, the co-occurrence and inter-domain network of the LRE, which was more affected by terrestrial input, was more complex and stable. Functional gene prediction revealed a higher gene expression of methane metabolism in LRE than in PURE, particularly those related to methane oxidation, and this conclusion could help better explore the impact of global warming on the methane cycle in the Arctic Marginal Seas. This study explored the increased freshwater runoffs under the background of global warming dramatically affect Arctic microplankton communities from community structure, assembly and gene expression aspects.

Host diet drives gut microbiome convergence between coral reef fishes and mammals

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

Linking microbial community coalescence to ecological diversity, community assembly and species coexistence in a typical subhumid river catchment in northern China

Community coalescence denotes the amalgamation of biotic and abiotic factors across multiple intact ecological communities. Despite the growing attention given to the phenomenon of coalescence, there remains limited investigation into community coalescence in single and multiple source habitats and its impact on microbial community assemblages in sinks. This study focused on a major river catchment in northern China. We investigated microbial community coalescence across different habitats (i.e., water, sediment, biofilm, and riparian soil) and seasons (i.e., summer and winter). Using 16S rRNA gene amplicon sequence variants, we examined the relationship between community coalescence and microbial diversity, assembly processes, and species coexistence. The results showed that the intensity of microbial community coalescence was higher in the same habitat pairs compared to disparate habitat pairs in both summer and winter. During the occurrence of microbial community coalescence, the assembly processes regulated the intensity of coalescence. When the microbial community exhibited strong heterogeneous selection (heterogeneous environmental conditions leading to more dissimilar community structures), the intensity of community coalescence was low. With the assembly process shifted towards stochasticity, coalescence intensity increased gradually. However, when homogeneous selection (homogeneous environmental conditions leading to more similar community structures) predominantly shaped microbial communities, coalescence intensity exceeded the threshold of 0.25-0.30. Moreover, the enhanced intensity of community coalescence could increase the complexity of microbial networks, thereby enhancing species coexistence. Furthermore, the assembly processes mediated the relationship between community coalescence and species coexistence, underscoring the pivotal role of intermediate intensity of community coalescence in maintaining efficient species coexistence. In conclusion, this study highlights the crucial role of community coalescence originating from single and multiple source habitats in shaping microbial communities in sinks, thus emphasizing its central importance in watershed ecosystems.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures

The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely polluted soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils subjected to phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all PTEs in CDH-enriched soil (compared to unenriched soil) appeared in FTC. Furthermore, under the influence of FTC, in the relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. The analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in both cases high pollutant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.

Microeukaryote community coalescence strengthens community stability and elevates diversity

Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.

Mitigating salinity stress through interactions between microalgae and different forms (free-living & alginate gel-encapsulated) of bacteria isolated from estuarine environments

Salinity stress in estuarine environments poses a significant challenge for microalgal survival and proliferation. The interaction between microalgae and bacteria shows promise in alleviating the detrimental impacts of salinity stress on microalgae. Our study investigates this interaction by co-cultivating Chlorella sorokiniana, a freshwater microalga, with a marine growth-promoting bacterium Pseudomonas gessardii, both of which were isolated from estuary. In this study, bacteria were encapsulated using sodium alginate microspheres to establish an isolated co-culture system, preventing direct exposure between microalgae and bacteria. We evaluated microalgal responses to different salinities (5 PSU, 15 PSU) and interaction modes (free-living, gel-encapsulated), focusing on growth, photosynthesis, cellular metabolism, and extracellular polymeric substances (EPS) properties. High salinity inhibited microalgal proliferation, while gel-fixed interaction boosted Chlorella growth rate by 50.7 %. Both attached and free-living bacteria restored Chlorella's NPQ to normal levels under salt stress. Microalgae in the free-living interaction group exhibited a significantly lower respiratory rate compared to the pure algae group (-17.2 %). Increased salinity led to enhanced EPS polysaccharide secretion by microalgae, particularly in interaction groups (19.7 %). Both salt stress and interaction increased the proportion of aromatic proteins in microalgae's EPS, enhancing its stability by modulating EPS glycosidic bond C-O-C and protein vibrations. This alteration caused microalgal cells to aggregate, free-living bacteria co-culture group, and fixed co-culture group increasing by 427.5 %, 567.1 %, and 704.1 %, respectively. In gel-fixed bacteria groups, reduced neutral lipids don't accumulate starch instead, carbon redirects to cellular growth, aiding salt stress mitigation. These synergistic activities between salinity and bacterial interactions are vital in mitigating salinity stress, improving the resilience and growth of microalgae in saline conditions. Our research sheds light on the mechanisms of microalgal-bacterial interactions in coping with salt stress, offering insights into the response of estuarine microorganisms to global environmental changes and their ecological stability.

