Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes

Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China

Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.

Prokaryotic Communities Vary with Cultivation Modes of Shrimp (Litopenaeus vannamei)

In response to the growing market demand for Litopenaeus vannamei, a variety of single-species, high-density, intensive, and high-yield aquaculture modes have arisen. These aquacultural systems are teeming with microorganisms, which play roles in water quality and host health. To uncover the prokaryotic community composition across cultivation modes, we investigated the prokaryotic community composition at two fractionated sizes in the water of three culture modes of Litopenaeus vannamei, including high-level pond culture, biofloc technology (BFT), and pond culture. The 16S rRNA gene high-throughput sequencing results indicated that the taxa particularly enriched by high-level pond culture modes were mainly Deltaproteobacteria, while Alpha- and Gammaproteobacteria and Flavobacteria were enriched in the BFT culture modes. The pond culture enriched Bacteroidetes, Sphingobacteriia, Actinobacteria, and Cyanobacteria. PCoA analysis showed that for the pond samples, there were significant differences in the community composition compared with the samples from the other two modes. However, the high-level pond and biofloc samples showed similar community compositions. Furthermore, Canonical Correspondence Analysis (CCA) and Variance Partitioning Analysis (VPA) revealed that NH4+-N, salinity (Sal), and NO3--N were key factors affecting the aquaculture communities.

Phyllospheric application of Bacillus mucilaginosus mediates the recovery of tea plants exposed to low-temperature stress by alteration of leaf endophytic community and plant physiology

BACKGROUND

In winter, tea plants are highly susceptible to low-temperature freezing damage. The rapid recovery of tea plant vigor in spring is crucial for tea yield and quality. Some studies have reported that Bacillus mucilaginosus could improve the stress resistance of plants. However, there were no reports on the effect of B. mucilaginosus on the recovery of tea plant vigor after low-temperature stress. This study firstly used different concentrations of B. mucilaginosus to spray tea leaves and used 16S rRNA high-throughput sequencing technology to study the impact of different treatments on tea leaf endophytic populations. Meanwhile, physiological indexes such as Soil and plant analyzer development values (SPAD), maximum photochemical quantum yield of PS II (Fv/Fm), and superoxide dismutase (SOD) were measured and analyzed in tea plant leaves of different treatments, and the correlation between them and the bacterial community was studied.

RESULTS

Microbial results showed that the diversity of leaf endophytic populations treated with different concentrations of Bacillus mucilaginosus (T1, T2, T3) was higher than that in control group (CK) leaves, and T2 treatment had the highest diversity. The dominant bacterial phyla of all samples were Proteobacteria, Actinobacteriota, Firmicutes, and Bacteroidota. At the phylum level, the relative abundance of Actinobacteriota, Firmicutes, and Bacteroidota in leaves treated with B. mucilaginosus was significantly higher than that in the control. At the genus level, the relative abundance of Paenibacillus, Nocardioides, and Marmoricola in leaves treated with B. mucilaginosus was significantly higher than that in the control. Different concentrations of B. mucilaginosus affected the distribution of leaf endophytic populations. At the level of bacterial function, abundant metabolic functional features were observed, including amino acid transport and metabolism, as well as energy production and conversion, indicating that bacterial metabolism in tea plant leaf samples tends to be vigorous. The treatment with B. mucilaginosus significantly increased the activity of antioxidant enzymes and osmolyte content, promoted the recovery of Fv/Fm in tea plants after low-temperature stress, and improved the resistance of tea leaves to low-temperature stress, thereby promoting recovery.

CONCLUSIONS

This study showed that B. mucilaginosus could significantly change the community structure of leaf endophytic populations, and increase antioxidant enzyme activity and osmolyte content in tea plants after low-temperature stress, promoting the rapid recovery of photosynthesis, and thereby benefiting the recovery of tea plant leaves. This study provided a theoretical basis for the application of B. mucilaginosus in practical production and also provided new ideas for the recovery of tea plants exposed to low-temperature stress.

Soil Bacterial Community Characteristics and Functional Analysis of Estuarine Wetlands and Nearshore Estuarine Wetlands in Qinghai Lake

Qinghai Lake, the largest inland saline lake in China, plays a vital role in wetland carbon cycling. However, the structure and function of soil bacterial communities in its estuarine and nearshore estuarine wetlands remain unclear. This study examined the effects of wetland type and soil depth on bacterial diversity, community composition, and functional potential in the Shaliu, Heima, and Daotang River wetlands using high-throughput sequencing. The results showed that wetland type and soil depth significantly influenced bacterial communities. Nearshore wetlands exhibited lower bacterial diversity in the 0-10 cm layer, while deeper soils (10-20 cm) showed greater regional differentiation. Estuarine wetlands were enriched with Proteobacteria, Actinobacteriota, and Chloroflexi, whereas nearshore wetlands were dominated by Actinobacteriota and Cyanobacteria. Functionally, estuarine wetlands had higher sulfate reduction and anaerobic decomposition potential, with Desulfovibrio, Desulfobacter, and Desulfotomaculum regulating sulfur cycling and carbon decomposition. In contrast, nearshore wetlands showed greater nitrogen fixation and organic matter degradation, facilitated by Rhizobium, Azotobacter, Clostridium, and nitrogen-fixing Cyanobacteria (e.g., Anabaena, Nostoc). Microbial metabolic functions varied by depth: surface soils (0-10 cm) favored environmental adaptation and organic degradation, whereas deeper soils (10-20 cm) exhibited lipid metabolism and DNA repair strategies for low-oxygen adaptation. These findings highlight the spatial heterogeneity of bacterial communities and their role in biogeochemical cycles, providing insights into wetland carbon dynamics and informing conservation strategies.

