Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake

Response of sulfate concentration to eutrophication on spatio-temporal scale in freshwater lakes

The dramatical increase of sulfur concentration in eutrophic lakes, especially sulfate (SO42-), has brought attention to the impact on the lake ecosystem; however, the mechanisms driving the intensification of eutrophication and the role of SO₄2- concentrations remain poorly understood. To assess the impact of eutrophication on SO42- dynamics in lakes, this study monitored SO42- concentrations in water and sediments across seven lakes with varying trophic statuses on a spatial scale, and in the eutrophic Lake Taihu over one year on a temporal scale, as well as a series of microcosms with different initial SO42- concentrations. Exogenous sulfur input is the primary driver of increased SO42- concentrations in lakes, the highest SO42- concentration in overlying water was 100 mg/L, as well as which reached 310.9 mg/L in sediment. The concurrent input of nutrients such as nitrogen and phosphorus exacerbated eutrophication, resulting in the destabilization of the sulfur cycle. Eutrophication promoted the SO42- concentration on the spatio-temporal scale, especially in sediment, and trophic lake index (TLI) showed a positive correlation with the SO42- in sediments (R2 = 0.99; 0.88). The SO42- concentration in water and TLI showed a nonlinear correlation on the temporal scale (R2 = 0.44), and showed a positive correlation on the spatial scale (R2 = 0.49). Microscopic experiments demonstrate that the anaerobic environment created by cyanobacteria decomposition induced sulfate reduction and significantly reduces SO42- concentrations. Concurrently, the anaerobic environment facilitates the coupling of iron reduction with sulfate reduction, leading to a substantial increase in Acid Volatile Sulfides (AVS) in the sediment. These findings reveal that eutrophication has a dual effect on the dynamic change of SO42- concentrations in overlying water, which is helpful to accurately evaluate and predict the change of SO42- concentrations in lakes.

Different patterns of bacterioplankton in response to inorganic and organic phosphorus inputs in freshwater lakes - a microcosmic study

Phosphorus (P) is a limiting factor in fresh waters and is also the main cause of water eutrophication and deterioration, However, the practical effect of elevated P level on bacterioplankton is less evaluated. In this study, we investigated the bacterioplankton in a 96 hours microcosm experiment with P additions in two forms (organic/inorganic P, OP/IP) and three levels (final conc., 0.040, 0.065 and 0.125 g/L), aiming to find out the response pattern of bacterioplankton in coping with the increasing P levels. Results showed a more dramatic change of water properties and bacterioplankton between P forms (OP and IP) than among the addition levels, and a more remarkable effect of OP addition than the IP. Both OP and IP treatments significantly decreased the water pH, dissolved oxygen (DO), Electrical Conductivity (EC), Nitrate Nitrogen (NO3--N) and Total Organic Carbon (TOC), and reduced the α-diversity of bacterioplankton and relative abundance of Cyanobacteria, but increased the abundance of Proteobacteria. The IP addition decreased Actinobacteria abundance (especially for HgcI) and showed higher denitrification potentials, while the OP addition depressed the Bateroidota and exhibited lowed methylotrophic functions, but such trends decreased with increasing addition concentrations. The network analysis showed that both IP and OP additions increased the proportion of positively correlated edges and reduced the network complexity and stability, but the OP network was more stable than the IP network. The study clarifies the response pattern of bacterioplankton to the P input with different forms and levels, and deepens our understanding of the eutrophication process, which provides a scientific basis for the management and control of freshwater lakes facing eutrophication.

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea

Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.

Eutrophication-induced shifts cause diverse responses in the phoD community of a plateau freshwater lake

