Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient

Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions

Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3-]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.

Coral microbiome in estuary coral community of Pearl River Estuary: insights into variation in coral holobiont adaptability to low-salinity conditions

BACKGROUND

Low salinity is a crucial environmental stressor that affects estuarine coral ecosystems considerably. However, few studies have focused on the effects of low-salinity conditions on coral-associated microorganisms and the adaptability of coral holobionts.

METHODS

We explored the community structure of coral symbiotic Symbiodiniaceae and associated bacteria in low-salinity conditions using samples of six coral species from the Pearl River Estuary and analyzed the adaptability of coral holobionts in estuaries.

RESULTS

The symbiotic Symbiodiniaceae of all six studied coral species were dominated by Cladocopium, but, the Symbiodiniaceae subclades differed among these coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of symbiotic Symbiodiniaceae but low Symbiodiniaceae density, with different adaptability to low-salinity stress in the Pearl River Estuary. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by associating with specific Symbiodiniaceae subclades and with high Symbiodiniaceae density under low-salinity stress. The microbiome associated with the coral species were dominated by Proteobacteria, Chloroflexi, and Bacteroidetes; however, its diversity and composition varied among coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of associated bacteria, with different adaptability owing to low-salinity stress. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by having minority bacterial dominance under low-salinity stress.

CONCLUSIONS

High Symbiodiniaceae density and high bacterial diversity may be conducive to increase the tolerance of coral holobiont to low-salinity environments. Different coral species have distinct ways of adapting to low-salinity stress, and this difference is mainly through the dynamic regulation of the coral microbiome by corals.

Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks

Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.

Trait-environmental relationships reveal microbial strategies of environmental adaptation

Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.

Genome-resolved adaptation strategies of Rhodobacterales to changing conditions in the Chesapeake and Delaware Bays

The abundant and metabolically versatile aquatic bacterial order, Rhodobacterales, influences marine biogeochemical cycles. We assessed Rhodobacterales metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed Rhodobacterales genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. Rhodobacterales genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. Planktomarina genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These Rhodobacterales also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine Rhodobacterales within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.

IMPORTANCE

In the complex web of global biogeochemical nutrient cycling, the Rhodobacterales emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of Rhodobacterales genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine Rhodobacterales, revealing their various energy production pathways and diverse resource management, especially during phytoplankton or algal blooms. Whether adopting a free-living or particle-attached existence, these organisms demonstrate remarkable flexibility in their metabolic strategies, underscoring their pivotal role in driving ecosystem dynamics within estuarine ecosystems.

Tidal levels significantly change bacterial community composition in a tropical estuary during the dry season

Estuaries are usually characterized by strong spatial and temporal variability in water physicochemical conditions and are often largely affected by human activities. One important source of variability is caused by tides that can swiftly alter not only physicochemical conditions but also the abundance and composition of the biota. The effect of the diurnal tidal cycle on microbial community composition during different seasons remains uncertain, although this knowledge underlies having effective monitoring programs for water quality and potential identification of health risk conditions. In this study, we assessed the bacterioplankton community composition and diversity across four tidal water levels in a tropical estuary characterized by a mixed semidiurnal tide regime (i.e., two high and two low tides of varying amplitudes) during both dry and wet seasons. The bacterial community composition varied significantly among the four tidal levels, but only during the dry season, when the influence of the seawater intrusion was largest. Bacterial indicators' taxa identified using the Indicator Value Index were found within Cyanobacteria, Actinobacteriota, Bacteroidota, and Proteobacteria. The indicator taxon Cyanobium sp. had a prominent presence across multiple tidal levels. The main predicted phenotypes of the bacterial communities were associated with potential pathogenicity, gram-negative, and biofilm formation traits. While there were no marked predicted phenotypic differences between seasons, pathogenic and gram-negative traits were more prevalent in the dry season, while biofilm formation traits dominated in the wet season. Overall, our findings underscore the intricate relationship between river hydrodynamics and bacterial composition variability and hint a significant human impact on the water quality of the Bangpakong River.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00254-w.

A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea

Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.

Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France

Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.

Coupling between microbial assemblages and environmental drivers along a tropical estuarine gradient

The change in the community structure of phytoplankton and bacterioplankton, and in the degree of coupling between them as well as the environmental conditions, have substantial impacts on the transfer of energy to higher trophic levels and finally on the fate of organic matter. The microbial community structure, usually described only by the abundance of the different taxonomic or functional groups, can be extended to include other levels of descriptors, like physiological state and single-cell properties. These features play a role in the ecological regulation of microbial communities but are not generally studied as additional descriptors of the community structure. Here, we show the changes in abundance and single-cell characteristics based on flow cytometry measurements of picocyanobacteria, photoautotrophic pico- and nanoeukaryotes, and heterotrophic bacteria during the rainy and dry seasons along the estuarine gradient of the inner Gulf of Nicoya. The spatiotemporal distribution of these microbial assemblages showed different patterns in surface and bottom waters along the estuarine gradient and seasonally, both in their abundances and single-cell traits, which suggest differences in their ecological regulation. The changes in the structure of the microbial community along the estuary correlated most significantly with the changes in environmental variables during the dry season. This seems to occur due to changes in salinity, concentration and lability of DOC, concentration of DIN and PO43- and net community production, largely affected by the differences in the river flow. In addition, during the dry season, small-size phytoplankton and bacterioplankton assemblages, characterised by abundance and single-cell traits, presented a higher level of coupling, leading to a more complex ecological network with respect to the rainy season.

