Key roles for freshwater A ctinobacteria revealed by deep metagenomic sequencing

Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes

In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.

A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.

From small water bodies to lakes: Exploring the diversity of freshwater bacteria in an Alpine Biosphere Reserve

Small water bodies, although supporting high biodiversity, are often understudied in the Alpine region. In this work, we characterized the planktic and benthic bacterial communities, as well as the water chemistry, of a wide physiographic range of 19 freshwater bodies within an Alpine Biosphere Reserve, including ponds, pasture ponds, peat bogs, shallow lakes, and lakes. We collected both water and surface sediment samples, followed by metabarcoding analysis based on the V3-V4 regions of the 16S rRNA gene. We investigated the changes in biodiversity and the distribution of unique and shared amplicon sequence variants (ASVs) between water (11,829 ASVs) and surface sediment (19,145 ASVs) habitats, as well as across different freshwater typologies. The majority of ASVs (78 %) were unique to a single sample, highlighting the variability and uniqueness of bacterial communities in such freshwater bodies. Most freshwater environments showed higher α-diversity in sediment samples (median, 1469 ASVs) compared to water (468 ASVs). We found that water and sediment habitats harboured unique bacterial communities with significant differences in their taxonomic compositions. Benthic bacteria were associated with several biogeochemical and degradative processes occurring in the sediments, with no notable differences among freshwater typologies and with phylogenetically and ecologically similar species. Conversely, planktic communities showed greater heterogeneity: small water bodies and peat bogs were characterized by higher relative abundances of Patescibacteria (up to 33 %), while lakes and shallow lakes were dominated by Actinobacteriota (up to 36 %). Cyanobacteria (426 ASVs) were generally distributed at low abundances in both water and sediment habitats. Overall, our results provided essential insights into the bacterial ecology of understudied environments such as ponds and pasture ponds and highlighted the importance of further exploring their rich pelagic and benthic bacterial biodiversity.

Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment-Water Interface in a Subalpine Lake

The sediment-water interface is the most active region for biogeochemical processes and biological communities in aquatic ecosystems. As the main drivers of biogeochemical cycles, the assembly mechanisms and the distribution characteristics of microbial communities at this boundary remain unclear. This study investigated the microbial communities across the sediment-water interface in a natural subalpine lake in China. The results indicated that the diversity of bacterial communities in middle sediment was significantly higher than that in overlying water and other sediments (p < 0.001). Pearson's correlation analysis indicated that the diversity was significantly influenced by biotic factors (e.g., diversity of fungus, protozoan and alga) and physicochemical parameters (e.g., total carbon, total organic carbon, nitrate, ammonium and pH) (p < 0.01). Null model analysis revealed that the homogeneous selection dominated the assembly of the bacteria community in sediment, whereas the heterogeneous selection dominated that in overlying water. The least squares path analysis showed that interactions between protozoa and bacteria had a greater impact on bacterial community assembly (p < 0.001). Important taxa influence the assembly by regulating biotic interactions. These findings provided a basis for understanding the importance of biotic interactions in maintaining subalpine lakes' ecosystems across the sediment-water interface.

Diversity and networking of uni-cyanobacterial cultures and associated heterotrophic bacteria from the benthic microbial mat of a desert hydrothermal spring

Thermal springs harbour microorganisms, often dominated by cyanobacteria, which form biofilms and microbial mats. These phototrophic organisms release organic exudates into their immediate surroundings, attracting heterotrophic bacteria that contribute to the diversity and functioning of these ecosystems. In this study, the microbial mats from a hydrothermal pool in the Ksar Ghilane oasis in the Grand Erg Oriental of the Desert Tunisia were collected to obtain cyanobacterial cultures formed by single cyanobacterial species. High-throughput analysis showed that while the microbial mat hosted diverse cyanobacteria, laboratory cultures selectively enriched cyanobacteria from the Leptolyngbya, Nodosilinea, and Arthronema. Per each of these genera, multiple non-axenic uni-cyanobacterial cultures were established, totalling 41 cultures. Cyanobacteria taxa mediated the assembly of distinct heterotrophic bacterial communities, with members of the Proteobacteria and Actinobacteria phyla dominating. The bacterial communities of uni-cyanobacterial cultures were densely interconnected, with heterotrophic bacteria preferentially co-occurring with each other. Our study highlighted the complex structures of non-axenic uni-cyanobacterial cultures, where taxonomically distinct cyanobacteria consistently associate with specific groups of heterotrophic bacteria. The observed associations were likely driven by common selection pressures in the laboratory, such as cultivation conditions and specific hosts, and may not necessarily reflect the microbial dynamic occurring in the spring microbial mats.

