Deep-sea cold seeps are formed by the leakage of hydrocarbons such as methane, creating unique eco-environments that foster novel and phylogenetically diverse prokaryotes, eukaryotes, and viruses. Cold seep microorganisms obtain energy and substances through chemosynthesis, driving the biogeochemical cycles of elements such as carbon, sulfur, and nitrogen, thereby maintaining the stability of the cold seep ecosystem. Cold seep habitats contain rich microbial genetic resources, especially enzymes and secondary metabolites produced under extreme conditions, which exhibit dehalogenating, nitrogen-fixing, and antimicrobial activities, with potential applications in agriculture, drug development, and environmental protection. Additionally, cold seep microorganisms are closely related to the environmental impact assessment of natural gas hydrate extraction and play a significant role in global climate change. To effectively develop the microbial genetic resources in deep-sea cold seeps, researchers should combine in situ sampling, sequencing, and culture methods with environmental parameter monitoring to explore the ecological roles and evolutionary mechanisms of these microorganisms, delve into their genetic resources, and investigate microbial responses during hydrate extraction. Such efforts will provide a scientific basis for comprehensively developing microbial genetic resources and hydrate resources in deep-sea cold seeps.

Cable bacteria are a new group of filamentous electroactive microorganisms with the ability of long-distance electron transfer (LDET), playing an important role in the geochemical cycling of elements. Their unique structural and functional characteristics make them like "biological cables". Since the first discovery in marine sediments in 2012, cable bacteria have attracted widespread attention. They have shown unique ecological potential in maintaining the health of aquatic ecosystems, environmental restoration, and climate regulation. Focusing on the "biological cable" structures and functions of cable bacteria, this paper reviews their filamentous structural characteristics, electrogenic sulfur oxidation characteristics, diversity and distribution characteristics, and LDET mechanism in sediments, and summarizes their influences on the cycling of key elements such as S, C, N, and P and the migration and transformation of metal ions. In addition, this paper summarizes the interactions of cable bacteria with other organisms and their roles in the natural restoration of ecosystems and analyzes the existing problems and future development directions, with a view to providing a reference for further giving play to the role of "biological cables" in the natural restoration of ecosystems.

[Objective] To explore the environmental drivers of prokaryotic microbial communities and carbon-fixing microbial groups in the upper and lower reaches of the Xiaolangdi Reservoir of the Yellow River during the dry season. [Methods] Water and surface sediment samples were collected from the upper and lower reaches of Xiaolangdi Reservoir during the dry season (November, 2020), and the physiochemical factors were measured. The composition of prokaryotic microbial communities and their carbon fixation functions were investigated by high-throughput sequencing of bacterial and archaeal 16S rRNA genes and PICRUSt2 prediction. The composition of carbon-fixing microbial groups was analyzed by high-throughput sequencing of cbbL and cbbM. [Results] Proteobacteria (24.74%), Actinobacteria (17.55%), and Firmicutes (11.43%) were the dominant bacterial phyla. Crenarchaeota (63.26%), Thermoplasmatota (18.29%), and Halobacterota (11.31%) were the dominant archaea. Proteobacteria (13.14%), Cyanobacteria (1.70%), and Actinobacteria (0.76%) were the dominant phyla of cbbL-carrying carbon-fixing microorganisms. Proteobacteria (3.52%), Actinobacteria (0.03%), and Gemmatimonadota (0.02%) were the dominant phyla of cbbM-carrying carbon-fixing microorganisms. The main environmental drivers of the bacterial community structure were temperature (T), turbidity, chemical oxygen demand (COD), and total ammonia nitrogen, which, however, had mild influences on archaea and carbon-fixing microbial groups. In bacteria, the relative abundance of the reductive tricarboxylic acid cycle (rTCA), the dicarboxylate-hydroxybutyrate cycle (DC/4HB), the 3-hydroxypropionate bi-cycle (3HP), and the Calvin-Benson-Bassham (CBB) were higher than that of other detected carbon fixation pathways. Notably, the relative abundance of the hydroxypropionate-hydroxybutylate cycle (3HP/4HB) in the upper reaches was significantly higher than that in the lower reaches. In archaea, the relative abundance of carbon fixation pathways such as rTCA, DC/4HB, and incomplete rTCA was higher, and the abundance of the Wood-Ljungdahl pathway (WL) in the lower reaches was markedly higher than that in the upper reaches of the Xiaolangdi Reservoir. Turbidity was a key factor affecting the abundance of the bacterial 3HP and incomplete rTCA, while temperature, dissolved oxygen, turbidity, COD, and total phosphorus were the main factors affecting the abundance of carbon fixation pathways in archaea. [Conclusion] This study revealed the environmental drivers of prokaryotic microbial communities and carbon-fixing microbial groups in the upper and lower reaches of the Xiaolangdi Reservoir during the dry season. The results contribute to a deeper understanding of the microbial carbon fixation process and the environmental driving mechanisms in the Yellow River during the dry season.