Eutrophication is a critical environmental challenge affecting lakes globally. Mitigating trophic level under endogenous phosphorus release is an unsolved problem in eutrophic lakes. However, understanding the dynamics and assembly of microbial communities encoding the alkaline phosphatase (phoD community) and their responses during trophic transitions in eutrophic lakes is limited. In this study, we compared the composition and assembly mechanisms of phoD communities in four seasons in the Yilong Lake, a shallow lake of the Yunnan-Guizhou Plateau. The lake exhibits slightly eutrophic conditions in summer and mesotrophic conditions in spring, autumn, and winter. By analyzing seasonal variations, we observed that during summer, the relative abundance of Pseudomonas in the water had the highest value, while the Shannon-Wiener index of phoD communities was lowest. Mantel tests showed an increased Bray-Curtis dissimilarity of phoD communities in the water with rising eutrophication, a trend not observed in sediment. Notably, eutrophication heightened the homogeneity selection governing the assembly of phoD communities in water. The co-occurrence networks showed that the OTUs in the summer exhibited closer interconnections than those in other seasons. Additionally, the topological parameters from networks indicated that eutrophication is poised to instigate changes and modulate the dynamics of the microbial phoD community, resulting in markedly distinct seasonal behaviors. pH was identified as a critical factor directly influencing phoD community diversity via partial least squares path modeling (PLS-PM). This study shed light on our understanding of the seasonal dynamics of phoD communities and their pivotal role in phosphorus cycling in eutrophic lakes.

The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake

Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.

Microbial and environmental medium-driven responses to phosphorus fraction changes in the sediments of different lake types during the freezing period

The comparative study of the transformation among sediment phosphorus (P) fractions in different lake types is a global issue in lake ecosystems. However, interactions between sediment P fractions, environmental factors, and microorganisms vary with the nutrient status of lakes. In this study, we combine sequential extraction and metagenomics sequencing to assess the characteristics of P fractions and transformation in sediments from different lake types in the Inner Mongolian section of the Yellow River Basin. We then further explore the response of relevant microbial and environmental drivers to P fraction transformation and bioavailability in sediments. The sediments of all three lakes exhibited strong exogenous pollution input characteristics, and higher nutritional conditions led to enhanced sediment P fraction transformation ability. The transformation capacity of the sediment P fractions also differed among the different lake types at the same latitudes, which is affected by many factors such as lake environmental factors and microorganisms. Different drivers reflected the mutual control of weakly adsorbed phosphorus (WA-P), potential active phosphorus (PA-P), Fe/Al-bound phosphorus (NaOH-P), and Ca-bound phosphorus (HCl-P) with the bio-directly available phosphorus (Bio-P). The transformation of NaOH-P in reducing environments can improve P bioavailability, while HCl-P is not easily bioavailable in weakly alkaline environments. There were significant differences in the bacterial community diversity and composition between the different lake types at the same latitude (p < 0.05), and the role of P fractions was stronger in the sediments of lakes with rich biodiversity than in poor biodiversity. Lake eutrophication recovery was somewhat hindered by the microbial interactions of P cycling and P fractions within the sediment. This study provides data and theoretical support for exploring the commonalities and differences among different lake types in the Inner Mongolian section of the Yellow River Basin. Besides, it is representative and typical for promoting the optimization of ecological security patterns in ecologically fragile watersheds.

Nitrate input inhibited the biodegradation of erythromycin through affecting bacterial network modules and keystone species in lake sediments

Antibiotic contamination and excessive nitrate loads are generally concurrent in aquatic ecosystems. However, little is known about the effects of nitrate input on the biodegradation of antibiotics. In this study, the effects of nitrate input on microbial degradation of erythromycin, a typical macrolide antibiotic widely detected in lake sediments, were investigated. The results showed that the nitrate input significantly inhibited the erythromycin removal and such an inhibitory effect was strengthened with the increased input dosages. Nitrate input significantly increased sediment nitrite concentration, indicating enhanced denitrification under high nitrate pressure. Bacterial network module and keystone species analysis showed that nitrate input enriched the keystone species involved in denitrification (e.g., Simplicispira and Denitratisoma). In contrast, some potential erythromycin-degrading bacteria (e.g., Desulfatiglandales, Pseudomonadales, Nitrospira) were inhibited by nitrate input. The variations in dominant bacterial groups implied competition between denitrification and erythromycin degradation in response to nitrate input. Based on the partial least squares path modeling analysis, keystone species (total effect: 0.419) and bacterial module (total effect: 0.403) showed strong association with erythromycin removal percentage. This indicated that the inhibitory effect of nitrate input on erythromycin degradation was mainly explained by bacterial network modules and keystone species. These findings will help us to assess the bioremediation potential of antibiotic-contaminated sediments suffering from excessive nitrogen discharge concurrently.