Genome editing in ubiquitous freshwater Actinobacteria

Development of genome-editing tools in diverse microbial species is an important step both in understanding the roles of those microbes in different environments, and in engineering microbes for a variety of applications. Freshwater-specific clades of Actinobacteria are ubiquitous and abundant in surface freshwaters worldwide. Here, we show that Rhodoluna lacicola and Aurantimicrobium photophilum, which represent widespread clades of freshwater Actinobacteria, are naturally transformable. We also show that gene inactivation via double homologous recombination and replacement of the target gene with antibiotic selection markers can be used in both strains, making them convenient and broadly accessible model organisms for freshwater systems. We further show that in both strains, the predicted phytoene synthase is the only phytoene synthase, and its inactivation prevents the synthesis of all pigments. The tools developed here enable targeted modification of the genomes of some of the most abundant microbes in freshwater communities. These genome-editing tools will enable hypothesis testing about the genetics and (eco)physiology of freshwater Actinobacteria and broaden the available model systems for engineering freshwater microbial communities.

IMPORTANCE

To advance bioproduction or bioremediation in large, unsupervised environmental systems such as ponds, wastewater lagoons, or groundwater systems, it will be necessary to develop diverse genetically amenable microbial model organisms. Although we already genetically modify a few key species, tools for engineering more microbial taxa, with different natural phenotypes, will enable us to genetically engineer multispecies consortia or even complex communities. Developing genetic tools for modifying freshwater bacteria is particularly important, as wastewater, production ponds or raceways, and contaminated surface water are all freshwater systems where microbial communities are already deployed to do work, and the outputs could potentially be enhanced by genetic modifications. Here, we demonstrate that common tools for genome editing can be used to inactivate specific genes in two representatives of a very widespread, environmentally relevant group of Actinobacteria. These Actinobacteria are found in almost all tested surface freshwater environments, where they co-occur with primary producers, and genome-editing tools in these species are thus a step on the way to engineering microbial consortia in freshwater environments.

Regional and Longitudinal Dynamics of Cyanobacterial Blooms/Cyanobiome and Cyanotoxin Production in the Great Lakes Area

Cyanobacteria (blue-green algae) are a diverse group of prokaryotic microorganisms that impact global biogeochemical cycles. Under eutrophic conditions, cyanobacterial species can produce cyanotoxins, resulting in harmful algal blooms (cHABs) that degrade water quality and result in economic and recreational losses. The Laurentian Great Lakes, a key global freshwater source, are increasingly affected by these blooms. To understand the underlying mechanisms in cHAB formation, we investigated microcystin levels, cyanotoxin genes/transcripts, and taxonomic/microcystin metabarcoding across three sampling locations in the Canadian Great Lakes region, including Hamilton Harbour, Bay of Quinte, and Three Mile Lake (Muskoka), to observe the regional and longitudinal cyanobacterial dynamics. The results revealed a positive correlation between microcystin levels, the occurrence of cyanobacterial taxonomic/cyanotoxin molecular markers, and the relative widespread abundance of specific dominant cyanobacterial taxa, including Planktothrix, Microcystis, and Dolichospermum. The Cyanobium genus was not observed in Hamilton Harbor samples during late summer (August to September), while it was consistently observed in the Three Mile Lake and Bay of Quinte samples. Notably, Dolichospermum and saxitoxin genes were predominantly higher in Three Mile Lake (an inland lake), suggesting site-specific characteristics influencing saxitoxin production. Additionally, among the potential microcystin producers, in addition to Microcystis, Hamilton Harbour and Bay of Quinte samples showed consistent presence of less dominant microcystin-producing taxa, including Phormidium and Dolichospermum. This study highlights the complexity of cHAB formation and the variability in cyanotoxin production in specific environments. The findings highlight regional and site-specific factors that can influence cyanobacterial taxonomic and molecular profiles, necessitating the integration of advanced molecular technologies for effective monitoring and targeted management strategies.

Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses

Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.

Single-/Co-Driving of Tetracycline, Triclocarban and Zinc on Microbial Community, Resistome and Function in the Cyanobacteria-Blooming Freshwater Ecosystem

Environmental concentrations of antimicrobials can inhibit Cyanobacteria, but little is known about their effects on Cyanobacteria-blooming freshwater ecosystem. Here, a 21 days' outdoor freshwater mesocosm experiment was established to study effects of single and combined tetracycline, triclocarban and zinc at environmental concentrations on microbial community, microbial function and antimicrobial resistance using amplicon- and metagenomic-based methods. Results showed that three chemicals reshaped the microbial community with magnified effects by chemical combinations. Relative abundance of Cyanobacteria was decreased in all chemical groups, especially from 74.5 to 0.9% in combination of three chemicals. Microbial community networks were more simplified after exposure. Proteobacteria and Bacteroidetes predominated in Cyanobacteria-degraded ecosystems, and their relative abundances were significantly correlated with antibiotic resistome, suggesting that they might host antibiotic resistance genes. Notably, relative abundance (copy per 16 S rRNA gene) of total antibiotic resistome reached five to nine folds higher than the initial abundance in chemical-combined groups. The affected antibiotic resistance genes referred to a wide range of antibiotic classes. However, weak effects were detected on biocide/metal resistance and microbial virulence. Three chemicals posed complicated effects on microbial function, some of which had consistent variations across the groups, while some varied greatly in chemical groups. The findings highlight sensitivity of Cyanobacteria-blooming ecosystem to antimicrobials.

AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides

BACKGROUND

Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.

RESULTS

In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.

CONCLUSION

The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.

AVAILABILITY

A python package is available at: https://github.com/SayehSobhani/AFITBin .

Life in the PFAS lane: The impact of perfluoroalkyl substances on photosynthesis, cellular exudates, nutrient cycling, and composition of a marine microbial community

Perfluoroalkyl substances (PFAS) are of great ecological concern, however, exploration of their impact on bacteria-phytoplankton consortia is limited. This study employed a bioassay approach to investigate the effect of unary exposures of increasing concentrations of PFAS (perfluorooctane sulfonate (PFOS) and 6:2 fluorotelomer sulfonate (6:2 FTS)) on microbial communities from the northwestern Gulf of Mexico. Each community was examined for changes in growth and photophysiology, exudate production and shifts in community structure (16S and 18S rRNA genes). 6:2 FTS did not alter the growth or health of phytoplankton communities, as there were no changes relative to the controls (no PFOS added). On the other hand, PFOS elicited significant phototoxicity (p < 0.05), altering PSII antennae size, lowering PSII connectivity, and decreasing photosynthetic efficiency over the incubation (four days). PFOS induced a cellular protective response, indicated by significant increases (p < 0.001) in the release of transparent exopolymer particles (TEP) compared to the control. Eukaryotic communities (18S rRNA gene) changed substantially (p < 0.05) and to a greater extent than prokaryotic communities (16S rRNA gene) in PFOS treatments. Community shifts were concentration-dependent for eukaryotes, with the low treatment (5 mg/L PFOS) dominated by Coscinodiscophyceae (40 %), and the high treatment (30 mg/L PFOS) marked by a Trebouxiophyceae (50 %) dominance. Prokaryotic community shifts were not concentration dependent, as both treatment levels became depleted in Cyanobacteriia and were dominated by members of the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. Further, PFOS significantly decreased (p < 0.05) the Shannon diversity and Pielou's evenness across treatments for eukaryotes, and in the low treatment (5 mg/L PFOS) for prokaryotes. These findings show that photophysiology was not impacted by 6:2 FTS but PFOS elicited toxicity that impacted photosynthesis, exudate release, and community composition. This research is crucial in understanding how PFOS impacts microbial communities.