Microbial Metabolic Limitations and Their Relationships with Sediment Organic Carbon Across Lake Salinity Gradient in Tibetan Plateau

Inland lakes, contributing substantially to the global storage of sediment organic carbon (SOC), are subject to marked changes in salinity due to climate warming. The imbalance in the supply of resources, such as carbon, nitrogen, and phosphorus, in sediments leads to microbial metabolic limitations (MMLs). This, in turn, triggers the secretion of extracellular enzymes by microorganisms to mine for deficient resources by decomposing complex organic carbon. This process is a rate-limiting step in the degradation of organic carbon and, as a result, has the potential to regulate organic carbon stocks. However, the general understanding of MML patterns and their relationships with SOC content along lake salinity gradients remains elusive. This study examined 25 lakes on the Tibetan Plateau with salinity ranging from 0.13‱ to 31.06‱, analyzing MMLs through enzymatic stoichiometry. The results showed that sediment microbial metabolism was mainly limited by carbon and nitrogen, with stronger limitations at higher salinity. Water salinity and sediment pH were the main factors influencing microbial limitations, either directly or indirectly, through their effects on nutrients and microbial diversity. Additionally, the SOC content was negatively correlated with microbial carbon limitation, a relationship weakened when salinity and pH were controlled. These findings suggest that the decrease in SOC with increased salinity or pH could be driven by stronger microbial carbon limitations, offering insights into the impact of salinity changes on SOC stocks in inland lakes due to climate change.

Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

Spatiotemporal variation in biomass abundance of different algal species in Lake Hulun using machine learning and Sentinel-3 images

Climate change and human activities affect the biomass of different algal and the succession of dominant species. In the past, phytoplankton phyla inversion has been focused on oceanic and continental shelf waters, while phytoplankton phyla inversion in inland lakes and reservoirs is still in the initial and exploratory stage, and the research results are relatively few. Especially for mid-to-high latitude lakes, the research is even more blank. Therefore, this study proposes a machine learning method based on OLCI/Sentinel-3 satellite imagery to retrieve algal biomass abundance. Remote sensing models were developed to estimate the biomass abundance of three major algal groups: Cyanophyta, Chlorophyta, and Bacillariophyta. This study compared and evaluated 6 commonly used machine learning models, including extreme gradient boosting (XGBoost), support vector regression (SVR), backpropagation neural network (BP), gradient boosting decision tree (GBDT), random forest (RF), and categorical boosting (CatBoost). The results indicated that XGBoost exhibited the highest accuracy (R2 = 0.92, RMSE = 1.78%, MAPE = 9.96%) in estimating Cyanophyta's biomass abundance. The RF model demonstrated the highest accuracy for estimating Chlorophyta's biomass abundance (R2 = 0.72, RMSE = 6.57%, MAPE = 50.8%), while the GBDT model exhibited the highest accuracy for estimating Bacillariophyta's biomass abundance (R2 = 0.9, RMSE = 4.66%, MAPE = 47.87%). The models were subsequently applied to all cloud-free OLCI images from Hulun Lake during the ice-free periods from 2016 to 2023, producing spatiotemporal distribution maps of the different phytoplankton biomass abundance. Cyanophyta dominated the biomass abundance (44.62 ± 3.47%), followed by Bacillariophyta (36.35 ± 2.68%), and Chlorophyta had the lowest proportion (10.42 ± 1.08%). Together, these three algae groups constituted 91.4 ± 1.55% of all phytoplankton in Hulun Lake. Significant annual variations in the biomass abundance of Cyanophyta and Bacillariophyta were observed, whereas those of Chlorophyta remained stable. Additionally, this study examined the effects of climatic factors and water quality parameters on the biomass abundance of algae. The findings suggest that temperature, wind speed, and atmospheric pressure are critical factors influencing the biomass abundance of the different algae groups. This study not only fills the gaps in the related field, but also provides a new method for monitoring algae, as well as a strong support for realizing the goals of sustainable management of water resources and ecological protection.

Microbiota Composition Associates With Mosquito Productivity Outcomes in Belowground Larval Habitats

Vector mosquitoes are well-adapted to habitats in urban areas, including belowground infrastructure such as stormwater systems. As a major source of larval habitat in population centers, control of larval populations in stormwater catch basins is an important tool for control of vector-borne disease. Larval development and adult phenotypes driving vectorial capacity in mosquitoes are modulated by the larval gut microbiota, which is recruited from the aquatic environment in which larvae develop. Laboratory studies have quantified microbe-mediated impacts on individual mosquito phenotypes, but more work is needed to characterise how microbiota variation shapes population-level outcomes. Here, we evaluated the relationship between habitat microbiota variation and mosquito population dynamics by simultaneously characterising microbiota diversity, water quality, and mosquito productivity in a network of stormwater catch basins in the Chicago metropolitan area. High throughput sequencing of 16S rRNA gene amplicons from water samples collected from 60 basins over an entire mosquito breeding season detected highly diverse bacterial communities that varied with measures of water quality and over time. In situ measurements of mosquito abundance in the same basins further varied by microbiota composition and the relative abundance of specific bacterial taxa. Altogether, these results illustrate the importance of habitat microbiota in shaping ecological processes that affect mosquito populations. They also lay the foundation for future studies to characterise the mechanisms by which specific bacterial taxa impact individual and population-level phenotypes related to mosquito vectorial capacity.

