Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Evolution and distribution of antibiotic resistance genes in submerged macrophytes and biofilm systems: From seasonal monitoring to mesocosm experiments

The aquatic ecosystem has been extensively investigated as a hotspot for the spread of antibiotic resistance genes (ARGs); yet, the evolution and distribution of ARGs profiles in submerged macrophytes biofilms and surrounding water remained unclear. In this study, the dynamic distribution and seasonal variations of microbial communities and ARGs profiles were investigated, alongside their assembly processes and mutual interactions. Bacitracin and multidrug resistance genes were predominant, constituting more than 60% of the total ARGs abundance. The deterministic processes (<65%), influenced by the physicochemical properties of the river environment, governed the assembly and composition of ARGs profiles, exhibiting significant seasonal variation. The peak diversity (21 types) and abundance (0.316 copy ratios) of ARGs were detected during the summer. Proteobacteria and Actinobacteria were the dominant bacterial phyla, accounting for 38.41-85.50% and 4.03-27.09% of the microbial community, respectively. Furthermore, Proteobacteria, especially genera such as Acinetobacter, Burkholderia, and Pseudomonas, with various resistance sequences, were the primary carriers of multiple ARGs. Notably, the genetic exchanges between biofilms and surrounding water facilitated the further propagation of high-risk ARGs, posing greater ecological risks. Redundancy analysis indicated that the total nitrogen and temperature in water determined the fate of pathogenic-resistant species. These findings provided theoretical support for the mitigation of ARGs contamination in aquatic environments.

Metagenomic Insights into Potential Impacts of Antibacterial Biosynthesis and Anthropogenic Activity on Nationwide Soil Resistome

The presence of antibiotic resistance genes (ARGs) in soils has received extensive attention regarding its impacts on environmental, animal, and human systems under One Health. However, the health risks of soil ARGs and microbial determinants of soil resistomes remain poorly understood. Here, a nationwide metagenomic investigation of ARGs in cropland and forest soils in China was conducted. The findings indicated that the abundance and richness of high-risk (i.e., mobilizable, pathogen-carriable and clinically relevant) ARGs in cropland soils were 25.7 times and 8.4 times higher, respectively, compared to those identified in forest soils, suggesting the contribution of agricultural practices to the elevated risk level of soil resistomes. The biosynthetic potential of antibacterials best explained the total ARG abundance (Mantel's r = 0.52, p < 0.001) when compared with environmental variables and anthropogenic disturbance. Both microbial producers' self-resistance and antagonistic interactions contributed to the ARG abundance, of which self-resistance ARGs account for 14.1 %- 35.1 % in abundance. With the increased biosynthetic potential of antibacterials, the antagonistic interactions within the microbial community were greatly enhanced, leading to a significant increase in ARG abundance. Overall, these findings advance our understanding of the emergence and dissemination of soil ARGs and provide critical implications for the risk control of soil resistomes.

Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species

Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.

Agricultural practices and ditch size drive microbial community assembly and mediate N- and P-transformation in multistage drainage networks of paddy fields: Insights from a large-scale irrigation district in eastern China

Agricultural drainage ditches (ADDs) are ubiquitous and regarded as active zones for biogeochemical reactions and microbe-mediated pollutant removal. However, little is known about the microbial distribution and community assembly in ADDs. Here, a typical large-scale irrigation district, including five orders of farmland drainage systems (namely field, sublateral, head, branch, and trunk ditches that could efficiently remove excess water from paddy fields to downstream water bodies), was selected to investigate the ecological processes of microbial communities and N- and P-transformation processes in multistage ditches. We found that scale effects drove distinct environmental gradients and microbial community dissimilarities and that the five ordered ditches were grouped into three clusters (field vs. sublateral vs. head, branch, and trunk ditches). Specifically, the microbial communities in the field ditches located adjacent to the paddy fields were strongly selected by agricultural fertilization and irrigation drainage, enriching salt-tolerant microbes with high nitrification and inorganic P solubilization capabilities. In comparison, the sublateral ditches showed the highest removal performance for total nitrogen (13.28-55.80%) and total phosphorus (9.06-65.07%) during the growth of rice, which was mainly attributed to the enrichment of versatile microbiota (e.g., C39, Nitrospira, and Novosphingobium) as a result of the increased stochastic processes driven by the low redox potential. Notably, the specific gene (i.e., hzsB) for anaerobic ammonium oxidation in sublateral ditches was 1-2 orders of magnitude higher than in adjacent ditches, further contributing to N loss. As field water was discharged into the large-sized head, branch, and trunk ditches, the nutrient levels decreased sharply. At the same time, deterministic processes gained more importance (∼82%), leading to the flourishing of Synechococcus and increasing the potential risk of eutrophication. Overall, the microbial communities in multistage ADDs were co-shaped by agricultural practices and ditch size, which further governed the N and P removal performance. These results provide unique insights into microbiota assembly patterns and dynamics in multistage ADDs and important ecological knowledge for controlling agricultural non-point source pollutants by managing of small-sized ditches.