Interactions between water quality and microbes in epiphytic biofilm and superficial sediment of lake in trophic agriculture area

Epiphytic and superficial sediment biofilm-dwelling microbial communities play a pivotal role in water quality regulation and biogeochemical cycling in shallow lakes. However, the interactions are far from clear between water physicochemical parameters and microbial community on aquatic plants and in surface sediments of lake in trophic agriculture area. This study employed Illumina sequencing, Partial Least Squares Path Modeling (PLS-PM), and physico-chemical analytical methods to explore the interactions between water quality and microbes (bacteria and eukaryotes) in three substrates of trophic shallow Lake Cyohoha North, Rwanda. The Lake Cyohoha was significantly polluted with total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), and ammonia nitrogen (NH3-N) in the wet season compared to the dry season. PLS-PM revealed a strong positive correlation (+0.9301) between land use types and physico-chemical variables in the rainy season. In three substrates of the trophic lake, Proteobacteria, Cyanobacteria, Firmicutes, and Actinobacteria were dominant phyla in the bacterial communities, and Rotifers, Platyhelminthes, Gastrotricha, and Ascomycota dominated in microeukaryotic communities. As revealed by null and neutral models, stochastic processes predominantly governed the assembly of bacterial and microeukaryotic communities in biofilms and surface sediments. Network analysis revealed that the microbial interconnections in Ceratophyllum demersum were more stable and complex compared to those in Eichhornia crassipes and sediments. Co-occurrence network analysis (|r| > 0.7, p < 0.05) revealed that there were complex interactions among physicochemical parameters and microbes in epiphytic and sediment biofilms, and many keystone microbes on three substrates played important role in nutrients removal, food web and microbial community stable. These findings emphasize that eutrophic water influence the structure, composition, and interactions of microbes in epiphytic and surface sediment biofilms, and provided new insights into the interconnections between water quality and microbial community in presentative substrates in tropical lacustrine ecosystems in agriculturally polluted areas. The study provides useful information for water quality protection and aquatic plants restoration for policy making and catchment management.

Microbial interaction patterns and nitrogen cycling regularities in lake sediments under different trophic conditions

Exploring how nitrogen (N) cycling microbes interact in eutrophic lake sediments and how biogenic elements influence the nitrogen cycle is crucial for understanding biogeochemical cycles and nitrogen accumulation mechanisms. In this study, sediment samples were collected from various areas of Taihu Lake with different trophic conditions in all four seasons from 2015 to 2017. Using high-throughput sequencing and molecular ecological network analysis, we investigated the microbial interaction patterns and the role of nitrogen cycling in sediments from lakes with different trophic conditions. The results showed distinct structures of sediment microbial networks between lake areas with different trophic conditions. In the more eutrophic region, network indices indicate higher transfer efficiency of energy, material, and information, more significant competition, and weaker niche differentiation of the microbial community. The sedimentary environment in the moderately eutrophic area exhibited greater potential for denitrification, nitrification, and anammox compared to the mesotrophic area, but the inhibition between N functional microbes and limitations in N removal processes were also more likely to occur. The topological structure of the networks showed that the carbon (C), sulfur (S), and iron (Fe) cycles had a strong influence on the nitrogen cycle in both lake areas. In the moderately eutrophic lake area, C- and S-cycling functional bacteria facilitated a closed cycle of the coupled N fixation-nitrification-DNRA (dissimilatory nitrate reduction to ammonium) process and reduced N removal. In the mesotrophic lake area, C- and S-cycling functional bacteria promoted both N fixation and mineralization, and Fe-cycling functional bacteria coupled with denitrifiers enhanced the nitrogen removal process of products from nitrogen fixation and mineralization. This study improved the understanding of the nitrogen cycling mechanism in lake sediments under different trophic conditions.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

β-Glucosidase-producing microbial community in composting: Response to different carbon metabolic pressure influenced by biochar

