Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment

Numerical computation and experimental assessment of a pressure-retaining gas-tight sediment sampler

The pressure of the recovered sample is intricately connected to seawater temperature, the recovery velocity, and the pressure of the pre-charged gas. To better understand the sample pressure dynamics during the sampling recovery process, we focus on a gas-tight sediment sampler, delving into its pressure-compensation and pressure-retaining mechanisms. A comprehensive thermal and thermodynamic analysis is conducted throughout the entire pressure-retaining sampling process, examining the temporal variations in the temperatures of seawater and nitrogen within the sampler at various descending velocities. The heat transfer and thermodynamics are examined throughout the entire pressure-retaining sampling process to determine how changes in the temperatures of seawater and nitrogen, as well as the descent velocity, affect the pressure-retaining performance. The influence of pre-charging pressure and recovery velocities on the pressure-retaining performance of the sampler is examined. Then the proposed numerical model was well verified by the ultra-high-pressure vessel experiments of the sampler under 115 MPa. Finally, the sea trial results further verified the accuracy of the numerical model.

Impact of Concurrent aerobic-anaerobic Methanotrophy on Methane Emission from Marine Sediments in Gas Hydrate Area

Microbial methane oxidation has a significant impact on the methane flux from marine gas hydrate areas. However, the environmental fate of methane remains poorly constrained. We quantified the relative contributions of aerobic and anaerobic methanotrophs to methane consumption in sediments of the gas hydrate-bearing Sakata Knoll, Japan, by in situ geochemical and microbiological analyses coupled with 13C-tracer incubation experiments. The anaerobic ANME-1 and ANME-2 species contributed to the oxidation of 33.2 and 1.4% methane fluxes at 0-10 and 10-22 cm below the seafloor (bsf), respectively. Although the aerobic Methylococcaceae species consumed only 0.9% methane flux in the oxygen depleted 0.0-0.5 cmbsf zone, their metabolic activity was sustained down to 6 cmbsf (based on rRNA and lipid biosyntheses), increasing their contribution to 10.3%. Our study emphasizes that the co-occurrence of aerobic and anaerobic methanotrophy at the redox transition zone is an important determinant of methane flux.

Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift

Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.

One-Step Process for Environment-Friendly Preparation of Agar Oligosaccharides From Gracilaria lemaneiformis by the Action of Flammeovirga sp. OC4

Oligosaccharides extracted from agar Gracilaria lemaneiformis (G. lemaneiformis) have stronger physiological activities and a higher value than agar itself, but the pollution caused by the extraction process greatly restricts the sustainable use of agar. In this study, four bacterial strains with a high ability to degrade G. lemaneiformis were isolated from seawater by in situ enrichment in the deep sea. Among them, Flammeovirga sp. OC4, identified by morphological observation and its 16S rRNA sequencing (98.07% similarity to type strain JL-4 of Flammeovirga aprica), was selected. The optimum temperature and pH of crude enzyme produced by Flammeovirga sp. OC4 were 50°C and 8, respectively. More than 60% of the maximum enzyme activity remained after storage at pH 5.0-10.0 for 60 min. Both Mn²⁺ and Ba²⁺ could enhance the enzyme activity. A "one-step process" for preparation of oligosaccharides from G. lemaneiformis was established using Flammeovirga sp. OC4. After optimization of the Plackett-Burman (PB) design and response surface methodology (RSM), the yield of oligosaccharides was increased by 36.1% from 2.71 to 3.09 g L^-1 in a 250-mL fermenter with optimized parameters: 30 g L^-1 G. lemaneiformis powder, 4.84 g L^-1 (NH4)₂SO₄, 44.8-mL working medium volume at 36.7°C, and a shaking speed of 200 × g for 42 h. The extracted oligosaccharides were identified by thin layer chromatography (TLC) and ion chromatography, which consisted of neoagarobiose, agarotriose, neoagarotetraose, agaropentaose, and neoagarohexaose. These results provided an alternative approach for environment-friendly and sustainable utilization of algae.