Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation

Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.

Temporal and spatial dynamic changes of planktonic bacteria community structure in Li River, China: a seasonal survey

A combined temporal and spatial research approach helps us to evaluate the ecological status of a river scientifically and comprehensively. To understand the response mechanisms of bacteria in the Li River to different environments, we conducted a 1-year study (2020-2021) and collected water samples from 18 sections of the river in October, January, April, and August. 16S sequencing was used to study the composition and structure of bacterial communities in Li River at different temporal and spatial scales. The results showed that NO3--N, TP, T, pH, and DO were significantly different on spatial and temporal scales. Alpha diversity of planktonic bacteria in Li River fluctuated significantly with the season, reaching its highest in summer. Proteobacteria remained the most dominant phylum in all seasons, but the differential microorganisms varied between seasons. Although the abundance of metabolic functions of planktonic bacteria did not show significant differences between seasons, we found that DO, TP, T, and COD were the key environmental factors affecting bacterial metabolism. In addition, the co-occurrence network analysis showed that the autumn network had a higher number of nodes and edges and exhibited a high degree of complexity, while the summer network had the highest degree of modularity and exhibited greater stability. These results deepen our knowledge of the response mechanisms of river microorganisms to temporal and spatial changes and provide a scientific reference for the study of river ecosystems.

Untangling microbiota diversity and assembly patterns in the world's longest underground culvert water diversion canal

The long-distance underground box culvert water transport system (LUBWT) is a crucial link between the source of drinking water and the consumers. It must ensure the stability of water quality during transportation. However, uncontrollable microbial growth can develop in the water delivery system during the long delivery process, posing a risk to health and safety. Therefore, we applied 16 s and 18 s gene sequence analysis in order to study microbial communities in box culvert waters sampled in 2021, as well as a molecular ecological network-based approach to decipher microbial interactions and stability. Our findings revealed that, in contrast to natural freshwater ecosystems, micro-eukaryotes in LUBWT have complex interactions such as predation, parasitism, and symbiosis due to their semi-enclosed box culvert environment. Total nitrogen may be the primary factor affecting bacterial community interactions in addition to temperature. Moreover, employing stability indicators such as robustness and vulnerability, we also found that microbial stability varied significantly from season to season, with summer having the higher stability of microbial communities. Not only that but also the stability of the micronuclei also varied greatly during water transport, which might also be related to the complex interactions among the micro-eukaryotes. To summarize, our study reveals the microbial interactions and stability in LUBWT, providing essential ecological knowledge to ensure the safety of LUBWT's water quality.

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors

Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.

Appropriate Irrigation and Fertilization Regime Restrain Indigenous Soil Key Ammonia-Oxidizing Archaeal and Bacterial Consortia to Mitigate Greenhouse Gas Emissions

Harnessing an ammonia-oxidizing microbiome has become an increasingly attractive form of management for mitigating greenhouse gas emissions in rice paddies; however, the relationship between greenhouse gas emissions and ammonia-oxidizing microbiomes, using a nitrogen application and irrigation regime, has not been well investigated. To decipher which of (and how) the specific mmonia-oxidizing bacterial species drive the greenhouse gas CH4 and N2O emissions, a field experiment with varying nitrogen application and irrigation regimes was initiated to investigate the succession of key bacterial consortia associated with GHG emissions. The results showed that water-saving irrigation (AWD) significantly increased NO3-N and NH4+-N concentrations, compared with conventional irrigation (FDF), whereas (total nitrogen) TN was little higher in FDF (1.38 g kg−1) compared with the AWD (1.36 g kg−1). During the rice-growing season, CH4 emissions ascended speedily, and emissions peaked at maximum values of 3.32 and 4.41 ug mg−2 h−1 on day 5 in FDF and AWD irrigation regimes, respectively, and then they rapidly decreased during the midseason period, maintaining a relatively low emission rate until the rice was harvested. The patterns of N2O emission fluxes had the same tendencies with N fertilization. Putative key taxa, such as Flavobacterium, Massilia, Arenimonas, Novosphingobium, Pseudomonas, exhibited significant positive relationships with higher GHG emissions, suggesting that they make particularly obvious contributions to N2O emissions. These putative taxa should be considered when designing a high nitrogen application and irrigation strategy. As such, the nitrogen application of N180, and the irrigation regimes of water-saving irrigation, are recommended methods for N conservation and the mitigation of greenhouse gas emissions in rice paddies.

Factors affecting seasonal variation of microbial community structure in Hulun Lake, China

Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there is a lack of research on the seasonal variation in lake water microorganisms in cold environments. In this study, 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors in Hulun Lake water during different seasons. The results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most important phyla in the microbial community of Hulun Lake, but they had significant seasonal differences in their distribution. In addition, significant seasonal differences were observed in the α diversity of microorganisms, with bacterial diversity being higher in winter than in summer. Changes in environmental variables were significantly correlated with changes in the microbial community, and the rapid changes in temperature, pH, and dissolved oxygen are potentially the major factors influencing seasonal bacterial diversity trends. The findings of the present study enhance our understanding of the microbial communities in alpine lake ecosystems and are of great significance for the management and protection of lake ecosystems.