Poor management of agricultural waste will cause a lot of environment pollution and the composting process is one of the most effective measures for resource reuse of agricultural waste. β-Glucosidase-producing microbial communities play a vital role in cellulose degradation during composting and regulate cellulase production via differentially expressed glucose/non-glucose tolerant β-glucosidase genes. Biochar is widely used as an amendment in compost to accelerate cellulose degradation during composting. However, Biochar-mediated impacts on β-glucosidase-producing microbial communities in compost are unclear. Here, different carbon metabolism pressures were set in natural and biochar compost to elucidate the regulation mechanism and interaction of the β-glucosidase microbial community. Results showed that the addition of biochar decreased the transcription of β-glucosidase genes and led to a reduction of β-glucosidase activity. Micromonospora and Cellulosimicrobium were the predominant functional communities determining cellulose degradation during biochar compost. Biochar addition strengthened the response of the functional microbial community to carbon metabolism pressure. And adding biochar altered the key β-glucosidase-producing microbial communities, influencing cellulase and the interaction between these communities to respond to the different carbon metabolic pressure of compost. Biochar also shifted the co-occurrence network of β-glucosidase-producing microbial community by changing the keystone species. Furthermore, co-occurrence network analysis revealed that high glucose decreased the complexity and stability of the functional microbial network. Most functional microorganisms from Streptomyces produce non-glucose tolerant β-glucosidase, which were the key bacterial communities affecting β-glucosidase activity in the non-glucose treatment. This study provides new insights into the response of functional microbial communities and the regulation of enzyme production during the transformation of cellulosic biomass.

Tidal flat microbial communities between the Huaihe estuary and Yangtze River estuary

Tidal flats have important ecological functions and offer great economic value. Using field sampling, numerical simulation, and high-throughput sequencing, the ecological state of typical tidal flats along the eastern coast of China was investigated. The findings demonstrated that the area may be separated into subregions with notable differences in the features of microbial communities due to the variations in water quality and total pollutant discharge of seagoing rivers. With a ratio of 62%, the development of the microbial community revealed that homogenous selection predominated. In general, the formation of microbial communities follows deterministic processes, especially those of environmental selection. The wetland microbial communities are impacted by pollutants discharged into the sea from the Huaihe River and the Yangtze River. The Yangtze River's nitrogen pollutants affected the wetland zone, and denitrification dominated. The study established ecological patterns between the river and the sea and we offer suggestions for managing watersheds and safeguarding the ecology of coastal tidal flats.

Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China

Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R2 = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.

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.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China

The antibiotic concentrations spanned from 11.2 to 173.8 ng/g, with quinolones and tetracyclines being observed to be prevalent. The amount of microbial biomass as determined by Phospholipid fatty acid (PLFA) ranged from 2.92 to 10.99 mg kg-1, with G- bacteria dominating. A total of 254 distinct ARGs and 10 MEGs were identified, with multidrug ARGs having the highest relative abundance (1.18 × 10-2 to 3.00 × 10-1 copies/16S rRNA gene copies), while vancomycin and sulfonamide resistance genes were the least abundant. Results from canonical-correlation analyses combined with redundancy analysis indicated that macrolides were significantly related to the shifts of microbial community structure in sediments, particularly in G+ bacteria that were more sensitive to antibiotic residues. It was observed that sulfonamide ARGs had a greater correlation with residual antibiotics than other ARGs. This study provided a field evidence that multiple residual antibiotics from coastal sites could cause fundamental shifts in microbial community and their associated ARGs.

Effect of microbial communities on nitrogen and phosphorus metabolism in rivers with different heavy metal pollution

Small urban and rural rivers usually face heavy metal pollution as a result of urbanization and industrial and agricultural activities. To elucidate the metabolic capacity of microbial communities on nitrogen and phosphorus cycle in river sediments under different heavy metal pollution backgrounds, this study collected samples in situ from two typical rivers, Tiquan River and Mianyuan River, with different heavy metal pollution levels. The microbial community structure and metabolic capacity of nitrogen and phosphorus cycles of sediment microorganisms were analyzed by high-throughput sequencing. The results showed that the major heavy metals in the sediments of the Tiquan River were Zn, Cu, Pb, and Cd with the contents of 103.80, 30.65, 25.95, and 0.44 mg/kg, respectively, while the major heavy metals in the sediments of the Mianyuan River were Cd and Cu with the contents of 0.60 and 27.81 mg/kg, respectively. The dominant bacteria Steroidobacter, Marmoricola, and Bacillus in the sediments of the Tiquan River had positive correlations with Cu, Zn, and Pb while are negatively correlated with Cd. Cd had a positive correlation with Rubrivivax, and Cu had a positive correlation with Gaiella in the sediments of the Mianyuan River. The dominant bacteria in the sediments of the Tiquan River showed strong phosphorus metabolic ability, and the dominant bacteria in the sediments of the Mianyuan River showed strong nitrogen metabolic ability, corresponding to the lower total phosphorus content in the Tiquan River and the higher total nitrogen content in the Mianyuan River. The results of this study showed that resistant bacteria became dominant bacteria due to the stress of heavy metals, and these bacteria showed strong nitrogen and phosphorus metabolic ability. It can provide theoretical support for the pollution prevention and control of small urban and rural rivers and have positive significance for maintaining the healthy development of rivers.