[Objective] Eukaryotic plankton are key components of a freshwater ecosystem, playing an important role in the food web. This study aims to explore the community dynamics and assembly mechanisms of three differently size-fractionated eukaryotic plankton communities (0.2–200, 0.2–3, and 3–200 μm) in two deep subtropical reservoirs (Shidou Reservoir and Tingxi Reservoir) in Xiamen. [Methods] From 2015 to 2018, samples were collected from both reservoirs in four seasons. The V9 region of eukaryotic 18S rRNA gene was amplified and sequenced to investigate the dynamic changes of eukaryotic plankton communities in the reservoirs. [Results] Overall, the temporal dynamics of dominant phyla of total eukaryotic plankton (0.2–200 μm) showed a strong correlation with that of micro-eukaryotic plankton (3–200 μm) and a weak correlation with that of pico-eukaryotic plankton (0.2–3 μm). Turnover was the main factor driving the temporal dynamics of eukaryotic plankton community composition in the two reservoirs. The proportions of the total number of sequences of the turnover species were higher in Shidou Reservoir than in Tingxi Reservoir in 2016 and 2017, while the opposite pattern was observed in 2018. Deterministic processes played a stronger role in the pico-eukaryotic plankton community assembly in Shidou Reservoir than in Tingxi Reservoir. The concentration of cyanobacterial chlorophyll a was weakly correlated with the eukaryotic plankton community in Tingxi Reservoir, while it was significantly correlated with the eukaryotic plankton community (especially the pico-eukaryotic plankton community) in Shidou Reservoir. [Conclusion] The pico-eukaryotic plankton community was more sensitive to cyanobacterial biomass than the micro-eukaryotic plankton community. The dynamics of the micro-eukaryotic plankton community largely determined the dynamics of the total eukaryotic plankton community. In the context of global changes, efforts should be made to monitor differently size-fractionated eukaryotic plankton and analyze the dynamics of community structure and functions for better understanding and protection of the reservoir ecosystem health and water quality.

Although the large scale of industrial nitrogen fixation and chemical nitrogen fertilizer application have increased crop yields and alleviated food crisis, the excess discharge of nitrogen nutrients have affected the environment and human health. The treatment of nitrogen contamination is largely dependent on the nitrogen cycle driven by microorganisms. In the last three decades, researchers have discovered the inorganic nitrogen metabolism pathways such as anaerobic ammonia oxidation (Anammox), complete ammonia oxidation (Comammox), and direct ammonia oxidation (Dirammox). Shewanella, a genus of known bacteria with abundant respiration pathways, are ubiquitous in natural habitats and have potential applications in both microbial fuel cells and environmental bioremediation. In this review, we described the modulation mechanisms of denitrification and dissimilatory nitrate reduction to ammonium pathways in Shewanella from the nitrate reductase systems, regulation of the cyclic AMP (cAMP) receptor proteins (Crp), and modulation and switching of nitrate reduction pathways, aiming to give insights into the microbial-driven nitrogen cycling mechanism in the hydrosphere and the development of novel biotechniques and bioreactors for the removal and mitigation of nitrogen pollution.

Dissolved organic matter (DOM) in the ocean encompasses complex and diverse organic compounds, and heterotrophic bacteria, the main DOM decomposers, also exhibit high biodiversity. The interactions between heterotrophic bacteria and DOM play an important role in biogeochemical cycles, which, however, are not fully understood.[Objective] To explore the dynamics of microbial communities with the addition of marine-derived concentrated DOM. [Methods] DOM with a molecular weight exceeding 1 kDa and enriched from coastal seawater was introduced into microcosm culture systems. Illumina amplicon sequencing, dissolved organic carbon (DOC) concentration measurement, and bacterial isolation were performed on different days of incubation. [Results] The addition of DOM significantly influenced bacterial community composition, inducing more pronounced changes in the high-DOM group. Specifically, the relative abundance of Campylobacterota, Nitrosococcales, and Nitrincolaceae increased in the high-DOM group on days 3, 10, and 30, respectively. The alpha diversity and evenness of the microbial community decreased during days 0-3 and increased during days 10-30, with a transition point occurring between days 3 and 10. The network analysis revealed that the high-DOM group exhibited a more tightly interconnected and complex network than the control group. In addition, bacterial isolates from the culture systems added with different concentrations of DOM were distinct. The specific genera of different DOM treatments were identified, which may be key groups in DOM degradation. [Conclusion] The addition of DOM triggers the succession of microbial community structures within microcosm culture systems, and the community composition may be associated with specific DOM components, which influence the direction of community succession. Furthermore, the varying DOM concentrations select for culturable bacteria with diverse survival strategies. This study provides a basis for enriching our understanding about the mechanisms underlying microbial responses to marine-derived DOM.