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China

It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Deterioration of single-use biodegradable plastics in high-humidity air and freshwaters over one year: Significant disparities in surface physicochemical characteristics and degradation rates

More single-use plastics are accumulating in the environment, and likewise biodegradable plastics (BPs), which are being vigorously promoted, cannot escape the fate. Currently, studies on the actual degradation of BPs in open-air and freshwaters are underrepresented despite they are potentially headmost leakage and contamination sites for disposable BPs. Herein, we compared the degradation behavior of six BP materials and non-degradable polypropylene (PP) plastics over a 1-year in situ suspension in the high-humidity air, a eutrophic river, and an oligotrophic lake. Moreover, a 3-months laboratory incubation was performed to detect the release of dissolved organic carbon (DOC) from BPs. In both air and freshwaters, poly(p-dioxanone) (PPDO) degraded significantly while PP and polylactic acid (PLA) showed no signs of degradation. The average degradation rates of three poly(butylene adipate-co-terephthalate) (PBAT)-based films varied: 100% in river, 55% in lake, and 10% in air. In addition to PLA, surface chemical groups, hydrophilicity, and thermal stability of BPs changed, and microplastics were found on their surfaces. Correspondingly, BPs with faster degradation rates released relatively higher amounts of DOC. Environmental microbial and chemical characteristics may contribute to differences in BP degradation besides polymer specificity. Altogether, our results indicate the need for appropriate monitoring of BPs.

Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System

Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.

Pollutants reduction via artificial mixing in a drinking water reservoir: Insights into bacterial metabolic activity, biodiversity, interactions and co-existence of core genera

Endogenous pollution due to long periods of hypolimnetic anoxia in stratified reservoirs has become a worldwide concern, which can threaten metabolic activity, biodiversity, water quality security, and ultimately human health. In the present study, an artificial mixing system applied in a drinking water reservoir was developed to reduce pollutants, and the biological mechanism involved was explored. After approximately 44 days of system operation, the reservoir content was completely mixed resulting in the disappearance of anoxic layers. Furthermore, the metabolic activity estimated by the Biolog-ECO microplate technique and biodiversity was enhanced. 16S rRNA gene sequencing indicated a great variability on the composition of bacterial communities. Co-occurrence network analysis showed that interactions among bacteria were significantly affected by the proposed mixing system. Bacteria exhibited a more mutualistic state and >10 keystone genera were identified. Pollutants, including nitrogen, phosphorus, organic matter, iron, and manganese decreased by 30.63-80.15 %. Redundancy discriminant analysis revealed that environmental factors, especially the temperature and dissolved oxygen, were crucial drivers of the bacterial community structure. Furthermore, Spearman's correlation analysis between predominant genera and pollutants suggested that core genus played a vital role in pollutant reduction. Overall, our findings highlight the importance and provide insights on the artificial mixing systems' microbial mechanisms of reducing pollutants in drinking water reservoirs.

Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming

Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 ℃). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.

Diversity characterization of bacteria and fungi in water, sediments and biofilms from Songhua River in Northeast China

Water, sediments, and biofilms are the typical microbial carriers in natural water environments. However, comparative analysis of the distribution of bacterial and fungal communities in different carriers within the same habitat is relatively lacking. Therefore, this study employed 16 S and ITS rRNA gene sequencing to identify bacterial and fungal community structures in water, sediments, and biofilm. The results show that (1) the OTUs numbers revealed that the bacterial abundance, at the levels of species, genus, and family, followed the order of sediments > water > biofilms, while the fungal abundance order was water > sediments > biofilms. In addition, bacteria were mainly present in sediments, while fungi were mainly present in water. (2) The α diversity index (Shannon, ACE, Simpson, and Chao1) order, for bacteria was: sediments > water > biofilms, indicating that the diversity and homogeneity of bacteria in sediments were relatively higher; for fungi was: water > sediments > biofilms, indicating that the diversity and abundance of fungi in water were high. (3) The core phylum of bacterial in the water, sediments, and biofilms was Cyanobacteria (31.3-46.1%) and Actinobacteria (27.6-36.1%); Proteobacteria (35.0-41.8%), Cyanobacteria (14.7-36.6%); and Proteobacteria (63.3-69.2%), respectively. (4) The mainly colonized fungal phyla in biofilms in the water, sediments, and biofilms were Basidiomycota (29.3-38.7%) and Ascomycota (16.2-27.7%); Zygomycota (13.1-17.5%), Basidiomycota (5.6-17.6%); and Zygomycota (23.8-44.2%). (5) There were significant species differences in bacterial and fungal communities in water, sediments, and biofilm by NMDS analysis. Findings are useful for guiding significance for the Biogeochemical cycle of elements, the environmental fate of pollutants, and the study of water ecosystems.

