Bacterioplankton communities in a high-altitude freshwater wetland

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

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

Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China

Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.

A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors

The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland.

Pollutant removal from municipal sewage by a microaerobic up-flow oxidation ditch coupled with micro-electrolysis

The development of efficient and low-cost wastewater treatment processes remains an important challenge. A microaerobic up-flow oxidation ditch (UOD) with micro-electrolysis by waterfall aeration was designed for treating real municipal wastewater. The effects of influential factors such as up-flow rate, waterfall height, reflux ratio, number of stages and iron dosing on pollutant removal were fully investigated, and the optimum conditions were obtained. The elimination efficiencies of chemical oxygen demand (COD), ammonia nitrogen (NH₄ ⁺-N), total nitrogen (TN) and total phosphorus (TP) reached up to 84.33 ± 2.48%, 99.91 ± 0.09%, 93.63 ± 0.60% and 89.27 ± 1.40%, respectively, while the effluent concentrations of COD, NH₄ ⁺-N, TN and TP were 20.67 ± 2.85, 0.02 ± 0.02, 1.39 ± 0.09 and 0.27 ± 0.02 mg l^-1, respectively. Phosphorous removal was achieved by iron-carbon micro-electrolysis to form an insoluble ferric phosphate precipitate. The microbial community structure indicated that carbon and nitrogen were removed via multiple mechanisms, possibly including nitrification, partial nitrification, denitrification and anammox in the UOD.

Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

Responses of submerged macrophytes Vallisneria natans and epiphytic biofilm to floating plants Eichhornia crassipes in eutrophic water

The degeneration of submerged macrophytes and the invasion of Eichhornia crassipes (E. crassipes) destroyed the balance of aquatic ecosystems environments. In this study, responses of Vallisneria natans (V. natans) and the leaf-epiphytic biofilms to E. crassipes were analyzed to provide a technical scheme for V. natans restoration and E. crassipes control in eutrophic water. The results showed that a significant improvement of water quality achieved in 1100 ind·m^-2 E. crassipes density group and TN removal rate reached 63.53%. The presence of E. crassipes changed the morphological characteristics of V. natans, which stimulated the adaptive mechanisms via promotion of shoot height and root length. Concentrations of the antioxidant enzymes, peroxidase, superoxide dismutase, and catalase in the V. natans leaves remained stable. But E. crassipes greatly increased the microbial diversity on V. natans leave biofilms. Furthermore, the greatest richness in bacterial community diversity was observed at 700, 1100, and 1200 ind·m^-2 E. crassipes densities in heatmap, which was beneficial to the stability of the water ecological environment. These results showed that the combination of V. natans with E. crassipes of 1100 ind m^-2 providing more favorable conditions for the growth and restoration of submerged macrophytes and improve the water quality. PRACTITIONER POINTS: The responses of submerged macrophytes to floating plants were studied. The optimal density of Eichhornia crassipes was 1100 ind m^-2 . The biofilm microbial community changed in response to Eichhornia crassipes.

Effect of different types of anthropogenic pollution on the bacterial community of urban rivers

The health of urban rivers is threatened by multiple anthropogenic stressors. Bacterial communities in rivers can quickly respond to different types of polluted environments, making them useful for water quality assessments and predictive insights. However, research on river bacterial communities has largely ignored interactions between these communities. Here, 16S rRNA amplicon sequencing analysis is used to comprehensively analyze the bacterial communities in the water and sediments in different types of anthropogenically impacted urban river. The results show that distinct differences occur in the bacterial communities in the river sediment and water with different pollution types. The changes in the bacterial communities in sediments were more pronounced than those in the water. A modular analysis further showed that the microbial co-occurrence network under different types of pollution had a nonrandom modular structure, and this structure was mainly driven by classification correlation and bacterial function. Genes identified for nitrogen cycling in all the river water and sediment samples included major functional genes for nitrogen fixation, assimilatory nitrogen reduction, nitrification, denitrification, and ammonification. Carbon degradation genes were mainly observed in the carbon cycle. Taken together, the above findings provide further insights into microbial communities in urban river ecosystems under anthropogenic contamination. PRACTITIONER POINTS: The physical and chemical indicators of the four types of pollution drive bacterial community structure. Bacterial community has C, N, P metabolic genes indicating its ecological effect. River bacteria were connected more frequently in the same or similar type of pollution in the co-occurrence network. Microbe-environment correlations and microbe-microbe interactions were combined to determine crucial indicators.