Variation of bacterial community diversity and composition in saline-alkali soils reclaimed with flood irrigation and crop cultivation is driven by salinity and edaphic factors

Reclamation is crucial for improving the fertility and productivity of saline-alkali soils, but the evolution of soil bacterial communities during the course of reclamation, which is an important feedback of soil micro-ecosystem, has received little attention. This study was conducted to investigate the variation of bacterial community diversity and composition in reclaimed saline-alkali soils based on space-for-time substitution, elucidate the underlying ecological mechanisms of bacterial community assembly processes, and identify the key driving factors of bacterial community evolution. The soil bacterial communities in undeveloped saline-alkali land and farmlands with different reclamation history (1-4, 5-6, and 10-25 years) in the Yellow River Delta, China, was analyzed by 16S rRNA gene amplicon sequencing. Soil bacterial diversity was found to increase significantly with reclamation history, and the entire bacterial community composition varied remarkably in the saline-alkali soils at different stages of reclamation. Halophilic and halotolerant bacteria dominated in the soils of undeveloped saline-alkali land (33.7 %), but their abundance diminished largely in the reclaimed soils. Analysis of bacterial community assembly processes suggested that heterogeneous selection dominated the change of bacterial communities in the saline-alkali soils that had been reclaimed for 1-4 years (52.8 %), 5-6 years (93.1 %), and 10-25 years (94.4 %). Salinity, soil organic carbon, pH, and moisture content were found to be the key environmental factors driving the evolution of bacterial communities in the reclaimed saline-alkali soils. While salinity directly shaped the bacterial community diversity, the other key drivers primarily governed the composition of bacterial communities in the saline-alkali soils during reclamation. These findings shed light on the probable ecological mechanisms of assembly processes and the environmental factors driving the soil bacterial communities during reclamation of saline-alkali lands, which could help better understand the evolution of soil bacterial communities under declining saline stress and optimize strategies to improve the agroecosystem health of saline-alkali lands.

Functional traits and adaptation of lake microbiomes on the Tibetan Plateau

BACKGROUND

Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.

RESULTS

Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.

CONCLUSIONS

Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.

Low salinity stress increases the risk of Vibrio parahaemolyticus infection and gut microbiota dysbiosis in Pacific white shrimp

BACKGROUND

Extreme precipitation events often cause sudden drops in salinity, leading to disease outbreaks in shrimp aquaculture. Evidence suggests that environmental stress increases animal host susceptibility to pathogens. However, the mechanisms of how low salinity stress induces disease susceptibility remain poorly understood.

METHODS

We investigated the acute response of shrimp gut microbiota exposed to pathogens under low salinity stress. For comparison, shrimp were exposed to Vibrio infection under two salinity conditions: optimal salinity (Control group) and low salinity stress (Stress group). High throughput 16S rRNA sequencing and real-time PCR were employed to characterize the shrimp gut microbiota and quantify the severity level of Vibrio infection.

RESULTS

The results showed that low salinity stress increased Vibrio infection levels, reduced gut microbiota species richness, and perturbed microbial functions in the shrimp gut, leading to significant changes in lipopolysaccharide biosynthesis that promoted the growth of pathogens. Gut microbiota of the bacterial genera Candidatus Bacilliplasma, Cellvibrio, and Photobacterium were identified as biomarkers of the Stress group. The functions of the gut microbiota in the Stress group were primarily associated with cellular processes and the metabolism of lipid-related compounds.

CONCLUSIONS

Our findings reveal how environmental stress, particularly low salinity, increases shrimp susceptibility to Vibrio infection by affecting the gut microbiota. This highlights the importance of avoiding low salinity stress and promoting gut microbiota resilience to maintain the health of shrimp.

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme environments, remain obscured. Here we unravel the metabolic potential of microbial dark matters (MDMs) in four deep-inland hypersaline lakes in Xinjiang, China. Utilizing metagenomic binning, we uncovered a rich diversity of 3030 metagenome-assembled genomes (MAGs) across 82 phyla, revealing a substantial portion, 2363 MAGs, as previously unclassified at the genus level. These unknown MAGs displayed unique distribution patterns across different lakes, indicating a strong correlation with varied physicochemical conditions. Our analysis revealed an extensive array of 9635 biosynthesis gene clusters (BGCs), with a remarkable 9403 being novel, suggesting untapped biotechnological potential. Notably, some MAGs from potentially new phyla exhibited a high density of these BGCs. Beyond biosynthesis, our study also identified novel biodegradation pathways, including dehalogenation, anaerobic ammonium oxidation (Anammox), and degradation of polycyclic aromatic hydrocarbons (PAHs) and plastics, in previously unknown microbial clades. These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation, emphasizing the untapped potential of microbial diversity in hypersaline environments.

