Search Results (110)

Coastal sediment bacteria mediate essential biogeochemical cycles, yet their functional gene potential to anthropogenic stress gradients remains insufficiently understood. This study presents a comparative analysis of sediment bacterial communities and carbon, nitrogen, phosphorus, and sulfur (C/N/P/S) cycling genes between the west and east coasts of Shenzhen, China, a region exemplifying sharp contrasts between intensive urbanization and relatively pristine marine environments. We integrated 16S rRNA gene high-throughput sequencing with QMEC (Quantitative Microbial Element Cycling), a high-throughput quantitative PCR chip to profile both bacterial taxonomic composition and quantitatively measured gene abundances across C/N/P/S biogeochemical pathways. Western sediments, under strong terrestrial input, exhibited higher ammonium and organic carbon, while eastern sediments had higher salinity. Bacterial alpha diversity was significantly higher in the west, and community structure differed markedly between regions (ANOSIM R = 0.334, p = 0.001). Although dominant phyla (Pseudomonadota, Bacteroidota, and Planctomycetota) were shared, genus-level taxa diverged: Sulfurovum (sulfur cycling) was enriched in the west, while organic-degrading Burkholderia-Caballeronia-Paraburkholderia and Phaeodactylibacter prevailed in the east. Notably, functional gene abundance for all four biogeochemical cycles was an order of magnitude higher in western sediments, with denitrification genes dominating there and nitrification genes in the east. Redundancy analysis (RDA) and the Mantel test identified nitrate as the primary environmental driver of bacterial variation (r = 0.574, p = 0.001), alongside salinity, temperature, ammonium, and total organic carbon. These findings reveal distinct bacterial adaptations to contrasting anthropogenic pressures and demonstrate that sediment bacterial functional gene profiles can serve as sensitive indicators of ecosystem health, providing a quantitative microbiological basis for targeted pollution management in urbanized coastal zones. Full article

Climate warming and atmospheric nitrogen deposition are altering carbon (C), nitrogen (N), and phosphorus (P) cycling in alpine wetlands. However, how these drivers jointly reorganize microbial communities and their biogeochemical cycling potential remains poorly understood, particularly in cold, nutrient-limited alpine wetlands. We conducted a four-year field experiment combining open-top chamber warming and nitrogen addition. Soil physicochemical measurements were integrated with shotgun metagenomic sequencing to assess microbial community structure and the functional potential associated with C, N, and P cycling. The results showed that archaeal and bacterial community composition remained stable following warming and nitrogen addition, whereas fungal composition changed. Functional gene richness was positively correlated with archaeal and bacterial richness but was not correlated with fungal richness, indicating asynchronous responses between taxonomic–functional dimensions. Warming and nitrogen addition did not consistently increase the overall abundance of C, N, and P cycling functional genes. Instead, they induced pathway-specific responses: compensatory shifts among C fixation pathways, decreases in complex C degradation genes, increases in nitrification genes, and decreases in genes associated with P acquisition and homeostatic regulation. Soil moisture and enzyme activities were significantly correlated with C, N, and P cycling genes. These findings highlight domain-specific taxonomic responses and process-specific re-organization of microbial functional potential and emphasize the importance of hydro-thermal constraints when predicting alpine-wetland biogeochemical responses to future warming and increasing N inputs. Full article

Mineral springs in the Andean–Amazonian transition represent poorly explored aquatic ecosystems whose hydrogeochemical heterogeneity may favor the establishment of specialized microbial communities. In this study, bacterial communities in sediments from 19 mineral springs in northern Peru were characterized using 16S rRNA gene sequencing, and their relationships with hydrogeochemical conditions and predicted functional potential were evaluated. The springs exhibited temperatures ranging from 15.1 to 38.2 °C and total dissolved solids (TDS) concentrations ranging from 0.022 to 162.5 mg L⁻¹, reflecting marked variation in thermal and mineralization conditions. Bacterial communities were dominated by Desulfobacteraceae, Desulfosarcinaceae, Chlorobiaceae, Nitrosomonadaceae, Nitrospiraceae, and Rhodobacteraceae, including representative genera such as Halanaerobium, Chlorobium, Thiothrix, and Sulfurovum. Although alpha diversity did not differ significantly among hydrogeochemical categories, beta diversity analyses indicated compositional differentiation among thermal categories, while RDA revealed a significant multivariate association between bacterial community composition and the combined hydrogeochemical gradient (F = 1.0934, p = 0.035). Co-occurrence network analysis identified Desulfotignum, Roseimarinus, Halanaerobium, and Anaerophaga among the most highly connected taxa. PICRUSt2 predicted functional potential associated with carbon fixation, nitrogen and sulfur transformations, phosphorus acquisition and polyphosphate-related metabolism, and ferrous iron uptake. These findings provide the first integrated characterization of these bacterial communities and establish a baseline for future research on microbial ecology, biogeochemical cycling, and environmental biotechnology in Andean–Amazonian ecosystems of Peru. Full article

As key drivers of soil biogeochemical cycles, soil microbial communities play essential roles in maintaining soil fertility, nutrient cycling, and plant growth. In this study, high-throughput sequencing of 16S rRNA and ITS genes was used to investigate the diversity, the composition, and the driving factors of bacterial and fungal communities in bulk soils across four soil groups collected from different vegetation covers (forest soil (FS), soybean field (PGS), and two Atractylodes japonica cultivation soils (ALO and ALR)) under identical climatic conditions. The results showed that the bacterial α-diversity remained stable across all the vegetation types, whereas the fungal α-diversity and richness were more sensitive to the vegetation type, with the PGS generally exhibiting lower Shannon and Chao1 indices. The β-diversity analysis revealed significant differences in the microbial community structure among the vegetation types, with a stronger effect on fungi (R² = 0.737, p = 0.001) than on bacteria (R² = 0.493, p = 0.001). At the phylum and genus levels, the fungal communities displayed more pronounced shifts than the bacterial communities, which remained relatively stable. A redundancy analysis indicated that the soil chemical properties significantly shaped the microbial community structure (p = 0.002). The microbial communities in the A. japonica soils (ALO and ALR) were primarily driven by pH, available phosphorus, and available potassium, while the FS and PGS communities were more strongly influenced by soil organic carbon, total nitrogen, and nitrogen forms (NH₄⁺-N and NO₃⁻-N). The Spearman correlation and functional prediction analyses further confirmed that the key soil factors differentially regulated the abundance and ecological functions of the dominant microbial taxa. These findings demonstrate the vegetation-specific assembly of soil microbial communities and highlight the distinct edaphic drivers associated with A. japonica cultivation, providing a scientific basis for soil health management and the sustainable cultivation of this medicinal plant. Full article

Rice is a globally important staple crop and a major dietary source of inorganic arsenic (As). Compared with upland crops, flooded rice cultivation profoundly alters soil redox conditions, making paddy soils one of the most active agricultural interfaces for As mobilization, transformation, and food-chain transfer. While previous research has primarily focused on total As and inorganic As [As(III)/As(V)], methylated and thiolated As species also carry critical agronomic and health implications. Dimethylarsinic acid (DMA) can accumulate in grain and induce straighthead disease, whereas dimethylmonothioarsenate (DMMTA) shows substantially higher toxicity and uptake potential; DMMTA root uptake can be approximately 10 times higher than DMA, and its straighthead-inducing potency can exceed DMA by more than fivefold. This review synthesizes the sources, biogeochemical transformations, plant uptake, grain accumulation, safety assessment, and management implications of As along the paddy soil–rice–grain continuum. Particular emphasis is placed on how water regimes, redox potential, Fe/Mn/Al oxides, sulfur cycling, dissolved organic matter (DOM), microbial functional genes, and crop genotypes regulate diverse As species. Quantitative evidence indicates that alternate wetting and drying (AWD) can reduce grain total As and inorganic As by medians of 32% and 22%, respectively, but may increase grain cadmium (Cd) by a median of 58%; meanwhile, DMA and DMMTA can account for approximately 10–90% and 1–21% of total grain As, respectively, emphasizing that grain-As risk cannot be evaluated using inorganic As alone. Future research should establish speciation-based monitoring systems for inorganic, methylated, and thiolated As; develop process models linking water regime, Fe/S cycling, microbial transformations, and plant transport; and translate these mechanisms into field decision tools that balance As–Cd risk reduction, crop yield, and rice safety under changing environmental conditions. Full article

Microplastics (MPs) are increasingly accumulating in agricultural soils, while their effects on crop-associated rhizosphere microbial communities and ecological functions remain insufficiently understood, particularly for different polymer types. In this study, polyethylene (PE) and polystyrene (PS) microplastics with the same particle size (2 μm) were applied at different concentrations (0, 0.1%, 0.5%, 1%, and 5%, w/w) to investigate their effects on oat rhizosphere bacterial communities and predicted functional potentials. The results showed that microplastic addition significantly altered bacterial community diversity, composition, and predicted functional profiles. Compared to the control (Ctrl), the 1% PE treatment significantly reduced bacterial richness-related indices (p < 0.05), whereas PS mainly affected bacterial diversity. Microplastic treatments also reshaped dominant bacterial taxa and altered the predicted functional potentials associated with carbon and nitrogen cycling. In particular, the 1% PE treatment significantly reduced the predicted relative abundance of the carbon fixation-related gene cbbL (p < 0.05). In addition, high-concentration (5%) PE enhanced several predicted functional potentials related to nitrogen cycling, including nifH, ureA, and amoC. Overall, PE and PS microplastics induced polymer- and concentration-dependent changes in oat rhizosphere bacterial communities. These findings suggest that microplastic accumulation in agricultural soils may influence ecosystem processes by modifying microbial diversity and potential biogeochemical functions. This study provides new insights into the ecological consequences of different microplastic polymers in crop rhizosphere ecosystems and highlights the importance of considering polymer-specific effects when evaluating soil microplastic pollution. Full article

Rhizosphere microorganisms play critical roles in biogeochemical processes including carbon cycling; however, their linkages to carbon-cycling functions under distinct mine restoration approaches remain unclear. In this study, we compared natural and artificial vegetation restoration via metagenomic sequencing to characterize rhizosphere microbial communities and carbon-cycling functional genes. Artificial restoration (AR) decreased soil electrical conductivity (EC) and salt content (SC) while increasing total phosphorus and available phosphorus by 12.33% and 16.44%, respectively. AR also elevated the relative abundances of genes responsible for degrading aromatic compounds, lignin and starch, along with genes participating in carbon-fixation pathways. Taxa of the Actinomycetia, Chloroflexi, and Solirubrobacterales served as the primary contributors to genes encoding 2-isopropylmalate synthase, α-glucosidase, malate synthase, and α-mannosidase, as well as carbon-fixation-related genes, including aconitate hydratase (ACO), methylmalonyl-CoA mutase subunit (E5.4.99.2A), pyruvate orthophosphate dikinase (ppdK), and phosphoenolpyruvate carboxylase (ppc). Moreover, the relative abundances of carbon-fixation genes exhibited significant positive correlations with EC, SC, nitrate nitrogen (NO₃⁻-N) and ammonium nitrogen (NH₄⁺-N). Overall, microorganisms in AR soils hold relatively high genetic potential for carbon sequestration and decomposition. Such rhizosphere carbon-cycling functions are jointly shaped by restoration strategies and vegetation community composition, and our findings offer key theoretical support for mine ecological restoration. Full article

Mangrove microorganisms play a fundamental role in regulating sediment biogeochemical processes, particularly carbon storage and trace element cycling. Although numerous studies have examined microbial roles in individual processes, an integrated understanding of how microbial communities simultaneously regulate carbon storage and trace element dynamics in natural and restored mangrove ecosystems remains limited. This review synthesizes the global status of mangrove microbial research and the influence of microbes on carbon storage, trace element accumulation, and speciation in natural and restored mangrove ecosystems, while identifying emerging research trends and knowledge gaps. Our investigation revealed that research on the influence of microbes on carbon storage in mangrove sediments is increasing globally, with considerably increasing trends after 2017. However, less research has been reported on microbial trace metal interrelations than on carbon storage relationships, suggesting that there is limited focus from researchers on this topic. The available evidence indicates that sulfate reduction, microbial extracellular polymeric substances (EPS), microbial necromass formation, redox-driven biogeochemical coupling, and microbially mediated mineral transformations are the principal mechanisms promoting long-term carbon stabilization in mangrove sediments. Therefore, several studies have also suggested that microbial diversity regulates trace element accumulation and speciation through different pathways, such as redox transformation, bioadsorption, EPS-mediated binding or aggregation, biomineralization, and sulfide precipitation, in mangrove sediment. The principal conceptual contribution of this review is the development of an integrated framework demonstrating that microbial processes act as a central biogeochemical bridge connecting carbon storage and trace element cycling, rather than regulating these functions independently. Finally, we identify critical challenges and research priorities, including functional gene characterization, integrated metal–microbe–plant interactions, multi-omics approaches, long-term monitoring, and global meta-analyses, to improve mechanistic understanding and support evidence-based mangrove restoration and blue carbon management. Full article

