Microorganisms In Sediments Research Articles

Limited Microbial Contribution in Salt Lake Sediment and Water to Each Other’s Microbial Communities

Climate change and human activities have led to frequent exchanges of sedimentary and aquatic microorganisms in lakes. However, the ability of these microorganisms to survive in their respective habitats between saline lake sediment and water remains unclear. In this study, we investigated microbial sources and community composition and metabolic functions in sediments and water in Yuncheng Salt Lake using a combination of source tracking and Illumina MiSeq sequencing. The results showed that 0.10–8.47% of the microbial communities in the sediment came from the corresponding water bodies, while 0.12–10.78% of the sedimentary microorganisms contributed to the aquatic microbial populations, and the microbial contributions depended on the salinity difference between sediment and water. Habitat heterogeneity and salinity variations led to the differences in microbial diversity, community composition, and assembly between sediment and water communities. The assembly of sedimentary communities was mainly controlled by stochastic processes (>59%), whereas the assembly of aquatic communities was mainly controlled by deterministic processes (>88%). Furthermore, sediments had a higher potential for metabolic pathways related to specific biogeochemical functions than lake water. These results provide insights into the survival ability of microorganisms and the mechanisms of microbial community assembly under frequent exchange conditions in saline lakes.

Novel Photoelectron-Assisted Microbial Reduction of Arsenate Driven by Photosensitive Dissolved Organic Matter in Mine Stream Sediments.

The microbial reduction of arsenate (As(V)) significantly contributes to arsenic migration in mine stream sediment, primarily driven by heterotrophic microorganisms using dissolved organic matter (DOM) as a carbon source. This study reveals a novel reduction pathway in sediments that photosensitive DOM generates photoelectrons to stimulate diverse nonphototrophic microorganisms to reduce As(V). This microbial photoelectrophic As(V) reduction (PEAsR) was investigated using microcosm incubation, which showed the transfer of photoelectrons from DOM to indigenous sediment microorganisms, thereby leading to a 50% higher microbial reduction rate of As(V). The abundance of two marker genes for As(V) reduction, arrA and arsC, increased substantially, confirming the microbial nature of PEAsR rather than a photoelectrochemical process. Photoelectron ion is unlikely to stimulate photolithoautotrophic growth. Instead, diverse nonphototrophic genera, e.g., Cupriavidus, Sphingopyxis, Mycobacterium, and Bradyrhizobium, spanning 13 orders became enriched by 10-50 folds. Metagenomic binning revealed their genetic potential to mediate the photoelectron-assisted reduction of As(V). These microorganisms contain essential genes involved in respiratory As(V) reduction, detoxification As(V) reduction, dimethyl sulfoxide reductase family, c-type cytochromes, and multiple heavy-metal resistance but lack a complete photosynthesis system. The novel microbial PEAsR pathway offers new insights into the interaction between photoelectron utilization and nonphototrophic As(V)-reducing microorganisms, which may have profound implications for arsenic pollution transportation in mine stream sediment.

Comparative metagenomics highlights the habitat-related diversity in taxonomic composition and metabolic potential of deep-sea sediment microbiota

Sediment plays a pivotal role in deep-sea ecosystems by providing habitats for a diverse range of microorganisms and facilitates the cycling processes of carbon, sulfur and nitrogen. Beyond the normal seafloor (NS), distinctive geographical features such as cold seeps (CS) and hydrothermal vent (HV) are recognized as life oases harboring highly diverse microbial communities. A global atlas of microorganisms can reveal the notable association between geological processes and microbial colonization. However, a comprehensive understanding of the systematic comparison of microbial communities in sediments across various deep-sea regions worldwide and their contributions to Earth's elemental cycles remains limited. Analyzing metagenomic data from 163 deep-sea sediment samples across 73 locations worldwide revealed that microbial communities in CS sediments exhibited the highest richness and diversity, followed by HV sediments, with NS sediments showing the lowest diversity. The NS sediments were predominantly inhabited by Nitrosopumilaceae, a type of ammonia-oxidizing archaea (AOA). In contrast, CSs and HVs were dominated by ANME-1, a family of anaerobic methane-oxidizing archaea (ANME), and Desulfofervidaceae, a family of sulfate-reducing bacteria (SRB), respectively. Microbial networks were established for each ecosystem to analyze the relationships and interactions among different microorganisms. Additionally, we analyzed the metabolic patterns of microbial communities in different deep-sea sediments. Despite variations in carbon fixation pathways in ecosystems with different oxygen concentrations, carbon metabolism remains the predominant biogeochemical cycle in deep-sea sediments. Benthic ecosystems exhibit distinct microbial potentials for sulfate reduction, both assimilatory and dissimilatory sulfate reduction (ASR and DSR), in response to different environmental conditions. The presence of nitrogen-fixing microorganisms in CS sediments may influence the global nitrogen balance. In this study, the significant differences in the taxonomic composition and functional potential of microbial communities inhabiting various deep-sea environments were investigated. Our findings emphasize the importance of conducting comparative studies on ecosystems to reveal the complex interrelationships between marine sediments and global biogeochemical cycles.