Ecological processes shaping highly connected bacterial communities along strong environmental gradients

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Role of methanotrophic communities in atmospheric methane oxidation in paddy soils

Wetland systems are known methane (CH4) sources. However, flooded rice fields are periodically drained. The paddy soils can absorb atmospheric CH4 during the dry seasons due to high-affinity methane-oxidizing bacteria (methanotroph). Atmospheric CH4 uptake can be induced during the low-affinity oxidation of high-concentration CH4 in paddy soils. Multiple interacting factors control atmospheric CH4 uptake in soil ecosystems. Broader biogeographical data are required to refine our understanding of the biotic and abiotic factors related to atmospheric CH4 uptake in paddy soils. Thus, here, we aimed to assess the high-affinity CH4 oxidation activity and explored the community composition of active atmospheric methanotrophs in nine geographically distinct Chinese paddy soils. Our findings demonstrated that high-affinity oxidation of 1.86 parts per million by volume (ppmv) CH4 was quickly induced after 10,000 ppmv high-concentration CH4 consumption by conventional methanotrophs. The ratios of 16S rRNA to rRNA genes (rDNA) for type II methanotrophs were higher than those for type I methanotrophs in all acid-neutral soils (excluding the alkaline soil) with high-affinity CH4 oxidation activity. Both the 16S rRNA:rDNA ratios of type II methanotrophs and the abundance of 13C-labeled type II methanotrophs positively correlated with high-affinity CH4 oxidation activity. Soil abiotic factors can regulate methanotrophic community composition and atmospheric CH4 uptake in paddy soils. High-affinity methane oxidation activity, as well as the abundance of type II methanotroph, negatively correlated with soil pH, while they positively correlated with soil nutrient availability (soil organic carbon, total nitrogen, and ammonium-nitrogen). Our results indicate the importance of type II methanotrophs and abiotic factors in atmospheric CH4 uptake in paddy soils. Our findings offer a broader biogeographical perspective on atmospheric CH4 uptake in paddy soils. This provides evidence that periodically drained paddy fields can serve as the dry-season CH4 sink. This study is anticipated to help in determining and devising greenhouse gas mitigation strategies through effective farm management in paddy fields.

Flooding promotes the coalescence of microbial community in estuarine habitats

Microbial community coalescence describes the mixing of microbial communities and their integration with the surrounding environment, which is common in natural ecosystems and has potential impacts on ecological processes. However, few studies have focused on microbial community coalescence between different habitats in estuarine regions. In this study, we comprehensively investigated the environmental characteristics and bacterial community changes of different habitats (water body (Water), subtidal sediments (SS) and intertidal salt marsh sediments (SM)) in Luanhe estuary during flood and normal flow periods. The results showed that flood event significantly reduced the salinity of the estuarine habitats, changed the nutrient structure and intensified the eutrophication of estuarine water. By calculating the proportion of overlapping groups and applying the 'FEAST' algorithm, we revealed that flood event facilitated the migration of bacterial communities along alternative pathways across habitats, markedly enhanced the cross-habitat mobility of bacterial communities, which underscores the pivotal role of flood event in driving bacterial community coalescence. Flood-induced community coalescence not only increased the α-diversity of bacterial communities within habitats, but also increased the proportion of overlapped species between habitats, ultimately leading to homogenization between habitats. Canonical correlation analysis combined co-occurrence network analysis revealed that flood event attenuated the role of environmental filtration in microbial assembly, while increased the impact of dispersal processes and intensified interspecific competition among microorganisms, led to the change of keystone species and reduced the complexity and stability of bacterial communities. In conclusion, this study demonstrates the complex effects of flood events on estuarine microbial communities from the perspective of multi-habitat interactions in the estuary, and emphasizes the key role of river hydrodynamic conditions in facilitating the coalescence of estuarine microbial communities. We look forward to further attention and research on estuarine microbial coalescence, which will provide new insights into assessing the stability and resilience of estuarine ecosystems under flood challenges and the sustainable management of estuarine wetlands.

