Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes

Aggregating Synechococcus contributes to particle organic carbon export in coastal estuarine waters: Its lineage features and assembly processes

The release and deposition of phytoplankton-derived particulate organic matter is crucial in marine carbon export, yet the roles of picoplankton in these processes were seldom considered. Therefore, this study aimed to shed light on the matter by investigating the aggregating (AG) lifestyle of Synechococcus, a main group of picoplankton, in the coastal waters of the Yellow River Estuary with ample sediments acting as ballast minerals. We revealed that AG Synechococcus constituted a substantial portion, maximally reaching up to 85.4 %, of the total Synechococcus population. Pearson correlations and random forest (RF) regression analyses found significant connections (p < 0.01) between AG Synechococcus and the content of particulate organic carbon (POC), which emphasized its underlying role in facilitating POC export in this region. Furthermore, by employing high-throughput sequencing of the RNA polymerase gene (rpoC1), it was demonstrated that S5.1 clade I exhibited a significantly higher proportion in the AG fraction than in the free-living (FL) fraction (p < 0.05). This suggests distinct inclinations in the phylogenetic preference for different Synechococcus lineages between different lifestyles in the studied area. Finally, we ascertained "small-world" and higher robustness attributes of aggregates formed through the co-occurrence construction between Synechococcus and heterotrophic bacteria, likely facilitated by the reciprocal exchange of carbon and nitrogen elements. Overall, these findings have implications for our understanding of the role of Synechococcus in the ecology and biogeochemistry of marine ecosystems, and they are significant for more accurately evaluating the contribution of picophytoplankton in ocean carbon export.

Grass-legume mixtures maintain forage biomass under microbial diversity loss via gathering Pseudomonas in root zone soil

IMPORTANCE

Grass-legume mixtures are a common practice for establishing artificial grasslands, directly or indirectly contributing to the improvement of yield. In addition, this method helps maintain soil and plant health by reducing the use of chemical fertilizers. The impact of grass-legume mixtures on yield and its underlying microbial mechanisms have been a focus of scientific investigation. However, the benefits of mixtures in the context of soil microbial diversity loss remain a problem worthy of exploration. In this study, we examined different aboveground and belowground diversity combinations to elucidate the mechanisms by which grass-legume mixtures help maintain stable yields in the face of diversity loss. We identified the significantly enriched Pseudomonas genus microbial ASV53, which was gathered through homogeneous selection and served as a keystone in the co-occurrence network. ASV53 showed a strong positive correlation with biomass and the abundance of nitrogen-fixing genes. These findings provide a new theoretical foundation for utilizing grass-legume mixtures to enhance grass yields and address the challenges posed by diversity loss.

Assessing the impacts of fine sediment removal on endogenous pollution release and microbial community structure in the shallow lakes

Resuspension is a crucial process for releasing endogenous pollution from shallow lakes into the overlying water. Fine particle sediment, which has a higher contamination risk and longer residence time, is the primary target for controlling endogenous pollution. To this end, a study coupling aqueous biogeochemistry, electrochemistry, and DNA sequencing was conducted to investigate the remediation effect and microbial mechanism of sediment elution in shallow eutrophic water. The results indicated that sediment elution can effectively remove some fine particles in situ. Furthermore, sediment elution can inhibit the release of ammonium nitrogen and total dissolved phosphorous into the overlying water from sediment resuspension in the early stage, resulting in reductions of 41.44 %-50.45 % and 67.81 %-72.41 %, respectively. Additionally, sediment elution greatly decreased the concentration of nitrogen and phosphorus pollutants in pore water. The microbial community structure was also substantially altered, with an increase in the relative abundance of aerobic and facultative aerobic microorganisms. Redundancy analysis, PICRUSt function prediction, and the correlation analysis revealed that loss on ignition was the primary factor responsible for driving changes in microbial community structure and function in sediment. Overall, the findings provide novel insights into treating endogenous pollution in shallow eutrophication water.

