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Bacteria communities, as key drivers of energy flow and nutrient recycling in rivers, usually consist of a few abundant taxa and many rare taxa. During the last decades, rivers on the Tibetan Plateau have experienced dramatic land surface changes under climate change and anthropogenic disturbances. However, the responses of abundant and rare taxa to such changes and disturbances still remains unclear. In this study, we explored the biogeography and drivers of the abundant and rare bacteria in Yarlung Tsangpo River sediments on the Tibetan Plateau. Our study demonstrated that changes in surrounding land-use patterns, especially in forest land, bare land and cropland, had profound influences on the distribution of the abundant and rare sediment bacteria in the Yarlung Tsangpo River. Although both communities exhibited significant distance-decay patterns, dispersal limitation was the dominant process in the abundant community, while the rare community was mainly driven by heterogeneous selection. Our results also revealed that the abundant bacteria exhibited stronger adaptation across environmental gradients than the rare bacteria. The similar biogeographic patterns but contrasting assembly processes in abundant and rare communities may result from the differences in their environmental adaptation processes. This work provides valuable insights into the importance of land surface changes in influencing the biogeographic patterns of bacteria in fluvial sediments, which helps to predict their activities and patterns in Tibetan rivers under future global climate change and anthropogenic disturbances.

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.

Microeukaryotes play a significant role in biogeochemical cycling and can serve as bioindicators of water quality in freshwater ecosystems. However, there is a knowledge gap on how freshwater microeukaryotic communities are assembled, especially that how terrestrial microeukaryotes influence freshwater microeukaryotic assemblages. Here, we used a combination of 18S rRNA gene amplicon sequencing and community-based microbial source tracking (MST) approaches (i.e., SourceTracker and FEAST) to assess the contribution of microeukaryotes from surrounding environments (i.e., soils, river sediments, swine wastewater, influents and effluents of decentralized wastewater treatment plants) to planktonic microeukaryotes in the main channel, tributaries and reservoir of a peri-urban watershed, China in wet and dry seasons. The results indicated that SAR (~ 49% of the total communities), Opithokonta (~ 34%), Archaeplastida (~ 9%), and Amoebozoa (~ 2%) were dominant taxa in the watershed. The community-based MST analysis revealed that sewage effluents (7.96 – 21.84%), influents (2.23 – 13.97%), and river sediments (2.56 – 11.71%) were the major exogenous sources of riverine microeukaryotes. At the spatial scale, the downstream of the watershed (i.e., main channel and tributaries) received higher proportions of exogenous microeukaryotic OTUs compared to the upstream reservoirs, while at the seasonal scale, the sewage effluents and influents contributed higher exogenous microeukaryotes to river water in wet season than in dry season. Moreover, the swine and domestic wastewater led to the presence of Apicomplexa in wet season only, implying rainfall runoff may enhance the spread of parasitic microeukaryotes. Taken together, our study provides novel insights into the immigration patterns of microeukaryotes and their dominant supergroups between terrestrial and riverine habitats.

Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.

Summary Although the health of rivers is threatened by multiple anthropogenic stressors with increasing frequency, it remains an open question how riverine microbial communities respond to emerging micropollutants. Here, by using 16S rDNA amplicon sequencing of 60 water samples collected during different hydrological seasons, we investigated the spatio-temporal variation and the co-occurrence patterns of microbial communities in the anthropogenically impacted Jiulong River in China. The results indicated that the riverine microbial co-occurrence network had a non-random, modular structure, which was mainly shaped by the taxonomic relatedness of co-occurring species. Fecal indicator bacteria may survive for prolonged periods of time in river water, but they formed an independent module which had fewer interactions with typical freshwater bacteria. Multivariate analysis demonstrated that nutrients and micropollutants (i.e. pharmaceuticals and personal care products, PPCPs) exerted combined effects in shaping α- and β-diversity of riverine microbial communities. Remarkably, we showed that a hitherto unrecognized disruptive effect of PPCPs on the abundance variations of central species and module communities was stronger than the influence of physico-chemical factors, suggesting the key role played by micropollutants for the microbial co-occurrence relationships in lotic ecosystems. Overall, our findings provide novel insights into community assembly in aquatic environments experiencing anthropogenic stresses. This article is protected by copyright. All rights reserved.