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning

Microbial life forms are among the most ubiquitous on Earth, yet many remain understudied in Caribbean estuaries. We report on the prokaryote community composition of the Urabá Estuary in the Colombian Caribbean using 16S rRNA gene-transcript sequencing. We also assessed potential functional diversity through 38 metabolic traits inferred from 16S rRNA gene data. Water samples were collected from six sampling stations at two depths with contrasting light-penetration conditions along an approximately 100 km transect in the Gulf of Urabá in December 2019. Non-metric multidimensional scaling analysis grouped the samples into two distinct clusters along the transect and between depths. The primary variables influencing the prokaryote community composition were the sampling station, depth, salinity, and dissolved oxygen levels. Twenty percent of genera (i.e., 58 out 285) account for 95% of the differences between groups along the transect and among depths. All of the 38 metabolic traits studied showed some significant relationship with the tested environmental variables, especially salinity and except with temperature. Another non-metric multidimensional scaling analysis, based on community-weighted mean of traits, also grouped the samples in two clusters along the transect and over depth. Biodiversity facets, such as richness, evenness, and redundancy, indicated that environmental variations-stemming from river discharges-introduce an imbalance in functional diversity between surface prokaryote communities closer to the estuary's head and bottom communities closer to the ocean. Our research broadens the use of 16S rRNA gene transcripts beyond mere taxonomic assignments, furthering the field of trait-based prokaryote community ecology in transitional aquatic ecosystems.IMPORTANCEThe resilience of a dynamic ecosystem is directly tied to the ability of its microbes to navigate environmental gradients. This study delves into the changes in prokaryote community composition and functional diversity within the Urabá Estuary (Colombian Caribbean) for the first time. We integrate data from 16S rRNA gene transcripts (taxonomic and functional) with environmental variability to gain an understanding of this under-researched ecosystem using a multi-faceted macroecological framework. We found that significant shifts in prokaryote composition and in primary changes in functional diversity were influenced by physical-chemical fluctuations across the estuary's environmental gradient. Furthermore, we identified a potential disparity in functional diversity. Near-surface communities closer to the estuary's head exhibited differences compared to deeper communities situated farther away. Our research serves as a roadmap for posing new inquiries about the potential functional diversity of prokaryote communities in highly dynamic ecosystems, pushing forward the domain of multi-trait-based prokaryote community ecology.

Deciphering assembly processes, network complexity and stability of potential pathogenic communities in two anthropogenic coastal regions of a highly urbanized estuary

The existence of potential pathogens may lead to severe water pollution, disease transmission, and the risk of infectious diseases, posing threats to the stability of aquatic ecosystems and human health. In-depth research on the dynamic of potential pathogenic communities is of significant importance, it can provide crucial support for assessing the health status of aquatic ecosystems, maintaining ecological balance, promoting sustainable economic development, and safeguarding human health. Nevertheless, the current understanding of the distribution and geographic patterns of potential pathogens in coastal ecosystems remains rather limited. Here, we investigated the diversity, assembly, and co-occurrence network of potential pathogenic communities in two anthropogenic coastal regions, i.e., the eight mouths (EPR) and nearshore region (NSE), of the Pearl River Estuary (PRE) and a total of 11 potential pathogenic types were detected. The composition and diversity of potential pathogenic communities exhibited noteworthy distinctions between the EPR and NSE, with 6 shared potential pathogenic families. Additionally, in the NSE, a significant pattern of geographic decay was observed, whereas in the EPR, the pattern of geographic decay was not significant. Based on the Stegen null model, it was noted that undominant processes (53.36%/69.24%) and heterogeneous selection (27.35%/25.19%) dominated the assembly of potential pathogenic communities in EPR and NSE. Co-occurrence network analysis showed higher number of nodes, a lower average path length and graph diameter, as well as higher level of negative co-occurrences and modularity in EPR than those in NSE, indicating more complex and stable correlations between potential pathogens in EPR. These findings lay the groundwork for the effective management of potential pathogens, offering essential information for ecosystem conservation and public health considerations in the anthropogenic coastal regions.

Comprehensive profiles of sulfur cycling microbial communities along a mangrove sediment depth

The sulfur (S) cycle is an important biogeochemical cycle with profound implications for both cellular- and ecosystem-level processes by diverse microorganisms. Mangrove sediments are a hotspot of biogeochemical cycling, especially for the S cycle with high concentrations of S compounds. Previous studies have mainly focused on some specific inorganic S cycling processes without paying specific attention to the overall S-cycling communities and processes as well as organic S metabolism. In this study, we comprehensively analyzed the distribution, ecological network and assembly mechanisms of S cycling microbial communities and their changes with sediment depths using metagenome sequencing data. The results showed that the abundance of gene families involved in sulfur oxidation, assimilatory sulfate reduction, and dimethylsulfoniopropionate (DMSP) cleavage and demethylation decreased with sediment depths, while those involved in S reduction and dimethyl sulfide (DMS) transformation showed an opposite trend. Specifically, glpE, responsible for converting S2O32- to SO32-, showed the highest abundance in the surface sediment and decreased with sediment depths; in contrast, high abundances of dmsA, responsible for converting dimethyl sulfoxide (DMSO) to DMS, were identified and increased with sediment depths. We identified Pseudomonas and Streptomyces as the main S-cycling microorganisms, while Thermococcus could play an import role in microbial network connections in the S-cycling microbial community. Our statistical analysis showed that both taxonomical and functional compositions were generally shaped by stochastic processes, while the functional composition of organic S metabolism showed a transition from stochastic to deterministic processes. This study provides a novel perspective of diversity distribution of S-cycling functions and taxa as well as their potential assembly mechanisms, which has important implications for maintaining mangrove ecosystem functions.