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats

Microplastics (MPs) have the potential to modify aquatic microbial communities and distribute microorganisms, including pathogens. This poses a potential risk to aquatic life and human health. Despite this, the fate of 'hitchhiking' microbes on MPs that traverse different aquatic habitats remains largely unknown. To address this, we conducted a 50-day microcosm experiment, manipulating estuarine conditions to study the exchange of bacteria and microeukaryotes between river, sea and plastisphere using a long-read metabarcoding approach. Our findings revealed a significant increase in bacteria on the plastisphere, including Pseudomonas, Sphingomonas, Hyphomonas, Brevundimonas, Aquabacterium and Thalassolituus, all of which are known for their pollutant degradation capabilities, specifically polycyclic aromatic hydrocarbons. We also observed a strong association of plastic-degrading fungi (i.e., Cladosporium and Plectosphaerella) and early-diverging fungi (Cryptomycota, also known as Rozellomycota) with the plastisphere. Sea MPs were primarily colonised by fungi (70%), with a small proportion of river-transported microbes (1%-4%). The mere presence of MPs in seawater increased the relative abundance of planktonic fungi from 2% to 25%, suggesting significant exchanges between planktonic and plastisphere communities. Using microbial source tracking, we discovered that MPs only dispersed 3.5% and 5.5% of river bacterial and microeukaryotic communities into the sea, respectively. Hence, although MPs select and facilitate the dispersal of ecologically significant microorganisms, drastic compositional changes across distinct aquatic habitats are unlikely.

Assembly dynamics of eukaryotic plankton and bacterioplankton in the Yangtze River estuary: A hybrid community perspective

Estuaries, acting as transitional habitats receiving species introductions from both freshwater and marine sources, undergo significant impacts from global climate changes. Planktonic microorganisms contribute significantly to estuarine biodiversity and ecological stability. These microorganisms primarily fall into three groups: eukaryotic plankton, particle-associated bacteria, and free-living bacteria. Understanding the structural characteristics and interactions within these subcommunities is crucial for comprehending estuarine dynamics. We collected samples from three distinct locations (< 0.1 PSU, 6.6 PSU, and 19 PSU) within the Yangtze River estuary. Samples underwent analysis for physicochemical indicators, while microbial communities were subjected to 16S/18S rRNA amplicon sequencing. Additionally, simulated mixing experiments were conducted using samples of varying salinities. Estuary samples, combined with simulated experiments, were employed to collectively examine the structural characteristics and assembly processes of estuarine microbes. Our research highlights the considerable impact of phylogenetic classification on prokaryotic behavior in these communities. We observed a transition in assembly processes from primarily stochastic for particle-associated bacteria to a predominant influence of homogeneous selection as salinity increased. Particle-associated bacterial communities exhibited a greater influence of stochastic processes compared to free-living bacteria, showcasing higher stability in diversity. The variations in composition and structure of estuarine microbial subcommunities were influenced by diverse environmental factors. Particle-associated bacteria displayed elevated network characterization values and established closer interactions with eukaryotic plankton. Structural equation modeling (SEM) analysis revealed that free-living bacteria displayed a heightened sensitivity to environmental factors and exerted a more significant influence on assembly processes and network characteristics. Simulated mixing in these environments resulted in the loss of species with similar microbial taxonomic relationships. The functioning of bacterioplankton is influenced by salinity and the processes governing their assembly, particularly in relation to different living states. These findings significantly contribute to our understanding of the intricate interplay between prokaryotic and eukaryotic plankton microorganisms in highly dynamic environments, laying a robust foundation for further exploration into the ecological mechanisms governing microbial dynamics in estuaries.