Influences of hydrodynamics on microbial community assembly and organic carbon composition of resuspended sediments in shallow marginal seas

Hydrodynamic processes play a crucial role in driving the transmission of sediments, likely harboring diverse microbes and heterogeneous organic carbon (OC) in the ocean. Here we conducted continuous micro-erosion experiments on surface sediments retrieved from shallow marginal seas, and analyzed the microbial community structures, OC content, and isotope compositions (δ13C and Δ14C) of resuspended sediments to investigate the effects of hydrodynamics on microbial assembly and OC composition in marginal seas. Our results showed that gene abundance and major microbial compositions in resuspended sediments changed with varying benthic shear stresses, which evolved towards diversification after continuous hydrodynamic erosion. Aerobic bacteria were more likely to be eroded out from sediments under lower shear stresses compared with anaerobic bacteria. Our study provides evidence that hydrodynamic disturbances shape the assembly of microbial communities with different metabolic functions, especially for bacteria, which may spatially influence the microbial-mediated biogeochemical transformation in marginal seas. Isotopic results revealed that more terrestrial OC was resuspended under initial erosion, while more marine OC was eroded out with increasing shear stresses, suggesting that hydrodynamics may control the redistribution of different sourced OC and contribute to the dispersion and degradation of terrestrial OC during transport process. Our findings further suggest that the nature of resuspended OC may influence the assembly of sediment-attached microbes due to their metabolic preference for carbon sources, as evidenced by correlations between OC compositions and microbial diversity and abundance. We thus suggest that hydrodynamic disturbance is an extrinsic physical driver of OC redistribution and microbial reassembly, whereas OC may be an intrinsic factor influencing microbial colonization, helping to interpret the spatial heterogeneity of microbes and OC compositions observed in marginal sea sediments. Our study underscores the significant roles of hydrodynamic-driven sediment resuspension in shaping diverse microbial communities and redistributing OC in aquatic systems, and highlights the importance of this process in biogeochemical cycles and ecological environment evolution in shallow marginal sea systems.

Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains

Introduction

Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.

Methods

The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology.

Results

The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential.

Discussion

This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.

Effects of microplastics on denitrification and associated N2O emission in estuarine and coastal sediments: insights from interactions between sulfate reducers and denitrifiers

Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N2O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N2O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N2O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO3-), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO3- levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO3- levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems.

Size-dependent promotion of micro(nano)plastics on the horizontal gene transfer of antibiotic resistance genes in constructed wetlands

Constructed wetlands (CWs) have been identified as significant sources of micro(nano)plastics (MPs/NPs) and antibiotic resistance genes (ARGs) in aquatic environments. However, little is known about the impact of MPs/NPs exposure on horizontal gene transfer (HGT) of ARGs and shaping the corresponding ARG hosts' community. Herein, the contribution of polystyrene (PS) particles (control, 4 mm, 100 μm, and 100 nm) to ARG transfer was investigated by adding an engineered fluorescent Escherichia coli harboring RP4 plasmid-encoded ARGs into CWs. It was found MPs/NPs significantly promoted ARG transfer in a size-dependent manner in each CW medium (p < 0.05). The 100 μm-sized PS exhibited the most significant promotion of ARG transfer (p < 0.05), whereas 100 nm-sized PS induced limited promotion due to its inhibitory activity on microbes. The altered RP4-carrying bacterial communities suggested that MPs/NPs, especially 100 µm-PS, could recruit pathogenic and nitrifying bacteria to acquire ARGs. The increased sharing of RP4-carrying core bacteria in CW medium further suggested that ARGs can spread into CW microbiome using MPs/NPs as carriers. Overall, our results highlight the high risks of ARG dissemination induced by MPs/NPs exposure and emphasize the need for better control of plastic disposal to prevent the potential health threats.