Salinity and nutrient modulate soil bacterial communities in the coastal wetland of the Yellow River Delta, China

The Yellow River Delta is the largest and youngest estuarine and coastal wetland in China and is experiencing the most active interactions of seawater and freshwater in the world. Bacteria played multifaceted influence on soil biogeochemical processes, and it was necessary to investigate the intermodulation between the soil factors and bacterial communities. Soil samples were collected at sites with different salinity degree, vegetations, and interference. The sequences of bacilli were tested using 16S rRNA sequencing method and operational taxonomic units were classified with 97% similarity. The soil was highly salinized and oligotrophic, and the wetland was nitrogen-restricted. Redundancy analysis suggested that factors related with seawater erosion were principal to drive the changes of soil bacterial communities and then the nutrient level and human disturbance. A broader implication was that, in the early succession stages of the coastal ecosystem, seawater erosion was the key driver of the variations of marine oligotrophic bacterial communities, while the increasing nutrient availability may enhance in the abundance of the riverine copiotrophs in the late stages. This study provided new insights on the characteristics of soil bacterial communities in estuarine and coastal wetlands.

Bacterial community in a freshwater pond responding to the presence of perfluorooctanoic acid (PFOA)

Microbial community is an essential component of freshwater, providing valuable self-purification ecosystem service. Poly-and perfluoroalkyl substances (PFAS) have attracted increasing concerns in light of their potential ecotoxicological effects and ubiquitous occurrence in the aquatic environment. Knowledge about their influences on the microbial community, however, remains largely unknown. In the present study, Illumina high-throughput sequencing of 16S ribosomal DNA was applied to explore the changes in the dynamic and composition of the bacterial community upon exposure to perfluorooctanoic acid (PFOA) at different concentrations, i.e. 0.45 µg L^-1, 130 µg L^-1 and 5.0 mg L^-1. Principal component analysis (PCA) revealed variations of 57.2% for Principal Component 1 and 16.0% for Principal Component 2 of the total community. This clearly demonstrated changes in the bacterial community structure between the controls and PFOA-amended water samples. At the phylum level, the predominant bacteria in the original pond water included Proteobacteria (64.47%), Armatimonadetes (11.87%), Actinobacteria (10.81%), Bacteroidetes (6.36%), Chloroflexi (1.44%), Verrucomicrobia (0.61%) and Firmicutes (0.14%). The relative abundance of Actinobacteria, Bacteroidetes, and Verrucomicrobia decreased 26.5-38.8%, 40.5-70.7%, and 47.4-87.5%, respectively, upon PFOA exposure. By contrast, PFOA led to an obvious increase of Proteobacteria, by 12.5-18.6% and Chloroflexi by 19.1-74.4%. Results from this study provided the needed evidence that PFAS at high concentrations could affect the microbial community in a freshwater ecosystem. Principle Component Analysis (PCA) results suggest clear distinctions of bacterial community structure between the original pond water and the water samples spiked with PFOA based on pyrosequencing of 16S rRNA gene.

Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake

As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p < 0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.

Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO₄-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China

Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake

Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.

Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau

High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (≥4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. Operational taxonomic units (OTUs) composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.

