Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China

Bacterioplankton diversity and potential health risks in volcanic lakes: A study from Arxan Geopark, China

Bacterioplankton play a vital role in maintaining the functions and services of lake ecosystems. Understanding the diversity and distribution patterns of bacterioplankton, particularly the presence of potential pathogenic bacterial communities, is crucial for safeguarding human health. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the diversity and geographic patterns of bacterioplankton communities, as well as potential pathogens, in eight volcanic lakes located in the Arxan UNESCO Global Geopark (in the Greater Khingan Mountains of China). Our results revealed that the bacterial communities primarily comprised Bacteroidota (45.3%), Proteobacteria (33.1%), and Actinobacteria (9.0%) at the phylum level. At the genus level, prominent taxa included Flavobacterium (31.5%), Acinetobacter (11.0%), Chryseobacterium (7.9%), and CL500-29 marine group (5.6%). Among the bacterioplankton, we identified 34 pathogen genera (165 amplicon sequence variants [ASVs]), with Acinetobacter (59.8%), Rahnella (18.3%), Brevundimonas (9.6%), and Pseudomonas (5.8%) being the most dominant. Our findings demonstrated distinct biogeographic patterns in the bacterial communities at the local scale, driven by a combination of dispersal limitation and environmental factors influenced by human activities. Notably, approximately 15.3% of the bacterioplankton reads in the Arxan lakes were identified as potential pathogens, underscoring the potential risks to public health in these popular tourist destinations. This study provides the first comprehensive insight into the diversity of bacterioplankton in mountain lake ecosystems affected by high tourist activity, laying the groundwork for effective control measures against bacterial pathogens.

Fine-Scale Structuring of Planktonic Vibrio spp. in the Chinese Marginal Seas

Vibrio is ubiquitous in marine environments with high metabolism flexibility and genome plasticity. Studies have investigated the ecological distribution of Vibrio spp. in several narrow zones, but a broad scale pattern of distribution and community assembly is still lacking. Here, we elucidated the distribution of Vibrio spp. in seawater along the Chinese marginal seas with a high spatial range. Comparison of Vibrio abundance between 3- and 0.2-μm-pore-size membranes showed distinction in preferential lifestyle. Vibrio spp. in the Yellow Sea (YS) was low in abundance and adopted a particle-associated lifestyle, whereas that in the East China Sea (ECS) and South China Sea (SCS) was more abundant and was likely in a temporary free-living state as a strategy to cope with nutrient limitation. Vibrio community compositions were also separated by sampling area, with different dominant groups in YS (Vibrio chagasii and Vibrio harveyi), ECS and SCS (Vibrio japonicus and V. chagasii). The community niche breadth was significantly wider in ECS and SCS than that of YS. Among species, V. chagasii and V. harveyi had the largest niche breadths likely reflecting strong competitive positions. Stochastic processes played important roles in shaping the geographical pattern of the vibrionic community. Environmental selection (e.g., temperature, salinity, and dissolved oxygen) had a much greater impact on the community in surface than in bottom water. The large proportions of unexplained variations (78.9%) imply complex mechanisms in their community assembly. Our study provides insights into the spatial distribution patterns and underlying assembly mechanisms of Vibrio at a broad spatial scale. IMPORTANCE Vibrio spp. may exert large impacts on biogeochemical cycling in coastal habitats, and their ecological importance has drawn increasing attention. Here, we investigated the spatial distribution pattern and community assembly of Vibrio populations along the Chinese marginal seas, spanning a wide spatial scale. Our results showed that the abundances of the Vibrio population increased with decreasing latitude and their preferential lifestyle differed among adjacent coastal areas. The compositions of Vibrio spp. were also separated by geographical location, which was mainly attributable to stochastic processes. Overall, this work contributes to the understanding of the ecological distribution patterns and the community assembly mechanisms of marine vibrios at a high spatial range. The large proportion of unexplained variations indicates the existence of complex mechanisms in the assembly of vibrionic community which should be considered comprehensively in future.

Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance

Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.