Microbial ecological responses of partial nitritation/anammox granular sludge to real water matrices and its potential application

Granular sludges are commonly microbial aggregates used to apply partial nitritation/anammox (PN/A) processes during efficient biological nitrogen removal from ammonium-rich wastewater. Considering keystone taxa of anammox bacteria (AnAOB) in granules and their sensitivity to unfavorable environments, it is essential to investigate microbial responses of autotrophic PN/A granules to real water matrices containing organic and inorganic pollutants. In this study, tap water, surface water, and biotreated wastewater effluents were fed into a series of continuous PN/A granular reactors, respectively, and the differentiation in functional activity, sludge morphology, microbial community structure, and nitrogen metabolic pathways was analyzed by integrating kinetic batch testing, size characterization, and metagenomic sequencing. The results showed that feeding of biotreated wastewater effluents causes significant decreases in nitrogen removal activity and washout of AnAOB (dominated by Candidatus Kuenenia) from autotrophic PN/A granules due to the accumulation of heavy metals and formation of cavities. Microbial co-occurrence networks and nitrogen cycle-related genes provided evidence for the high dependence of symbiotic heterotrophs (such as Proteobacteria, Chloroflexi, and Bacteroidetes) on anammox metabolism. The enhancement of Nitrosomonas nitritation in the granules would be considered as an important contributor to greenhouse gas (N₂O) emissions from real water matrices. In a novel view on the application of microbial responses, we suggest a bioassay of PN/A granules by size characterization of red-color cores in ecological risk assessment of water environments.

Unraveling the response of water quality and microbial community to lake water backflowing in one typical estuary of Lake Taihu, China

To investigate the effect of lake water backflowing on the aquatic ecosystem in the estuary, surface water samples in the backflowing and unbackflowing areas were collected from one typical estuary of Lake Taihu, Xitiaoxi River. 16S rRNA sequencing and redundancy analysis were conducted to quantitatively elucidate the correlation between microbial community and water quality parameters. Results indicated lake water backflowing would affect the relative distribution of nitrogen species and increase the concentration of total nitrogen (TN) and nitrate, especially in the outlets of municipal sewage and agricultural drainage. For backflowing areas, more frequent water exchange could lower the seasonal fluctuation of the abundance and diversity of microbial community. RDA results showed crucial water quality parameters that greatly influence bacterial community were total organic carbon (TOC), total dissolved solids (TDS), salinity (SAL), ammonia, nitrate, TN for backflowing areas, and TOC, TDS, SAL, ammonia, TN without nitrate for unbackflowing areas. Verrucomicrobia, Proteobacteria, Microcystis, and Arcobacter were dominant with 27.7%, 15.7%, 30.5%, and 25.7% contribution to the overall water quality in backflowing areas. Chloroflexi, Verrucomicrobia, Flavobacterium, and Nostocaceae were dominant with 25.0%, 18.4%, 22.3%, and 11.4% contribution to the overall water quality in unbackflowing areas. And lake water backflowing might mainly affect the amino acid and carbohydrate metabolism based on the metabolism function prediction. A better understanding of the spatiotemporal changes in water quality parameters and microbial community was obtained from this research to comprehensively assess the effect of lake water backflowing on the estuarine ecosystem.

Diversity and interaction of bacterial and microeukaryotic communities in sediments planted with different submerged macrophytes: Responses to decabromodiphenyl ether