A watershed impacted by anthropogenic activities: Microbial community alterations and reservoir of antimicrobial resistance genes

Water is the main resource for maintaining life. Anthropic activities influence the microbial epidemiological chain in watersheds, which can act as ways of disseminating microorganisms resistant to antimicrobial drugs, with impacts on human, animal, and environmental health. Here, we characterized aquatic microbial communities and their resistomes in samples collected along Rio das Ostras watershed during two seasons. Surface water samples were collected at eleven sites from the Jundiá, Iriry, and Rio das Ostras rivers in two seasons (dry and wet season). Microbial DNA was extracted, high-throughput sequenced and screened for antimicrobial resistance genetic (ARG) markers. The physicochemical characteristics and the microbiota data confirmed that Rio das Ostras watershed can be divided into three well defined portions: rural, urban, and marine. Rural areas were enriched by bacteria typically found in limnic environments and Patescibacteria phyla. The urban portion was characterized by sites with low pH and groups associated with iron oxidation. Some genera of clinical relevance were also identified, though in relatively low abundance. The marine site was enriched mainly by Cyanobacteria and bacteria that showed strong correlation with conductivity, salinity, and chloride. Twenty-six ARG markers were identified on the resistome, being found most frequently in the urban area, despite being present in rural sites. Among them were some related to classes of great clinical concern, such as genes coding for extended-spectrum beta-lactamase (bla_CTX-M and bla_TEM), resistance to carbapenems (bla_KPC) and to methicillin by Staphylococcus aureus (mecA). These results broaden our understanding of the microbial community of a watershed impacted by anthropogenic actions. The large number of ARGs detected along the Rio das Ostras watershed contrasts with the small number of microorganisms of clinical relevance observed, suggesting that antimicrobial resistance has arisen from non-clinical environments and microbes. Our results corroborate that freshwater acts as a reservoir of antimicrobial resistance genes.

Effects of shading levels on the composition and co-occurrence patterns of bacterioplankton and epibiotic bacterial communities of Cabomba caroliniana

Epibiotic bacterial community colonized on the plant leaf plays important roles in promoting plant growth and nutrient absorption, but is sensitive to environmental changes. As one of the most important environmental factors affecting the growth of plants and photosynthetic microorganisms, light may affect the diversity, composition, and interactions of the epibiotic bacterial community. Submerged plants in the aquatic ecosystem may be more sensitive to light intensity variations compared to the terrestrial plants since they usually receive less light. However, the effects of light on the interactions between the submerged plants and their epibiotic microbial communities remain uncertain. Here we used the 16S rRNA gene high-throughput sequencing to investigate the diversity and composition of the bacterioplankton and epibiotic bacterial communities of the Cabomba caroliniana under four different shading levels. A total of 24 water and leaf samples were collected from the experimental microcosms near Lake Taihu. We found the epibiotic bacterial community possessed a higher diversity than that of the bacterioplankton community, although the alpha diversity of the bacterioplankton community was more susceptible to different levels of shading. SourceTracker analysis revealed that with the increase of shading, the colonization of bacterioplankton to epibiotic bacteria decreased. Network analysis showed that the bacterial community network at 50% shading level had the lowest modularity and highest clustering coefficient compared to the bacterial community networks of other shading levels. Our findings provided new understandings of the effects of different light intensities on the epibiotic bacterial communities of submerged macrophytes.

Bacterial diversity, community composition and metabolic function in Lake Tianmuhu and its dammed river: Effects of domestic wastewater and damming

Anthropogenic disturbances, such as pollution discharge and damming, can lead to a global decline in biodiversity in aquatic ecosystems. However, how such disturbances affect microbial community composition and function remains poorly understood. In November 2019, we explored bacterial diversity, community composition and metabolic function in Lake Tianmuhu, China, and in its upstream dammed river, using Illumina MiSeq sequencing and Biolog EcoPlate method based on carbon source utilization. Our results revealed higher variations in bacterial α- and β-diversity in the dammed river ecosystem than in the lake ecosystem. In addition, the dammed river and lake ecosystems were significantly different in bacterial community compositions and metabolic structures. No significant relationship between species richness and functional (metabolic) diversity was observed in this study. The site that was most impacted by domestic wastewater had the lowest taxonomic diversity but highest metabolic capacity and activity, suggesting that community composition rather than species diversity is more important in determining ecosystem functioning. Overall, our findings indicate that anthropogenic disturbances can significantly alter bacterial community and function, and taxonomic diversity is a weak proxy for ecosystem functioning in a natural freshwater habitat.

Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

Although bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

High heterogeneity of bacterioplankton community shaped by spatially structured environmental factors in West Lake, a typical urban lake in eastern China

Elucidating the bacterioplankton spatial distribution patterns and its determinants is a central topic in ecological research. However, research on the distribution patterns of bacterioplankton community composition (BCC) within a small-sized, highly dynamic freshwater lake remains unclear. In this study, we collected surface water samples from West Lake to investigate the spatiotemporal variation of BCC by 16S rRNA gene high-throughput sequencing. Clear spatial heterogeneity in BCC was identified both in summer and winter. The relatively high abundant taxa exhibited greater correlations with environmental factors and other abundant species in summer than in winter. Variation partitioning analysis was used to unravel the relative importance of environmental factors and spatial processes and further explore the underlying mechanism of BCC successions. Our results showed the predominant shared effect of environmental and spatial factors on BCC in summer (68.41%) and winter (57.37%), indicating that spatially structured environmental factors were the key determinants of structuring BCC spatial heterogeneity in West Lake in the two seasons. Furthermore, environmental factors alone explained a higher proportion of the variation in summer whereas spatial factors explained a higher proportion in winter. These divergences may be related to seasonal environmental changes and anthropogenic disturbances. Our study provided knowledge on BCC spatial heterogeneity in small freshwater habitats and their underlying determinants in different seasons.

Bacterial Diversity in a Dynamic and Extreme Sub-Arctic Watercourse (Pasvik River, Norwegian Arctic)

Microbial communities promptly respond to the environmental perturbations, especially in the Arctic and sub-Arctic systems that are highly impacted by climate change, and fluctuations in the diversity level of microbial assemblages could give insights on their expected response. 16S rRNA gene amplicon sequencing was applied to describe the bacterial community composition in water and sediment through the sub-Arctic Pasvik River. Our results showed that river water and sediment harbored distinct communities in terms of diversity and composition at genus level. The distribution of the bacterial communities was mainly affected by both salinity and temperature in sediment samples, and by oxygen in water samples. Glacial meltwaters and runoff waters from melting ice probably influenced the composition of the bacterial community at upper and middle river sites. Interestingly, marine-derived bacteria consistently accounted for a small proportion of the total sequences and were also more prominent in the inner part of the river. Results evidenced that particular conditions occurring at sampling sites (such as algal blooms, heavy metal contamination and anaerobiosis) may select species at local scale from a shared bacterial pool, thus favoring certain bacterial taxa. Conversely, the few phylotypes specifically detected in some sites are probably due to localized external inputs introducing allochthonous microbial groups.

Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat

Teleost fish represent an invaluable repertoire of host species to study the factors shaping animal-associated microbiomes. Several studies have shown that the phylogenetic structure of the fish gut microbiome is driven by species-specific (e.g., host ancestry, genotype, or diet) and habitat-specific (e.g., hydrochemical parameters and bacterioplankton composition) factors. However, our understanding of other host-associated microbial niches, such as the skin mucus microbiome, remains limited. The goal of our study was to explore simultaneously the phylogenetic structure of the fish skin mucus and gut microbiome and compare the effect of species- and habitat-specific drivers on the structure of microbial communities in both tissues. We sampled 114 wild fish from 6 populations of 3 ecologically and phylogenetically contrasting Amazonian teleost species. Water samples were collected at each site, and 10 physicochemical parameters were characterized. The skin mucus, gut, and water microbial communities were characterized using a metabarcoding approach targeting the V3-V4 regions of the 16S rRNA. Our results showed a significant distinction between the phylogenetic profile and diversity of the microbiome from each microbial niche. Skin mucus and bacterioplankton communities were significantly closer in composition than gut and free-living communities. Species-specific factors mostly modulated gut bacterial communities, while the skin mucus microbiome was predominantly associated with environmental physicochemistry and bacterioplankton community structure. These results suggest that the variable skin mucus community is a relevant target for the development of microbial biomarkers of environmental status, while the more conserved gut microbiome is better suited to study long-term host-microbe interactions over evolutionary time scales.IMPORTANCE Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a light on this topic as we investigate how the phylogenetic structure of microbial communities from two distinct fish tissues are shaped by species- and habitat-specific factors. Our study showed that in contrast to the teleost gut microbiome, skin mucus communities are highly environment dependent. This result has various implications: (i) the skin mucus microbiome should be used, rather than the gut, to investigate bacterial biomarkers of ecosystem perturbance in the wild, and (ii) the gut microbiome is better suited for studies of the drivers of phylosymbiosis, or the coevolution of fish and their symbionts.

Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca²⁺–Mg²⁺–HCO₃⁻–SO₄²⁻ water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.