Anthropogenic activities change the relationship between microbial community taxonomic composition and functional attributes

Functional redundancy is considered common in microbial systems, but recent studies have challenged this idea. The mechanism for this contradictory result is not clear. However, in this study, we hypothesize that strong environmental filtering which links to the anthropogenic activities is able to weaken microbial functional redundancy. We used metagenome and 16S rRNA gene high-throughput sequencing to investigate planktonic microbial communities in a subtropical river. We found that the weak anthropogenic activities might result in a low selection pressure in the river upstream area. Therefore, the microbial community functional attributes were stable although the community composition changed with the water temperature and NO₃ -N in upstream area (this indicates functional redundancy). However, the strong anthropogenic activities in river downstream area selected pollutant-degraded functions (e.g. nitrogen metabolism, toluene, xylenes and ethylbenzene degradation) and potentially pollutant-degraded (tolerant) microbes, and therefore caused the microbial community composition synchronously changed with the variation of community functional attributes. Our results reveal that strong environmental filtering which associates with the anthropogenic activities not only has effects on microbial community composition and community functional attributes but also on their relationships. These results provide a new insight to refine the functional redundancy idea.

Bacterial diversity and predicted enzymatic function in a multipurpose surface water system - from wastewater effluent discharges to drinking water production

BACKGROUND

Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics -from the source of contamination, through the watershed to the DW production process-may help safeguard human health and the environment.

RESULTS

The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemäenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <  0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 ± 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 ± 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66-80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (≥13%) than in other groups (≤3%). Acidobacteria was more abundant in the DW treatment process (≥13%) than in others (≤2%). In total, the share of PHRB reads was higher in sewage and surface water than in the DW treatment samples. The seasonal effect in bacterial communities was observed only on surface water samples, with the lowest diversity during summer.

CONCLUSIONS

The low bacterial diversity and absence of PHRB read in the DW samples indicate AGR can produce biologically stable and microbiologically safe drinking water. Furthermore, the significantly different bacterial communities at the pollution sources compared to surface water and DW samples highlight the importance of effective wastewater treatment for protecting the environment and human health.

River temperature research and practice: Recent challenges and emerging opportunities for managing thermal habitat conditions in stream ecosystems

There is growing evidence that river temperatures are increasing under climate change, which is expected to be exacerbated by increased abstractions to satisfy human water demands. Water temperature research has experienced crucial advances, both in terms of developing new monitoring and modelling tools, as well as understanding the mechanisms of temperature feedbacks with biogeochemical and ecological processes. However, water practitioners and regulators are challenged with translating the widespread and complex technological, modelling and conceptual advances made in river temperature research into improvements in management practice. This critical review provides a comprehensive overview of recent advances in the state-of-the-art monitoring and modelling tools available to inform ecological research and practice. In so doing, we identify pressing research gaps and suggest paths forward to address practical research and management challenges. The proposed research directions aim to provide new insights into spatio-temporal stream temperature dynamics and unravel drivers and controls of thermal river regimes, including the impacts of changing temperature on metabolism and aquatic biogeochemistry, as well as aquatic organisms. The findings of this review inform future research into ecosystem resilience in the face of thermal degradation and support the development of new management strategies cutting across spatial and temporal scales.

Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics

Lotic surface water sites (e.g. creeks) are important resources for localized agricultural irrigation. However, there is concern that microbial contaminants within untreated surface water may be transferred onto irrigated soil and crops. To evaluate this issue, water samples were collected between January 2017 and August 2018 from a freshwater creek used to irrigate kale and radish plants on a small farm in the Mid-Atlantic, United States. In addition, on one sampling date, a field survey was conducted in which additional water (creek source and point-of-use) and soil samples were collected to assess the viral and bacterial communities pre- and post- irrigation. All samples were processed for DNA extracts and shotgun sequenced on the Illumina HiSeq platform. The resulting metagenomic libraries were assembled de novo and taxonomic and functional features were assigned at the contig and peptide level. From these data, we observed that Betaproteobacteria (e.g. Variovorax) dominated the water, both at the source and point-of-use, and Alphaproteobacteria (e.g. Streptomyces) dominated both pre- and post-irrigated soil. Additionally, in the creek source water there were variations in the abundance of the dominant bacterial genera and functional annotations associated with seasonal characteristics (e.g. water temperature). Antibiotic resistance genes and virulence factors were also identified in the creek water and soil, with the majority specific to their respective habitat. Moreover, an analysis of clustered regularly interspaced short palindromic repeat (CRISPR) arrays showed the persistence of certain spacers through time in the creek water, as well as specific interactions between creek bacteriophages and their hosts. Overall, these findings provide a more holistic picture of bacterial and viral composition, dynamics, and interactions within a freshwater creek that can be utilized to further our knowledge on its suitability and safety for irrigation.