Shifts in Microbial Community Structure and Co-occurrence Network along a Wide Soil Salinity Gradient

The response of microbiomes to salinity has been clarified in different geographic scales or ecosystems. However, how soil microbial community structure and interaction respond to salinity across wide salinity range and climatic region is still unclearly resolved. To address this issue, we examined the microbial community's composition in saline soils from two climatic regions (coastal wetland and arid desert). Our research confirms that soil salinity had a negative effect on soil nutrient content. Salinity decreased the relative abundance of bacteria, but increased archaea abundance, leading to the shifts from bacteria dominant community to archaea dominant community. Low-water medium-salinity soil (LWMS) had the most complex archaeal community network, whereas for bacteria, the most complex bacterial community network was observed in low-water high-salinity soils (LWHS). Key microbial taxa differed in three salinity gradients. Salinity, soil water content, pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors for the composition of archaeal and bacterial community. Salinity directly affected archaeal community, but indirectly influenced bacteria community through SOC; pH affected archaeal community indirectly through TN, but directly affected bacterial community. Our study suggests that soil salinity dramatically influences diversity, composition, and interactions within the microbial community.

Response of microbial diversity and function to the degradation of Barkol Saline Lake

Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.

Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity

Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.

Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions

Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.

Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach

The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments

The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.

Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient

Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.

Horizontal and Vertical Comparison of Microbial Community Structures in a Low Permeability Reservoir at the Local Scale

Petroleum microorganisms play a crucial role in the application of microbial-enhanced oil recovery, and the community structures of petroleum microorganisms have been widely studied. Due to variations in reservoir geological conditions, reservoir microbial communities exhibit unique characteristics. However, previous studies have primarily focused on microbial community changes within a single well, a single block, and before and after water flooding, and thus, cross-horizon and cross-regional comparative studies of in situ microbial communities are lacking. In this study, the 16S rRNA full-length sequencing method was adopted to study bacterial communities in crude oil samples taken from two wells at the same depths (depths of 2425 m and 2412 m) but approximately 20 km apart in the Hujianshan oilfield, located in the Ordos Basin. At the same time, the results were combined with another layer of research data from another article (from a depth of 2140 m). The aim was to compare the differences in the microbial community structures between the oil wells on a horizontal scale and a vertical scale. The results revealed that there were minimal differences in the microbial community structures that were influenced by the horizontal distances within a small range (<20 km), while differences were observed at a larger spatial scale. However, the dominant bacteria (Proteobacteria and Bacteroidetes) in the different oilfields were similar. Vertical depth variations (>300 m) had significant impacts on the communities, and this was mainly controlled by temperature. The greater the depth, the higher formation temperature, leading to an increase in thermophilic and anaerobic bacteria within a community.

Sediment Bacteria in the Alpine Lake Sayram: Vertical Patterns in Community Composition

Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm long sediment core from the center of Lake Sayram, the largest alpine lake in Xinjiang Uygur autonomous area, China, and used 16S rRNA gene-targeted amplicon sequencing to examine the bacterial populations. The results showed that bacterial diversity, as estimated by the Shannon index, was highest at the surface (6.9849 at 0-4 cm) and gradually decreased with depth up to 3.9983 at 68-72 cm, and then increased to 5.0927 at 96-100 cm. A total of 56 different phyla and 1204 distinct genera were observed in the sediment core of Lake Sayram. The bacterial community structure in the sediment samples from the various layers was dissimilar. The most abundant phyla in alpine Lake Sayram were Proteobacteria, Firmicutes, and Planctomycetes, accounting for 73%, 6%, and 4% of the total reads, respectively; the most abundant genera were Acinetobacter, Hydrogenophaga, and Pseudomonas, accounting for 18%, 12%, and 8% of the total reads, respectively. Furthermore, the relative abundance of Acinetobacter increased with sediment depth, while the relative abundance of Hydrogenophaga and Pseudomonas decreased with sediment depth. Our findings indicated that the nitrate-reducing bacteria (Acinetobacter, Hydrogenophaga, and Pseudomonas) may be prevalent in the sediment core of Lake Sayram. Canonical correspondence analysis showed that carbonate and total organic carbon (TOC) may be the main environmental factors affecting the vertical patterns of bacterial community composition (BCC) in the sediment of Lake Sayram. This work significantly contributes to our understanding of the BCC of sediments from alpine lakes in arid and semiarid regions.

Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = -0.924, p < 0.01; r = -0.800, p < 0.01; r = -0.933, p < 0.01) and salinity (r = -0.615, p < 0.05; r = -0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Different Responses of Bacteria and Archaea to Environmental Variables in Brines of the Mahai Potash Mine, Qinghai-Tibet Plateau

