Grassland soil microorganisms play a pivotal role in maintaining the health and stability of grassland ecosystems. However, systematic studies on the diversity, geographical distribution, isolation techniques, and functional potential of novel bacterial taxa in grassland soils remain limited. Here, we conducted a meta-analysis of 104 novel bacterial taxa described in 74 studies from grassland ecosystems across 19 countries between 2004 and 2025. We further predicted their functions via whole-genome data and compared them with background soil bacterial communities in grassland soils. Our results showed that novel bacterial taxa in grassland soils were mainly affiliated with the phyla Actinomycetota and Pseudomonadota, and their discovery frequency closely matched the abundance of background soil microorganisms. Their geographical distribution exhibited clear latitudinal zonality, with high-latitude regions being enriched with dormant taxa adaptive to harsh environments. Functional potential analysis suggested that these novel species not only provide the physiological verification of microbial dark matter, but may also play important roles in key ecosystem processes. Several representative taxa showed distinct ecological functional potential. Amnibacterium soli contributes to carbon and nitrogen cycling through efficient hydrolase systems; Chthonobacter albigriseus mediates methane oxidation to mitigate the greenhouse effect; Noviherbaspirillum agri possesses nitrogen-fixing, plant growth-promoting, and salt-alkali adaptation capabilities; and Streptomyces ziwulingensis can contribute to microbial defenses through secondary metabolite production. Together, these findings highlight the ecological and biotechnological potential of core grassland microbial taxa. Future studies integrating multidisciplinary approaches are needed to elucidate the functions and evolution of novel phyllosphere and rhizosphere taxa and bridge the gap between genomic sequences and ecological functions, thus providing microbiological support for improving the productivity and maintaining the ecosystem stability of grassland.

Mangrove ecosystems, situated at the land-sea interface, serve as vital blue carbon sinks, playing a key role in the global carbon cycle and climate regulation with their efficient carbon sequestration capacity. Microorganisms are central drivers of carbon sequestration in mangrove sediments, capable of fixing carbon through diverse metabolic pathways. This review first summarizes the currently identified microbial carbon fixation pathways and carbon sequestration mechanisms in mangrove sediments, with a focus on three primary processes: the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, and the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Furthermore, we discuss the influences of key environmental factors, such as vegetation type, sediment physicochemical properties, and nutrient inputs, on microbial carbon fixation and sequestration. Finally, we propose the future directions for studies on microbial carbon fixation and sequestration in mangrove sediments, including the couplings of nutrient cycling processes, microbiome engineering, and microorganism-plant interactions. This review proposes potential novel strategies for enhancing blue carbon capacity in mangrove ecosystems.

Objective Coastal wetlands are important natural sources of nitrous oxide (N₂O), and the distribution of denitrification genes nirS and nirK directly influences their N₂O emission potential. Vegetation types can significantly regulate the abundance of these genes by altering soil physicochemical properties and carbon-nitrogen availability, while the underlying mechanisms remain unclear. Methods Soils were collected from five representative habitats—Kandelia obovata (mangrove), Spartina alterniflora, Cyperus malaccensis, Phragmites australis, and unvegetated mudflat—in the Minjiang River estuary wetland at depths of 0-10, 10-20, and 20-30 cm. The abundance of nirS and nirK was quantified by real-time quantitative PCR, and their environmental drivers were analyzed through random forest modeling and correlation analysis. Results The abundance of nirS and nirK in all the vegetated soils was significantly higher than that in the unvegetated mudflat, with the highest values observed in the surface soil (0-10 cm) under P. australis. Both genes showed significantly decreased abundance as the soil depth increased, presenting a distinct surface enrichment effect. The nirS/nirK ratio was greater than 5 across all soil samples, indicating the dominance of nirS-type denitrifiers. The mangrove surface soil exhibited the highest nirS/nirK ratio, likely due to low dissolved organic carbon (DOC) levels limiting nirK-type denitrifiers. Random forest analysis identified soil electrical conductivity as the primary driver of nirS and nirK abundance, while available phosphorus (AP) was the dominant factor influencing the nirS/nirK ratio. High salinity promoted the enrichment of both genes, whereas high AP concentrations increased the nirS/nirK ratio. Conclusion Vegetation type and soil depth jointly shape the distribution patterns of nitrite reductase genes in the Minjiang River estuary wetland by regulating soil salinity, DOC, and nutrient availability. The results provide insights for nitrogen cycle management in coastal wetlands.