Wastewater treatment plants (WWTPs) rely mainly on the microbial assemblages to contribute significantly for the removal of organic pollutants and nutrients. However, limited information is available on the ecological driving forces underlying the turnover of prokaryotic communities across wastewater treatment processes (i.e., from influents (IFs) and effluents (EFs)) within WWTPs. Here, we used a combination of the 16S rRNA gene amplicon sequencing and a quantitative ecological null model analysis to explore the ecological processes governing the turnover of the prokaryotic communities and the dominant taxonomic taxa across wastewater treatment processes of five full-scale WWTPs in China. Our results indicated that a significant variation in the composition of prokaryotic communities and the dominant taxa between IFs and EFs. The analysis of the environmental sources of indicator OTUs showed that a relatively lower abundance of the sludge/sewage and human guts associated OTUs in EFs than in IFs. Ecological null models revealed that among the ecological processes, deterministic processes were dominant in controlling the turnover of the overall communities from IFs to EFs, whereas the relative importance of deterministic processes varied among the dominant taxa (i.e., Bacteroidetes > Proteobacteria > Gammaproteobacteria > Firmicutes > Betaproteobacteria). However, the assembly of IF and EF communities was influenced mainly by the deterministic and stochastic processes, respectively. In addition, our results indicated that EF communities have a higher phylogenetic diversity than those of the IF communities, but the abundance of prokaryotic 16S rRNA genes was lower in EFs than in IFs. Overall, our study provides a novel insight of the assembly mechanisms underlying the turnover of prokaryotic communities during wastewater treatment processes.

Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1, 388 and 369 core operational taxonomic units (OTUs), 1, 038 and 1, 683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH4-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.

The occurrence, dissemination and assembly processes of antibiotic resistance genes (ARGs) in urban water ecosystems are far from being understood. Here, we examined the diversity and abundance of ARGs in urban water ecosystems including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city, China through high-throughput quantitative PCR. A total of 237 ARGs were identified, where multidrug, aminoglycoside and beta-lactamase resistance genes were the most abundant. Urban ponds had a comparatively high diversity and large numbers of shared ARGs with IFs and EFs. The average absolute abundance of ARGs (1.38 × 107 copies/mL) and mobile genetic elements (MGEs) (4.19 × 106 copies/mL) in ponds were only one order of magnitude lower than those of IFs, but higher than those of EFs and reservoirs. Stochastic processes dominated the ARG community assembly in IFs and ponds due to the random horizontal gene transfer caused by MGEs. These results imply that urban ponds are hotspots of ARGs. We further identified 25, 3, and 11 indicator ARGs for tracing the ARG contamination from IFs, EFs and ponds, respectively. Our study represents the first to highlight the role of urban ponds in the dissemination of ARGs.

Microeukaryotic communities are sensitive to environmental changes; and are considered essential for microbial food webs and biogeochemical cycles. Therefore, understanding the community responses of microeukaryotes to environmental changes is of great ecological significance. Very little is known about the assembly mechanisms underlying the microeukaryotic communities, especially for the key ecological groups (e.g., habitat generalists/specialists) in the riverine ecosystems. Here, we employed 18S rDNA amplicon sequencing to study the assembly processes governing the microeukaryotic communities and their habitat generalists and specialists across three hydrological seasons in a subtropical river in China. The results showed that deterministic and stochastic processes jointly shaped the microeukaryotic communities, where the relative importance of stochastic processes decreased in the following order: wet > normal > dry seasons. However, deterministic processes played more important role in shaping the microeukaryotic communities than those of prokaryotes. Meanwhile, stochastic and deterministic processes were responsible for structuring the microeukaryotic habitat generalists and specialists, respectively. Generally, the pure effects of physicochemical factors on the microeukaryotic communities and their key ecological groups were ~ 1.7 folds than those of the micropollutants. However, several micropollutants (e.g., acetaminophen, benzophenone-3, bisphenol A, sulfadiazine, triclocarban and triclosan) were found to have a strong effect on the habitat specialists. Altogether, we suggested that the ecological responses of the riverine microeukaryotes to micropollutants may vary among species due to the intrinsic differences in their environmental plasticity.

