Objective Although the coupling of carbon (C), nitrogen (N), and sulfur (S) cycles is crucial in mangrove ecosystems, direct experimental evidence from pure microbial cultures demonstrating this coupling remains scarce. This work aims to elucidate the coupling process of C, N, and S cycles in mangrove-derived Vibrio ziniensis ZWAL4003. Methods An integrated approach combining genomic analysis, phylogenetic analysis, 16S rRNA gene abundance quantification, and physiological-biochemical characterization was employed to explore the potential coupling process of element metabolism in ZWAL4003. Results The genome of ZWAL4003 carried genes associated with complete metabolic pathways including tricarboxylic acid cycle, oxidative phosphorylation, dissimilatory nitrate reduction to ammonium, and assimilatory sulfur reduction. Glucose, sucrose, starch, and glycerol as C sources significantly enhanced the nitrate reduction activity of ZWAL4003. NaNO₃ as the N source inhibited the sulfate reduction activity of ZWAL4003. Na₂S₂O₃, Na₂SO₄, and Na₂SO₃ as the S sources inhibited the nitrate reduction activity. Furthermore, V. ziniensis strains were widely distributed in the mangrove sediments along the southeast coast of China, with the relative abundance of 0.004 19%-0.073 04%, showing an increasing trend from north to south. Conclusion This study demonstrates that C source utilization promotes nitrate and sulfate reductions, while mutual inhibition exists between nitrate and sulfate reductions, forming the coupling process of C, N, and S metabolisms in ZWAL4003. The wide distribution of V. ziniensis strains in the mangrove ecosystems of China suggests the potential important role of V. ziniensis as an executor in coupling element cycles. These findings enrich our understanding of the integrity of microbe-driven geochemical processes in mangrove ecosystems.

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.

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.

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.

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.

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.

As a crucial group of probiotics, lactic acid bacteria (LAB) play a vital role in the gut microbial ecosystem of insects. This article comprehensively reviewed the species composition, ecological functions, and practical values of LAB in the guts of major insect orders, including Hymenoptera, Diptera, Coleoptera, Hemiptera, Lepidoptera, Blattodea, and Orthoptera. To date, multiple LAB genera including Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Enterococcus, Bifidobacterium, and Weissella were successfully identified from insect guts. The community composition of these bacteria was shaped by factors such as host phylogeny, dietary traits, developmental stages, gut microenvironment, and external ecological conditions. The LAB in insect guts not only assist the hosts in degrading recalcitrant complexes by secreting extracellular enzymes but also inhibit pathogens through the synthesis of antimicrobial substances such as bacteriocins. Additionally, they modulate host immune responses, promote growth and development, regulate host behavior, and participate in the metabolic detoxification of xenobiotics, thereby enhancing host survival and adaptability. Furthermore, insect-derived LAB held great potential in the production of resource insects, pest management, agricultural waste utilization, and green manufacturing. In summary, insect guts represent an important reservoir for the discovery and isolation of novel LAB.

Objective Earthworm intestines, rich in carbohydrates and organic acids, are considered potential hotspots for the horizontal transfer of antibiotic resistance genes (ARGs). However, direct evidence is lacking regarding whether reactive oxygen species (ROS) are produced under anaerobic conditions in earthworm intestines and how ROS regulate plasmid conjugation. This study aimed to investigate the contribution of organic matter metabolism to ROS generation in earthworm intestines and how ROS affected the conjugative transfer of plasmids. Methods Pheretimaguillelmi was used as a model organism to establish the anaerobic microcosm systems simulating in-situ substrate concentrations of earthworm intestines. Four treatments with glucose, lactate, acetate, and amino acids as sole carbon sources were set up. The role of ROS was verified by adding ROS scavengers. Using the fluorescent probe technology, ion chromatography, and qPCR, we determined the production levels of •OH, O₂^•-, and H₂O₂, the consumption of organic substrates, and the abundance changes of the conjugation-related genes gfp, mCherry, trfA, and trbB, respectively. Results ROS was detected in all the treatments. The glucose group showed the highest •OH, O₂^•-, and H₂O₂ yields (0.684, 0.988, and 6.371 μmol/L, respectively) on day 2, which were significantly higher than those in other groups, while the acetate group showed the lowest yields. The substrate consumption rate followed the trend of glucose>lactate>amino acids>acetate, which was consistent with the ROS generation trend. Correspondingly, the glucose group exhibited the highest abundance of gfp, trfA, and trbB (3.47×10⁶, 6.73×10⁶, and 7.86×10⁶ copies/μg DNA) and conjugation frequency (8.9×10^-4), which were the lowest in the acetate group. After ROS scavenging, the conjugation frequencies in all the treatments significantly decreased by 73%‒92%. Mantel analysis revealed that hydroxyl radical showed the most significant correlation with conjugation frequency and abundance of trfA and trbB, indicating that •OH was the core ROS driving conjugative transfer. Unclassified Enterobacteriaceae and Clostridiumsensu stricto 10 were identified as the core microbial taxa coupling ROS generation and conjugation. Conclusion Organic matter metabolism in the anaerobic earthworm intestine can significantly promote ROS generation. ROS further regulates the conjugative transfer of ARGs among microbial strains by altering the abundance of conjugation-related genes.

Objective To analyze the expression profile of the β-glucan-binding protein (Acβ-GBP) gene of Apis cerana cerana in response to Ascosphaera apis infection and to investigate the impacts of Acβ-GBP knockdown on the larval mortality and the incidence of chalkbrood disease following A. apis infection. These findings will provide a foundation for further functional research. Methods The sequence and structural characteristics of Acβ-GBP were analyzed via bioinformatics approaches. RT-qPCR was employed to investigate the expression profiles of Acβ-GBP in the larval midgut following A. apis infection. Furthermore, RNA interference (RNAi) was utilized to explore the impacts of Acβ-GBP on the larval mortality and the incidence of chalkbrood disease. Results The CDS length of Acβ-GBP was 1 440 bp, encoding a protein with a molecular weight of 54.68 kDa and a grand average of hydropathicity value of -0.22, which contained a typical transmembrane domain and signal peptide. Phylogenetic analysis revealed that β-GBP of A. c. cerana, Apis florea and Apis dorsata clustered into a single major clade. After A. apis infection, the expression level of Acβ-GBP in the midgut of A. c. cerana worker larvae was downregulated at 1-3 days post-infection (dpi) (P<0.05). Following RNA interference (RNAi)-mediated silencing of Acβ-GBP, its expression level was lower than that in the ds-egfp group at 2 and 3 dpi (P<0.01). The cumulative larval mortality and the incidence of chalkbrood disease both increased over the infection time, and the overall mortality was higher than that of the control group (P<0.000 1). Conclusion Acβ-GBP was capable of responding to A. apis infection, and knockdown of Acβ-GBP expression significantly impaired the resistance of honeybee larvae to A. apis. Collectively, β-GBP acts as an important immune recognition protein in A. c. cerana, and plays an important role in defending against fungal invasion.