Global warming is profoundly altering the structure and function of permafrost peatland ecosystems, but how soil microorganisms as core regulators of biogeochemical cycles respond to the process remains unclear. We investigated peatlands of the continuous, the discontinuous, and the isolated permafrost zones in the climatically sensitive high-latitude Greater Khingan Mountains using 16S rRNA gene high-throughput sequencing and soil physicochemical analysis to systematically reveal the spatial differentiation patterns, community assembly processes, and primary environmental factors of bacterial communities. The results indicated that bacterial alpha diversity was highest in the discontinuous permafrost zone, and both permafrost type and soil depth exerted significant effects on bacterial community composition. From the continuous to the isolated permafrost zones, the relative abundance of the dominant phylum Proteobacteria decreased, while phylum Chloroflexota showed a gradual increasing trend. Co-occurrence network analysis suggested that bacterial network complexity was highest in the continuous permafrost zone, and network stability decreased along the permafrost gradient. From the continuous to the isolated permafrost zone, the relative contribution of stochastic processes declined, whereas that of deterministic processes increased. Partial least squares path modeling (PLS-PM) further demonstrated that soil pH, total organic carbon (TOC), total nitrogen (TN), and soil water content (SWC) were major drivers of bacterial communities, with their effects differing among permafrost zones. Our study elucidated the synergistic evolutionary patterns of bacterial community composition, assembly mechanisms, and environmental drivers under permafrost degradation, providing key scientific evidence for predicting the feedback of high-latitude peatlands to climate warming. Full article

Microorganisms in sediments participate actively in biogeochemical cycling and are essential for maintaining the stability of marine ecosystems. To investigate the spatial impact of seaweed mariculture on sediment bacterial communities, three distinct zones were selected along the Zhanjiang coast, China: the Gracilaria salicornia aquaculture zone, a transition zone (adjacent to the aquaculture area), and a control zone (with no direct mariculture influence). In this study, 16S rRNA gene amplicon sequencing was employed to examine the composition, diversity, and potential functions of sediment bacterial communities across these three zones. The dominant microbial communities identified included Pseudomonadota, Thermodesulfobacteriota, Chloroflexota, and Acidobacteriota. Analyses of α-diversity, β-diversity, and molecular ecological network revealed that the bacterial community in the G. salicornia aquaculture zone exhibited significant differences in species composition, community structure, and interspecies interaction compared with those in the transition and control zones. Environmental factors such as pH, dissolved oxygen (DO) and nitrate (NO₃⁻) exerted significant influence on the bacterial community composition and structure. Predicted functional potential analyses indicated high abundances of pathways related to carbohydrate metabolism and amino acid metabolism. Overall, this study characterizes the spatial distribution patterns of microbial communities in a coastal seaweed mariculture ecosystem and provides important data to support further research on biogeochemical processes mediated by sediment bacteria and their response mechanisms to mariculture activities. Full article

Bacterial communities play vital roles in coastal biogeochemical cycling and ecological stability. Despite their importance, a significant knowledge gap exists regarding their spatiotemporal dynamics and assembly mechanisms in the tropical coastal waters of the Leizhou Peninsula, China. To investigate the bacterial community structure, co-occurrence networks, and assembly processes, we conducted 16S rRNA gene amplicon sequencing on water samples collected seasonally from August 2022 to June 2023. The bacterial communities were dominated by Proteobacteria and Cyanobacteria, and were characterized by a distinct warm-season peak in the relative of Cyanobium. Alpha diversity indices exhibited significant seasonal fluctuations, reaching a minimum in August (autumn) and a maximum in December (winter). These variations were strongly regulated by water temperature and phosphate availability. Redundancy analysis (RDA) identified salinity as the primary deterministic factor shaping community composition. Seasonal environmental heterogeneity, rather than spatial variation, primarily governed bacterial community dynamics. We also observed a seasonal succession in community assembly mechanisms with deterministic filtering dominated in autumn, whereas stochastic processes prevailed in other seasons. Predicted functional profiles indicated a stable core metabolism, although local anthropogenic inputs stimulated specific metabolic adaptations in industrial and aquaculture zones. Our findings reveal that seasonal environmental filtering (especially temperature and salinity) and a shifting balance between stochastic and deterministic assembly processes govern bacterial dynamics in this tropical coastal ecosystem, with anthropogenic inputs modulating local metabolic functions. This study provides fundamental insights into the mechanisms maintaining microbial diversity and stability in tropical coastal waters facing seasonal and human pressures. Full article