Objective To investigate the changes in microbial community structure and function in degraded mangrove sediment, and to explore their potential relationships with environmental factors and mangrove degradation. Methods Sedimental samples were collected from degraded mangroves in Guangxi Beihai Coastal National Wetland Park, marked as healthy (ZC), early-stage/deteriorating (BY), and necrotic (SW) groups. The physicochemical factors, including total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), oils, and various heavy metals, were analyzed using standard methods. High-throughput sequencing of 16S rRNA gene and ITS region was performed. Subsequent analyses, including diversity indices, Venn plot, LEfSe analysis, Z_i-P_i analysis, and FAPROTAX/FUNGuild functional prediction, were employed to compare the composition and functional differences of bacterial and fungal communities and to identify their driving environmental factors. Results The richness and diversity of the bacterial community followed the order of SW>ZC≈BY. The dominant phyla were Pseudomonadota and Chloroflexi. In contrast, fungal richness and diversity were lowest in SW, where Ascomycota was the dominant phylum. LEfSe analysis indicated that the bacterial community in ZC was characterized by Actinomycetota and several Desulfobacterota; BY was enriched in Gemmatimonadota; SW was dominated by Bacillota, Campylobacterota, and Spirochaetota. Z_i-P_i analysis revealed that keystone fungal taxa in BY were mainly from Ascomycota, while those in SW contained both Ascomycota and Basidiomycota. Functional prediction suggested that bacterial communities were predominantly chemoheterotrophic, with fermentation as a major pathway. Fungal communities were primarily saprotrophic and notably pathogenic. Correlation analysis further demonstrated that TN, TP, oils, and heavy metals (e.g., As, Cu) significantly influenced microbial community structure. Conclusion By investigating microbial community structure and function, this study elucidates the dynamic response of microbial communities to environmental shifts in degrading mangrove ecosystems, thus providing a crucial microbiological reference for future ecosystem health assessment and restoration efforts.

Objective The survival mechanisms of aerobic methylotrophs in oxygen-deficient environments represent a focal topic in current microbial ecology. This study aims to investigate the extracellular electron transfer (EET) mechanism by which the aerobic methylotroph Methylophilus sp. 14 utilizes insoluble iron minerals (ferrihydrite) under oxygen-deficient conditions and to elucidate the synergistic role of exogenous and endogenous electron shuttles in this process. Methods Anaerobic culture (initial O₂ level: 2%) of Methylophilus sp. 14 isolated from sediments of Fuxian Lake was conducted with methanol as the carbon source and ferrihydrite as the sole terminal electron acceptor. Iron reduction kinetics were measured along with electrochemical analyses (differential pulse voltammetry and cyclic voltammetry) and microscopic characterization (scanning/transmission electron microscopy) to systematically evaluate the iron-reducing capacity of the strain and explore the roles of exogenous shuttles (humic substances, HS; anthraquinone-2,6-disulfonate, AQDS) and endogenous flavins in electron transfer. Results Methylophilus sp. 14 coupled methanol oxidation with ferrihydrite reduction, increasing the Fe(II) concentration from 0.49 μmol/L to 8.29 μmol/L within 20 days and promoting the partial transformation of ferrihydrite into magnetite. Exogenous addition of HS and AQDS further enhanced Fe(II) production to 10.73 μmol/L and 11.22 μmol/L, respectively, improving the cumulative electron transfer efficiency by approximately 1.5 folds. Electrochemical analyses indicated that the redox potential of the bacterial cells was lower than that of ferrihydrite, thermodynamically favoring spontaneous electron transfer. Soluble AQDS formed a conductive microenvironment that accelerated electron flux. Notably, this study first revealed that Methylophilus sp. 14 synthesized and secreted flavins, whose extracellular concentration showed a strong positive correlation with the EET rate (r=0.94, P<0.001). Furthermore, exogenous shuttles stimulated increases of 30%‒50% in total flavin secretion. Flavins functioned as a critical electron bridge, mediating electron transfer from intracellular metabolism to exogenous shuttles and thereby establishing a cooperative electron transport chain. Conclusion This work reveals a novel EET strategy employed by aerobic methylotrophs to adapt to oxygen-deficient conditions. That is, exogenous electron shuttles not only construct an extracellular conductive microenvironment but also stimulate the secretion of endogenous flavins, resulting in a synergistic electron transfer mechanism that efficiently drives the reduction of solid-phase iron minerals. These findings deepen our understanding of the metabolic flexibility of aerobic microorganisms and their ecological role at aerobic-anerobic interfaces.