Although various persistent organic pollutants (POPs) can affect microbial communities and functions in aquatic ecosystems, little is known about how bacteria and microeukaryotes respond to the POPs in sediments planted with different submerged macrophytes. Here, a 60-day microcosm experiment was carried out to investigate the changes in the diversity and interaction of bacterial and microeukaryotic communities in sediments collected from Taihu lake, either with decabromodiphenyl ether (BDE-209) own or combined with two common submerged macrophyte species (Vallisneria natans and Hydrilla verticillate). The results showed that BDE-209 significantly decreased the bacterial α-diversity but increased the microeukaryotic one. In sediments planted with submerged macrophytes, the negative effect of BDE-209 on bacterial diversity was weakened, and its positive effect on microeukaryotic one was strengthened. Co-occurrence network analysis revealed that the negative relationship was dominant in bacterial and microeukaryotic communities, while the cooperative relationship between microbial species was increased in planted sediments. Among nine keystone species, one belonging to bacterial family Thermoanaerobaculaceae was enriched by BDE-209, and others were inhibited. Notably, such inhibition was weakened, and the stimulation was enhanced in planted sediments. Together, these observations indicate that the responses of bacteria and microeukaryotes to BDE-209 are different, and their communities under BDE-209 contamination are more stable in sediments planted with submerged macrophytes. Moreover, the effects of plant species on the microbial responses to BDE-209 need to be explored by more specific field studies in the future.

Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions

PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H₂S and CH₄ emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.

Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau

Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated β-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated β-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of β-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in β-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.

Combining historical maps and landsat images to delineate the centennial-scale changes of lake wetlands in Taihu Lake Basin, China

Lake wetlands (LWs) are essential components of the ecosystem and play an irreplaceable role in flood regulation, carbon fixation, and biodiversity maintenance. Continuous monitoring of LWs' change is necessary in the context of increased human disturbance and climate change, particularly in Taihu Lake Basin, China, an area exposed to early human exploitation. Yet, long-time series of LWs detection in this region is still unavailable due to the data limitation. To quantify the spatiotemporal dynamics of LWs and the associated driving forces, we combined 236 historical topographic maps and thousands of Landsat satellite images from the 1910s to 2021 to delineate the centennial-scale changes of lake wetlands for the first time in this region. We also applied land use transitions and statistical analyses to quantitively explore the climatic and anthropogenic factors behind LWs variations. Our results document a dramatic decline in the area and number of LWs in the Taihu Lake Basin over the last century and a shift in the 2000s: Taihu Lake Basin has seen a total of 89.15% loss in lake littoral wetlands and a decrease of 14.5% in the whole lake wetlands area, with a net reduction of 68 (from 156 in the 1910s to 88 in the 2021) lakes. This decrease has been especially predominant during the 1910s-2000s, because of the policy initiatives for reclamation and aquacultural industries. The area and number of LWs have gradually been recovered since the 2000s as the country strengthened concern on the ecological restoration and sustainable development. The statistical results suggested that human activities played a dominant role in the LWs changes, with GDP and population explained 80.74% of the changes, coupled with climatic contribution of only around 20%. This long-term investigation will provide baseline information for future lake wetlands monitoring. Our findings could also provide a guidance for decision makers regarding water resources management, environmental protection and land-use planning in urban areas.

Construction of the comprehensive evaluation system of waterbody pollution degree and the response of sedimentary microbial community

This study proposed and established a comprehensive evaluation system for the pollution degree of the waterbody by taking overlying water and sediment as a whole. By dividing different sampling points into three gradients according to the pollution degree, the changes in sedimentary microbes under various pollution gradients were compared. The results showed that microbial diversity, abundance and specific OTUs decreased significantly with the increase in pollution degree. Meanwhile, Firmicutes, Bacteroidota and Caldiseriota increased in the severely polluted group, while Chloroflexi and Acidobacteriota decreased. Spearman correlation analysis and co-occurrence network revealed that COD, pH in overlying water, and Mn, Fe in sediments were the most significant pollution degree evaluation indicators affecting sedimentary microorganisms, which drove the sedimentary microbial communities dominated by Proteobacteria and Firmicutes. FAPROTAX functional prediction indicated that increased pollution levels led to the weakening of functional genes related to nitrogen metabolism and sulfur metabolism and the increase of functional genes related to carbon metabolism in sediment microorganisms. This study not only provided new insights into waterbody pollution evaluation but also verified the feasibility of this evaluation method by the response of sedimentary microbial communities to different pollution degrees.