Interkingdom network analyses reveal microalgae and protostomes as keystone taxa involved in nutrient cycling in large freshwater lake sediment

Few studies have explored the role of interkingdom interactions between bacteria and microeukaryotes in nutrient cycling in lake ecosystems. We conducted sediment sampling from 40 locations covering Hongze Lake and analyzed their chemical properties. Intra- and interkingdom networks were constructed using 16S and 18S rRNA gene amplicon sequencing. Microeukaryotic intranetworks were more complex in spring than in autumn, while no clear variation in the complexity of bacterial intranetworks was found between autumn and spring. Larger and more complex bacterial-microeukaryotic bipartite networks emerged in spring than in autumn, correlated with lower carbon, nitrogen, and phosphorus levels in spring, likely resulting in intense microbial competition. Bacteria and microeukaryotes played different topological roles in interkingdom networks, with microeukaryotes contributing to the networks' greater complexity. Seven keystone modules were identified in spring and autumn nutrient cycling. Importantly, keystone taxa in these modules belonged to photoautotrophic microalgae or predatory protostomes, indicating that these organisms are key drivers in lake sediment nutrient cycling. Our results suggested that nutrient content variation in autumn and spring changes interkingdom networks' topological structure between bacteria and microeukaryotes. Microalgae and protostomes are essential in freshwater lake nutrient cycling and may be targeted to modulate nutrient cycling in large freshwater ecosystems.

Enhanced nitrogen removal in low-carbon saline wastewater by adding functional bacteria into Sesuvium portulacastrum constructed wetlands

Functional bacterial communities (FBC) have members of different taxonomic biochemical groups, such as N2-fixation, nitrification and denitrification. This study explored the mechanism of the FBC from an upflow three-dimensional biofilm electrode reactor on enhancing the nitrogen removal efficiencies in a Sesuvium potulacastum (S. potulacastum) constructed wetland. There were high abundances of denitrifying bacteria detected in the FBC, and they had potential metabolic processes for nitrogen reduction. In the constructed wetland, cellular nitrogen compounds of S. potulacastum were enriched by overexpressed differentially expressed genes (DEGs), and the napA, narG, nirK, nirS, qnorB, and NosZ genes related to the denitrification process had more copies under FBC treatment. Nitrogen metabolism in root bacterial communities (RBCs) was activated in the FBC group compared with the control group without FBC. Finally, these FBCs improved the removal efficiencies of DTN (dissolved total nitrogen), NO3¯-N, NO2¯-N, and NH4+-N by 84.37 %, 87.42 %, 67.51 %, and 92.57 %, respectively, and their final concentrations met the emission standards of China. These findings indicate that adding FBC into S. potulacastum-constructed wetlands would result in high nitrogen removal efficiencies from wastewater and have large potential applications in further water treatment technology.

Profiles and spatial distributions of heavy metals, microbial communities, and metal resistance genes in sediments from an urban river

The occurrence and propagation of resistance genes due to exposure to heavy metals (HMs) in rivers is an emerging environmental issue. Little is known about resistance genes in microbial communities in river sediments with low HM concentrations. The profiles and spatial distributions of HMs, the microbial community, and metal resistance genes (MRGs) were analyzed in sediment samples from the Zhilong River basin in Yangjiang city, near the Pearl River Delta. Concentrations of copper (Cu), cadmium (Cd), lead (Pb), chromium (Cr), and nickel (Ni) were relatively low compared with those in other urban river sediments in China. HM chemical composition and fractions and the structure of the microbial community varied along the main channel, but the composition and abundance of MRGs were relatively homogeneous. Variations in HMs and microbial communities in mid- to upstream areas were related to the presence of tributaries, whose inputs were one of the major factors affecting HM chemical fractions and genera structure in mainstream sediments. There were no significant correlations (p < 0.05) between HM concentrations, bacterial communities, and the MRG profiles; thus, HM concentrations were not the main factor affecting MRGs in sediments. These results contribute to understanding the propagation of MRGs in urban rivers in developing cities.

Microbial carbon fixation and its influencing factors in saline lake water

Microbial carbon fixation in saline lakes constitutes an important part of the global lacustrine carbon budget. However, the microbial inorganic carbon uptake rates in saline lake water and its influencing factors are still not fully understood. Here, we studied in situ microbial carbon uptake rates under light-dependent and dark conditions in the saline water of Qinghai Lake using a carbon isotopic labeling (¹⁴C-bicarbonate) technique, followed by geochemical and microbial analyses. The results showed that the light-dependent inorganic carbon uptake rates were 135.17-293.02 μg C L^-1 h^-1 during the summer cruise, while dark inorganic carbon uptake rates ranged from 4.27 to 14.10 μg C L^-1 h^-1. Photoautotrophic prokaryotes and algae (e.g. Oxyphotobacteria, Chlorophyta, Cryptophyta and Ochrophyta) may be the major contributors to light-dependent carbon fixation processes. Microbial inorganic carbon uptake rates were mainly influenced by the level of nutrients (e.g., ammonium, dissolved inorganic carbon, dissolved organic carbon, total nitrogen), with dissolved inorganic carbon content being predominant. Environmental and microbial factors jointly regulate the total, light-dependent and dark inorganic carbon uptake rates in the studied saline lake water. In summary, microbial light-dependent and dark carbon fixation processes are active and contribute significantly to carbon sequestration in saline lake water. Therefore, more attention should be given to microbial carbon fixation and its response to climate and environmental changes of the lake carbon cycle in the context of climate change.

