Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts

Eco-friendly reagents derived from plants represent a promising strategy to mitigate the occurrence of toxic cyanobacterial blooms. The use of an amentoflavone-containing Selaginella tamariscina extract (STE) markedly decreased the number of Microcystis aeruginosa cells, thus demonstrating significant anti-cyanobacterial activity. In particular, the Microcystis-killing fraction obtained from pulverized S. tamariscina using hot-water-based extraction at temperatures of 40 °C induced cell disruption in both axenic and xenic M. aeruginosa. Liquid chromatographic analysis was also conducted to measure the concentration of amentoflavone in the STE, thus supporting the potential M. aeruginosa-specific killing effects of STE. Bacterial community analysis revealed that STE treatment led to a reduction in the relative abundance of Microcystis species while also increasing the 16S rRNA gene copy number in both xenic M. aeruginosa NIBR18 and cyanobacterial bloom samples isolated from a freshwater environment. Subsequent testing on bacteria, cyanobacteria, and algae isolated from freshwater revealed that STE was not toxic for other taxa. Furthermore, ecotoxicology assessment involving Aliivibrio fischeri, Daphnia magna, and Danio rerio found that high STE doses immobilized D. magna but did not impact the other organisms, while there was no change in the water quality. Overall, due to its effective Microcystis-killing capability and low ecotoxicity, aqueous STE represents a promising practical alternative for the management of Microcystis blooms.

The Diversity and Composition of Soil Microbial Communities Differ in Three Land Use Types of the Sanjiang Plain, Northeastern China

In recent years, the Sanjiang Plain has experienced drastic human activities, which have dramatically changed its ecological environment. Soil microorganisms can sensitively respond to changes in soil quality as well as ecosystem function. In this study, we investigated the changes in soil microbial community diversity and composition of three typical land use types (forest, wetland and cropland) in the Sanjiang Plain using phospholipid fatty acid analysis (PLFA) technology, and 114 different PLFA compounds were identified. The results showed that the soil physicochemical properties changed significantly (p < 0.05) among the different land use types; the microbial diversity and abundance in cropland soil were lower than those of the other two land use types. Soil pH, soil water content, total organic carbon and available nitrogen were the main soil physico-chemical properties driving the composition of the soil microbial community. Our results indicate that the soil microbial community response to the three different habitats is complex, and provide ideas for the mechanism by which land use changes in the Sanjiang Plain affect the structure of soil microbial communities, as well as a theoretical basis for the future management and sustainable use of the Sanjiang plain, in the northeast of China.

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms

Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.

Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs

Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.

Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile

Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.

Specific characteristics of the microbial community in the groundwater fluctuation zone

Groundwater level fluctuation is a common natural phenomenon that causes alternate changes in oxygen, moisture, and biogeochemical processes in sediments. Microbes are sensitive to these environmental changes. Therefore, a specific microbial community is proposed to form in the groundwater fluctuation zone (GFZ). The vertical distributions of microbial abundance, diversity, and functional microbes and genes in sediment profiles were investigated, focusing on the GFZ, using high-throughput 16S rRNA gene sequencing, qPCR, and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) approach. The relationships between chemical variables and microbial community structure were investigated by redundancy analysis (RDA). Results showed that the microbial abundance and microbial community richness and diversity were higher in the sediments of the GFZ. The nitrate reducers prefer to stay just below the groundwater level in the GFZ. The predominant microbes in the GFZ functioned as nitrifiers and Fe-oxidizers. The specific community in the GFZ is mainly related to NO₃^- and Fe(III) in the sediment. Consequently, the biochemical processes nitrification and Fe- and Mn-oxidation sequentially happen above the nitrate-reduction zone near the groundwater level in the GFZ. These results provide new knowledge in the biogeochemistry cycle of the GFZ and its disturbance on the vertical distribution and transport of biogenic elements and contaminants.

Effects of Land Use Conversion on the Soil Microbial Community Composition and Functionality in the Urban Wetlands of North-Eastern China

Urban wetlands are undergoing intensive conversion from natural wetlands to farmlands, woodlands, and even alkaline land. This study aimed to determine the effects of land conversion on soil microbial communities of urban wetlands in the hinterland of Songnen Plain, Northeastern China. Soil samples were collected from various sites of Longfeng wetland, including swamp wetland (SW), meadow wetland (MW), woodland (WL), farmland (FL), and alkaline land (AL). High-throughput sequencing followed by bioinformatic analysis was conducted to evaluate the structure, composition, and function of soil bacterial and fungal communities. The most dominant bacterial and fungal phylum among the land-use types were Proteobacteria and Ascomycota, respectively. In addition, the bacterial diversity and functions varied significantly across different land-use types. However, no remarkable differences in fungal communities were observed under various land-use types. Edaphic parameters, including exchange sodium percent (ESP) and total nitrogen (TN), remarkably influenced the abundance and diversity of soil microbial communities. These results show that land-use type shapes various aspects of soil microbial communities, including soil physicochemical properties, microbial taxa structure, potential functional genes, and correlation with environmental factors. This study provides reliable data to guide land use management and supervision by decision-makers in this region.