Removal of Chloroxylenol Disinfectant by an Activated Sludge Microbial Community

Chloroxylenol (CHL) is an antimicrobial ingredient that is frequently used in antiseptics/disinfectants for skin (e.g. hand soap) and non-living surfaces. CHL is an alternative to triclosan and triclocarban, the use of which has recently been banned in some countries. Accordingly, the more widespread use of CHL may significantly increase its occurrence and level in aquatic environments in the near future, eventually resulting in potential ecological risks. Wastewater treatment plants (WWTPs) may be a point source of CHL in natural environments due to extensive discharge through urban waste stream disposal. While the satisfactory removal of CHL in WWTPs is critical for maintaining healthy aquatic ecosystems, the extent of CHL removal and whether CHL causes system upset/failure in WWTPs currently remain unknown. In the present study, we conducted bioreactor operation and batch experiments to investigate the fate and effects of CHL and elucidate the mechanisms underlying degradation at various levels from environmentally relevant to high levels (0.5–5 mg L⁻¹). Bioreactors partially removed CHL (44–87%) via a largely biological route. Microbial association networks constructed using 16S rRNA gene sequencing data revealed selective enrichment and a correlation between Sphingobium and CHL, implying its involvement in the biological breakdown of CHL through dehalogenation and ring hydroxylation pathways. The present results provide insights into the behavior and effects of CHL in activated sludge communities and important information for the sustainable management of CHL that may be an emerging issue in the urban water cycle.

Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands

Coastal ecosystems experience some of the most active land–ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4^th most abundant phylum (range 1.7–41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.

Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs

Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA). Analysis of the metagenomic amplicon datasets, including quality filtering, clustering of Operational Taxonomic Units and taxonomy assignment revealed that 78.45% of the microbial communities between the two reservoirs were overlapping. The diversity (H) and Pielou's evenness (J) indices declined along the longitudinal axis of both reservoirs. The estimated values for the Shannon diversity index are typically observed in oligotrophic lakes. The microbial communities of both reservoirs were dominated by Proteobacteria, followed by Actinobacteria and Bacteroidetes all comprised over 95% of the relative abundance, regardless of the reservoir's large hydrogeological differences. The bacterioplankton was characterized by high phylogenetic heterogeneity in the taxonomic structure, being distributed among 211 genera. The genera Limnohabitans and Rhodoferax held the absolute predominance, implying their significance in the aquatic food webs. The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments.

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes

Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution. The results uncovered a 1,000-fold increase in the total amount of sequences harvested and a reverse relationship between trophic level and the bacterial diversity in most seasons of a year. A total of 65 phyla, 221 classes, 436 orders, 624 families, and 864 genera were identified in the study area. Delta-proteobacteria and gamma-proteobacteria prevailed in spring/summer and winter, respectively, regardless trophic conditions; meanwhile, the two classes dominated in the eutrophication and mesotrophication lake regions, respectively, but exclusively in the Fall. For LEfSe analysis, bacterial taxon that showed the strongest seasonal or spatial variation, majority had the highest abundance in spring/summer or medium eutrophication region, respectively. Pearson's correlation analysis indicated that 5 major phyla and 18 sub-phylogenetic groups showed significant correlation with trophic status. Canonical correspondence analysis further revealed that porewater NH₄⁺ -N as well as sediment TOM and NO_x -N are likely the dominant environmental factors affecting bacterial community compositions.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water

Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.

Influence of substrate type on microbial community structure in vertical-flow constructed wetland treating polluted river water

Microorganisms attached on the surfaces of substrate materials in constructed wetland play crucial roles in the removal of organic and inorganic pollutants. However, the impact of substrate material on wetland microbial community structure remains unclear. Moreover, little is known about microbial community in constructed wetland purifying polluted surface water. In this study, Illumina high-throughput sequencing was applied to profile the spatial variation of microbial communities in three pilot-scale surface water constructed wetlands with different substrate materials (sand, zeolite, and gravel). Bacterial community diversity and structure showed remarkable spatial variation in both sand and zeolite wetland systems, but changed slightly in gravel wetland system. Bacterial community was found to be significantly influenced by wetland substrate type. A number of bacterial groups were detected in wetland systems, including Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Cyanobacteria, Nitrospirae, Planctomycetes, Actinobacteria, Firmicutes, Chlorobi, Spirochaetae, Gemmatimonadetes, Deferribacteres, OP8, WS3, TA06, and OP3, while Proteobacteria (accounting for 29.1-62.3 %), mainly composed of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, showed the dominance and might contribute to the effective reduction of organic pollutants. In addition, Nitrospira-like microorganisms were abundant in surface water constructed wetlands.

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.