How bacterioplankton community can go with cascade damming in the highly regulated Lancang-Mekong River Basin

Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang-Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming. The results showed that dam constructions increased nutrient concentrations and threatened water quality in cascade reservoirs. Bacterioplankton cell abundance was reduced by damming, and α-diversity was inhibited in cascade reservoirs. Fortunately, however, river ecosystems were resilient after the remarkable disturbance caused by damming. Moreover, bacterioplankton community composition was significantly altered by cascade dams, including a shift in the dominant phylum from r-strategists to k-strategists. Meanwhile, according to GeoChip analysis, the functional composition of bacterioplankton was less affected than taxonomic composition. In addition, geographic and environmental features both followed a distance-decay relationship with community and functional composition, but the local environment condition was the dominant driver in the Lancang River. Therefore, the impoundments of cascade dams had significant impacts on bacterioplankton communities and more attention should be paid to the potential ecological consequences of river regulation.

The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation

Benthic microeukaryotes are key ecosystem drivers in marine sandy beaches, an important and dynamic environment; however, little is known about their diversity and biogeography on a large spatial scale. Here, we investigated the community composition and geographical distributions of benthic microeukaryotes using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors and spatial separation on the distribution patterns of both rare and abundant taxa. We collected 36 intertidal samples at 12 sandy beaches from four regions that spanned distances from 0.001 to 12,000 km. We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) including members of all eukaryotic super-groups and several phyla of uncertain position. Arthropoda and Diatomeae dominated the sequence reads in abundance, but Ciliophora and Discoba were the most diverse groups across all samples. About one-third of the OTUs could not be definitively classified at a similarity level of 80%, supporting the view that a large number of rare and minute marine species may have escaped previous characterization. We found generally similar geographical patterns for abundant and rare microeukaryotic sub-communities, and both showed a significant distance-decay similarity trend. Variation partitioning showed that both rare and abundant sub-communities exhibited a slightly stronger response to environmental factors than spatial (distance) factors. However, the abundant sub-community was strongly correlated with variations in spatial, environmental and sediment grain size factors (66% of variance explained), but the rare assemblage was not (16%). This suggests that different or more complex mechanisms generate and maintain diversity in the rare biosphere in this habitat.

Patterns and Processes in Marine Microeukaryotic Community Biogeography from Xiamen Coastal Waters and Intertidal Sediments, Southeast China

Microeukaryotes play key roles in the structure and functioning of marine ecosystems. Little is known about the relative importance of the processes that drive planktonic and benthic microeukaryotic biogeography in subtropical offshore areas. This study compares the microeukaryotic community compositions (MCCs) from offshore waters (n = 12) and intertidal sediments (n = 12) around Xiamen Island, southern China, using high-throughput sequencing of 18S rDNA. This work further quantifies the relative contributions of spatial and environmental variables on the distribution of marine MCCs (including total, dominant, rare and conditionally rare taxa). Our results showed that planktonic and benthic MCCs were significantly different, and the benthic richness (6627 OTUs) was much higher than that for plankton (4044 OTUs) with the same sequencing effort. Further, we found that benthic MCCs exhibited a significant distance-decay relationship, whereas the planktonic communities did not. After removing two unique sites (N2 and N3), however, 72% variation in planktonic community was explained well by stochastic processes. More importantly, both the environmental and spatial factors played significant roles in influencing the biogeography of total and dominant planktonic and benthic microeukaryotic communities, although their relative effects on these community variations were different. However, a high proportion of unexplained variation in the rare taxa (78.1–97.4%) and conditionally rare taxa (49.0–81.0%) indicated that more complex mechanisms may influence the assembly of the rare subcommunity. These results demonstrate that patterns and processes in marine microeukaryotic community assembly differ among the different habitats (coastal water vs. intertidal sediment) and different communities (total, dominant, rare and conditionally rare microeukaryotes), and provide novel insight on the microeukaryotic biogeography and ecological mechanisms in coastal waters and intertidal sediments at local scale.