Lose-lose consequences of bacterial community-driven invasions in soil

BACKGROUND

Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.

RESULTS

Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.

CONCLUSIONS

Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Toward an integrative framework for microbial community coalescence

Community coalescence is defined as the mixing of intact ecological communities. From river confluences to fecal microbiota transplantation, community coalescence constitutes a common ecological occurrence affecting natural and engineered microbial systems. In this opinion article, we propose an integrative framework for microbial community coalescence to guide advances in our understanding of this important - yet underexplored - ecological phenomenon. We start by aligning community coalescence with the unified framework of biological invasion and enumerate commonalities and idiosyncrasies between these two analogous processes. Then, we discuss how organismal interactions and cohesive establishment affect coalescence outcomes with direct implications for community functioning. Last, we propose the use of ecological null modeling to study the interplay of ecological processes structuring community reassembly following coalescence.

Contrary effects of increasing temperatures on the spread of antimicrobial resistance in river biofilms

River microbial communities regularly act as the first barrier of defense against the spread of antimicrobial resistance genes (ARGs) that enter environmental microbiomes through wastewater. However, how the invasion dynamics of wastewater-borne ARGs into river biofilm communities will shift due to climate change with increasing average and peak temperatures remains unknown. Here, we aimed to elucidate the effects of increasing temperatures on the naturally occurring river biofilm resistome, as well as the invasion success of foreign ARGs entering through wastewater. Natural biofilms were grown in a low-anthropogenic impact river and transferred to artificial laboratory recirculation flume systems operated at three different temperatures (20°C, 25°C, and 30°C). After 1 week of temperature acclimatization, significant increases in the abundance of the naturally occurring ARGs in biofilms were detected at higher temperatures. After this acclimatization period, biofilms were exposed to a single pulse of wastewater, and the invasion dynamics of wastewater-borne ARGs were analyzed over 2 weeks. After 1 day, wastewater-borne ARGs were able to invade the biofilms successfully with no observable effect of temperature on their relative abundance. However, thereafter, ARGs were lost at a far increased rate at 30°C, with ARG levels dropping to the initial natural levels after 14 days. Contrary to the lower temperatures, ARGs were either lost at slower rates or even able to establish themselves in biofilms with stable relative abundances above natural levels. Hence, higher temperatures come with contrary effects on river biofilm resistomes: naturally occurring ARGs increase in abundance, while foreign, invading ARGs are lost at elevated speeds.IMPORTANCEInfections with bacteria that gained resistance to antibiotics are taking millions of lives annually, with the death toll predicted to increase. River microbial communities act as a first defense barrier against the spread of antimicrobial resistance genes (ARGs) that enter the environment through wastewater after enrichment in human and animal microbiomes. The global increase in temperature due to climate change might disrupt this barrier effect by altering microbial community structure and functions. We consequently explored how increasing temperatures alter ARG spread in river microbial communities. At higher temperatures, naturally occurring ARGs increased in relative abundance. However, this coincided with a decreased success rate of invading foreign ARGs from wastewater to establish themselves in the communities. Therefore, to predict the effects of climate change on ARG spread in river microbiomes, it is imperative to consider if the river ecosystem and its resistome are dominated by naturally occurring or invading foreign ARGs.

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample

MOTIVATION

In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low-abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome.

RESULTS

We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of ANI, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach.

AVAILABILITY AND IMPLEMENTATION

The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.

Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession

Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.

Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages from an intermittent stream