Tropical lacustrine sediment microbial community response to an extreme El Niño event

Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

Exploring the impacts of physicochemical characteristics and heavy metals fractions on bacterial communities in four rivers

Heavy metals contamination in sediment poses serious threats to bacterial communities that play critical roles in sediment biogeochemical processes. However, the physicochemical factors and the major heavy metals fractions that affect sediment bacterial communities are still unclear. Here, we performed heatmap and redundancy analyses to examine the effects of physico-chemical characteristics and heavy metals fractions on the sediment bacterial community from rivers in the UK (River Tyne and Ouseburn) and India (River Ganga and Yamuna). The results revealed that physicochemical characteristics and heavy metals fractions altered the diversity, richness, and structures of the bacterial community. Moreover, the fractions of Co, Zn, Pb, Cr, and Cu played significant roles in shaping the bacterial community structure, and physicochemical variables, particularly NH₄⁺-N and NO₂^--N, also influenced the bacterial diversity and structure. Firmicutes showed strong associations with both physicochemical factors and heavy metals fractions. Chloroflexi and Actinobacteriota can be used as biomarkers for Zn contamination. Overall, our study identified the significance of sediment chemical characteristics and heavy metals fractions in determining the bacterial community structure as well as bioremediation and environmental management of metals contaminated sites.

Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles

In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.

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.

Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary

Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO₂^-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.

Bacterial Metabolic Potential in Response to Climate Warming Alters the Decomposition Process of Aquatic Plant Litter—In Shallow Lake Mesocosms

Increased decomposition rates in shallow lakes with global warming might increase the release of atmospheric greenhouse gases, thereby producing positive feedback for global warming. However, how climate warming affects litter decomposition is still unclear in lake ecosystems. Here, we tested the effects of constant and variable warming on the bacterial metabolic potential of typically submerged macrophyte (Potamogeton crispus L.) litters during decomposition in 18 mesocosms (2500 L each). The results showed that warming reduced main chemoheterotrophic metabolic potential but promoted methylotrophy metabolism, which means that further warming may alter methane-cycling microbial metabolism. The nitrate reduction function was inhibited under warming treatments, and nitrogen fixation capability significantly increased under variable warming in summer. The changes in dissolved oxygen (DO), pH, conductivity and ammonium nitrogen driven by warming are the main environmental factors affecting the bacteria’s metabolic potential. The effects of warming and environmental factors on fermentation, nitrate reduction and ammonification capabilities in stem and leaf litter were different, and the bacterial potential in the stem litter were more strongly responsive to environmental factors. These findings suggest that warming may considerably alter bacterial metabolic potential in macrophyte litter, contributing to long-term positive feedback between the C and N cycle and climate.

Microbial ecology of biofiltration used for producing safe drinking water

Abstract

Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application.

Key points

• Biofilters are composed of complex microbiomes, primarily shaped by water quality.

• Conventional biofilters contribute to address safety challenges in drinking water.

• Studies may underestimate the active/functional role of microbiomes in biofilters.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12013-x.

16S rRNA gene sequencing analysis reveals an imbalance in the intestinal flora of Eriocheir sinensis with hepatopancreatic necrosis disease