Methane fluxes in tidal marshes of the conterminous United States

Methane (CH4) is a potent greenhouse gas (GHG) with atmospheric concentrations that have nearly tripled since pre-industrial times. Wetlands account for a large share of global CH4 emissions, yet the magnitude and factors controlling CH4 fluxes in tidal wetlands remain uncertain. We synthesized CH4 flux data from 100 chamber and 9 eddy covariance (EC) sites across tidal marshes in the conterminous United States to assess controlling factors and improve predictions of CH4 emissions. This effort included creating an open-source database of chamber-based GHG fluxes (https://doi.org/10.25573/serc.14227085). Annual fluxes across chamber and EC sites averaged 26 ± 53 g CH4 m-2 year-1, with a median of 3.9 g CH4 m-2 year-1, and only 25% of sites exceeding 18 g CH4 m-2 year-1. The highest fluxes were observed at fresh-oligohaline sites with daily maximum temperature normals (MATmax) above 25.6°C. These were followed by frequently inundated low and mid-fresh-oligohaline marshes with MATmax ≤25.6°C, and mesohaline sites with MATmax >19°C. Quantile regressions of paired chamber CH4 flux and porewater biogeochemistry revealed that the 90th percentile of fluxes fell below 5 ± 3 nmol m-2 s-1 at sulfate concentrations >4.7 ± 0.6 mM, porewater salinity >21 ± 2 psu, or surface water salinity >15 ± 3 psu. Across sites, salinity was the dominant predictor of annual CH4 fluxes, while within sites, temperature, gross primary productivity (GPP), and tidal height controlled variability at diel and seasonal scales. At the diel scale, GPP preceded temperature in importance for predicting CH4 flux changes, while the opposite was observed at the seasonal scale. Water levels influenced the timing and pathway of diel CH4 fluxes, with pulsed releases of stored CH4 at low to rising tide. This study provides data and methods to improve tidal marsh CH4 emission estimates, support blue carbon assessments, and refine national and global GHG inventories.

Microbial ecology of northern Gulf of Mexico estuarine waters

Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.

Succession of diversity, assembly mechanisms, and activities of the microeukaryotic community throughout Scrippsiella acuminata (Dinophyceae) bloom phases

Harmful algal bloom (HAB) is a rapidly expanding marine ecological hazard. Although numerous studies have been carried out about the ecological impact and the ecological mechanism of HAB outbreaks, few studies have comprehensively addressed the shifts of species composition, metabolic activity level, driving factors and community assembly mechanisms of microeukaryotic plankton in the course of the bloom event. To fill the gap of research, we conducted 18S ribosomal DNA and RNA sequencing during the initiation, development, sustenance and decline stages of a Scrippsiella acuminata (S. acuminata) bloom at the coastal sea of Fujian Province, China. We found that the bloom event caused a decrease in microeukaryotic plankton species diversity and increase in community homogeneity. Our results revealed that the RNA- and DNA-inferred communities were similar, but α-diversity was more dynamic in RNA- than in DNA-inferred communities. The main taxa with high projected metabolic activity (with RNA:DNA ratio as the proxy) during the bloom included dinoflagellates, Cercozoa, Chlorophyta, Protalveolata, and diatoms. The role of deterministic processes in microeukaryotic plankton community assembly increased during the bloom, but stochastic processes were always the dominant assembly mechanism throughout the bloom process. Our findings improve the understanding of temporal patterns, driving factors and assembly mechanisms underlying the microeukarytic plankton community in a dinoflagellate bloom.

Effects of forest fire smoke deposition on soil physico-chemical properties and bacterial community

The number of forest fires has increased globally, together with considerable smoke emission that significantly impacts the atmospheric environment and associated ecosystems. Most current studies have focused on the in situ effects of fire on the forest ecosystem. However, the mechanisms by which smoke particles affect adjacent ecosystems are largely unexplored. In this study, a simulated forest fire combustion system was developed to evaluate the effect of different smoke concentrations (control, low and high) on soil physico-chemical properties of adjacent farmland at two soil depths. The abundance and diversity of bacterial community were also determined. The results showed that smoke deposition increased the contents of total carbon (TC), total nitrogen (TN), and total phosphorus (TP) in the 0-10 cm soil layer; however, no significant changes in soil water content (SWC) and pH values was observed. The ACE(Abundance Coverage-based Fastimator) and Chao1 diversity indices of bacterial community generally showed a downward trend whereas the PD_whole_ tree diversity index increased after 180 d of smoke deposition. The relative abundance of Proteobacteria remained stable, while abundance of Firmicutes in soil decreased after 180 d of smoke deposition. Smoke deposition slightly affected the physical and chemical properties of the 10-20 cm soil, but the range of variation of the relative abundance and diversity dominant bacteria exceeded that of the 0-10 cm soil. A significant positive correlation was found between the soil properties and the alpha diversity indices during the first 30 d after smoke deposition; the correlation then decreased gradually. Redundancy analysis revealed that Proteobacteria, Firmicutes, and Actinobacteria were generally positively correlated with TC, TN, and SWC. As a whole, the study reveals that the effects of smoke deposition on soil physico-chemical properties and bacterial community depends on smoke concentration where relatively low concentration appears to be beneficial to soil bacterial community.

Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay

Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.

Microbial interactions strengthen deterministic processes during community assembly in a subtropical estuary

Systematic studies on the assembly process and driving mechanisms of microbial communities in estuaries with diverse seasonal and spatial scales are still limited. In this study, high-throughput sequencing, and microbial network analysis were combined to decipher the impact of environmental changes and biological interactions on the maintenance of microbial diversity patterns in the Jiulong River Estuary (JRE). The results showed that overall, stochastic processes dominated the bacterioplankton community assembly in the estuary, accounting for 49.66-74.78 % of the total. Additionally, bacterioplankton community diversity varied significantly across seasons and subzones. Specifically, the concentration of soluble reactive phosphorus (SRP) in the estuary steadily reduced from winter to summer, and the corresponding bacterioplankton community interactions gradually shifted from the weakest interaction in winter to the strongest in summer. The deterministic processes contributed more than half (50.34 %) to microbial assembly in the summer, but only 25.22 % in winter. Deterministic processes prevailed in the seaward with low SRP concentrations and strong bacterioplankton community interactions, while stochastic processes contributed 70.14 % to the assembly of microbial communities riverward. Biotic and abiotic factors, such as nutrients and microbial interactions, jointly drove the seasonal and spatial patterns of bacterioplankton community assembly, but overall, nutrients played a dominant role. Nevertheless, the contributions of nutrients and microbial interactions were equivalent in spatial assembly processes, albeit nutrients were the primary seasonal driver of the bacterioplankton community assembly process. This study emphasizes the significance of microbial interactions in the bacterioplankton community assemblage. These findings provide new and comprehensive insights into the microbial communities' organization in estuaries.

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.

The active free-living bathypelagic microbiome is largely dominated by rare surface taxa

A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.

Field experiments on chemical and biological changes of thin-layer oyster shells capping sediments in dense aquaculture area

Thin-layer oyster shell capping has been proposed as a method for improving contaminated coastal environments. Field experiments were conducted to investigate the effects of oyster shell capping on nutrient concentrations, microorganisms, and macrobenthic communities. The concentration of PO4-Pin the experimental area decreased by approximately 38% more than in the control, due to phosphorus fixation of oyster shells and the presence of Proteobacteria. Ammonia-oxidizing bacteria such as the order Pirellulales (phylum Planctomycetes) were related to the low ratio of NH3-N found in dissolved inorganic nitrogen in the experimental area, indicating nitrification promotion. The reduction in annular benthic organisms observed in the experimental area indicates a decline in sediment organic matter, which could potentially mitigate eutrophication. Oyster shell capping was confirmed to be an effective material for restoring coastal sediments by improving their chemical and biological properties.

Soil salinity is the main factor influencing the soil bacterial community assembly process under long-term drip irrigation in Xinjiang, China

Identifying the potential factors associated with the impact of long-term drip irrigation (DI) on soil ecosystems is essential for responding to the environmental changes induced by extensive application of DI technology in arid regions. Herein, we examined the effects of the length of time that DI lasts in years (NDI) on soil bacterial diversity as well as the soil bacterial community assembly process and the factors influencing it. The results showed that long-term DI substantially reduced soil salinity and increased soil bacterial diversity while affecting the soil bacterial community structure distinctly. Null model results showed that the soil bacterial community assembly transitioned from stochastic processes to deterministic processes, as NDI increased. Homogeneous selection, a deterministic process, emerged as the dominant process when NDI exceeded 15 years. Both random forest and structural equation models showed that soil salinity was the primary factor affecting the bacterial community assembly process. In summary, this study suggested that soil bacteria respond differently to long-term DI and depends on the NDI, influencing the soil bacterial community assembly process under long-term DI.

Aromatic compounds depurative and plant growth promotion rhizobacteria abilities of Allenrolfea vaginata (Amaranthaceae) rhizosphere microbial communities from a solar saltern hypersaline soil

Introduction

This work investigates whether rhizosphere microorganisms that colonize halophyte plants thriving in saline habitats can tolerate salinity and provide beneficial effects to their hosts, protecting them from environmental stresses, such as aromatic compound (AC) pollution.

Methods

To address this question, we conducted a series of experiments. First, we evaluated the effects of phenol, tyrosine, 4-hydroxybenzoic acid, and 2,4-dichlorophenoxyacetic (2,4-D) acids on the soil rhizosphere microbial community associated with the halophyte Allenrolfea vaginata. We then determined the ability of bacterial isolates from these microbial communities to utilize these ACs as carbon sources. Finally, we assessed their ability to promote plant growth under saline conditions.

Results

Our study revealed that each AC had a different impact on the structure and alpha and beta diversity of the halophyte bacterial (but not archaeal) communities. Notably, 2,4-D and phenol, to a lesser degree, had the most substantial decreasing effects. The removal of ACs by the rhizosphere community varied from 15% (2,4-D) to 100% (the other three ACs), depending on the concentration. Halomonas isolates were the most abundant and diverse strains capable of degrading the ACs, with strains of Marinobacter, Alkalihalobacillus, Thalassobacillus, Oceanobacillus, and the archaea Haladaptatus also exhibiting catabolic properties. Moreover, our study found that halophile strains Halomonas sp. LV-8T and Marinobacter sp. LV-48T enhanced the growth and protection of Arabidopsis thaliana plants by 30% to 55% under salt-stress conditions.

Discussion

These results suggest that moderate halophile microbial communities may protect halophytes from salinity and potential adverse effects of aromatic compounds through depurative processes.

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BACKGROUND

Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.

RESULTS

The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.

CONCLUSIONS

Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis

Growth and survival are key determinants of bacterial fitness. However, how resource allocation of bacteria could reconcile these two traits to maximize fitness remains poorly understood. Here, we find that the resource allocation strategy of Bacillus subtilis does not lead to growth maximization on various carbon sources. Survival-related pathways impose strong proteome constraints on B. subtilis. Knockout of a master regulator gene, spo0A, triggers a global resource reallocation from survival-related pathways to biosynthesis pathways, further strongly stimulating the growth of B. subtilis. However, the fitness of spo0A-null strain is severely compromised because of various disadvantageous phenotypes (e.g., abolished sporulation and enhanced cell lysis). In particular, it also exhibits a strong defect in peptide utilization, being unable to efficiently recycle nutrients from the lysed cell debris to maintain long-term viability. Our work uncovers a fitness trade-off between growth and survival that governed by Spo0A-mediated proteome allocation constraints in B. subtilis, further shedding light on the fundamental design principle of bacteria.

Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones

MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.

Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants

Organohalide pollutants are prevalent in coastal regions due to extensive intervention by anthropogenic activities, threatening public health and ecosystems. Gradients in salinity are a natural feature of coasts, but their impacts on the environmental fate of organohalides and the underlying microbial communities remain poorly understood. Here we report the effects of salinity on microbial reductive dechlorination of tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) in consortia derived from distinct environments (freshwater and marine sediments). Marine-derived microcosms exhibited higher halotolerance during PCE and PCB dechlorination, and a halotolerant dechlorinating culture was enriched from these microcosms. The organohalide-respiring bacteria (OHRB) responsible for PCE and PCB dechlorination in marine microcosms shifted from Dehalococcoides to Dehalobium when salinity increased. Broadly, lower microbial diversity, simpler co-occurrence networks, and more deterministic microbial community assemblages were observed under higher salinity. Separately, we observed that inhibition of dechlorination by high salinity could be attributed to suppressed viability of Dehalococcoides rather than reduced provision of substrates by syntrophic microorganisms. Additionally, the high activity of PCE dechlorinating reductive dehalogenases (RDases) in in vitro tests under high salinity suggests that high salinity likely disrupted cellular components other than RDases in Dehalococcoides. Genomic analyses indicated that the capability of Dehalobium to perform dehalogenation under high salinity was likely owing to the presence of genes associated with halotolerance in its genomes. Collectively, these mechanistic and ecological insights contribute to understanding the fate and bioremediation of organohalide pollutants in environments with changing salinity.

Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake

Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH₄⁺. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China

Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.

Microbial community structural response to variations in physicochemical features of different aquifers

Introduction

The community structure of groundwater microorganisms has a significant impact on groundwater quality. However, the relationships between the microbial communities and environmental variables in groundwater of different recharge and disturbance types are not fully understood.

Methods

In this study, measurements of groundwater physicochemical parameters and 16S rDNA high-throughput sequencing technology were used to assess the interactions between hydrogeochemical conditions and microbial diversity in Longkou coastal aquifer (LK), Cele arid zone aquifer (CL), and Wuhan riverside hyporheic zone aquifer (WH). Redundancy analysis indicated that the primary chemical parameters affecting the microbial community composition were NO3 -, Cl-, and HCO3 -.

