Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean

Diversities and interactions of phages and bacteria in deep-sea sediments as revealed by metagenomics

Phages are found virtually everywhere, even in extreme environments, and are extremely diverse both in their virion structures and in their genomic content. They are thought to shape the taxonomic and functional composition of microbial communities as well as their stability. A number of studies on laboratory culture and viral metagenomic research provide deeper insights into the abundance, diversity, distribution, and interaction with hosts of phages across a wide range of ecosystems. Although most of these studies focus on easily accessible samples, such as soils, lakes, and shallow oceans, little is known about bathypelagic phages. In this study, through analyzing the 16S rRNA sequencing and viral metagenomic sequencing data of 25 samples collected from five different bathypelagic ecosystems, we detected a high diversity of bacteria and phages, particularly in the cold seep and hydrothermal vent ecosystems, which have stable chemical energy. The relative abundance of phages in these ecosystems was higher than in other three abyssal ecosystems. The low phage/host ratios obtained from host prediction were different from shallow ecosystems and indicated the prevalence of prophages, suggesting the complexity of phage-bacteria interactions in abyssal ecosystems. In the correlation analysis, we revealed several phages-bacteria interaction networks of potential ecological relevance. Our study contributes to a better understanding of the interactions between bathypelagic bacteria and their phages.

Salinity effect on an anaerobic methane- and ammonium-oxidising consortium: Shifts in activity, morphology, osmoregulation and syntrophic relationship

Nitrate-dependent anaerobic methane oxidation (AOM) is a microbial process of both ecological significance for global methane mitigation and application potential for wastewater treatment. It is mediated by organisms belonging to the archaeal family 'Candidatus Methanoperedenaceae', which have so far mainly been found in freshwater environments. Their potential distribution in saline environments and their physiological responses to salinity variation were still poorly understood. In this study, the responses of the freshwater 'Candidatus Methanoperedens nitroreducens'-dominated consortium to different salinities were investigated using short- and long-term setups. Short-term exposure to salt stress significantly affected nitrate reduction and methane oxidation activities over the tested concentration range of 15-200‰ NaCl, and 'Ca. M. nitroreducens' showed the higher tolerance to high salinity stress than its partner of anammox bacteria. At high salinity concentration, near marine conditions of 37‰, the target organism 'Ca. M. nitroreducens' showed stabilized nitrate reduction activity of 208.5 µmol day-1 gCDW-1 in long-term bioreactors over 300 days, in comparison to 362.9 and 334.3 µmol day-1 gCDW-1 under low-salinity conditions (1.7‰ NaCl) and control conditions (∼15‰ NaCl). Different partners of 'Ca.  M. nitroreducens' evolved in the consortia with three different salinity conditions, suggesting the different syntrophic mechanisms shaped by changes in salinity. A new syntrophic relationship between 'Ca. M. nitroreducens' and Fimicutes and/or Chloroflexi denitrifying populations was identified under the marine salinity condition. Metaproteomic analysis shows that the salinity changes lead to higher expression of response regulators and selective ion (Na+/H+) channeling proteins that can regulate the osmotic pressure between the cell and its environment. The reverse methanogenesis pathway was, however, not impacted. The finding of this study has important implications for the ecological distribution of the nitrate-dependent AOM process in marine environments and the potential of this biotechnological process for the treatment of high-salinity industrial wastewater.

Increasing sulfate concentration and sedimentary decaying cyanobacteria co-affect organic carbon mineralization in eutrophic lake sediments

Sulfate (SO₄^2-) concentrations in eutrophic lakes are continuously increasing; however, the effect of increasing SO₄^2- concentrations on organic carbon mineralization, especially the greenhouse gas emissions of sediments, remains unclear. Here, we constructed a series of microcosms with initial SO₄^2- concentrations of 0, 30, 60, 90, 120, 150, and 180 mg/L to study the effects of increased SO₄^2- concentrations, coupled with cyanobacterial blooms, on organic carbon mineralization in Lake Taihu. Cyanobacterial blooms promoted sulfate reduction and released a large amount of inorganic carbon. The SO₄^2- concentrations in cyanobacteria treatments significantly decreased and eventually reached close to 0. As the initial SO₄^2- concentration increased, the sulfate reduction rates significantly increased, with maximum values of 9.39, 9.44, 28.02, 30.89, 39.68, and 54.28 mg/L∙d for 30, 60, 90, 120, 150, and 180 mg/L SO₄^2-, respectively. The total organic carbon content in sediments (51.16-52.70 g/kg) decreased with the initial SO₄^2- concentration (R² = 0.97), and the total inorganic carbon content in overlying water (159.97-182.73 mg/L) showed the opposite pattern (R² = 0.91). The initial SO₄^2- concentration was positively correlated with carbon dioxide (CO₂) emissions (R² = 0.68) and negatively correlated with methane (CH₄) emissions (R² = 0.96). The highest CO₂ concentration and lowest CH₄ concentration in the 180 mg/L SO₄^2- treatment were 1688.78 and 1903 μmol/L, respectively. These biogeochemical processes were related to competition for organic carbon sources between sulfate reduction bacteria (SRB) and methane production archaea (MPA) in sediments. The abundance of SRB was positively correlated with the initial SO₄^2- concentration and ranged from 6.65 × 10⁷ to 2.98 × 10⁸ copies/g; the abundance of MPA showed the opposite pattern and ranged from 1.99 × 10⁸ to 3.35 × 10⁸copies/g. These findings enhance our understanding of the effect of increasing SO₄^2- concentrations on organic carbon mineralization and could enhance the accuracy of assessments of greenhouse gas emissions in eutrophic lakes.

Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites

Methane is a strong greenhouse gas that plays a key role in Earth’s climate. At methane seeps, large amounts of methane move upward through the seafloor, where microbial communities consume much of it. A full accounting of methane’s sources and sinks has evaded researchers—in part, perhaps, because key habitats including carbonate rock mounds have been largely neglected. We sampled seven methane seeps representing four geological settings and found that all sites had rock-hosted microbes capable of consuming methane; in lab-based incubations, some did so at the highest rates reported to date. We demonstrate several factors that help determine a sample’s methane-consuming potential and propose that carbonate rocks at methane seeps may represent a methane sink of far-reaching importance.

At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated V_max, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample’s methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.

"Sifarchaeota," a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode diverse metabolic capacities and which play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off the Costa Rica margin, defining a novel lineage phylogenetically married to "Candidatus Thorarchaeota"; as such, we propose the name "Sifarchaeota" for this phylum. The two Sifarchaeota MAGs encode an anaerobic pathway for methylotrophy enabling the utilization of C1 to C3 compounds (methanol and methylamines) to synthesize acetyl coenzyme A (acetyl-CoA). The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di-, and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between Sifarchaeota and "Candidatus Odinarchaeota" MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within Sifarchaeota MAGs, which hypothetically expanded Sifarchaeota capacities for substrate utilization, energy production, and niche adaptation.IMPORTANCE The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important, since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.