Functional Genes and Metabolic Pathways of Nitrogen Metabolism Microorganisms in Lake Sediments：A Case Study of Hongfeng Lake, Guizhou Province

The nitrogen cycle is of great importance for material circulation and energy flow in lake ecosystems. It is driven by microorganisms in lake sediments and can contribute to balancing lake ecosystems. In this study, physical and chemical properties of the sediments sampled from Hongfeng Lake in Guizhou Province were assayed and analyzed using metagenomics to reveal relevant microorganisms, functional genes, metabolic pathways, and their relationships throughout nitrogen metabolism. The results showed that bacteria were dominant, and the top three relative abundant genera were Thiobacillus （16.64%）, Rubrivivax（9.43%）, and Nitrospira （7.09%）. Only six pathways, including nitrogen fixation, nitrification, denitrification, assimilatory nitrate reduction, dissimilatory nitrate reduction, and complete nitrification, were detected in total, of which denitrification and dissimilatory nitrate reduction were the primary processes, but anaerobic ammonia oxidation was not detected. Bacteria and archaea participated in these six pathways, while eukaryotes only functioned in dissimilatory nitrate reduction, denitrification, and complete nitrification. Ammonia nitrogen, nitrate nitrogen, and total phosphorus, as main environmental factors affecting the distribution of functional genes for nitrogen metabolism, differentiated with each other in their respective real-world conditions. A positive correlation （95.04%） was observed between the functional genes and microorganisms, and narG, narZ, and nxrA possessed the highest abundance and the highest host genes. On this basis, these findings are expected to further elucidate the nitrogen cycle of typical karst lakes in Guizhou Province.

The Source of Thermophilic Bacteria in Lake Baikal Cold Sediments – Coastal Hydrotherms or Deep Fluids?

The sources of thermophilic bacteria revealed in cold Lake Baikal sediments are considered. Comparative analysis of the taxonomic position of thermophilic microorganisms from four terrestrial hot springs at Lake Baikal coast and from the bottom sediments associated with hydrocarbon discharge was carried out. The sequences of thermophilic microorganisms with the same taxonomic position were revealed both in the hot springs and bottom sediments. Some microbial species occurred only in the hydrotherm samples or only in those from the sediments. Gas-saturated fluids from the hydrocarbon generation zone at the depth of 4‒6 km are the most probable source of thermophilic microorganisms in the bottom sediments.

Influences and mechanisms of iron input for methane productions in peatlands.

Atmospheric deposition provides a stable iron source for peatlands. The influences of Fe input on methane (CH4) productions and the underlying mechanisms remain unclear. We conducted a microcosm experiment with peat sediments collected from the Qinghai-Tibet Plateau of China to explore the effects of ferrihydrite reductionfor CH4 productions in peatlands by using geochemical analyses including 57Fe Mössbauer spectroscopy and three-dimensional fluorescence spectroscopy (3D-EEM) in combination with high-throughput sequencing of 16S rRNA and real-time fluorescence quantitative PCR (qPCR). Results showed that ferrihydrite reduction significantly increased CH4 production, being 30 times of that under the control. Selective extractions for iron oxides and 57Fe Mössbauer spectroscopy measurements revealed that no crystalline secondary iron minerals were formed during the ferrihydrite reduction process. The addition of ferrihydrite enhanced the degradation of dissolved organic matter (DOM) in peat soil, resulting in a reduction in the concentration of dissolved organic carbon (DOC). Furthermore, the relative abundance of typical fermentative microorganisms in peat sediments, including Acidobacteriota and Bacteroidota, significantly increased. Such a result indicated that reduction of ferrihydrite accelerated organic matter decomposition and increased substrate concentration required for methanogenesis. Furthermore, a co-increase in relative abundance of Geobacter, Geothrix, and Methanobacterium in the ferrihydrite-amended group suggested a potential synergistic interaction that may promote the CH4 production. Our results demonstrated that ferrihydrite reduction could significantly enhance CH4 production and play a vital role in regulating CH4 emissions in peatlands.

Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea.

Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.

This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50°C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2cm) and bottom depth (250cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

Degradation of pyrene at high concentrations in sediment and the implications for the microbiome in microbial electrochemical systems

The polycyclic aromatic hydrocarbons (PAHs) frequently accumulate in sediments, particularly those near industrial sites. The efficacy of microbial electrochemical systems (MESs) in electricity generation and PAHs degradation is intricately linked to the microbiome’s response to high contaminant levels. Metabolomics and metagenomics were applied to elucidate the impact of a high pyrene concentration on the functional structure and metabolic dynamics of sediment microbiomes within MES. In sediment with a high pyrene concentration, both the electrical output of MES and efficiency of their microbiomes in degrading organic substrates and pyrene were markedly reduced. These conditions were associated with the enrichment of PAH-degrading microorganisms, such as Hydrogenophaga and Flavobacterium. Analyses of metabolites and genetic profiles revealed that metabolic pathways were primarily influenced in MES exposed to low pyrene concentrations whereas fewer metabolic pathways were activated in MES exposed to high concentrations; instead, pathways representing functions critical for microbial survival and communication were activated as well. According to enzymatic analyses, low pyrene levels promoted carbohydrate metabolism by sediment microorganisms, whereas high levels had an inhibitory effect. An examination of electron transport enzymes revealed that intracellular electron transfer was facilitated by both low and high concentrations. However, high levels impeded enzymes associated with outer membrane electron transfer, hindering electron movement from intracellular to extracellular electron acceptors and thus negatively affecting the electrical output of MES. Our study provides crucial theoretical insight and mechanistic understanding for addressing the challenges that may be encountered when MES are used to treat pyrene-contaminated sediment near industrial sites.

Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench.

The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments

Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing. We found that the N removal activities could be affected through potential competition and inhibition among microbial metabolic pathways. High-diversity microbial communities generally increased the abundance and expression of N removal functional genes. Further enrichment experiments showed that the enrichment of N removal microorganisms led to a development of simplified but more stable microbial communities, characterized by similar evolutionary patterns among N removal microorganisms, tighter interactions, and increased adaptability. Notably, the sustained provision of NH4+ and NO2− during the enrichment could potentially strengthen the interconnections among denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, the identification of shared metabolic traits among denitrification, anammox and DNRA implies important cooperative associations and adaptability of N removal microorganisms. Our findings highlight the microbial interactions affect the adaptive strategies of key microbial taxa involved in N removal.

Microorganisms Directly Affected Sediment Carbon–Nitrogen Coupling in Two Constructed Wetlands

Clarifying the carbon–nitrogen coupling pattern in wetlands is crucial for understanding the driving mechanism of wetland carbon sequestration. However, the impacts of plants and environmental factors on the coupling of carbon–nitrogen in wetland sediments are still unclear. Sediment samples from plant (Typha angustifolia and Phragmites australis)-covered habitats and bare land were collected in two constructed wetlands in northern China. The contents of different forms of carbon and nitrogen in sediments and plants, and the sediment microbial community were detected. It was found that the sediment carbon to nitrogen (C/N) ratios did not differ significantly in the bare sites of different wetlands, but did in the plant-covered sites, which highlighted the different role of plants in shifting the carbon–nitrogen coupling in different constructed wetlands. The effects of plants on the sediment carbon–nitrogen coupling differed in two constructed wetlands, so the structural equation model was used and found that sediment microorganisms directly affected sediment C/N ratios, while water and sediment physicochemical properties indirectly affected sediment C/N ratios by altering sediment microbial functions. Multiple linear regression models showed that water pH, sediment moisture content, water dissolved oxygen, and water depth had a greater influence on the carbon metabolism potential of the sediment microbial community, while sediment moisture content had the greatest impact on the sediment microbial nitrogen metabolism potential. The study indicates that variations in environmental conditions could alter the influence of plants on the carbon and nitrogen cycles of wetland sediments. Water environmental factors mainly affect microbial carbon metabolism functions, while soil physicochemical factors, especially water content, affect microbial carbon and nitrogen metabolism functions.

Dynamic Changes of Environment and Gut Microbial Community of Litopenaeus vannamei in Greenhouse Farming and Potential Mechanism of Gut Microbial Community Construction

The aim of this study was to investigate the dynamic changes in the microbial communities of both the environment and gut of Litopenaeus vannamei, as well as to elucidate the mechanisms underlying microbial community assembly in greenhouse farming. 16S rDNA high-throughput sequencing and bioinformatics methods were used to carry out the research on the community structure of the microorganisms under greenhouse culture conditions in water, sediment, and gut microorganisms; correlations pertaining to environmental factors; the feasibility of using Source Tracker; and the mechanisms of community construction. The results show that the dominant microorganisms in water, sediment, and gut farming in a greenhouse environment varied and were subject to dynamic change. A variety of beneficial microbiota such as Bacillus were found in the gut, whereas a variety of microorganisms such as Marivita and Pseudomonas, which function as nitrogen and phosphorus removers, were present in water. Source Tracker and environmental correlation analyses showed that changes in the gut were associated with eutrophication indicators (total nitrogen, total phosphorus, ammonia nitrogen) and changes in environmental microorganisms (in water and sediment). The results of the community-building mechanism analysis show that stochastic processes determine the community-building directions of environmental and gut microorganisms. These findings will help us to understand the microbiota characteristics of shrimp ponds under greenhouse farming conditions, and the complex interactions between the shrimp gut and the environmental microbiota and environmental variables, as well as revealing the changing rules of the gut microbiota.

Exploring the optimal integrated multi-trophic aquaculture (IMTA) patterns benefiting culture animals and natural water environment

Despite bringing various benefits, rapid developments in aquaculture have contributed to the eutrophication of natural water environments. Therefore, it is imperative to mitigate nutrient load in natural water bodies while ensuring sustainable development of aquaculture. On the basis, we proposed an integrated multi-trophic aquaculture (IMTA) system, which considered a perfect solution and constructed an optimised IMTA pattern. Silver and bighead carps and freshwater pearl mussels were used as purification organisms. Six experimental groups were established for a land-based enclosure experiment: giant freshwater prawn monoculture group (G); giant freshwater prawn and freshwater pearl mussel polyculture group (GH2); giant freshwater prawn and silver and bighead carp polyculture group (GSB); giant freshwater prawn, freshwater pearl mussel and silver and bighead carp polyculture groups (GSBH1, GSBH2 and GSBH3) in different densities of freshwater pearl mussels. Each group had four replicates. Control of cyanobacterial blooms, productivity index, outputs of total nitrogen and total phosphorus and microbial community composition were studied and compared in different culturing patterns. Results showed that the GSBH1 group had the most obvious comprehensive advantages in the above four aspects (no cyanobacterial bloom occurred; the best comprehensive productivity index of giant freshwater prawn; the abundance of beneficial microorganisms in sediments was the highest; reduced phosphorus emissions in tailwater by 60.34%; the utilisation rates of nitrogen and phosphorus increased by 10.99% and 13.05%, respectively). Even so, however, the GSBH1 group might not be the most optimal IMTA pattern in practice because the mortality rate of the mussels reached 12.33% and the weight gain was −3.66%. Additionally, the presence of freshwater pearl mussel at its lowest density in this experiment had exhibited detrimental impacts on the growth of silver and bighead carps. Therefore, the most optimal IMTA pattern needs to be determined by further research.

Redox conditions and biochar pyrolysis temperature affecting As and Pb biogeochemical cycles and bacterial community of sediment from mining tailings

Despite the widespread use of biochar for soil and sediment remediation, little is known about the impact of pyrolysis temperature on the biogeochemistry of arsenic (As) and lead (Pb) and microorganisms in sediment under reducing conditions. In this study, we investigated the effects of pyrolysis temperature and the addition of glucose on the release and transformation of As and Pb, as well as their potential effects on the bacterial community in contaminated sediments. The addition of biochar altered the geochemical cycle of As, as it favors specific bacterial groups capable of changing species from As(V) to As(III) through fermentation, sulfate respiration and nitrate reduction. The carbon quality and content of N and S in solution shaped the pH and redox potential in a way that changed the microbial community, favoring Firmicutes and reducing Proteobacteria. This change played a fundamental role in the reductive dissolution of As and Pb minerals. The addition of biochar was the only efficient way to remove Pb, possibly as a function of its sorption and precipitation mechanisms. Such insights could contribute to the production or choice of high-efficiency biochar for the remediation of sediments subjected to redox conditions.