Combined sewer overflows (CSO) are used to avoid overloading unitary sewers and wastewater treatment plants. Following the European Council Directive on Urban Wastewater Treatment (UWT), CSO discharges are regulated using guidelines that aim to reduce their ecological impact on aquatic systems. A model CSO, which is part of a long-term experimental field observatory, was modified according to these guidelines and used to evaluate the benefits of compliance through analyses of the bacteriological and chemical states of the receiving intermittent stream. The benthic and hyporheic sediments of similar geomorphic units located upstream and downstream of a monitored CSO outlet were compared before and after changes in CSO regimes. Hydrological, pollutants (Metal Trace Elements, MTE; Polycyclic Aromatic Hydrocarbons, PAH; fecal indicator bacteria, FIB), and tpm-based DNA meta-barcoding datasets resolving the occurrences of >700 bacterial species of nearly 200 genera were studied. The frequency of overflow was confirmed to have significantly decreased following the application of the UWT guidelines. Overflows became almost limited to periods of heavy summer thunderstorm events. These changes were not associated with a significant decrease in most of the surveyed MTE, PAH, and FIB among stream sediments, except for chromium. Ecological benefits were highlighted by significant changes in tpm-based meta-barcoding community patterns between the UWT compliant sampling period and the previous one. Bacterial community change point analyses confirmed this segregation in the meta-barcoding dataset according to hydrological indices such as the number of CSO events and discharged volumes. A significant decline in CSO bacterial taxa in the benthic and hyporheic sediments was observed. Thirty-four CSO indicator species were identified, including Aeromonas caviae, Aeromonas media, and Pseudomonas oleovorans. These indicators, often documented as opportunistic pathogens (to humans, animals or plants) and/or pollutant degraders, were proposed as ecological sentinels for the assessment of CSO impacts.

Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland

Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.

Effect of freeze-thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes

The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing-thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing-thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT's role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC's negative effect on microbial diversity and increased Planctomycetia abundance.

Functional redundancy in response to runoff input upholds microbial community in hydrocarbon-contaminated land-sea continuum

An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.

The ecology of scale: impact of volume on coalescence and function in methanogenic communities

Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon

The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.

Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

Groundwater depth regulates assembly processes of abundant and rare bacterial communities across arid inland river basin

Although numerous studies on bacterial biogeographic patterns in dryland have been conducted, bacterial community assembly across arid inland river basins is unclear. Here, we assessed the ecological drivers that regulate the assembly processes of abundant (ABS) and rare (RBS) bacterial subcommunities based on 162 soil samples collected in an arid inland river basin of China. The results showed that: (1) ABS exhibited a steeper distance-decay slope, and were more strongly affected by dispersal limitation (75.5% and 84.5%), than RBS in surface and subsurface soil. RBS were predominantly controlled by variable selection (54.6% and 50.2%). (2) Soil electric conductivity played a decisive role in mediating the balance between deterministic and stochastic processes of ABS and RBS in surface soil, increasing soil electric conductivity increased the importance of deterministic process. For subsurface soil, soil available phosphorus (SAP) and soil pH drove the balance in the assembly processes of ABS and RBS, respectively. The RBS shifted from determinism to stochasticity with decreased pH, while the dominance of deterministic processes was higher in low-SAP sites. (3) Groundwater depth seasonality had substantial effects on the assembly processes of ABS and RBS, but groundwater depth seasonality affected them indirectly mainly by regulating soil properties. Collectively, our study provides robust evidence that groundwater-driven variations in soil properties mediates the community assembly process of soil bacteria in arid inland river basins. This finding is of importance for forecasting the dynamics of soil microbial community and soil process in response to current and future depleted groundwater.

Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type

Anthropogenic freshwater salinization is an emerging and widespread water quality stressor that increases salt concentrations of freshwater, where specific upland land-uses produce distinct ionic profiles. In-situ studies find salinization in disturbed landscapes is correlated with declines in stream bacterial diversity, but cannot isolate the effects of salinization from multiple co-occurring stressors. By manipulating salt concentration and type in controlled microcosm studies, we identified direct and complex effects of freshwater salinization on bacterial diversity in the absence of other stressors common in field studies using chloride salts. Changes in both salt concentration and cation produced distinct bacterial communities. Bacterial richness, or the total number of amplicon sequence variants (ASVs) detected, increased at conductivities as low as 350 μS cm^-1, which is opposite the observations from field studies. Richness remained elevated at conductivities as high as 1500 μS cm^-1 in communities exposed to a mixture of Ca, Mg, and K chloride salts, but decreased in communities exposed to NaCl, revealing a classic subsidy-stress response. Exposure to different chloride salts at the same conductivity resulted in distinct bacterial community structure, further supporting that salt type modulates responses of bacterial communities to freshwater salinization. Community variability peaked at 125-350 μS cm^-1 and was more similar at lower and upper conductivities suggesting possible shifts in deterministic vs. stochastic assembly mechanisms across freshwater salinity gradients. Based on these results, we hypothesize that modest freshwater salinization (125-350 μS cm^-1) lessens hypo-osmotic stress, reducing the importance of salinity as an environmental filter at intermediate freshwater ranges but effects of higher salinities at the upper freshwater range differ based on salt type. Our results also support previous findings that ~300 μS cm^-1 is a biological effect concentration and effective salt management strategies may need to consider variable effects of different salt types associated with land-use.