Effect of erythromycin on epiphytic bacterial communities and water quality in wetlands

The occurrence of antibiotics such as erythromycin (ERY) under macrolide group, has long been acknowledged for negatively affecting ecosystems in freshwater environments. However, the effects of ERY on water quality and microbial communities in epiphytic biofilms are poorly understood. Here, Scanning Electron Microscopy (SEM), High-throughput sequencing, and physicochemical analytical methods were employed to unravel the impact of ERY on the water quality and bacterial morphology, biodiversity, composition, interaction, and ecological function in epiphytic biofilms attached to Vallisneria natans and artificial plants in mesocosmic wetlands. The study showed that ERY exposure significantly impaired the nutrient removal capacity (TN, TP, and COD) and altered the epiphytic bacterial morphology of V. natans and artificial plants. ERY did not affect the bacterial α-diversity. Notwithstanding ERY decreased the bacterial composition, but the relative abundance of Proteobacteria and Patescibacteria spiked by 62.2 % and 54 %, respectively, in V. natans, while Desulfobacteria and Chloroflexi increased by 8.9 % and 11.2 %, respectively, in artificial plants. Notably, ERY disturbed the food web structure and metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, membrane transport, and signal transduction. This study revealed that ERY exposure disrupted the bacterial morphology, composition, interaction or food web structure, and metabolic functions in epiphytic biofilm. These data underlined that ERY negatively impacts epiphytic bacterial communities and nutrient removal in wetlands.

Responses of abundant and rare prokaryotic taxa in a controlled organic contaminated site subjected to vertical pollution-induced disturbances

Soil microbiota as the key role mediates the natural attenuation process of organic contaminated sites, and therefore illuminating the mechanisms underlying the responses of abundant and rare species is essential for understanding ecological processes, maintaining ecosystem stability, and regulating natural attenuation well. Here, we explored the distributional characteristics, ecological diversities, and co-occurrence patterns of abundant and rare prokaryotic subcommunities using 16S rRNA high-throughput sequencing in vertical soil profiles of a controlled organic contaminated site. Results showed that abundant prokaryotic taxa were widespread across all soil samples, whereas rare counterparts were unbalancedly distributed. Rare subcommunity had more taxonomic groups and higher α- and β-diversities than abundant subcommunity. Both of these two subcommunities surviving in the organic polluted site possessed the potential of degrading organic contaminants. Abundant subcommunity was little affected by abiotic factors and mainly shaped by soil depth, while rare one was sensitive to environmental disturbances and presented a non-depth-dependent structure. Co-occurrence analysis revealed that rare taxa were more situated at the center of the network and more inclined to cooperate with non-abundant species than abundant taxa, which might play crucial roles in enhancing the resilience and resistance of prokaryotic community and maintaining its structure and stability. Overall, our results suggest that abundant and rare prokaryotic subcommunities present different responses to physicochemical factors and pollution characteristics along vertical soil profiles of organic contaminated sites undergoing natural attenuation.

Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu

Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.

The mechanism of C-N-S interconnection degradation in organic-rich sediments by Ca(NO3)2 - CaO2 synergistic remediation

The rebound of black-odorous occurred in organic-rich sediments has become a critical issue due to its great harm to the ecological environment. Elements such as S, C, and N play a crucial role in the biogeochemical cycle of black-odorous rivers. As electronic acceptors, Ca(NO₃)₂ and CaO₂ can effectively remove acidified volatile sulfide (AVS) and organic matter to control the black-odorous rebound. However, the remediation mechanisms in organic-rich sediments by Ca(NO₃)₂ and CaO₂ are unclear. The present study explored the mechanism of C-N-S interconnection degradation in organic-rich urban river sediments by adding different ratios and sequences of Ca(NO₃)₂ and CaO₂. The results showed that Ca(NO₃)₂ remediation followed by CaO₂ and the accepted electron ratio 1:1 of Ca(NO₃)₂ to CaO₂ is an effective method for controlling the rebound of black-odorous and reducing the accumulation NO₂^--N. Mainly attributed to that, CaO₂ enhanced the degradation of organic matter by stimulating enzymatic activities in the sediments, which is also the main reason for controlling the rebound of black-odorous. Since CaO₂ releases O₂ and •OH, which inhibit nosZgenes, NO₂^--N accumulates when remedied simultaneously with Ca(NO₃)₂ and CaO₂. Co-occurrence network analysis illustrated that sulfur-driven autotrophic denitrification bacteria, heterotrophic denitrifying bacteria, and sulfate-reducing bacteria interact strongly inside one module, clarifying a solid interaction of C-N-S substances among these bacteria. Our results reveal the C-N-S interconnection degradation mechanism and provide a new perspective on applying biochemical remediation in organic-rich urban river sediments.