Exploring correlations between microplastics, microorganisms, and water quality in an urban drinking water source

The microplastic pollution in freshwater system is gradually becoming more severe, which has led to increasing attention on the distribution and potential harmful effects of microplastics. Moreover, microplastics may have an impact on river ecology and pose risks to ecosystems. Therefore, it is important to reveal this process. This study aimed to explore correlations between microplastics and free-living microorganisms in an urban drinking water source of Xiangjiang River by using multivariate statistical analysis. The results indicated that the abundance of microplastics (size 50 μm to 5 mm) in surface water and sediments ranged from 0.72 to 18.6 (mean ± SD: 7.32 ± 2.36) items L−1 and 26.3–302 (150 ± 75.6) items kg−1 dry weight (dw), respectively, suggesting potential microplastic pollution despite the protected status as a drinking water source. Higher microplastic abundances were observed in urban areas and the downstream of wastewater plants, with mostly granular shape, transparent and black color as well as 50–100 μm in size. The multivariate statistical analysis presented that the abundance of microplastics is not significantly correlated with water indicators, due to the complexity of the abundance data. The water indicators showed an obvious correlation with microplastics in colors of transparent and black, and smaller sizes of 50–100 μm. This is also true for microplastics and microorganisms in water and sediment. Proteobacteria was the main prokaryote in water and sediments, being positively correlated with 50–100 μm microplastics; while Chloroplastida was the dominated eukaryotes, presenting a weak correlation with smaller-size microplastics. Overall, when considering the properties of microplastics such as shape, color and size, the potential correlations with water indicators and microorganisms were more evident than abundance. This study provides new insights into the multivariate statistical analysis, explaining the potential correlations among microplastic properties, microorganisms and environmental factors in a river system.

Characteristics of bacterial community structure in the sediment of Chishui River (China) and the response to environmental factors

Sediment microorganisms performed an essential function in the biogeochemical cycle of aquatic ecosystems, and their structural composition was closely related to environmental carrying capacity and water quality. In this study, the Chishui River (Renhuai section) was selected as the research area, and the concentrations of environmental factors in the water and sediment were detected. High⁃throughput sequencing was adopted to reveal the characteristics of bacterial community structures in the sediment. In addition, the response of bacteria to environmental factors was explored statistically. Meanwhile, the functional characteristics of bacterial were also analyzed based on the KEGG database. The results showed that the concentration of environmental factors in the water and sediment displayed spatial differences, with the overall trend of midstream > downstream > upstream, which was related to the wastewater discharge from the Moutai town in the midstream directly. Proteobacteria was the most dominant phylum in the sediment, with the relative abundance ranged from 52.06% to 70.53%. The distribution of genus-level bacteria with different metabolic activities varied in the sediment. Upstream was dominated by Massilia, Acinetobacter, and Thermomonas. In the midstream, Acinetobacter, Cloacibacterium and Comamonas were the main genus. Nevertheless, the abundance of Lysobacter, Arenimonas and Thermomonas was higher in the downstream. Redundancy analysis (RDA) showed that total nitrogen (TN) and total phosphorus (TP) were the main environmental factors which affected the structure of bacterial communities in sediment, while total organic carbon (TOC) was the secondary. The bacterial community was primarily associated with six biological pathway categories such as metabolism. Carbohydrate metabolism and amino acid metabolism were the most active functions in the 31 subfunctions. This study could contribute to the understanding of the structural composition and driving forces of bacteria in the sediment, which might benefit for the ecological protection of Chishui River.

Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity

Marine sediments constitute the world’s most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle. In this study, we employ a metagenomic methodology to investigate the distribution and abundance of carbohydrate-active enzymes (CAZymes) in 37 marine sediments sites. These sediments exhibit varying oxygen availability and were isolated in diverse regions worldwide. Our comparative analysis is based on the metabolic potential for oxygen utilisation, derived from genes present in both oxic and anoxic environments. We found that extracellular CAZyme modules targeting the degradation of plant and algal detritus, necromass, and host glycans were abundant across all metagenomic samples. The analysis of these results indicates that the oxic/anoxic conditions not only influence the taxonomic composition of the microbial communities, but also affect the occurrence of CAZyme modules involved in the transformation of necromass, algae and plant detritus. To gain insight into the sediment microbial taxa, we reconstructed metagenome assembled genomes (MAG) and examined the presence of primary extracellular carbohydrate active enzyme (CAZyme) modules. Our findings reveal that the primary CAZyme modules and the CAZyme gene clusters discovered in our metagenomes were prevalent in the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. We compared those MAGs to organisms from the same taxonomic classes found in soil, and we found that they were similar in its CAZyme repertoire, but the soil MAG contained a more abundant and diverse CAZyme content. Furthermore, the data indicate that abundant classes in our metagenomic samples, namely Alphaproteobacteria, Bacteroidia and Gammaproteobacteria, play a pivotal role in carbohydrate transformation within the initial few metres of the sediments.