Shift in bacterioplankton diversity and structure: Influence of anthropogenic disturbances along the Yarlung Tsangpo River on the Tibetan Plateau, China

River systems have critical roles in the natural water environment and the transportation of nutrients. Anthropogenic activities, including wastewater discharge and river damming, raise adverse impacts on ecosystem and continuum of rivers. An increasing amount of attention has been paid to riverine bacterioplankton as they make vital contributions to biogeochemical nutrient cycle. A comprehensive study was conducted on the bacterioplankton community along the Yarlung Tsangpo River, which is the longest plateau river in China and is suffering from various anthropogenic impacts. The results indicated that nutrient variations corresponded to anthropogenic activities, and silica, nitrogen and phosphorus were retained by the dam. River damming influenced the biomass and diversity of the bacterioplankton, but significant alterations in the community structure were not observed between upstream and downstream of the dam. Moreover, the spatial distribution of the bacterioplankton community changed gradually along the river, and the dominant bacterioplankton in the upstream, midstream and downstream portions of the river were Firmicutes, Bacteroidetes and Proteobacteria, respectively. Soluble reactive phosphorus, elevation, ammonium nitrogen, velocity and turbidity were the main environmental factors that shape the bacterioplankton community. Our study offers the first insights into the variation of a bacterioplankton community of a large river in plateau region.

Bacterial community composition and structure in an Urban River impacted by different pollutant sources

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment.

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality

Select bacteria, such as Escherichia coli or coliforms, have been widely used as sentinels of low water quality; however, there are concerns regarding their predictive accuracy for the protection of human and environmental health. To develop improved monitoring systems, a greater understanding of bacterial community structure, function, and variability across time is required in the context of different pollution types, such as agricultural and urban contamination. Here, we present a year-long survey of free-living bacterial DNA collected from seven sites along rivers in three watersheds with varying land use in Southwestern Canada. This is the first study to examine the bacterial metagenome in flowing freshwater (lotic) environments over such a time span, providing an opportunity to describe bacterial community variability as a function of land use and environmental conditions. Characteristics of the metagenomic data, such as sequence composition and average genome size (AGS), vary with sampling site, environmental conditions, and water chemistry. For example, AGS was correlated with hours of daylight in the agricultural watershed and, across the agriculturally and urban-affected sites, k-mer composition clustering corresponded to nutrient concentrations. In addition to indicating a community shift, this change in AGS has implications in terms of the normalization strategies required, and considerations surrounding such strategies in general are discussed. When comparing abundances of gene functional groups between high- and low-quality water samples collected from an agricultural area, the latter had a higher abundance of nutrient metabolism and bacteriophage groups, possibly reflecting an increase in agricultural runoff. This work presents a valuable dataset representing a year of monthly sampling across watersheds and an analysis targeted at establishing a foundational understanding of how bacterial lotic communities vary across time and land use. The results provide important context for future studies, including further analyses of watershed ecosystem health, and the identification and development of biomarkers for improved water quality monitoring systems.

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river

The spatiotemporal distribution of microbial diversity, community composition, and their major drivers are fundamental issues in microbial ecology. In this study, the planktonic bacterial and microeukaryotic communities of the Jiulong River were investigated across both wet and dry seasons by using denaturing gradient gel electrophoresis (DGGE). We found evidence of temporal change between wet and dry seasons and distinct spatial patterns of bacterial and microeukaryotic communities. Both bacterial and microeukaryotic communities were strongly correlated with temperature, NH4-N, PO4-P, and chlorophyll a, and these environmental factors were significant but incomplete predictors of microbial community composition. Local environmental factors combined with spatial and temporal factors strongly controlled both bacterial and microeukaryotic communities in complex ways, whereas the direct influence of spatial and temporal factors appeared to be relatively small. Path analysis revealed that the microeukaryotic community played key roles in shaping bacterial community composition, perhaps through grazing effects and multiple interactions. Both Betaproteobacteria and Actinobacteria were the most dominant and diverse taxa in bacterial communities, while the microeukaryotic communities were dominated by Ciliophora (zooplankton) and Chlorophyta (phytoplankton). Our results demonstrated that both bacterial and microeukaryotic communities along the Jiulong River displayed a distinct spatiotemporal pattern; however, microeukaryotic communities exhibited a stronger distance-decay relationship than bacterial communities and their spatial patterns were mostly driven by local environmental variables rather than season or spatial processes of the river. Therefore, we have provided baseline data to support further research on river microbial food webs and integrating different microbial groups into river models.