The distribution and ecological risks of antibiotics in the sediments from a diverging area of the bifurcated river: Effects of hydrological properties

The hydrodynamics in the diverging area become complicated because of the basin hydrological conditions, making the distribution of antibiotics largely uncertain and thus bringing uncertain ecological risks of antibiotics. Through field sampling, experiments and numerical simulations, the distribution of antibiotics, its responses to hydrological conditions were studied. Antibiotics in the bifurcated river sediments was mainly distributed in the branch mouth. The hydrodynamic regions were affected by the hydrological frequency. Notably, the center of the low-velocity area moved upstream and gradually expands to the entire tributary as the hydrological frequency shifted from high to low. ENRO (enrofloxacin) and OFC (ofloxacin) were the key hazardous antibiotics affecting the ecological health in the diverging area, and their concentrations are mainly affected by sediment particle size (D < 0.15 mm) and oxygen content. The ecological risk of antibiotics in the diverging area were gradually decreased with the increase of the distance from the central area. The water physical and chemical properties, altered by the river basin hydrological conditions, play an important role in influencing the distribution of antibiotic concentrations, and ultimately posing great threat to aquatic ecosystem. The research provides a scientific basis for antibiotic risk control in the diverging area under different hydrological conditions.

Comparison and interpretation of freshwater bacterial structure and interactions with organic to nutrient imbalances in restored wetlands

Chemical oxygen demand to nitrogen (COD/N) and nitrogen to phosphorus (N/P) ratios have distinct effects on bacterial community structure and interactions. However, how organic to nutrient imbalances affect the structure of freshwater bacterial assemblages in restored wetlands remains poorly understood. Here, the composition and dominant taxa of bacterial assemblages in four wetlands [low COD/N and high N/P (LH), low COD/N and low N/P (LL), high COD/N and high N/P (HH), and high COD/N and low N/P (HL)] were investigated. A total of 7,709 operational taxonomic units were identified by high throughput sequencing, and Actinobacteria, Proteobacteria, and Cyanobacteria were the most abundant phyla in the restored wetlands. High COD/N significantly increased bacterial diversity and was negatively correlated with N/P (R 2 = 0.128; p = 0.039), and the observed richness (Sobs) indices ranged from 860.77 to 1314.66. The corresponding Chao1 and phylogenetic diversity (PD) values ranged from 1533.42 to 2524.56 and 127.95 to 184.63. Bacterial beta diversity was negatively related to COD/N (R 2 = 0.258; p < 0.001). The distribution of bacterial assemblages was mostly driven by variations in ammonia nitrogen (NH4 +-N, p < 0.01) and electrical conductivity (EC, p < 0.01), which collectively explained more than 80% of the variation in bacterial assemblages. However, the dominant taxa Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Deinococcus-Thermus were obviously affected by variation in COD/N and N/P (p < 0.05). The highest node and edge numbers and average degree were observed in the LH group. The co-occurrence networkindicated that LH promoted bacterial network compactness and bacterial interaction consolidation. The relationships between organic to nutrient imbalances and bacterial assemblages may provide a theoretical basis for the empirical management of wetland ecosystems.

The Spatiotemporal Characteristics of Water Quality and Main Controlling Factors of Algal Blooms in Tai Lake, China

Taking Tai Lake in China as the research area, a 3D water environment mathematical model was built. Combined with the LHS and Morris uncertainty and sensitivity analysis methods, the uncertainty and sensitivity analysis of total phosphorus (TP), total nitrogen (TN), dissolved oxygen (DO), and chlorophyll a (Chl-a) were carried out. The main conclusions are: (1) The performance assessment of the 3D water environment mathematical model is good (R2 and NSE > 0.8) and is suitable for water quality research in large shallow lakes. (2) The time uncertainty study proves that the variation range of Chl-a is much larger than that of the other three water quality parameters and is more severe in summer and autumn. (3) The spatial uncertainty study proves that Chl-a is mainly present in the northwest lake area (heavily polluted area) and the other three water quality indicators are mainly present in the center. (4) The sensitivity results show that the main controlling factors of DO are ters (0.15) and kmsc (0.12); those of TN and TP are tetn (0.58) and tetp (0.24); and those of Chl-a are its own growth rate (0.14), optimal growth temperature (0.12), death rate (0.12), optimal growth light (0.11), and TP uptake rate (0.11). Thus, TP control is still the key treatment method for algal blooms that can be implemented by the Chinese government.