Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides

Abstract

Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca 2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl 2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.

Facultative methanotrophs – diversity, genetics, molecular ecology and biotechnological potential: a mini-review

“…tundrae strains PC1 and PC4, which contain only Xox-MDHs [45]. These two strains were unable to grow on methanol in the absence of a rare-earth element, in common with a relatively small number of other methylotrophs [61, 77–79], which require these elements for methylotrophic growth. Subsequent to the isolation of these Xox-only Methylocella strains, additional methylotrophic (not methanotrophic) Xox-only members of the Beijerinckiaceae have been discovered [80].…”

Reductive Transformation of Fe(III) (oxyhydr)Oxides by Mesophilic Homoacetogens in the Genus Sporomusa

“…The genomic DNA of strain GT1 was isolated and purified as reported previously ( Kato et al, 2020 ). Extracted DNA was used to generate Illumina shotgun paired-end (2 × 101 base pair) sequence libraries, which were sequenced on an Illumina HiSeq 2500 platform (Illumina, San Diego, CA, United States), yielding 4.3 Gb raw read data.…”

Autocatalytic reaction cycles for non-enzymatic synthesis of life-sustaining sugars in neutral media

“…Soil microbes were collected from forest soil near the National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido. Samples were added to an inorganic medium 47 containing a ltersterilized formose solution, and incubated at 30 °C with agitation. The formose solution fed to the microbial cultures were obtained as follows; 1 M HCHO aqueous solution containing 10 mM C2a and 60 mM Na 2 WO 4 in the presence of 10% CH 3 OH was maintained at 80 °C for 4 h. After the reaction, catalysts were removed from the solution with an anion exchange resin.…”