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.

Acidic soil accounts for approximately 50% of the world’s available arable land. Its highly active aluminum ions and low pH environment not only directly inhibit plant growth but also significantly alter the microbial community structure in the rhizosphere, weaken the functions of beneficial microorganisms, and exacerbate soil-borne diseases. Brassinolide (BR), as a group of important plant signaling molecules, play a core role in enhancing the plant stress resistance in acidic soil by precisely regulating plant-microorganism interactions. BR promote the root secretion of organic acids such as malic acid and oxalic acid by activating BZR1/BES1 and transcription factors. These secretions act as carbon sources and chemotactic signals to specifically recruit beneficial microorganisms such as Paenibacillus azotofixans, Pseudomonas, and ectomycorrhizal fungi, reshaping the microbial community structure in the rhizosphere. The microbial community reassembly induced by BR significantly enhances aluminum ion chelation, nutrient activation, and pathogen inhibition. For instance, nitrogen-fixing bacteria enriched utilize malic acid for metabolic activities and secrete auxin and other substances to promote plant growth in acidic environments. Ectomycorrhizal fungi alleviate aluminum toxicity through oxalic acid secretion. Meanwhile, BR, in collaboration with plant hormones such as auxin and gibberellin, optimizes the root structure, expands the microbial colonization niche, and forms a complex synergistic network for enhancing stress resistance. Future research should focus on the specific regulatory mechanisms of BR on the rhizosphere microbiome, unveil the direct action pathways of BR as microbial signaling molecules, and develop efficient BR-microbial compound preparations in combination with microbial community engineering, providing innovative strategies and application solutions for the regulation of acidic soil microorganisms.

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.

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.

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.

Perfluorooctanoic acid (PFOA), a representative per- and polyfluoroalkyl substance (PFAS), has emerged as a priority-controlled emerging contaminant of global concern due to its extreme environmental persistence, bioaccumulation potential, and toxicity. It poses a serious threat to ecosystem stability and human health. Microbial degradation has become one of the most promising technological approaches for PFOA remediation, owing to its core advantages of being environmentally friendly, cost-effective, and amenable to large-scale application. This paper systematically reviews the research progress in PFOA-degrading microorganisms in terms of the characteristics, degradation efficiency, and underlying mechanisms of isolated and identified functional strains (bacteria and fungi). Subsequently, this paper synthesizes the response patterns of microbial communities and strategies for resource exploration in various contaminated habitats harboring potential PFOA degraders. Finally, it highlights key scientific challenges currently facing the field and makes an outlook on future research directions. This review aims to provide a reference for the resource development, mechanism elucidation, and engineering application of PFOA-degrading microorganisms, offering theoretical support and forward-looking perspectives for advancing microbial remediation technologies targeting global PFOA contamination.

The deep sea encompasses a wide range of ecosystems, including cold seeps, hydrothermal vents, seamounts, and hadal trenches, whose extreme environmental conditions support diverse and unique microbial communities. Among them, viruses, as one of the most abundant biological entities on Earth, exhibit remarkable novelty in terms of genome composition, functional proteins, and evolutionary lineages and play crucial roles in regulating microbial community structure, driving biogeochemical cycles, and facilitating horizontal gene transfer. In recent years, with the rapid development of deep-sea sampling technologies, high-throughput sequencing, multi-omics approaches, and artificial intelligence-based analyses, a vast number of uncultivated deep-sea viral genomes have been identified, revealing a substantial reservoir of viral “dark matter” and significantly expanding our understanding of viral diversity, ecological functions, and adaptive strategies in deep-sea environments. Accumulating evidence indicates that deep-sea viruses participate in ecological processes through diverse infection strategies, including lytic, lysogenic, and chronic infections. During long-term adaptation to extreme environments and virus-host coevolution, deep-sea viruses have accumulated a rich repertoire of unique genetic resources, including virus-encoded functional genes and enzymes with significant potential for biotechnological applications. This review systematically summarizes recent advances in the abundance, distribution, diversity, ecological functions, and genetic resource exploration of deep-sea viruses. Furthermore, this paper discusses the main challenges and future perspectives in this field, with the aim of providing a theoretical framework for a deeper understanding of deep-sea microbial ecological processes and the sustainable utilization of deep-sea genetic resources.

Objective To elucidate the community structures and environmental adaptation mechanisms of bacteria and archaea in the sodium sulfate-type Yuncheng Salt Lake in Shanxi Province, China and explore the assembly patterns of microbial interaction networks under extreme hypersaline conditions. The findings are expected to provide a theoretical basis for assessing the ecosystem functions of salt lakes and developing halophilic microbial resources. Methods Water samples were collected from 10 sampling sites with salinity gradients of 6.0%-34.2% in Yuncheng Salt Lake. The physicochemical analysis of water quality, high-throughput 16S rRNA gene sequencing, molecular ecological network analysis, and multivariate statistical methods were employed to systematically investigate the microbial community structure and its interactions with environmental factors. Results The dominant taxa included Euryarchaeota, Pseudomonadota, and Bacteroidota. Archaea were primarily represented by Halarchaeum and Halorubrum, while the dominant bacterial genera were Roseovarius and Spiribacter. A microbial network consisting of 53 nodes and 73 edges was constructed, with negative correlations accounting for 63%. Key taxa included Halolamina, Geitlerinema, and Halorubrum. Salinity, nitrogen, and sulfide emerged as the three core drivers with high connectivity in the network, exhibiting significant correlations with multiple microbial groups. Conclusion Microbial community assembly in Yuncheng Salt Lake is dominated by negative correlations (e.g., potential competition, niche differentiation, or environmental stress), and this highly competitive network structure enhances the system resistance to environmental disturbances. The study reveals unique microbial adaptation strategies in sodium sulfate-type salt lakes and provides new insights for the exploitation of extremophilic microbial resources.

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.