Mitigating nitrous oxide (N₂O) emissions from cropland soils is a pressing challenge for climate change mitigation. This study evaluated rockwool-based fertigation (RF) in reducing N₂O emissions from tea plantations. A 17-month field experiment was conducted comparing RF with conventional surface fertilization (CK), measuring tea plant biomass, new tea shoots yield, new tea shoots quality indices, soil N₂O fluxes, physicochemical properties, and nitrogen (N)-cycling functional genes across different soil layers. Results showed that RF treatment significantly increased the aboveground pruning biomass of tea plants, suggesting that RF promotes tea plant growth. The RF treatment showed lower N₂O fluxes and cumulative N₂O emissions within 90 days post-fertilization across the tea-growing season compared with CK, demonstrating that RF effectively mitigates N₂O emissions from tea plantation soils. Random forest analysis further revealed that the RF-induced vertical redistribution of nutrients and N-cycling functional genes was the primary driver of N₂O mitigation. Our findings demonstrate that RF is an effective dual-benefit strategy that simultaneously enhances tea plant productivity and mitigates N₂O emissions by reshaping soil biogeochemical processes and their spatial distribution. Full article

Soil biofilms are structured, dynamic microbial consortia embedded within extracellular polymeric substances that regulate microscale physicochemical heterogeneity and drive biogeochemical transformations in soils. Despite increasing interest in biofilm-mediated remediation, current reviews have largely examined microbial ecology, engineered biofilm functions, and predictive modelling independently, limiting systems-level understanding of pollutant fate in complex soils. This review, therefore, proposes a revised conceptual framework integrating biofilm ecology, synthetic biology, and AI-driven predictive modelling to improve mechanistic and predictive understanding of emerging pollutant detoxification. Emerging pollutants, including pharmaceuticals, pesticides, per- and polyfluoroalkyl substances, micro- and nanoplastics, and heavy metals, exhibit persistence, bioaccumulation, and mixture-dependent effects that challenge conventional remediation strategies. Biofilm matrices function as reactive interfaces facilitating adsorption, sequestration, and enzymatic transformation, while steep redox and nutrient gradients support metabolically diverse processes such as cometabolism, syntrophic degradation, and biomineralisation. Increasing evidence indicates that quorum sensing, horizontal gene transfer, and low-abundance microbial taxa contribute significantly to adaptive responses and functional plasticity within biofilms. Advances in high-resolution imaging, spatial multi-omics, and microfluidic platforms have resolved previously inaccessible biofilm architectures and processes; however, integration with machine learning and process-based modelling remains limited, restricting field-scale prediction of pollutant behaviour and remediation outcomes. Synthetic biology enables targeted optimisation of biofilm functions, whereas AI-driven models enhance prediction of contaminant transport, transformation, and detoxification. Soil biofilms function both as sinks and catalytic hotspots, and resolving this duality through a predictive, systems-level framework represents a major advance beyond existing descriptive reviews. Full article

In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl₃), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl₃ caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level. Full article

Aquatic–terrestrial ecotones are highly dynamic biogeochemical hotspots where hydrological fluctuations profoundly influence microbial community structure and ecosystem functioning. However, the mechanisms underlying microbial community responses across hydrological gradients remain insufficiently understood. In this study, 16S rRNA gene sequencing was used to comparatively analyze bacterial communities in the waterward and landward zones of the drawdown area of the Danjiangkou Reservoir. The results showed that bacterial community composition differed significantly between the two zones, and waterlogging markedly increased bacterial α-diversity. Community variation was primarily associated with key environmental factors, including total phosphorus (TP), soil moisture content (SMC), and nitrate nitrogen (NO₃⁻-N). Compared with the landward zone, stochastic processes contributed more to community assembly in the waterward zone, which also exhibited higher network complexity and topological stability. In addition, several keystone taxa were identified, suggesting their potential roles in maintaining network structure and ecological stability. Functional prediction further revealed distinct metabolic potentials between zones, with enhanced anaerobic and redox-related functions in the waterward zone and predominantly aerobic metabolism in the landward zone. These findings suggest that hydrological fluctuations reshape bacterial community structure and potential ecological functions by jointly regulating water availability and nutrient dynamics. This study provides new insights into microbial ecological processes in reservoir riparian zones and offers a scientific basis for the management of aquatic–terrestrial ecotone ecosystems. Full article