Hepatopancreas necrosis disease (HPND) is a highly fatal disease that first appeared in Jiangsu Province, China, in 2015, and later spread to many other provinces, which had a severe impact on the culture of Chinese mitten crab (Eriocheir sinensis). Here, changes in the intestinal flora of healthy and HPND-affected Chinese mitten crabs were compared via 16S rRNA sequencing. Our findings indicated that Firmicutes, Bacteroidota, and Proteobacteria were the three dominant phyla in both healthy and HPND-affected crabs and exhibited no significant differences in α-diversity (richness p = 0.0892; evenness and diversity p = 0.0630). Furthermore, there were no significant changes in the abundance of Proteobacteria between the experimental groups. However, the abundance of Bacteroidota in the HPND group was significantly higher than that of the control group (HPND: 30.12%, Control: 16.60%), whereas the abundance of Firmicutes was significantly lower (HPND: 29.90%, Control: 50.55%). At the genus level, the abundance of Candidatus Bacilloplasma, Desulfovibrio, Bacteroides, and Aeromonas also differed significantly between groups (P < 0.05). Collectively, our study confirms an imbalance in the gut microbiota of Chinese mitten crabs with HPND and we speculate that this alteration may affect the metabolism and immune function of these organisms. Furthermore, we suspect that the structural changes in the intestinal flora of sick crabs observed in our study may be related to HPND.

Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season

Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH₄⁺, and NO₃^–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.

Response of bacterial community structure to different ecological niches and their functions in Korean pine forests

A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.

The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism

In densely populated cities with limited land, storage of surface water in underground spaces is a potential solution to meet the rising demand of clean water. In addition, due to the imperative need of renewable solar energy and limited land resources, the deployment of floating solar photovoltaic (PV) systems over water has risen exponentially. In both scenarios, microbial communities in the water do not have access to sunlight. How the absence of sunlight influences microbial community function and the water quality is largely unknown. The objective of this study was to reveal microbial processes in surface water stored in the dark and water quality dynamics. Water from a freshwater reservoir was stored in the dark or light (control) for 6 months. Water quality was monitored at regular intervals. RNA sequencing was performed on the Illumina MiSeq platform and qPCR was used to substantiate the findings arising from the sequencing data. Our results showed that storage of surface water in the dark resulted in the accumulation of nitrate in the water. Storage in the dark promoted the decay of algal cells, increasing the amount of free nitrogen in the water. Most of the free nitrogen was eventually transformed into nitrate through microbial processes. RNA sequencing-based microbial community analyses and pure culture experiments using nitrifying bacteria Nitrosomonas europaea and Nitrobacter sp. revealed that the accumulation of nitrate in the dark was likely due to an increase in nitrification rate and a decrease in the assimilation rate of nitrate back into the biomass. IMPORTANCE Microbial communities play an essential role in maintaining a healthy aquatic ecosystem. For example, in surface water reservoirs, microorganisms produce oxygen, break down toxic contaminants and remove excess nitrogen. In densely populated cities with limited land, storing surface water in underground spaces and deploying floating solar photovoltaic (PV) systems over water are potential solutions to address water and energy sustainability challenges. In both scenarios, surface water is kept in the dark. In this work, we revealed how the absence of sunlight influences microbial community function and water quality. We showed that storage of surface water in the dark affected bacterial activities responsible for nitrogen transformation, resulting in the accumulation of nitrate in the water. Our findings highlight the importance of monitoring nitrate closely if raw surface water is to be stored in the dark and the potential need of downstream treatment to remove nitrate.

K-strategy species plays a pivotal role in the natural attenuation of petroleum hydrocarbon pollution in aquifers

The natural attenuation of petroleum hydrocarbons is inseparable from the action of microorganisms, while the degradation methods and ecological strategies of microorganisms in petroleum-contaminated aquifers are still under debate. In the present study, 16 S rRNA sequencing and quantitative real-time polymerase chain reaction were used to assess the potential microbial degradation of petroleum hydrocarbons, and the ecological strategy of microorganisms under petroleum stress was analyzed through a co-occurrence network. The results showed that the microbial community in sediments exhibit higher efficiency and stability and stronger ecological function than that in groundwater. Keystone species coordinated with the community to execute ecosystem processes and tended to choose a K-strategy to survive, with the aquifer sediment being the main site of petroleum hydrocarbon degradation. Under natural conditions, the presence of petroleum hydrocarbons at concentrations higher than 126 μg kg^-1 and 5557 μg kg^-1 was not conducive to the microbial degradation of polycyclic aromatic hydrocarbons and alkanes, respectively. These results can be used as a reference for an enhanced bioremediation of contaminated groundwater. Overall, these findings provide support to managers for developing environmental management strategies.