Salt mines feature both autochthonous and allochthonous microbial communities introduced by industrialization. It is important to generate the information on the diversity of the microbial communities present in the salt mines and how they are shaped by the environment representing ecological diversification. Brine from Mahai potash mine (Qianghai, China), an extreme hypersaline environment, is used to produce potash salts for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. In this study, using high-throughput 16S rRNA gene amplicon sequencing and estimation of physicochemical variables, we examined brine samples collected from locations with the gradient of industrial activity intensity and discrete hydrochemical compositions in the Mahai potash mine. Our findings revealed a highly diverse bacterial community, mainly composed of Pseudomonadota in the hypersaline brines from the industrial area, whereas in the natural brine collected from the upstream Mahai salt lake, most of the 16S rRNA gene reads were assigned to Bacteroidota. Halobacteria and halophilic methanogens dominated archaeal populations. Furthermore, we discovered that in the Mahai potash mining area, bacterial communities tended to respond to anthropogenic influences. In contrast, archaeal diversity and compositions were primarily shaped by the chemical properties of the hypersaline brines. Conspicuously, distinct methanogenic communities were discovered in sets of samples with varying ionic compositions, indicating their strong sensitivity to the brine hydrochemical alterations. Our findings provide the first taxonomic snapshot of microbial communities from the Mahai potash mine and reveal the different responses of bacteria and archaea to environmental variations in this high-altitude aquatic ecosystem.

Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture

AIM

The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.

METHODS AND RESULTS

Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.

CONCLUSIONS

The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.

VP3 Phage Combined with High Salt Promotes the Lysis of Biofilm-Associated Vibrio cholerae

Cholera, caused by pathogenic Vibrio cholerae, poses a significant public health risk through water and food transmission. Biofilm-associated V. cholerae plays a crucial role in seasonal cholera outbreaks as both a reservoir in aquatic environments and a direct source of human infection. Although VP3, a lytic phage, shows promise in eliminating planktonic V. cholerae from the aquatic environment, its effectiveness against biofilm-associated V. cholerae is limited. To address this limitation, our proposed approach aims to enhance the efficacy of VP3 in eliminating biofilm-associated V. cholerae by augmenting the availability of phage receptors on the surface of Vibrio cholerae. TolC is a receptor of VP3 and a salt efflux pump present in many bacteria. In this study, we employed NaCl as an enhancer to stimulate TolC expression and observed a significant enhancement of TolC expression in both planktonic and biofilm cells of V. cholerae. This enhancement led to improved adsorption of VP3. Importantly, our findings provide strong evidence that high salt concentrations combined with VP3 significantly improve the elimination of biofilm-associated V. cholerae. This approach offers a potential strategy to eliminate biofilm-formation bacteria by enhancing phage-host interaction.

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.

Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment

BACKGROUND

High mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment.

METHODS

Five sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks.

RESULTS

Almost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils.

CONCLUSIONS

The results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.

Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes

Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community's composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion.

Active microbial arsenic methylation in saline-alkaline paddy soil

Seawater rice has been cultivated to ensure food security. The salt-tolerant rice strains are resistant to saline and alkali but may be vulnerable to elevated arsenic (As) near coastal regions. Herein, the saline-alkaline paddy soil was incubated with natural irrigation river for three months to explore the mobility and transformation of As. The incubation results showed that 65 ± 1.2 % solid-bound As(V) was reduced to As(III) within two weeks with the release of As(III) to porewater. The dissolved As(III) was methylated after two weeks, resulting in dimethyl arsenate (DMA) as the dominant As species (87 %-100 %). The elevated As methylation was attributed to the most abundant arsenite methyltransferase gene (arsM) (4.1-10.4 × 10⁷/g dry soil), over three orders of magnitude higher than As redox-related genes. The analysis of arsM operational taxonomic units (OTUs) suggested the highest sequence similarity to Proteobacteria (25.7-39.5 %), Actinobacteria (24.9-30.5 %), Gemmatimonadetes (7.5-11.9 %), Basidiomycota (5.1-12.5 %), and Chloroflexi (4.1-8.7 %). Specifically, Chloroflexi and Actinobacteria are salt-tolerant bacteria, probably responsible for As methylation. The As in grain was within a safe regulatory level, and the dominance of methylated As in porewater did not enhance its accumulation in rice grains.

Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments

The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.

Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species

It is of great significance to explore the structure and salinity response of microbial communities in salt-tolerant plants to understand the mechanisms of plant-microbe interactions. Herein, we investigated the phyllosphere and rhizosphere microbial communities of Avicennia marina, a pioneer salt-tolerant plant, at three sites with different salinities in the coastal intertidal zone. The results showed that salinity had different effects on phyllosphere and rhizosphere microbial communities and had a greater impact on bacterial communities and bacterial network interactions. The rhizosphere bacterial community alpha diversity significantly increased with increasing salinity. Moreover, the relative abundance of Proteobacteria decreased significantly, while that of Bacteroidota and Actinobacteriota, with stronger salt tolerance and nutrient utilization capacity, increased significantly. Functional prediction indicated that the microbial communities could produce catalase, peroxidase, 3-phytase, and tryptophan synthase, which may exert potential antistress and growth-promoting functions. Among them, catalase, 3-phytase, alkaline phosphatase, and acid phosphatase increased significantly in the phyllosphere and rhizosphere bacterial communities and the phyllosphere fungal community with increasing salinity. Importantly, the dominant taxa Kushneria and Bacillus, which are salt tolerant and growth promoting, were isolated from the phyllosphere and rhizosphere, respectively, and verified to have the ability to alleviate salt stress and promote the growth of rice. IMPORTANCE Avicennia marina is a pioneer salt-tolerant plant in coastal intertidal mangroves, an efficient blue carbon ecosystem. It is of great importance to explore how salinity affects the phyllosphere and rhizosphere microbial communities of A. marina. This study showed that the microbial communities in the phyllosphere and rhizosphere of A. marina had different constitutive properties, adaptive network interactions, and potential stress-promoting functions. Furthermore, the dominant bacteria Kushneria and Bacillus were obtained from the phyllosphere and rhizosphere, respectively, and their coculture with rice could effectively alleviate salt stress and promote rice growth. Additionally, the effects of salinity changes on microbial community structure, associations, and functional potential in the phyllosphere and rhizosphere of A. marina were observed. This study has enriched our understanding of the microbial community structure, function, and ecological stability of mangrove species in coastal intertidal zones and has practical significance for improving crop yield by using salt-tolerant plant microbiomes.

Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau

Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.

Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China

The study compare the diversity patterns and processes of microbial community assembly in the water and sediment of Lake Wuchang (China) using high-throughput sequencing of 16S rRNA gene amplicons. A higher microbial α-diversity in the sediment was revealed (P < 0.01), and the most common bacterial phyla in water column were Proteobacteria, Cyanobacteria and Actinobacteria, while Proteobacteria, Acidobacteria, Chloroflexi and Nitrospirae were dominant in sediment. Functions related to phototrophy and nitrogen metabolism primarily occurred in the water column and sediment, respectively. The microbial communities in water column from different seasons were divided into three groups, while no such dispersion in sediment based on PCoA and ANOSIM. According to Pearson correlation analysis, water temperature, dissolved oxygen, water depth, total nitrogen, ammonium, and nitrite were key factors in determining microbial community structure in water column, while TN in sediment, conductivity, and organic matter were key factors in sediment. However, the stochastic processes (|βNTI| < 2) dominated community assembly in both the water column and sediment of Lake Wuchang. These data will provide a foundation for microbial development and utilization in lake water column and sediment under the circumstances of increasing tendency of lake ecological fishery in China.

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

Introduction

Microbial mats are complex communities of benthic microorganisms that occur at the soil-water interphase in lakes' shores, streams, and ponds. In the cold, mountainous desert of Eastern Pamir (Tajikistan), where scarce water bodies are influenced by extreme environmental conditions, photosynthetic cyanobacteria form diverse mats. The mats are characterized by different morphology and thickness. Their habitats exhibit a wide range of conditions; from oligosaline to hypersaline, oligotrophic to hypertrophic, and from cold ponds to hot springs. The aim of the present study was to reveal the taxonomic composition and structure of these mats and to examine which environmental factors influence them.

Methods

Fifty-one mats were collected from small water bodies around Bulunkul, Karakul, and Rangkul Lakes in 2015 and 2017. The physical and chemical properties of the water were measured in situ, while the concentration of nutrients was analyzed ex-situ. To reveal the taxonomic composition of the mats, the hypervariable V3-V4 region of the 16S rRNA gene was examined using NGS technology.

Results

The results of bioinformatic analyses were compared with microscopic observations. They showed that Cyanobacteria was the dominant phylum, constituting on average 35% of bacterial ASVs, followed by Proteobacteria (28%), Bacteroidota (11%), and Firmicutes (9%). Synechococcales, Oscillatoriales, and Nostocales orders prevailed in Oxyphotobacteria, with a low contribution of Chroococcales, Gloeobacterales, and Chroococcidiopsidales. Occasionally the non-photosynthetic Vampirivibrionia (Melainabacteria) and Sericytochromatia from sister clades to Oxyphotobacteria were noted in the samples. Moreover, there was a high percentage of unidentified cyanobacterial sequences, as well as the recently described Hillbrichtia pamiria gen. et sp. nov., present in one of the samples. Salinity, followed by Na and K concentrations, correlated positively with the composition and structure of Oxyphotobacteria on different taxonomic levels and the abundance of all bacterial ASVs.

Discussion

The study suggests that the investigated communities possibly host more novel and endemic species. Among the environmental factors, salinity influenced the Oxyphotobacteria communities the most. Overall, the microenvironmental factors, i.e. the conditions in each of the reservoirs seemed to have a larger impact on the diversity of microbial mats in Pamir than the "subregional" factors, related to altitude, mean annual air temperature and distance between these subregions.

Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors

Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.

Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing

Soda lakes are unique poly-extreme environments with high alkalinity and salinity that support diverse microbial communities despite their extreme nature. In this study, prokaryotic and eukaryotic microbial diversity in samples of the three soda lakes, Lake Abijata, Lake Chitu and Lake Shala in the East African Rift Valley, were determined using amplicon sequencing. Culture-independent analysis showed higher diversity of prokaryotic and eukaryotic microbial communities in all three soda lakes than previously reported. A total of 3,603 prokaryotic and 898 eukaryotic operational taxonomic units (OTUs) were found through culture-independent amplicon sequencing, whereas only 134 bacterial OTUs, which correspond to 3%, were obtained by enrichment cultures. This shows that only a fraction of the microorganisms from these habitats can be cultured under laboratory conditions. Of the three soda lakes, samples from Lake Chitu showed the highest prokaryotic diversity, while samples from Lake Shala showed the lowest diversity. Pseudomonadota (Halomonas), Bacillota (Bacillus, Clostridia), Bacteroidota (Bacteroides), Euryarchaeota (Thermoplasmata, Thermococci, Methanomicrobia, Halobacter), and Nanoarchaeota (Woesearchaeia) were the most common prokaryotic microbes in the three soda lakes. A high diversity of eukaryotic organisms were identified, primarily represented by Ascomycota and Basidiomycota. Compared to the other two lakes, a higher number of eukaryotic OTUs were found in Lake Abijata. The present study showed that these unique habitats harbour diverse microbial genetic resources with possible use in biotechnological applications, which should be further investigated by functional metagenomics.

Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.

Compositional and Metabolic Responses of Autotrophic Microbial Community to Salinity in Lacustrine Environments

The compositional and physiological responses of autotrophic microbiotas to salinity in lakes remain unclear. In this study, the community composition and carbon fixation pathways of autotrophic microorganisms in lacustrine sediments with a salinity gradient (82.6 g/L to 0.54 g/L) were investigated by using metagenomic analysis. A total of 117 metagenome-assembled genomes (MAGs) with carbon fixation potentially belonging to 20 phyla were obtained. The abundance of these potential autotrophs increased significantly with decreasing salinity, and the variation of sediment autotrophic microbial communities was mainly affected by salinity, pH, and total organic carbon. Notably, along the decreasing salinity gradient, the dominant lineage shifted from Desulfobacterota to Proteobacteria. Meanwhile, the dominant carbon fixation pathway shifted from the Wood-Lungdahl pathway to the less-energy-efficient Calvin-Benson-Bassham cycle, with glycolysis shifting from the Embden-Meyerhof-Parnas pathway to the less-exergonic Entner-Doudoroff pathway. These results suggest that the physiological efficiency of autotrophic microorganisms decreased when the environmental salinity became lower. Metabolic inference of these MAGs revealed that carbon fixation may be coupled to the oxidation of reduced sulfur compounds and ferrous iron, dissimilatory nitrate reduction at low salinity, and dissimilatory sulfate reduction in hypersaline sediments. These results extend our understanding of metabolic versatility and niche diversity of autotrophic microorganisms in saline environments and shed light on the response of autotrophic microbiomes to salinity. These findings are of great significance for understanding the impact of desalination caused by climate warming on the carbon cycle of saline lake ecosystems. IMPORTANCE The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. In this study, we used genome-resolved metagenomics to interpret the dynamic changes in the autotrophic microbial community and metabolic pathways along a salinity gradient. The results showed that desalination drove the shift of the dominant microbial lineage from Desulfobacterota to Proteobacteria, enriched autotrophs with lower physiological efficiency pathways, and enhanced coupling between the carbon cycle and other element cycles. These results can predict the future response of microbial communities to lake desalination and improve our understanding of the effect of climate warming on the carbon cycle in saline aquatic ecosystems.

Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem

BACKGROUND

Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea.

RESULTS

The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments.

CONCLUSIONS

This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.

Abundant microbial communities act as more sensitive bio-indicators for ecological evaluation of copper mine contamination than rare taxa in river sediments

Bacterial and fungal communities have been widely applied as bio-indicators for ecological evaluation of copper (Cu) mine pollution in river sediments. However, the response pattern of their abundant and rare sub-communities is still unknown, limiting the further development of biological diagnostics. Here, the alpha-diversity, community composition, environmental contribution and co-occurrence network of total, abundant and rare taxa for bacteria and fungi in the Jiaopingdu Cu Mine wastewater treatment plant (WWTP) were investigated through high-throughput sequencing. The results revealed different responses of microbial alpha-diversity for abundant and rare sub-communities. The abundant taxa were ubiquitous in all sediments, while rare taxa exhibited increases of species richness in polluted areas because of heterochthonous inputs of WWTP drainage. Nevertheless, the variations of community composition were consistent for bacterial and fungal abundant and rare taxa, all of which showed significant dissimilarity between control and polluted areas. Distance-decay relationship and canonical correlation analysis indicated that abundant taxa assemblies (r_bacteria = -0.924, r_fungi = -0.684) were more strongly driven by environmental changes than rare ones (r_bacteria = -0.626, r_fungi = -0.349), because abundant microbes had higher proportions of significant variations in abundance. Co-occurrence networks revealed more keystone species with high node degree and centrality among abundant taxa compared with rare ones. Moreover, bacterial abundant and rare taxa were more sensitive to Cu mine pollution than relevant fungal taxa owing to different Cu tolerance. In conclusion, among all microbial sub-communities, abundant bacteria had the highest environmental sensitivity, suggesting their important application in biological diagnosis of Cu mine pollution. Accordingly, the abundant taxa could act as "key reservoir" for future selection of specific indicator species, for example Thiobacillus, while rare taxa no longer need excessive in-depth analysis, which would greatly improve microbial diagnosis efficiency.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments

Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L-1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L-1 NaCl between pH values 2-10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.

Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes

Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0.67 g/L to 346 g/L). MPN results showed that the abundance of NRFeOx microorganisms significantly (P < 0.05) decreased with increasing lake salinity, from 7.55 × 10³ to 8.09 cells/g dry sediment. The community composition of the NRFeOx enrichment cultures obtained from the MPNs differed distinctly among the five lakes and clustered with lake salinity. Two stable enrichment cultures, named FeN-EHL and FeN-CKL, were obtained from microcosm incubations of sediment from freshwater Lake Erhai and hypersaline Lake Chaka. The culture FeN-EHL was dominated by genus Gallionella (68.4%), while the culture FeN-CKL was dominated by genus Marinobacter (71.2%), with the former growing autotrophically and the latter requiring an additional organic substrate (acetate) and Fe(II) oxidation, caused to a large extent by chemodenitrification [reaction of nitrite with Fe(II)]. Short-range ordered Fe(III) (oxyhydr)oxides were the product of Fe(II) oxidation, and the cells were partially attached to or encrusted by the formed iron minerals in both cultures. In summary, different types of interactions between Fe(II) and nitrate-reducing bacteria may exist in freshwater and hypersaline lakes, i.e., autotrophic NRFeOx and chemodenitrification in freshwater and hypersaline environments, respectively. IMPORTANCE NRFeOx microorganisms are globally distributed in various types of environments and play a vital role in iron transformation and nitrate and heavy metal removal. However, most known NRFeOx microorganisms were isolated from freshwater and marine environments, while their identity and activity under hypersaline conditions remain unknown. Here, we demonstrated that salinity may affect the abundance, identity, and nutrition modes of NRFeOx microorganisms. Autotrophy was only detectable in a freshwater lake but not in the saline lake investigated. We enriched a mixotrophic culture capable of nitrate-reducing Fe(II) oxidation from hypersaline lake sediments. However, Fe(II) oxidation was probably caused by abiotic nitrite reduction (chemodenitrification) rather than by a biologically mediated process. Consequently, our study suggests that in hypersaline environments, Fe(II) oxidation is largely caused by chemodentrification initiated by nitrite formation by chemoheterotrophic bacteria, and additional experiments are needed to demonstrate whether or to what extent Fe(II) is enzymatically oxidized.

Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics

Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00119-6.

Abundant and Rare Bacterial Taxa Structuring Differently in Sediment and Water in Thermokarst Lakes in the Yellow River Source Area, Qinghai-Tibet Plateau

Thermokarst lakes are forming from permafrost thaw and are severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remains largely unknown, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided into abundant and rare according to their relative abundance, and the Sorensen dissimilarity (β_sor) was partitioned into turnover (β_turn) and nestedness (β_nest). The whole bacterial communities and the abundant and rare subcommunities differed substantially between sediment and water in taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. In general, bacterial communities are predominantly governed by strong turnover processes (β_turn/β_sor ratio of 0.925). Bacterial communities in sediment had a significantly higher β_turn/β_sor ratio than in water. Abundant subcommunities were significantly lower in the β_turn/β_sor ratio compared with rare subcommunities. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by heterogeneity in the source material, environmental filtering, and geographical isolation, leading to compositionally distinct communities. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapidly changing and vulnerable ecosystems.

Microbial response to multiple-level addition of grass organic matter in lake sediments with different salinity

Water surface expansion of saline lakes usually causes the inundation of surrounding grassland, leading to the increase of terrestrial grass organic matter (OM) input to the lakes and the decrease of lake salinity. However, the influence of terrestrial grass OM input increase and salinity decrease on organic carbon mineralization and microbial community composition remains unknown in saline lakes. Here, microbial mineralization of terrestrial grass (Achnatherum splendens) OM at different quantity levels in lake sediments with different salinity was investigated by performing microcosm experiments. The results showed that the CO2 production rates increased with the increase of grass OM supply in the studied sediments with different salinity, which may be driven by certain microbial groups (e.g., Bacteroidota, Firmicutes and Ascomycota). The increase of grass OM supply reduced the richness of prokaryotic community, which will decrease the size and complexity of the studied microbial networks, but increase the interaction between prokaryotic and fungal taxa. Taken together, our results suggest that the increase of terrestrial grass OM input caused by lake expansion would enhance the mineralization of organic carbon and affect the community composition and interactions of related microorganisms in lake sediments with different salinity.

Community Assembly and Co-Occurrence Patterns of Microeukaryotes in Thermokarst Lakes of the Yellow River Source Area

Thermokarst lakes are important aquatic ecosystems in cold regions, experiencing several changes due to global warming. However, the fundamental assembly mechanisms of microeukaryotic communities in thermokarst lakes are unknown. In this study, we examined the assembly processes and co-occurrence networks of microeukaryotic communities in sediment and water of thermokarst lakes in the Yellow River Source Area. Sediment microeukaryotic communities had a significantly lower α-diversity but higher β-diversity than water microeukaryotic communities. pH, sediment organic carbon, and total phosphorus significantly affected taxonomic and phylogenetic diversity of sediment communities, while conductivity was a significant driver for water communities. Both sediment and water microeukaryotic communities were strongly governed by dispersal limitation. However, deterministic processes, especially homogenous selection, were more relevant in structuring microeukaryotic communities in water than those in sediment. Changes in total nitrogen and phosphorus in sediment could contribute to shift its microeukaryotic communities from homogeneous selection to stochastic processes. Co-occurrence networks showed that water microeukaryotic communities are more complex and interconnected but have lower modularity than sediment microeukaryotic communities. The water microeukaryotic network had more modules than the sediment microeukaryotic network. These modules were dominated by different taxonomic groups and associated to different environmental variables.