Global climate change and soil heavy metal pollution have raised higher requirements for the synergistic adaptability of conventional remediation technologies. Microbially induced carbonate precipitation (MICP) technology, with its unique biological metabolism and environmental interaction characteristics, provides a new pathway for the synergistic management of carbon sequestration and heavy metal stabilization. This technology induces calcium carbonate formation through two core enzyme-mediated pathways involving urease and carbonic anhydrase, enabling simultaneous CO₂ sequestration by mineralization and heavy metal immobilization. In carbon sequestration scenarios, MICP technology can enhance the geological stability of carbon sequestration sites through lithological improvement and strengthen carbon sequestration efficiency through high-efficiency mineralization reactions. In heavy metal remediation scenarios, it can achieve heavy metal stabilization through multiple mechanisms such as adsorption, co-precipitation, and surface complexation, and different calcium carbonate crystal forms can adapt to varied pollution scenarios. However, the large-scale application of MICP technology currently faces three major bottlenecks: insufficient tolerance of functional strains to extreme environments, compatibility conflicts between exogenous strains and native ecosystems, and coupling barriers between metabolic pathways for carbon sequestration and heavy metal immobilization. To address these issues, this paper proposes a three-stage synergistic process flow hypothesis for heavy metal immobilization, carbon sequestration by mineralization and long-term monitoring. Sequentially switching metabolic pathways theoretically resolves the pH requirement conflict between heavy metal immobilization and carbon sequestration by mineralization, providing new solutions for the engineering application of MICP technology. Future research should focus on the modification of functional strains for extreme habitats, regulation of interactions between exogenous and native microorganisms, and precise optimization of process parameters, to advance this synergistic model from theoretical design to on-site validation, providing technical support for achieving carbon neutrality and the safe utilization of polluted soils.

Microbial dark carbon fixation (DCF) is a key biogeochemical process in which chemoautotrophic or heterotrophic microbes convert inorganic carbon to organic carbon in the absence of light. Recent studies have shown that the contribution of this process to the global carbon cycle has long been underestimated, particularly in deep waters, sediments, soils, hot springs, and other extreme environments where it holds significant ecological importance. This review comprehensively summarizes the recent research advances in microbial DCF, with a focus on major carbon fixation pathways, functional microbial groups, and carbon fixation rates across different ecosystems. The published data demonstrate significant variations in microbial DCF rates across different ecosystems. The deep ocean exhibits the highest DCF rate, reaching approximately 2.14×10⁴ µmol C/(m²·d), followed by boreal lakes, where the maximum DCF rate reaches 1.33×10⁴ µmol C/(m²·d). Additionally, in the deep-water layer of stratified boreal lakes, the contribution of DCF to total primary productivity can be as high as 81.4%. In high-temperature hot spring environments, DCF can account for 80%-100% of the total carbon fixation. From the perspective of carbon fixation pathways, the Calvin cycle is the primary pathway for microbial DCF across various habitats, widely existing in ecosystems including lakes, oceans, soils, and hot springs. Meanwhile, different habitats adapt to their specific environmental conditions by incorporating additional metabolic pathways such as the Wood-Ljungdahl pathway and the reductive tricarboxylic acid cycle (rTCA) pathway to achieve efficient carbon fixation. Temperature, pH, salinity, oxygen concentration, nutrient conditions, and depth are key environmental factors regulating microbial DCF rates. These factors collectively determine the efficiency and contribution ratios of DCF processes in different ecosystems by influencing the community structure of DCF-related microorganisms, the selection of metabolic pathways, and enzyme activities. Finally, the review discusses current limitations in this field, including uncertainties in quantification methods and insufficient understanding of environmental response mechanisms, and highlights key directions for future research. These advances are expected to provide critical scientific evidence for improving the carbon cycle theory, assessing the impacts of climate change, and developing microbe-based carbon sequestration technologies.

Objective Microbial-Fenton process driven by dissimilatory iron reduction is increasingly recognized as a major source of hydroxyl radicals (•OH) in redox-fluctuating environments (e.g., tidal sediments), thereby playing an important role in biogeochemical element cycling. However, extracellular polymeric substances (EPS), which are ubiquitous and closely associated with the cell-mineral interface, remain poorly understood in terms of their regulatory roles in this process. This study aims to elucidate the mechanisms by which EPS derived from Shewanella decolorationis influence •OH generation under oxic-anoxic conditions. Methods S. decolorationis S12, its extracellular electron transfer-deficient mutants (S12ΔBA and S12ΔccmA), extracted EPS, and ferrihydrite were employed as model components. By simulating oxic-anoxic alternating conditions, we employed a combination of chemical and spectroscopic approaches to characterize the physicochemical properties of EPS and to investigate their effects on iron reduction and •OH generation. Results Although EPS exhibited intrinsic redox activity and could mediate electron transfer in S. decolorationis, they exerted inhibitory effects on iron reduction efficiency and •OH generation under oxic-anoxic conditions, decreasing the Fe(Ⅱ) accumulation and •OH production by up to (56.63±4.67)% and (26.86±5.30)%, respectively. This inhibition was primarily attributed to the strong affinity between EPS and iron minerals, which led to the formation of EPS-Fe(Ⅲ) complexes that hindered electron transfer efficiency. In addition, EPS promoted the transformation of ferrihydrite into secondary iron mineral phases with lower bioavailability, thereby decreasing the reducibility of Fe(Ⅲ) and further suppressing •OH generation. Conclusion EPS act as a critical interfacial chemical mediator in the microbe-iron mineral system, regulating dissimilatory iron reduction and consequently influencing •OH production. These findings provide new insights into the biogeochemical processes in tidal soil and water environments such as intertidal sediments.

