The characteristics and comparative analysis of methanotrophs reveal genomic insights into Methylomicrobium sp. enriched from marine sediments

Yu, Woon-Jong; Lee, Jae Won; Nguyen, Ngoc-Loi; Rhee, Sung‐Keun; Park, Soo-Je

doi:10.1016/j.syapm.2018.05.004

Cited by 17 publications

(5 citation statements)

References 81 publications

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“…Including the four gene ( rhlYZAB ) enzyme cassette from P. aeruginosa , the prerequisites for RL production are fatty acid biosynthesis/β-oxidation and an available pool of rhamnose. Fatty acid biosynthesis is well characterized for Methylotuvimicrobium buryatense 5GB(1), a methanotroph closely related to M. alcaliphilum (Yu et al, 2018 ); however, reports of R- 3-hydroxydecanoyl-CoA (direct precursor to RLs) and enzymes for RL synthesis are not known. Internal rhamnose pools have been reported earlier in M. alcaliphilum (Akberdin et al, 2018 ); additionally, the rhamnose concentration was also established during DASS strain characterization (Fig.…”

Section: Resultsmentioning

confidence: 99%

Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4

Awasthi

Tang

Amer

et al. 2022

Journal of Industrial Microbiology and Biotechnology

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Rhamnolipids (RL) are well-studied biosurfactants naturally produced by pathogenic strains of Pseudomonas aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however, methane (CH4) provides an intriguing alternative as a substrate for RL production because it is low-cost and may mitigate greenhouse gas emissions. Here we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum DSM19304. RLs are inhibitory to M. alcaliphilum growth (<0.05 g/L). Adaptive laboratory evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/L of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes, increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared to the parent strain. Expression of plasmid borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 μM of RLs, a 600-fold increase compared to the parent strain, solely from CH4. This work has promise for developing technologies to produce fatty acid-derived bioproducts, including biosurfactants, from CH4.

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Section: Resultsmentioning

confidence: 99%

Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4

Awasthi

Tang

Amer

et al. 2022

Journal of Industrial Microbiology and Biotechnology

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“…To estimate the frequency of genomic rearrangements in Thalassotalea spp., we analyzed prophage regions [ 33 ]. Most genomes had incomplete or no prophages, whereas two questionable prophage regions were identified in the T .…”

Section: Resultsmentioning

confidence: 99%

“…Protein sequences were annotated using the best basic local alignment search tool (BLAST) hit against the NCBI NR database, and tRNAs were identified using tRNAscan-SE [ 30 ]. A similarity analysis was performed using Clusters of Orthologous Groups (COGs), TIGRfam, Pfam, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database references, as described previously [ 31 , 32 , 33 ]. Secondary metabolite biosynthesis and carbohydrate utilization genes were identified using antiSMASH (version 5.1.0) [ 34 ] and dbCAN [ 35 ], respectively, and genome completeness was assessed using CheckM [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

et al. 2020

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Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

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“…Until now, methylotrophic bacterial species of the genus Methyloceanibacter , belonging to the order Rhizobiales (class Alphaproteobacteria ), have been discovered only in marine environments ( 1 – 3 ). Here, we report for the first time the metagenome-assembled genome (MAG) sequence of an uncultured Methyloceanibacter species retrieved from the activated sludge tank of a landfill site that was closed for nitrogen removal from the leachate.…”

Section: Announcementmentioning

confidence: 99%

Identification of a Metagenome-Assembled Genome of an Uncultured Methyloceanibacter sp. Strain Acquired from an Activated Sludge System Used for Landfill Leachate Treatment

Yasuda

Suenaga

Orschler

et al. 2020

Microbiol Resour Announc

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The characteristics and comparative analysis of methanotrophs reveal genomic insights into Methylomicrobium sp. enriched from marine sediments

Cited by 17 publications

References 81 publications

Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4

Adaptive evolution of Methylotuvimicrobium alcaliphilum to grow in the presence of rhamnolipids improves fatty acid and rhamnolipid production from CH4

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

Identification of a Metagenome-Assembled Genome of an Uncultured Methyloceanibacter sp. Strain Acquired from an Activated Sludge System Used for Landfill Leachate Treatment

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