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.

Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota

The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.

Adaptive genetic traits in pelagic freshwater microbes

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.

Diversity, distribution, and expression of opsin genes in freshwater lakes

Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have nontypical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.

Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons

The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.

Soil organic matter molecular composition with long-term detrital alterations is controlled by site-specific forest properties

Forest ecosystems are important global soil carbon (C) reservoirs, but their capacity to sequester C is susceptible to climate change factors that alter the quantity and quality of C inputs. To better understand forest soil C responses to altered C inputs, we integrated three molecular composition published data sets of soil organic matter (SOM) and soil microbial communities for mineral soils after 20 years of detrital input and removal treatments in two deciduous forests: Bousson Forest (BF), Harvard Forest (HF), and a coniferous forest: H.J. Andrews Forest (HJA). Soil C turnover times were estimated from radiocarbon measurements and compared with the molecular-level data (based on nuclear magnetic resonance and specific analysis of plant- and microbial-derived compounds) to better understand how ecosystem properties control soil C biogeochemistry and dynamics. Doubled aboveground litter additions did not increase soil C for any of the forests studied likely due to long-term soil priming. The degree of SOM decomposition was higher for bacteria-dominated sites with higher nitrogen (N) availability while lower for the N-poor coniferous forest. Litter exclusions significantly decreased soil C, increased SOM decomposition state, and led to the adaptation of the microbial communities to changes in available substrates. Finally, although aboveground litter determined soil C dynamics and its molecular composition in the coniferous forest (HJA), belowground litter appeared to be more influential in broadleaf deciduous forests (BH and HF). This synthesis demonstrates that inherent ecosystem properties regulate how soil C dynamics change with litter manipulations at the molecular-level. Across the forests studied, 20 years of litter additions did not enhance soil C content, whereas litter reductions negatively impacted soil C concentrations. These results indicate that soil C biogeochemistry at these temperate forests is highly sensitive to changes in litter deposition, which are a product of environmental change drivers.

Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient

Continental freshwater systems are particularly vulnerable to environmental variation. Climate change-induced desertification and the anthropogenic exploitation of hydric resources result in the progressive evaporation and salinization of inland water bodies in many areas of the globe. However, how this process impacts microbial communities and their activities in biogeochemical cycles is poorly known. Here, we take a space-for-time substitution approach and characterize the prokaryotic and eukaryotic microbial communities of two planktonic cell-size fractions (0.2-5 μm and 5-30 μm) from lakes of diverse trophic levels sampled along a salinity-alkalinity gradient located in the Trans-Mexican Volcanic Belt (TMVB). We applied a 16S/18S rRNA gene metabarcoding strategy to determine the microbial community composition of 54 samples from 12 different lakes, from the low-salinity lake Zirahuén to the hypersaline residual ponds of Rincón de Parangueo. Except for systems at both extremes of the salinity gradient, most lakes along the evaporation trend bear actively forming microbialites, which harbor microbial communities clearly distinct from those of plankton. Several lakes were sampled in winter and late spring and the crater lakes Alchichica and Atexcac were sampled across the water column. Physicochemical parameters related to salinity-alkalinity were the most influential drivers of microbial community structure whereas trophic status, depth, or season were less important. Our results suggest that climate change and anthropogenic-induced hydric deficit could significantly affect microbial communities, potentially altering ecosystem functioning.

