Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil.

Methylocapsa palsarum NE2T is an aerobic, mildly acidophilic, obligate methanotroph. Similar to other Methylocapsa species, it possesses only a particulate methane monooxygenase and is capable of atmospheric nitrogen fixation. The genome sequence of this typical inhabitant of subarctic wetlands and soils also contains genes indicative of aerobic anoxygenic photosynthesis.

GENOME ANNOUNCEMENT

Methylocapsa palsarum NE2T is a methanotroph of the class Alphaproteobacteria family Beijerinckiaceae. It was isolated from a Sphagnum-covered collapsed palsa soil in northern Norway (1). Cells of M. palsarum are Gram-negative, nonmotile, nonpigmented, slightly curved thick rods that multiply by binary fission. The cells possess only a particulate methane monooxygenase (MMO); the growth substrates are methane and methanol. M. palsarum NE2T is a mildly acidophilic, psychrotolerant methanotroph, which is capable of atmospheric nitrogen fixation under reduced oxygen tension.

The draft genome sequence was generated at the Department of Energy, Joint Genome Institute (JGI), using Illumina technology (2). An Illumina 300-bp insert standard shotgun library was constructed and sequenced using the Illumina HiSeq-2500 1 TB platform which generated 9,302,374 reads totaling 1,395.4 Mb. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov. All raw Illumina sequence data was filtered using BBDuk (http://sourceforge.net/projects/bbmap); artifact filtered Illumina reads were assembled using SPAdes (version 3.6.2) (3). Structural and functional annotations were performed using the JGI’s microbial genome annotation pipeline (4) and the genome was released through the Integrated Microbial Genomes (IMG) system (5). The final draft assembly contained 78 contigs. The total estimated size of the M. palsarum NE2T genome is 4.105 Mb (coverage of 339.9×), with G+C content of 61.7%. A single rRNA operon, 47 tRNAs, and 3,820 protein-coding genes were identified.

The genome of M. palsarum NE2T contains a single pmoCAB operon for particulate MMO; two additional pmoC homologues are also present. The absence of mmo operon encoding soluble MMO is typical for all Methylocapsa species (6, 7). Methanol oxidation capabilities are explained by the presence of two gene operons encoding MxaFI- and XoxF-methanol dehydrogenases (8). Genes involved in tetrahydromethanopterin-linked C1 transfer and formate oxidation were also identified. Similar to other Beijerinckiaceae methanotrophs (7), M. palsarum NE2T possesses the complete set of genes for the function of the Calvin-Benson-Bassham cycle and the serine pathway for carbon assimilation, as well as genes encoding enzymes of the tricarboxylic acid cycle. The genes involved in N2 fixation are organized as in Methylocapsa acidiphila B2T into one cluster (SAMN05444581_101312 to SAMN05444581_101348). Despite being described as a nonmotile bacterium, M. palsarum NE2T possesses a number of genes required for the flagellum assembly. Surprisingly, this methanotroph also harbors genes indicative of aerobic anoxygenic photosynthesis. This array of genes in strain NE2T is highly similar to that in many plant-associated Methylobacterium species (9) and includes genes encoding the light-harvesting complex (pufABCML), the reaction center (puhA), as well as genes involved in biosynthesis of bacteriochlorophyll and carotenoids. Most of these photosynthesis-related genes are assembled in gene clusters (SAMN05444581_1147 to SAMN05444581_1149, SAMN05444581_11410 to SAMN05444581_11450). It remains to be seen if these genes are expressed under some certain environmental conditions.

Accession number(s).

The Methylocapsa palsarum NE2T genome sequence was deposited in GenBank under the accession no. FOSN00000000. The version described in this paper is the first version, FOSN00000000.1.