Objective In view of the issues of reservoir acidification and pipeline corrosion caused by sulfate-reducing bacteria (SRB) during oil and gas field development, this study focused on the green synthesis of silver nanoparticles with bamboo leaf extract and systematically evaluated their effectiveness and mechanism in inhibiting SRB. Methods Under alkaline conditions (pH 11.0) and at 80 ℃, silver nanoparticles with a particle size of 20-50 nm and good monodispersity were successfully prepared through ultrasonically assisted ethanol extraction of active substances from bamboo leaves. Results Real-time quantitative PCR results showed that 50 μg/mL of silver nanoparticles reduced the total bacterial count from 5.21×10⁹ copies/mL to 2.01×10⁷ copies/mL. Meanwhile, the abundance of sulfate-reducing functional genes dsrB and aprA decreased from 1.76×10⁹ copies/mL and 2.03×10⁹ copies/mL to undetectable levels. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction assay indicated that silver nanoparticles reduced SRB activity in a dose-dependent manner, with the SRB activity in the 50 μg/mL silver nanoparticles group decreasing to 40% of that in the control group. The lactate dehydrogenase (LDH) release assay confirmed that the cytotoxic effect of the synthesized silver nanoparticles ranged from 32.8% to 42.1%. Under SEM/TEM, silver nanoparticles were observed to adsorb onto the cell membrane surface, forming a nanoscale coating that altered membrane permeability and disrupted the cell wall structure. At a concentration of 50 μg/mL, silver nanoparticles completely inhibited biofilm formation. Core simulation experiments further validated the effective inhibition of SRB by the nanoparticles in reservoir environments, with hydrogen sulfide production decreasing from 83.16 mg/L to below the limit of detection. Conclusion This study demonstrates that bamboo leaf-mediated synthesized silver nanoparticles exhibit high efficiency in inhibiting SRB, environmental friendliness, and resistance to microbial drug resistance. It provides a green prevention and control strategy for microbial corrosion in oil and gas development processes.

Open-air piling of coal gangue severely disrupts the soil structure and regional ecosystem health. Inoculation with sulfate-reducing bacteria (SRB) is an effective strategy to control acid pollution derived from coal gangue, as SRB can reduce sulfate and immobilize heavy metals. However, the remediation performance of SRB in coal gangue piles and the associated ecological response patterns along the depth gradient remain unclear. Objective To elucidate the overall ameliorating effect of SRB remediation on coal gangue piles, and to characterize the differentiation patterns and driving mechanisms of soil physicochemical properties, microbial community structure, and microbial functions along the vertical profile during remediation. Methods A typical coal gangue pile in an open-pit coal mine in Yulin City, Shaanxi Province, China was selected as the study site. Coal gangue piles with SRB remediation (treatment group) and without remediation (control group) were established. In the control dump, 0-20 cm mixed soil samples were collected to represent the background condition. In the SRB-remediated pile, soil samples were collected from the 0-5 cm shallow layer (SL), 5-10 cm middle layer (ML), and 10-20 cm deep layer (DL). Soil physicochemical properties were determined, and 16S rRNA gene high-throughput sequencing was performed. PICRUSt2 was used to predict microbial functions. Differences between groups and between vertical gradients within the treatment group were compared. Results Compared with the control, SRB remediation significantly increased the overall soil pH, electrical conductivity (EC), and soil organic matter (SOM) content of the coal gangue pile, and markedly enhanced the alpha diversity and altered the structure of the bacterial community. With the increase in depth of the remediated pile, pH, EC, and SOM increased progressively, while available potassium first increased and then decreased. The relative abundance of dominant bacterial phyla changed significantly along the depth gradient, and the complexity of the co-occurrence network (number of nodes, number of edges, and average degree) also increased. Soil pH and EC were identified as key environmental drivers of community structural variations. Functional prediction indicated that the abundance of genes related to carbon fixation, nitrogen cycling, and sulfur cycling in the deep layer was significantly higher than that in shallow and middle layers. Conclusion SRB bioremediation not only improved the overall soil environment and microbial community of the coal gangue pile but also shaped a depth-dependent differentiation pattern of environmental conditions and microbial functions within the pile. These findings provide an important theoretical basis for the long-term stable remediation of coal gangue piles and the regulation of microbially mediated processes.