Mounting evidence suggests that Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles, yet the pattern and its ecological drivers of biogeographic distribution of archaeal community in estuarine ecosystem are still not well understood. Here, we investigated planktonic and benthic archaeal communities in the human-impacted Jiulong River estuary (JRE), southern China by using real-time PCR (RT-PCR) and Illumina 16S ribosomal RNA (rRNA) amplicon sequencing. RT-PCR analysis indicated that Archaea accounted for an average of 0.79 and 5.31 % of prokaryotic biomass in water and sediment samples of the JRE, respectively. The diversity of planktonic archaeal community decreased gradually from the river runoff to seawater, whereas that of benthic community did not show the similar pattern. The results of taxonomic assignments indicated that Thaumarchaeota (Nitrosopumilus and Cenarchaeum), Methanocorpusculum, and Methanospirillum were significantly more abundant in planktonic than benthic communities, whereas the relative abundances of Miscellaneous Crenarchaeotic Group, Marine Benthic Group-B/-D, anaerobic methane-oxidizing Archaea -1/-2D, and South Africa Gold Mine Euryarchaeotic Group 1 were higher in sediments than in surface waters. Moreover, planktonic archaeal community composition varied significantly at broad and finer-scale taxonomic levels along the salinity gradient. Multivariate statistical analyses revealed that salinity is the main factor structuring the JRE planktonic but not benthic archaeal community at both total community and population level. SourceTrakcer analysis indicated that river might be a major source of archaea in the freshwater zone of the JRE. Overall, this study advances our understanding of the biogeographic patterns and its ecological drivers of estuarine archaeal communities.

Prokaryotes represent the largest biodiversity pool and drive the biogeochemical cycles in fluvial environments. However, the mechanisms underlying the assembly of prokaryotic communities are largely unexplored at taxonomic and functional levels, simultaneously. Here, we investigated the spatio-seasonal distribution of prokaryoplankton communities in a salinity-influenced watershed, China using 16S rRNA gene amplicon sequencing. The OTUs were divided into core and satellite, based on a statistical approach. Our results indicated that the core taxa accounted for 87.4% of all the communities, predominantly including Betaproteobacteria, Actinobacteria and Thaumarchaeota. Whereas 10 of 22 metabolic phenotypes annotated using METAGENassist had significantly higher relative abundances in the core than satellite communities. Temporal variations in the composition of ammonia-oxidizing prokaryotes could be attributed to the seasonal nutrient concentrations. Multivariate statistical analysis indicated that environmental filtering rather than dispersal limitation is the primary mechanism driving the assembly of the whole, core and satellite communities at both taxonomic and functional levels. Network analysis revealed that the mutualistic interactions might also have certain roles in the assembly of the core taxonomic community. However, taxonomic community fluctuations can only partially reflect the functional community variations. Collectively, this study significantly advanced our understanding of the biogeographic pattern of the fluvial prokaryotic communities.

This study used 16S rRNA gene-based pyrosequencing (16S-pyrotag) to investigate both planktonic and benthic bacterial communities in two main tributaries (North River and West River) of the Jiulong River Watershed (JRW), a mesoscale subtropical watershed that has experienced intensive human perturbation in recent decades. The results of 16S-pyrotag showed that benthic bacterial communities were clearly more diverse and uniform than surface bacterioplankton communities. The results of taxonomic assignments indicated that Betaproteobacteria, Actinobacteria and Firmicutes were significantly more abundant in planktonic than in benthic communities, whereas the relative abundances of Acidobacteria, Delta-, Gammaproteobacteria, Chloroflexi and Nitrospira were higher in sediment than in water samples. In particular, several sewer- and fecal-pollution bacterial indicators were observed in water samples, implying that the water bodies of the JRW were contaminated by fecal pollution. Using the typical freshwater bacteria (TFB) taxonomic framework, 57.6 ± 10%, 27.6 ± 10.9% and 10.4 ± 6.9% of sequences recovered from planktonic communities could be assigned to lineages, clades and tribes of TFB, respectively. The relatively lower abundance of TFB implied that some unknown or unique autochthonous bacterioplankton populations occurred in the JRW. The principal coordinate analysis (PCoA) and one way analysis of similarity (ANOSIM) analysis demonstrated that planktonic bacterial community structures were significantly different between North River and West River, whereas benthic communities from these two tributaries were grouped together. Multivariate statistical analysis revealed that nutrient concentrations and stoichiometry were the key drivers of both α- and β-diversity patterns of bacterioplankton communities. Overall, our results indicate that the diversity, composition and structure of planktonic bacterial communities are sensitive to water chemistry (e.g., nutrient concentrations and stoichiometry) in the JRW, and therefore can serve as a good sentinel of environmental changes in this watershed.