Plastic microbiome development in a freshwater ecosystem

To understand biological interactions of plastic litter in freshwater ecosystems, as well the potential effects of plastics on ecosystem processes, studies of the activity and composition of plastic-associated microbial communities are needed. The physical properties and chemical composition of plastic polymers are key components of plastic product design, and may also select for distinct microbial biofilms colonizing plastic litter. We monitored growth and succession of biofilm communities on plastic substrates of common morphotypes (i.e., hard, soft, foam, and film) and a natural surface (i.e., an unglazed ceramic tile) incubated in an urban stream. We measured biofilm biomass, metabolism, extracellular enzyme activity, and bacterial, fungal and algal community composition over four weeks during primary succession. Results demonstrated a general increase in biofilm biomass and enzymatic activity corresponding to carbon, nitrogen and phosphorus metabolism during biofilm development for all substrate types. We observed higher respiration rates and negative net ecosystem productivity on foam and tile surfaces in comparison to hard, soft and film plastic surfaces. Biofilm bacterial, fungal and algal assemblages showed few significant differences in composition among substrates. However, all microbial communities changed significantly in composition over time. While substrate type was not the major factor driving biofilm composition and activity, these data show plastic litter in streams is well colonized by an active and dynamic biofilm community. As plastic litter is increasing across all types of aquatic ecosystems, it should be considered a medium for biologically active organisms that contribute to key ecosystem processes.

Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes

Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.

The Evolutionary Kaleidoscope of Rhodopsins

Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.

α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats

RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.

Bacterial community composition and indicators of water quality in Caizi lake, a typical Yangtze-connected freshwater lake

Caizi Lake is an important lake connected to the Yangtze River in Anhui Province and a crucial connection for the Yangtze-to-Huaihe Water Diversion Project (YHWD). There were marked differences in trophic status of the six sampling sites based on the physicochemical characterization. The Bacterial Eutrophic Index (BEI), used to quantify water quality, was well related to Carlson's trophic state index (TSI) (Spearman's ρ = 0.829, P < 0.05). Mean TSI and BEI were 54 and 0.58, respectively, indicating that Caizi Lake was slightly eutrophic. Actinobacteriota were the predominant bacterial phylum in the water and Acidobacteriota in sediments. The diversity and composition of the bacterial community was markedly different between sites for water but not sediment samples. Unlike other Yangtze-connected freshwater lakes, the distance-based redundancy analysis (db-RDA) revealed that dissolved oxygen (DO) affected the composition of the planktonic bacterial community (P < 0.001) while total phosphorus (TP) was the major factor in the sediments (P < 0.05). Water quality of Caizi Lake significantly improved since a few years ago. These results contribute to the long-term monitoring of the ecological quality of the water environment along the Yangtze River to the Huaihe River.

Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir

Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.

Microbiome analysis reveals microecological advantages of emerging ditchless rice-crayfish co-culture mode

Ditchless rice-crayfish co-culture is an emerging model of rice-crayfish farming that circumvents the potential hazards of digging ditches in traditional rice-crayfish farming. However, due to the complex interactions among crayfish, ambient microbiota, and environmental variables, it is necessary to assess the differences in bacterial structure between ditchless and traditional rice-crayfish culture. In this study, the crayfish culture area in the Sichuan basin was selected as the study area, and the bacterial communities of two rice-crayfish culture systems were compared by high-throughput sequencing of 16S rDNA. The results showed that the ditchless system had lower water depth, higher dissolved oxygen, lower total ammonia nitrogen and lower morbidity. There are intuitive differences in the composition of environmental bacterial communities due to environmental changes, even if they are similar in composition at the phylum level. Microbiota in sediments from ditchless systems appear to produce less ammonia nitrogen. The abundance of the pathogens colonizing the intestine of ditchless crayfish was lower than ditched one, and the composition was similar to water. Ditch-farmed crayfish appear to be more susceptible to environmental microbes and have a more fragile intestinal structure. Water depth and dissolved oxygen are the main environmental factors that determine the distribution of microbiota. This study is the first to investigate the bacterial ecology of a ditchless rice- crayfish farming system. The results show that the ditchless rice-crayfish culture model has a more superior bacterial system than the traditional rice-crayfish culture.

Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China

We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH₃-N as well as NO₃^--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

Photodegradation, bacterial metabolism, and photosynthesis drive the dissolved organic matter cycle in the Heilongjiang River

Dissolved organic matter (DOM) plays a vital role in the biogeochemistry of aquatic ecosystems. However, the mechanisms of DOM cycling in the water column during different seasons have not been fully elucidated to date. The differences in DOM degradation in summer, autumn, and winter water columns were evaluated in this study. The results showed that bacteria played an essential role in the degradation of DOM in the summer water column. Photochemical degradation was the primary degradation pathway of DOM in the autumn and winter water columns. Notably, while DOM is degraded, photosynthetic bacteria produce organic matter through photosynthesis to replenish the water column. EEM-PARAFAC analysis indicated more tryptophan component C1 in summer, but the contents of humic substance component C2 and terrestrial substance C3 were higher in autumn and winter. In summer, more tryptophan-like components were consumed by bacteria, and Cyanobacteria produced more organic matter through photosynthesis to replenish the water column. Moreover, a similar bacterial community structure and a more active tryptophan biosynthesis pathway were found in autumn and winter. Random forest models identified representative bacteria involved in the DOM transformation process in different seasons. The above findings may be helpful to explore the degradation characteristics of DOM in different seasons and predict the fate of DOM in the water column in the future.

Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese

Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.

The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes

Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.

Anthropogenic activities and seasonal properties jointly drive the assemblage of bacterial communities in subtropical river basins

Anthropogenic activities have inevitably impacted riverine ecosystems, yet their overall contribution to the assemblage of bacterial communities at a large river basin scale remains unclear. In this study, 16S amplicon sequencing was implemented to investigate the bacterial ecosystems in paired water and sediment of North River and West River basins in South China., which contains various anthropogenic environments (e.g., rural/urban area, mining area and livestock area). Subsequently, the links between bacterial community and various types of emerging pollutants in river water were analyzed. The results show that the bacterial assemblage of water and sediment had their own properties that the bacterial community of sediment were mainly affected by seasonal properties, while the bacterial community of water were affected by both seasons and anthropogenic activities. Therein, the aquatic bacterial compositions and abundances were driven by changes in temperature, dissolved oxygen and the emerging pollutants. The dominant phyla Proteobacteria and Firmicutes exhibited adaptability to the mining-affected regions, therein many clades (e.g., Beijerinckiaceae, Acetobacteraceae and Mycobacteriaceae) were also prevalent in the livestock-affected and densely-populated regions. In addition, these two phyla presented associations to the antibiotic resistance in water. The levels of antibiotics, relative antibiotic resistance gens (ARGs) and non-antibiotic pharmaceuticals (NAPs) were closely related to bacterial community composition, diversity and functional diversity, indicating their drive in shifting bacterial communities. Collectively, this work provides a basis for understanding the contribution of anthropogenic activities in shifting bacterial community at a large river basin scale. Further, the results provide new insights for expansion of ecological assessment.

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.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria

Light is a ubiquitous source of both energy and information in surface environments, and regulates gene expression not only in photosynthetic microorganisms, but in a broad range of photoheterotrophic and heterotrophic microbes as well. Actinobacteria are keystone species in surface freshwater environments, where the ability to sense light could allow them to coordinate periods of nutrient uptake and metabolic activity with primary production. The model freshwater Actinobacteria Rhodoluna (R.) lacicola strain MWH-Ta8 and Aurantimicrobium (A.) photophilum strain MWH-Mo1 grow faster in the light than in the dark, but do not use light energy to support growth. Here, we characterize transcription throughout a light-dark cycle in R. lacicola and A. photophilum. In both species, some genes encoding carbohydrate metabolism and storage are upregulated in the light. However, expression of genes of the TCA cycle is only coordinated with light availability in R. lacicola. In fact, the majority of genes that respond to light and darkness in these two species are different, even though their light-responsive phenotypes are similar. The ability to respond to light and darkness may be widespread in freshwater Actinobacteria, but the genetic networks controlled by these two stimuli may vary significantly.

Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure

Bacteria, an integral part of aquatic ecosystems, are responsible for the circulation of matter and flow of energy. Since bacterioplankton rapidly responds to any natural and human-induced disturbances in the environment, it can serve as a bioindicator of these changes. Knowing factors that shape the microbial community structure may help the sustainable management of the water environment. However, the identification of environmental signals affecting the structure and function of bacterioplankton is still a challenge. The study analyses the impact of environmental variables on basic microbial parameters, which determines the effectiveness of ecological processes in rivers. Measurements of bacterioplankton abundance (BA) and extracellular enzyme activity (EEA) were based on fluorescent markers. The bacterial community structure was determined by 16S rRNA gene amplicon sequencing (Illumina). The results indicate spatial variation in bacterioplankton abundance. Temporal variation was not significant. Lipase and aminopeptidase had the highest level of activity. EEA was not correlated with bacterial abundance but was significantly correlated with temperature. Moreover, differences in lipase, α-glucosidase and β-glucosidase activity levels between spring and summer were noted. At the same time, the location of sampling site had a significant influence on aminopeptidase activity. The taxonomic analysis of bacterioplankton communities in the Brda River indicated that, although different numbers of OTUs were recorded in the studied river sections, bacterioplankton biodiversity did not change significantly along the river with distance downstream. Anthropogenically modified river sections were characterized by the dominance of Flavobacterium (Bacterioidetes) and hgcl clade (Actinobacteria) taxa, known for their ability to produce extracellular enzymes. PCoA analysis revealed that the sites located in the lower river course (urban area) had the most similar bacterial community structure (β-diversity). The study provides new insight into the changes in microbial communities along the river and emphasizes the potential impact of anthropogenization on these processes.

Bioavailable Nutrients (N and P) and Precipitation Patterns Drive Cyanobacterial Blooms in Missisquoi Bay, Lake Champlain

Anthropogenic activities release large amounts of nitrogen (N) and phosphorus (P) nutrients into the environment. Sources of nutrients include surface and sub-surface runoffs from agricultural practices with the application of chemical fertilizers and manure as well as combined sewer overflows (CSOs). Nutrient runoffs contribute to the eutrophication of aquatic ecosystems and enhance the growth of cyanobacteria. Precipitation is an important driving force behind the runoff of nutrients from agricultural fields into surrounding water bodies. To understand the dynamics between nutrient input, precipitation and cyanobacterial growth in Missisquoi Bay, Lake Champlain (Quebec), one location in Pike River (a major tributary into the bay) and four locations in Missisquoi Bay were monitored from April to November in 2017 and 2018. Biweekly water samples were analyzed using chemical methods and high-throughput sequencing of 16S rRNA gene amplicons. High concentrations of N and P were typically measured in April and May. Three major spikes in nutrient concentrations were observed in early and mid-summer as well as early fall, all of which were associated with intense cumulative precipitation events of 40 to 100 mm within 7 days prior to sampling. Despite the high concentrations of nutrients in the spring and early summer, the cyanobacterial blooms appeared in mid to late summer as the water temperature increased. Dolichospermum sp. was the major bloom-forming cyanobacterium during both summers. A second intense bloom event of Microcystis was also observed in the fall (October and November) for both years. Variation in the cyanobacteria population was strongly associated with inorganic and readily available fractions of N and P such as nitrites and nitrates (NOx), ammonia (NH₃) and dissolved organic phosphorus (DOP). During blooms, total Kjeldahl nitrogen (TKN) and total particulate phosphorus (TPP) fractions had a substantial influence on total nitrogen (TN) and total phosphorus (TP) concentrations, respectively. The abundance of bacteria involved in the metabolism of nitrogen compared to that of phosphorus revealed the importance of nitrogen on overall microbial dynamics as well as CB formation in the bay. Our findings emphasize the combined influence of precipitation events, temperature and several bioavailable fractions of nitrogen and phosphorus on cyanobacterial bloom episodes.

Insight into the hidden bacterial diversity of Lake Balaton, Hungary

In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.

Genome-resolved metagenomics using environmental and clinical samples

Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome

River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.