Ammonia stress influences intestinal histomorphology, immune status and microbiota of Chinese striped-neck turtle (Mauremys sinensis)

Ammonia is one of major pollutants in aquatic environment that induces severe stress and toxicity to organisms in aquatic system. The intestine acts a major defense line that protects living organisms from biotic and abiotic stresses. In the current study, we examined the effects of ammonia on intestinal histomorphology, transcriptional levels of intestinal barrier functioning genes and intestinal microbiota of Chinese striped-neck turtle (Mauremys sinensis). Thus, the turtles were placed in water with addition of ammonia at 0 (control), 100, 200 mg L^-1 for 30 days. Our findings showed that ammonia reduced the villus length and induced the inflammatory cells appearance. In addition, the epithelial tight junction genes, claudin and zonola occludin significantly downregulated in ammonia exposed groups as compared to control group (P < 0.05). Similarly, the mRNA expression levels of MUC-2 gene also significantly decreased in ammonia treated groups (P < 0.05). However, the expression levels of intestinal immune related genes such as IL-10, IL-12, TGF-β1, TNF-α and IFN-γ significantly increased (P < 0.05). Furthermore, ammonia changed gut microbial diversity variedly. At the phylum levels, Firmicutes increased, whereas Bacteroidota, Desulfobacterota and Synergistota decreased significantly. Likewise, Lachnospiraceae, Bacteroides, Eubacteriaceae, Desulfovibrio, Muribaculaceae, Bilophila, Cloacibacillus, Christensenellaceae, Ruminococcus and Parabacteroides decreased while, Romboutsia and Turicibacter increased in ammonia exposed groups. In conclusion, ammonia at 100 and 200 mg L^-1 could alter the intestinal barrier function and change the composition of intestinal microbiota, leading to bad health status in M. sinensis.

Dynamic changes in microbial community structure in farming pond water and their effect on the intestinal microbial community profile in juvenile common carp (Cyprinus carpio L.)

Water quality parameter dynamics, gut, sediment and water bacteria communities were studied to understand the environmental influence on the gut microbial community of a new strain of Huanghe common carp. A total of 3,384,078 raw tags and 5105 OTUs were obtained for the gut, water and sediment bacteria. The water quality had a stronger influence on the water bacteria community than gut and sediment bacteria communities. The ambient water quality parameters also significantly influenced the water and sediment bacteria communities. Comparing the gut, sediment, and water microbial communities, a relationship was found among them. However, gut bacteria were more closely related to sediment bacterial communities than to water bacteria communities. The results showed that the top three bacterial taxa were identical in gut and sediment samples in the early days of rearing. Interestingly, bacterial communities in the carp gut, water, and sediment had different adaptabilities to variations in environmental factors.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Different distribution patterns of microorganisms between aquaculture pond sediment and water

Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.

How do phytogenic iron oxide nanoparticles drive redox reactions to reduce cadmium availability in a flooded paddy soil?

While soil redox reactions are known to determine heavy metal soil availability, specific information on how iron (Fe) nanomaterials reduce heavy metal availability in bulk soil and in the rice rhizosphere is limited. Here a pot experiment was performed to examine the effect of phytogenic iron oxide nanoparticles (PION) on the availability of cadmium (Cd) in flooded soil. PION significantly reduced soil Cd availability, with Cd in rice shoot being 2.72, 1.21 and 0.40 mg kg^-1 for the control, 1 and 5% PION treatments, respectively. In addition, following PION application, Illumina MiSeq sequencing indicated that the abundance of Lentimicrobium and Anaeromyxobacter increased, while the abundance of Geobacter and Thiobacillus decreased. Structural equation model analysis revealed that redox reactions, driven by carbon, nitrogen, iron and sulfur cycling related functional groups, played an important role in the immobilization of Cd in flooded soil. Co-occurrence network analysis showed that the rhizosphere soil was far more complex than the bulk soil. Overall, PION addition enhanced the inherent soil microbe's activity and the involved in reducing Cd availability to rice by converting mobile Cd into stabler forms. This initial result paves the way for establishing a practical low-cost remediation strategy for Cd contaminated paddy soils.

Community structure of bacterioplankton and its relationship with environmental factors in the upper reaches of the Heihe River in Qinghai Plateau

Planktonic microorganisms play a key role in the biogeochemical processes of the aquatic system, and they may be affected by many factors. High-throughput sequencing technology was used in this study to investigate and study the bacterioplankton community of water bodies in the upper reaches of the Heihe River Basin in Qinghai Plateau. Results showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the predominant phyla in this river section, while the main genera are Thiomonas, Acidibacillus, Acidocella, Rhodanobacter, Acidithiobacter and Gallionella, which are autochthonous in the acid-mine drainage. Additionally, total nitrogen, total phosphorus, permanganate index and pH are significantly correlated with the bacterioplankton abundance and are the main limiting factors for the spatial distribution of the bacterioplankton. PICRUSt inferred that the mainstream microbial assemblages had a higher abundance of KOs belong to metabolism of terpenoids and polyketides, while the tributary had higher abundance of KOs belong to the immune system. The relationship between bacterioplankton community composition and environmental factors in the Heihe River basin was discussed for the first time in this study, which provides a theoretical basis for the healthy, orderly development of the water environment in the Heihe River Basin.

Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes

Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.

Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings

Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.

Surviving onshore soil microbial communities differ among the Qing-Tibetan lakes with different salinity

Little is known about the onshore microbial contribution to the microbial communities in nearby lakes and its response to salinity. In this study, transplanting experiments were established by caging onshore soils with dialysis bags followed by in situ 50-day incubation in nearby lakes with different salinity on the Qinghai-Tibetan Plateau. At the end of the experiment, geochemical and microbial analyses were performed on the original soils, caged soils and lake waters and sediments at the incubation sites. The results showed that the salinity increased significantly (P < 0.05) in the caged soils and such salinity increases showed significant (P < 0.05) positive correlation with the salinity of the studied lakes. The microbial community composition and predicted functions in the caged soils were significantly (P < 0.05) changed in comparison with their corresponding original soils, and such variation could be mainly explained by the succession of members of the Proteobacteria, Bacteroidetes and Actinobacteria from the original soils to their corresponding caged soils. The onshore microbial contribution appeared to be limited (up to 11.2% for sediment and negligible for water, respectively) to nearby lake microbial communities. Nevertheless, the survival of onshore soil microbial communities was mainly limited by the salinity of the receiving lakes.

Bacterial community rather than metals shaping metal resistance genes in water, sediment and biofilm in lakes from arid northwestern China

Lakes in arid northwestern China are valuable freshwater resources that drive socioeconomic development. Environmental pollution can significantly influence the composition of microbial communities and the distribution of functional genes in lakes. This study investigated heavy metal pollution to identify possible correlations with metal resistance genes (MRGs) and bacterial community composition in water, sediment and biofilm samples from Bosten Lake and Ebi Lake in northwestern China. High levels of zinc were detected in all samples. However, the metals detected in the sediment samples of both lakes were determined to be at low risk levels according to an ecological index. The mercury resistance gene subtype merP had the greatest average abundance (4.61 × 10^-3 copies per 16S rRNA) among all the samples, followed by merA and merC. The high abundance of merA in the pelagic zone rather than in benthic sediment suggests that the pelagic microbial community was important in mercury reduction. Proteobacteria were the main phylum found in the microbial communities in all samples. However, microbial communities in most of the water, sediment and biofilm samples had different compositions, indicating that the habitat niche plays an important role in shaping the bacterial communities in lakes. The microbial community, rather than the heavy metals, was the main driver of MRG distribution. The abundances of some bacterial genera involved in the decomposition of organic matter and the terrestrial nitrogen cycle were negatively correlated with heavy metals. This result suggests that metal pollution can adversely affect the biogeochemical processes that occur in lakes.

Bacterial community and eutrophic index analysis of the East Lake

This study investigated bacterial diversities in surface water and sediment of the East Lake located in Wuhan, China. Bacterial community of lake water was mainly composed of Proteobacteria (31.1%), Actinobacteria (25.0%), Bacteroidetes (18.6%), Cyanobacteria (18.9%), Planctomycetes (2.4%) and Verrucomicrobia (1.4%), while more abundant and richer bacterial community was found in the sediments, e.g. 46.1% for Proteobacteria, 10.1% for Bacteroidetes, 8.7% for Chloroflexi, 8.4% for Acidobacteria, 5.0% for Cyanobacteria, 3.6% for Firmicutes, 3.1% for Planctomycetes, 2.8% for Actinobacteria and 2.3% for Nitrospirae. The decreased bacterial community richness and abundance was found in poor-quality water. Moreover, Bacterial Eutrophic Index (BEI) was firstly put forward to quantitatively describe the water quality of a freshwater ecosystem, which was defined as the ratio of abundance of Cyanobacteria and Actinobacteria in water. It was demonstrated BEI was well correlated to Carlson's Trophic State Index (TSI) (Spearman's ρ = 0.848, p < 0.01). The average TSI and BEI were determined to be 64 and 0.81, suggesting that East Lake could be classified as a medium eutrophic level.