Will a heavy sediment load affect responses of phytoplankton functional groups to aquatic environmental changes in different water body types?

Sediment, as a natural component of rivers, directly affects the abundance and function of phytoplankton by altering water physicochemical properties. Despite mounting evidence for the sensitivity of phytoplankton to environmental factors, the responses of phytoplankton functional groups to complex environmental changes in rivers with a heavy sediment load are still poorly understood. Herein, the effectiveness of phytoplankton functional groups was evaluated as an indicator of aquatic environmental changes in a heavily sediment-laden river. Samples were collected from 44 sites (22 free-flowing river sections and 22 man-made reservoir sections) with a mean annual sediment concentration of 4.69 kg m^-3 in the Yellow River, China. A total of 31 phytoplankton functional groups were classified during spring (April-May) and autumn (September-October) in 2019. Groups C, MP, and D, which are well adapted to strong water disturbances and turbid habitats, showed distinct advantages over other groups. Despite no significant differences in many environmental variables between the river and reservoir sections, these variables (especially nitrogen nutrients) had remarkable effects on the phytoplankton community structure. The phytoplankton functional groups were sensitive to environmental changes even under sediment interference, although geo-climatic variables also exhibited non-trivial effects. The mean niche breadth of the abundant taxa (river: 11.16; reservoir: 7.93) was higher than that of the rare taxa (river: 5.64; reservoir: 4.86) in different water bodies. Thus, growth and diffusion of the abundant taxa played paramount roles in maintaining ecosystem stability. The results indicate that, in a large-scale sediment-laden river, phytoplankton functional groups can effectively indicate changes in the aquatic environment of either a free-flowing river or a man-made reservoir.

Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

The spatial heterogeneity of soil's microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray-Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.

Resilient biotic response to long-term climate change in the Adriatic Sea

Preserving adaptive capacities of coastal ecosystems, which are currently facing the ongoing climate warming and a multitude of other anthropogenic impacts, requires an understanding of long-term biotic dynamics in the context of major environmental shifts prior to human disturbances. We quantified responses of nearshore mollusk assemblages to long-term climate and sea-level changes using 223 samples (~71,300 specimens) retrieved from latest Quaternary sediment cores of the Adriatic coastal systems. These cores provide a rare chance to study coastal systems that existed during glacial lowstands. The fossil mollusk record indicates that nearshore assemblages of the penultimate interglacial (Late Pleistocene) shifted in their faunal composition during the subsequent ice age, and then reassembled again with the return of interglacial climate in the Holocene. These shifts point to a climate-driven habitat filtering modulated by dispersal processes. The resilient, rather than persistent or stochastic, response of the mollusk assemblages to long-term environmental changes over at least 125 thousand years highlights the historically unprecedented nature of the ongoing anthropogenic stressors (e.g., pollution, eutrophication, bottom trawling, and invasive species) that are currently shifting coastal regions into novel system states far outside the range of natural variability archived in the fossil record.

The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient

Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.

The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes

Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.

Glucocorticoids coordinate changes in gut microbiome composition in wild North American red squirrels

The gut microbiome impacts host health and fitness, in part through the diversification of gut metabolic function and pathogen protection. Elevations in glucocorticoids (GCs) appear to reduce gut microbiome diversity in experimental studies, suggesting that a loss of microbial diversity may be a negative consequence of increased GCs. However, given that ecological factors like food availability and population density may independently influence both GCs and microbial diversity, understanding how these factors structure the GC-microbiome relationship is crucial to interpreting its significance in wild populations. Here, we used an ecological framework to investigate the relationship between GCs and gut microbiome diversity in wild North American red squirrels (Tamiasciurus hudsonicus). As expected, higher GCs predicted lower gut microbiome diversity and an increase in metabolic taxa. Surprisingly, but in line with prior empirical studies on wild animals, gastrointestinal pathogens decreased as GCs increased. Both dietary heterogeneity and an upcoming food pulse exhibited direct effects on gut microbiome diversity, whereas conspecific density and reproductive activity impacted diversity indirectly via changes in host GCs. Our results provide evidence of a gut-brain axis in wild red squirrels and highlight the importance of situating the GC-gut microbiome relationship within an ecological framework.

Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.

Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining

The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities after draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macroinvertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, United States) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150-200 µS/cm that are substantially below the current U.S. Environmental Protection Agency aquatic life benchmark of 300 µS/cm for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering

Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence-the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems. We adopt the community coalescence framework, which integrates metacommunity theory and meta-ecosystem dynamics, and highlight the prevalence of these coalescence events within microbial systems. Specifically, we (i) describe fundamental types of community coalescences using naturally occurring and managed examples, (ii) offer ways forward to leverage community coalescence in managed systems, and (iii) emphasize the importance of microbial ecological theory to achieving desired coalescence outcomes. Further, considering the massive dispersal events of microbiomes and their coalescences is pivotal to better predict microbial community dynamics and responses to disturbances. We conclude our piece by highlighting some challenges and unanswered question yet to be tackled.

Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses

Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.

Transmission of Seed and Soil Microbiota to Seedling

The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa.

IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.

The microbial rare biosphere: current concepts, methods and ecological principles

Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Stream sediment bacterial communities exhibit temporally-consistent and distinct thresholds to land use change in a mixed-use watershed

Freshwater ecosystems are susceptible to biodiversity losses due to land conversion. This is particularly true for the conversion of land from forests for agriculture and urban development. Freshwater sediments harbor microorganisms that provide vital ecosystem services. In dynamic habitats like freshwater sediments, microbial communities can be shaped by many processes, although the relative contributions of environmental factors to microbial community dynamics remain unclear. Given the future projected increase in land use change, it is important to ascertain how associated changes in stream physico-chemistry will influence sediment microbiomes. Here, we characterized stream chemistry and sediment bacterial community composition along a mixed land-use gradient in West Virginia, USA across one growing season. Sediment bacterial community richness was unaffected by increasing anthropogenic land use, though microbial communities were compositionally distinct across sites. Community threshold analysis revealed greater community resilience to agricultural land use than urban land use. Further, predicted metagenomes suggest differences in potential microbial function across changes in land use. The results of this study suggest that low levels of urban land use change can alter sediment bacterial community composition and predicted functional capacity in a mixed-use watershed, which could impact stream ecosystem services in the face of global land use change.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.

Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

The immigration history of communities can profoundly affect community composition. For instance, early-arriving species can have a lasting effect on community structure by reducing the invasion success of late-arriving ones through priority effects. This can be particularly important when early-arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early-arriving communities and the invasion success of late-arriving taxa. Therefore, we implemented a full-factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early-arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing-based results showed that invasion success of better adapted late-arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late-arriving bacteria. Warming-enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.

Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift

Sea level rise is mixing formerly isolated freshwater communities with saltwater communities. The structure of these new aquatic communities is jointly controlled by pre- and post-colonization processes. Similarly, since salinity is a strong abiotic determinant of post-colonization survival in coastal systems, changes in salinity will likely impact community composition. In this study, we examine how a strong abiotic gradient affects the diversity and structure of bacterial and zooplankton communities and associated ecosystem functions (decomposition and carbon mineralization). We ran a six week dispersal experiment using mesocosm ponds with four distinct salinity profiles (0, 5, 9, and 13 psu). We find that salinity is the primary driver of both bacterial and zooplankton community composition. We find evidence that as bacterial richness increases so does the amount of decomposition. A phenomenological model suggests carbon mineralization may decrease at mid-salinities; this warrants future work into possible mechanisms for this apparent loss of function. Understanding how salinization changes community structure and ecosystem function may be paramount for managing and conserving coastal plain ecosystems where salinity is increasing due to sea level rise, saltwater intrusion, storm surges, and drought.

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.