Vitamin B₁₂ (VB₁₂) is an essential nutrient and growth cofactor for the majority of organisms. It exerts influence not only on the structure of microbial communities and marine primary productivity but also on the global biogeochemical cycles, thus justifying its designation as a "hard currency" in marine ecosystems. Ammonia-oxidizing archaea (AOA), initially isolated from the ocean in 2005, are distinguished by their chemolithoautotrophic characteristics. Genomic, metabolomic, and culture studies have demonstrated that AOA are among the few microbial groups capable of synthesizing VB₁₂ in the ocean. This capability is crucial for maintaining microbial community stability and biogeochemical functions. This review summarizes the measurement methods and distribution characteristics of VB₁₂ in the ocean and the pathways through which AOA produce VB₁₂. It discusses the importance of AOA in marine VB₁₂ supply and outlines the future research directions for VB₁₂ production by AOA.

Cyanobacteria have garnered great attention as important players in the marine hydrosphere and the source of bioactive compounds. Type Ⅳ pili (TFP) play a crucial role in cyanobacteria by participating in various physiological functions such as substrate surface movement, phototaxis, and natural transformation. With the continuous advancements in the visualization of pili, we have gained a deeper understanding of the TFP-mediated cell behaviors of cyanobacteria. We review the recent progress and applications of visualization of pili in the research on the twitching, phototaxis, and natural transformation of cyanobacteria. This review is expected to improve our understanding of the TFP-mediated cell behaviors and the ecological function and significance of cyanobacteria in the hydrosphere. Additionally, it provides new insights for developing TFP-based regulation on cell behaviors of cyanobacteria.

[Objective] To obtain a stable microbial consortium with a high yield of caproate and achieve high-value carbon recovery from Baijiu-making wastewater (Huangshui). [Methods] We used the plate screening approach to obtain a simplified caproate-producing microbial consortium, evaluated the preferred carbon source of the consortium, and optimized the substrate concentration, pH, and feeding strategy. The metagenomics based on nanopore sequencing was employed to determine the composition and stability characteristics of the simplified caproate-producing microbial consortium. [Results] SimpCom1, a simplified caproate-producing microbial consortium, demonstrated significantly higher conversion rate of lactate than glucose to caproate. When SimpCom1 was used to ferment unsterilized Huangshui, we controlled the working concentration of Huangshui between 30% and 50% and initial pH 5.50 to achieve stable growth and metabolism of the consortium for caproate production. The fermentation was carried out in a fed-batch manner with 50% Huangshui, initial pH 5.50, and pH 6.50–7.00 after 48 h. Within four fed-batch fermentation cycles, the average caproate titer, productivity, proportion of caproate in total acids, and conversion rate of lactate to caproate reached 16.83 g/L, 3.05 g/(L·d), 67.27%, and 0.42 g/g, respectively. The metagenomic analysis showed that Caproicibacterium lactatifermentans, Ligilactobacillus acidipiscis, Clostridium tyrobutyricum, and 'Butyriproducens baijiuensis BJN0003' were the core species of SimpCom1. C. lactatifermentans and 'B. baijiuensis BJN0003' remained stable growth and metabolism in the unsterilized Huangshui, with the relative abundance of 45.3% and 6.7%, respectively, at the end of fermentation with 50%-diluted Huangshui. [Conclusion] We successfully established an efficient and low-cost approach for producing caproate by fermentation of unsterilized Baijiu-making wastewater with a simplified microbial consortium containing C. lactatifermentans and 'B. baijiuensis BJN0003'.

[Objective] To study the sulfur oxidation characteristics of Halothiobacillus diazotrophicus LS2 under different oxygen levels and to decipher the mechanism of strain LS2 adapting to low-oxygen environments. [Methods] The concentrations of S₂O₃^2- and SO₄^2- were measured by ion chromatography. Bacterial growth was determined by plate dilution coating method. The differentially expressed genes and related metabolic pathways were identified and analyzed by transcriptome sequencing and bioinformatics technology. [Results] Strain LS2 oxidized reduced sulfur compounds and grew under 0.2%–21.0% oxygen, and it maintained high sulfur oxidation activity under the oxygen level above 1.6%. Comparative transcriptomic analysis screened out 851 differentially expressed genes that might be related to the adaptation to low oxygen, including 464 up-regulated genes and 387 down-regulated genes. In sulfur metabolism, thiosulfate sulfurtransferase, sulfur oxidase/reductase, and sulfide: quinone oxidoreductase were up-regulated, while the Sox enzyme system was down-regulated, which indicated that strain LS2 might change the sulfur oxidation pathway to adapt to low-oxygen environment. In the low-oxygen group, the cbb₃-type cytochrome c oxidase was up-regulated to increase the O₂-binding efficiency. Meanwhile, since less electron could be received by O₂, the nitrogenase genes nifDKH and Fix complex genes fixA, fixB, fixC, fixX were up-regulated, making N₂ and CO₂ the alternative electron accepters to maintain redox balance, which explained the higher maximum bacterial growth in low-oxygen environments. [Conclusion] Strain LS2 is a sulfur-oxidizing bacterium that can maintain high sulfur oxidation activity in the low-oxygen environment. Sulfide: quinone oxidoreductase, high-oxygen-affinity terminal oxidases, and nitrogenase play a role in the adaptation to the low-oxygen environment. This study is of positive significance for deciphering the mechanism of sulfur oxidation under low oxygen and provides a theoretical basis for optimizing the treatment process of sulfur-containing wastewater.