Water Level Has Higher Influence on Soil Organic Carbon and Microbial Community in Poyang Lake Wetland Than Vegetation Type

Although microorganisms play a key role in the carbon cycle of the Poyang Lake wetland, the relationship between soil microbial community structure and organic carbon characteristics is unknown. Herein, high-throughput sequencing technology was used to explore the effects of water level (low and high levels above the water table) and vegetation types (Persicaria hydropiper and Triarrhena lutarioriparia) on microbial community characteristics in the Poyang Lake wetland, and the relationships between soil microbial and organic carbon characteristics were revealed. The results showed that water level had a significant effect on organic carbon characteristics, and that soil total nitrogen, organic carbon, recombinant organic carbon, particle organic carbon, and microbial biomass carbon were higher at low levels above the water table. A positive correlation was noted between soil water content and organic carbon characteristics. Water level and vegetation type significantly affected soil bacterial and fungal diversity, with water level exerting a higher effect than vegetation type. The impacts of water level and vegetation type were higher on fungi than on bacteria. The bacterial diversity and evenness were significantly higher at high levels above the water table, whereas an opposite trend was noted among fungi. The bacterial and fungal richness in T. lutarioriparia community soil was higher than that in P. hydropiper community soil. Although both water level and vegetation type had significant effects on bacterial and fungal community structures, the water level had a higher impact than vegetation type. The bacterial and fungal community changes were the opposite at different water levels but remained the same in different vegetation soils. The organic carbon characteristics of wetland soil were negatively correlated with bacterial diversity but positively correlated with fungal diversity. Soil water content, soluble organic carbon, C/N, and microbial biomass carbon were the key soil factors affecting the wetland microbial community. Acidobacteria, Alphaproteobacteria, Verrucomicrobia, Gammaproteobacteria, and Eurotiomycetes were the key microbiota affecting the soil carbon cycle in the Poyang Lake wetland. Thus, water and carbon sources were the limiting factors for bacteria and fungi in wetlands with low soil water content (30%). Hence, the results provided a theoretical basis for understanding the microbial-driven mechanism of the wetland carbon cycle.

The bacterial community structure and N-cycling gene abundance in response to dam construction in a riparian zone

Dam construction has significantly altered riparian hydrological regime and environmental conditions in the reservoir region, yet knowledge concerning how bacterial community and N-cycling genes respond to these changes remains limited. In this study, we investigated the bacterial community composition, network structure and N-cycling genes in the water level fluctuation zones (WLFZs) of the Three Gorges Reservoir (TGR). Here, samples collected from five different water levels were divided into three groups: waterward sediments, interface sediments, and landward soils. Our results show that higher contents of NO₂^--N, SOC, DOC, NH₄⁺-N, and TP were characterized in waterward and interface sediments whereas higherNO₃^--N content was observed in landward soils. The α-diversity of bacterial community decreased gradually from waterward sediments to landward soils. Compared with waterward sediments and landward soils, the interface sediments showed a unique bacterial community pattern with diverse primary producers as well as N-cycling microbes. The interface sediments also had a much more complex co-occurrence network and a higher possible community stability. Among all of N-cycling genes, higher abundances of nrfA and AOA amoA genes were observed in interface sediments. The dissimilarity in bacterial community composition and N-cycling gene abundance was mainly driven by water-level. Moreover, random forest model revealed that AOA amoA and nirS genes were the most sensitive indicators in response to water level fluctuations. Overall, this study suggests distinct abundance, diversity, and network structure of microbes in riparian sediments and soils across the gradient of water levels and enhances our understanding with respect to comprehensive effects of dam construction on nitrogen cycle.

Seasonal Water Level Fluctuation and Concomitant Change of Nutrients Shift Microeukaryotic Communities in a Shallow Lake

Seasonal water level fluctuations (WLFs) impose dramatic influences on lake ecosystems. The influences of WLFs have been well studied for many lake biotas but the microeukaryotic community remains one of the least-explored features. This study employed high-throughput 18S rRNA gene sequencing to investigate the spatiotemporal patterns of microeukaryotic communities in the dry and wet seasons with concomitant change of nutrients in Poyang Lake, which experiences huge seasonal WLFs. The results showed that the dry season and wet season had distinct microeukaryotic community compositions and structures. In the dry season, Ciliophora (13.86–40.98%) and Cryptomonas (3.69–18.64%) were the dominant taxa, and the relative abundance of these taxa were significant higher in the dry season than wet season. Ochrophyta (6.88–45.67%) and Chlorophyta (6.31–22.10%) was the dominant taxa of microeukaryotic communities in the wet season. The seasonal variation of microeukaryotic communities was strongly correlated to seasonal nutrient variations. Microeukaryotic communities responded significantly to dissolved organic carbon, total nitrogen, nitrate, and soluble reactive phosphorus in the dry season, and correlated to nitrate and total phosphorus in the wet season. The microeukaryotic community showed different modular structures in two seasons, and nutrient variations were the key factors influencing seasonal variations of the modular structures. Moreover, microeukaryotic community networks based on different seasons indicated that the microeukaryotic community co-occurrence patterns were not constant but varied largely associating with the nitrogen and phosphorus variations under the effects of WLFs. Our results are important for understanding how microeukaryotic communities respond to nutrient variation under seasonal water level fluctuation.