Results

The species and quantity of microorganisms in the river-groundwater interaction area were considerably higher than those in areas with high salinity [Shannon: WH (6.28) > LK (4.11) > CL (3.96); Chao1: WH (4,868) > CL (1510) > LK (1,222)]. Molecular ecological network analysis demonstrated that the change in microbial interactions caused by evaporation was less than that caused by seawater invasion under high-salinity conditions [(nodes, links): LK (71,192) > CL (51,198)], whereas the scale and nodes of the microbial network were greatly expanded under low-salinity conditions [(nodes, links): WH (279,694)]. Microbial community analysis revealed that distinct differences existed in the classification levels of the different dominant microorganism species in the three aquifers.

Discussion

Environmental physical and chemical conditions selected the dominant species according to microbial functions. Gallionellaceae, which is associated with iron oxidation, dominated in the arid zones, while Rhodocyclaceae, which is related to denitrification, led in the coastal zones, and Desulfurivibrio, which is related to sulfur conversion, prevailed in the hyporheic zones. Therefore, dominant local bacterial communities can be used as indicators of local environmental conditions.

Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient

Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline

Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.

Soil salinity, not plant genotype or geographical distance, shapes soil microbial community of a reed wetland at a fine scale in the Yellow River Delta

Soil salinization is one of the most severe environmental problems restricting biodiversity maintenance and ecosystem functioning in a coastal wetland. Recent studies have well documented how salinization affects soil microbial communities along vegetation succession of coastal wetlands. However, the salinity effect is rarely assessed in the context of plant intraspecific variation. Here, we analyzed the soil bacterial and fungal communities of Phragmites australis wetland using amplicon high-throughput sequencing at a fine scale (within 1000 m) in the Yellow River Delta. Our results revealed that microbial diversity is significantly correlated to soil salinity (assessed as electrical conductivity, EC) but not to soil nutrients (N and P content) or plant intraspecific traits (leaf length, shoot height, and neutral genetic variation). Specifically, the microbial diversity tended to decrease with increased EC, and the bacterial community was more sensitive to EC change than the fungal community. The dominant bacterial phyla were Proteobacteria, Actinobacteria, and Chloroflexi, and the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The relative abundance of Actinobacteria was significantly negatively correlated to EC, while Proteobacteria were positively correlated to EC. In high salinity (> 1 mS/cm), the role of the stochastic processes became more important in community assembly according to habitat niche breadth estimation, neutral community model, C-score metric, and normalized stochasticity ratio. Additional common garden and microcosm experiments provided evidence that the genotype effect of P. australis on soil microbiome might only occur between lineages from different regions but not from the same region like the Yellow River Delta. Our findings provide new insights into soil microbial community assembly processes with the intraspecific variation of host plants in the wetland ecosystem and offer a scientific reference for salinity mitigation and vegetation management of coastal wetlands under future global changes.

The putative maintaining mechanism of gut bacterial ecosystem in giant pandas and its potential application in conservation

Animals living in captivity and the wild show differences in the internal structure of their gut microbiomes. Here, we performed a meta-analysis of the microbial data of about 494 fecal samples obtained from giant pandas (captive and wild giant pandas). Our results show that the modular structures and topological features of the captive giant panda gut microbiome differ from those of the wild populations. The co-occurrence network of wild giant pandas also contained more nodes and edges, indicating a higher complexity and stability compared to that of captive giant pandas. Keystone species analysis revealed the differences between geographically different wild populations, indicating the potential effect of geography on the internal modular structure. When combining all the giant panda samples for module analysis, we found that the abundant taxa (e.g., belonged to Flavobacterium, Herbaspirillum, and Escherichia-Shigella) usually acted as module hubs to stabilize the modular structure, while the rare taxa usually acted as connectors of different modules. We conclude that abundant and rare taxa play different roles in the gut bacterial ecosystem. The conservation of some key bacterial species is essential for promoting the development of the gut microbiome in pandas. The living environment of the giant pandas can influence the internal structure, topological features, and strength of interrelationships in the gut microbiome. This study provides new insights into the conservation and management of giant panda populations.

Moderate salinity improves the availability of soil P by regulating P-cycling microbial communities in coastal wetlands

Accelerated sea-level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling of P remain unexplored. We conducted a field experiment to investigate the effects of salinity on P cycling by soil microbial communities and their regulatory roles on P availability in coastal freshwater and brackish wetlands. Salinity was positively correlated with P availability, with higher concentrations of labile P but lower concentrations of moderately labile P in the brackish wetland. The diversity and richness of microbial communities involved in P cycling were higher in the brackish wetland than the freshwater wetland. Salinity substantially altered the composition of the P-cycling microbial community, in which those of the brackish wetland were separated from those of the freshwater wetland. Metagenomic sequence analysis indicated that functional genes involved in the solubilization of inorganic P and the subsequent transport and regulation of P were more abundant in coastal soils. The relative abundances of most of the target genes differed between the wetlands, with higher abundances of P-solubilization (gcd and ppa) and -mineralization (phoD, phy, and ugpQ) genes and lower abundances of P-transport genes (pstB, ugpA, ugpB, ugpE, and pit) in the brackish wetland. A significant positive correlation between the concentration of labile P and the abundances of the target genes suggested that salinity may, at least in part, improve P availability by regulating the P-cycling microbial community. Our results suggest that the P-cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance.

Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia

Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.

New insights into microbial community coalescence in the land-sea continuum

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion

Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH₄ daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH₄ daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.

A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors

The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland.

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.

Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism

Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.

Free-living and particle-attached bacterial community composition, assembly processes and determinants across spatiotemporal scales in a macrotidal temperate estuary

Bacteria play an important role in biogeochemical cycles as they transform and remineralize organic matter. Particles are notable hotspots of activity, hosting particle-attached (PA) communities that can differ largely from their free-living (FL) counterparts. However, long-standing questions remain concerning bacterial community assembly processes and driving factors. This study investigated the FL and PA community compositions and determinants within the Aulne estuary and the Bay of Brest coastal waters (France). Our results revealed that the FL and PA community compositions greatly varied with salinity and season, explaining a larger part of the variance than the sampling fraction. Both the FL and PA communities were driven by deterministic assembly processes and impacted by similar factors. The FL-PA dissimilarity varied across space and time. It decreased in the estuarine stations compared to the freshwater and marine ends, and in summer. Interestingly, a significant proportion of the FL and PA communities' β-diversity and dissimilarity was explained by cohesion, measuring the degree of taxa co-occurrence. This suggested the importance of co-occurrence patterns in shaping the FL and PA community compositions. Our results shed light on the factors influencing estuarine bacterial communities and provide a first step toward understanding their biogeochemical impacts.

Incubation habitats and aging treatments affect the formation of biofilms on polypropylene microplastics

Microbial colonization and biofilm formation associated with microplastics (MPs) have recently attracted wide attention. However, little is known about the effect of MP aging and different exposed habitats on biofilm formation and associated microbial community characteristics. To obtain a comprehensive understanding, virgin and aged polypropylene MPs were selected as attachment substrates and exposed to different aquatic habitats (marine, estuary, and river). The results showed that the aging process could destroy surface structure and increase oxygen-containing groups of MPs. The total biomass of the biofilms, attached-bacterial OTU numbers, and α diversities increased with exposure time. The biofilms biomass and α diversity of MPs in the river were significantly higher than those in the marine and estuary habitats, and temperature and salinity were primary factors affecting microbial colonization. Bacterial communities in MP-attached biofilms were significantly different from those in surrounding water. Microorganisms tend to adhere to aged MPs, and especially, genes related to human pathogens were significantly expressed on aged MPs, suggesting a potential ecological and health risk of aged MPs in aquatic ecosystems. Our results showed that aged MPs and different habitats have an important influence on microbial colonization, and the weathering process can accelerate biofilm formation on MPs.

Saltwater intrusion affecting NO2- accumulation in demersal fishery species by bacterially mediated N-cycling

To investigate the underlying effects of saltwater intrusion (SWI) on bottom aquatic ecosystems, a set of environmental parameters and the bacterial community were determined and analyzed by sampling bottom water and surface sediments at the Modaomen waterway of the Pearl River Estuary. Biodiversity of fishery species and their relationship with the environment variables were analyzed together. NO₃^- and NO₂^- concentration down-regulation and NH₄⁺ concentration up-regulation in water and sediment were observed along the resulting salinity gradient, indicating that SWI affected N-cycling. Further investigation via 16 s sequencing revealed that taxonomic and functional composition of the bacterial community in the sediment displayed greater discretization than in water, implying that SWI exerted a greater impact on the sedimentary bacterial community. Metagenomic sequencing showed that the sedimentary bacterial community was associated with NO₃^-, NO₂^-, and NH₄⁺ transformation under SWI, and that this was driven by salinity and conductivity. Nitrogen metabolism and denitrification related genes were expressed at higher levels in high salinity than in low salinity, consistent with the increased enzymatic activities of NiR and NR. The NO₂^- concentration in the muscle of six selected fishery species was significantly decreased by 11.15-65.74% (P < 0.05) along the salinity gradient, indicating that SWI reduced NO₂^- accumulation. The results suggest that SWI alleviates NO₂^- accumulation in demersal fishery species via bacterial mediation of N-cycling.

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China

As a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes (MAGs) from 30 subtropical estuaries at a large scale along South China. In total, 500 dereplicated MAGs with completeness ≥ 50% and contamination ≤ 10% were obtained, among which more than one-thirds (n = 207 MAGs) have a completeness ≥ 70%. These MAGs are dominated by taxa assigned to the phylum Proteobacteria (n = 182 MAGs), Bacteroidota (n = 110) and Actinobacteriota (n = 104). These draft genomes can be used to study the diversity, phylogenetic history and metabolic potential of microbiota in the estuary, which should help improve our understanding of the structure and function of these microorganisms and how they evolved and adapted to extreme conditions in the estuarine ecosystem.