Hydrogenotrophic methanogens overwrite isotope signals of subsurface methane.

Methane, a greenhouse gas and energy source, is commonly studied using stable isotope signals as proxies for its formation processes. In subsurface environments, methane often exhibits equilibrium isotopic signals, but the equilibration process has never been demonstrated in the laboratory. We cocultured a hydrogenotrophic methanogen with an H-producing bacterium under conditions (55°C, 10 megapascals) simulating a methane-bearing subsurface.

Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method.

The "duckweed-microbes co-cultivation method" is a microbial isolation technique that effectively recovers diverse microbes, including rarely cultivated bacterial phyla, from environmental samples. In this method, aseptic duckweed and microbes collected from an environmental sample are co-cultivated for several days, and duckweed-associated microbes are then isolated from its roots using a conventional agar plate-based cultivation method. We herein propose several improvements to the method in order to specifically obtain members of the rarely cultivated bacterial phylum, Verrucomicrobiota.

Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities.

Background: Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry.

Results: In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG).

A Marine Group A isolate relies on other growing bacteria for cell wall formation.

Most of Earth's prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or 'Candidatus Marinimicrobia') that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria.

Metabolism of novel potential syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats.

Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH. In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized.

Self-cloning of the Catalase Gene in Environmental Isolates Improves Their Colony-forming Abilities on Agar Media.

Hydrogen peroxide (HO) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower HO concentration in agar plates. Putative catalase genes, which degrade HO, were detected in their genomes.

Proposed minimal standards for description of methanogenic archaea.

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential.

Genome Sequences of Bacteria OS-1 and OS-4, Two Highly HO-Sensitive Strains Isolated from Pond Water.

The bacterial strains OS-1 and OS-4 were isolated from pond water and were found to be highly sensitive to hydrogen peroxide in the agar plates. Here, we report the nearly complete and complete genome sequences, respectively, of these two strains.

Subcellular Niche Segregation of Co-Obligate Symbionts in Whiteflies.

Many insects contain endosymbiotic bacteria within their bodies. In multiple endosymbiotic systems comprising two or more symbionts, each of the symbionts is generally localized in a different host cell or tissue. Bemisia tabaci (Sweet potato whitefly) possesses a unique endosymbiotic system where co-obligate symbionts are localized in the same bacteriocytes.

Critical Effect of HO in the Agar Plate on the Growth of Laboratory and Environmental Strains.

We previously showed that autoclaving in preparing agar media is one of the sources of hydrogen peroxide (HO) in the medium. This medium-embedded HO was shown to lower the total colony count of environmental microorganisms. However, the critical concentrations of HO detrimental to colony formation on the agar plate remain largely undetermined.

Complete Genomic Sequence of the Thermophilic Hydrogen-Oxidizing Methanogen Methanothermobacter tenebrarum Strain RMAS.

Methanothermobacter tenebrarum strain RMAS has a complete genomic length of 1,472,762 bp, a GC content of 42.1%, 1,599 coding DNA sequences (CDSs), 1 CRISPR array, 3 rRNAs, and 38 tRNAs.

Complete Genome Sequence of sp. Strain TBR-22.

We report a complete genome sequence of a novel bacterial isolate, strain TBR-22, belonging to the class of the phylum , which was isolated from duckweed fronds. The genome expands our knowledge of the lifestyle of this abundant but rarely characterized phylum.

Draft Genome Sequence of Strain F-183.

Here, we report a draft genome sequence of a bacterial strain, F-183, isolated from a duckweed frond. Strain F-183 belongs to the family of the phylum , and its genomic information would contribute to understanding the ecophysiology of this abundant but rarely characterized phylum.

Complete Genome Sequence of Bacterium Strain SO-S41, Isolated from Forest Soil.

The complete genome of hydrogen peroxide-sensitive alphaproteobacterial strain SO-S41 was sequenced. The complete genome contains a single chromosome, is 4,443,179 bp in length, contains a total of 4,632 genes, and has a G+C content of 66.2%.

Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.

Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments.

Novel Plant-Associated Promotes Growth of Common Floating Aquatic Plants, Duckweeds.

Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed-microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum , the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant-microbe interactions remain largely unclear.

Correction: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.

[This corrects the article DOI: 10.1371/journal.pone.

Parallel Evolution of Enhanced Biofilm Formation and Phage-Resistance in during Adaptation Process in Spatially Heterogeneous Environments.

An opportunistic pathogen has a versatile phenotype and high evolutionary potential to adapt to various natural habitats. As the organism normally lives in spatially heterogeneous and polymicrobial environments from open fields to the inside of hosts, adaptation to abiotic (spatial heterogeneity) and biotic factors (interspecies interactions) is a key process to proliferate. However, our knowledge about the adaptation process of in spatially heterogeneous environments associated with other species is limited.

Isolation of a member of the candidate phylum 'Atribacteria' reveals a unique cell membrane structure.

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum 'Candidatus Atribacteria' (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography.