Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil

Standards in Genomic Sciences (2013) 9:71-82 DOI:10.4056/sigs.4328031 Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil Suman R. Rawat1, Minna K. Männistö2, Valentin Starovoytov3, Lynne Goodwin4, Matt Nolan5 Loren J. Hauser6, Miriam Land6, Karen Walston Davenport4, Tanja Woyke5 and Max M. Häggblom1* 1 Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA 2 Finnish Forest Research Institute, Rovaniemi, Finland 3 Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 5 DOE Joint Genome Institute, Walnut Creek, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA *Corresponding author: Max M Häggblom () Keywords: cold adapted, acidophile, tundra soil, Acidobacteria Granulicella mallensis MP5ACTX8T is a novel species of the genus Granulicella in subdivision 1of Acidobacteria. G. mallensis is of ecological interest being a member of the dominant soil bacterial community active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates. These include gene modules encoding the carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides including plant based carbon polymers. The genome of Granulicella mallensis MP5ACTX8T consists of a single replicon of 6,237,577 base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes. Introduction Strain MP5ACTX8T (= ATCC BAA-1857T = DSM 23137T), is the type strain of the species Granulicella mallensis [1]. The genus Granulicella, in subdivision 1 of Acidobacteria, was first described by Pankratov et al. in 2010 [2]. Granulicella mallensis (mal.len' sis. N. L. fem. adj. mallensis; pertaining to its isolation from soil of Malla Nature Reserve, Kilpisjärvi, Finland; 69°01’N, 20°50’E) was described along with other species of the genus Granulicella isolated from tundra soil [1] and is one of the two with sequenced genomes, out of eight validly described Granulicella species. Acidobacteria is one of the most ubiquitous bacterial phyla found in diverse habitats and is abundant in most soil environments [3,4] including Arctic tundra soils [5,6]. Acidobacteria are phylogenetically and physiologically diverse [7] represented by 26 phylogenetic subdivisions [8] of which only subdivisions 1, 3, 4, 8, and 10 are defined by taxonomically characterized representatives. To date, subdivision 1 is comprised of eight genera: Acidobacterium [9], Terriglobus [10,11], Edaphobacter [12], Granulicella [1,2], Acidipila [13], Telmatobacter [14], Acidicapsa [15] and Bryocella [16]. Subdivision 3, 4 and 10 include only one genus each, namely Bryobacter [17], Blastocatella [18] and Thermotomaculum [19], respectively, while subdivision 8 includes three genera; Holophaga [20], Geothrix [21] and Acanthopleuribacter [22]. Three species, ‘Candidatus Koribacter versatilis’ [23], ‘Candidatus Solibacter usitatus’ [23] and ‘Candidatus Chloracidobacterium thermophilum’ [24] have been described as ‘Candidatus’ taxa. Acidobacteria are relatively difficult to cultivate with slow growth The Genomic Standards Consortium Granulicella mallensis type strain MP5ACTX8T rates and typically require up to several weeks to develop visible colonies on solid media. Nevertheless, the phylogenetic diversity, ubiquity and abundance of this group suggest that they play important ecological roles in soils. The abundance of Acidobacteria has been found to correlate with soil pH [25,26] and carbon [27,28], with subdivision 1 Acidobacteria being most abundant in slightly acidic soils. Our previous studies have shown that Acidobacteria dominate in the acidic tundra heaths of northern Finland [25,29-31]. Using selective isolation techniques we have been able to isolate several slow growing and fastidious strains of Acidobacteria [1,11]. On the basis of phylogenetic, phenotypic and chemotaxonomic data, including 16S rRNA, rpoB gene sequence similarity and DNA– DNA hybridization, strain MP5ACTX8T was classified as a novel species of the genus Granulicella [1]. Here, we summarize the physiological features together with the complete genome sequence, annotation and data analysis of Granulicella mallensis MP5ACTX8T (Table 1). Classification and features Within the genus Granulicella, eight species are described with validly published names: G. mallensis MP5ACTX8T, G. tundricola MP5ACTX9T, G. arctica MP5ACTX2T and G. sapmiensis S6CTX5AT isolated from Arctic tundra soil [1] and G. paludicola OB1010T, G. pectinivorans TPB6011T, G. rosea TPO1014T and G. aggregans TPB6028T isolated from sphagnum peat bogs [3]. Strain MP5ACTX8T showed 95.5 -96.1% 16S rRNA gene sequence identity to tundra soil strains, G. tundricola MP5ACTX9T (95.5%), G. sapmiensis S6CTX5AT (96.2%) and G. arctica MP5ACTX2T (96.1%) and 94.6 – 97.4% to G. rosea TPO1014T (94.6%), G. aggregans TPB6028T (96.0%), G. pectinivorans TPB6011T (96.1%), G. paludicola OB1010T (96.5%) and G. paludicola LCBR1 (97.4%). Phylogenetic analysis based on the 16S rRNA gene of taxonomically classified strains of family Acidobacteriaceae placed G. paludicola type strain OB1010 T as the closest taxonomically classified relative of G. mallensis MP5ACTX8T (Figure 1). Figure 1. Phylogenetic tree highlighting the position of G. mallensis MP5ACTX8 (shown in bold) relative to the other type strains within SD1 Acidobacteria. The maximum likelihood tree was inferred from 1,361 aligned positions of the 16S rRNA gene sequences and derived based on the Tamura-Nei model using MEGA 5 [41]. Bootstrap values >50 (expressed as percentages of 1,000 replicates) are shown at branch points. Bar: 0.02 substitutions per nucleotide position. The corresponding GenBank accession numbers are displayed in parentheses. Strains whose genomes have been sequenced, are marked with an asterisk; G. mallensis MP5ACTX8 (CP003130), G. tundricola MP5ACTX9 (CP002480), T. saanensis SP1PR4 (CP002467), T. roseus KBS63 (CP003379) and A. capsulatum ATCC 51196 (CP001472). Bryobacter aggregatus MPL3 (AM162405) in SD3 Acidobacteria was used as an outgroup. T T T T T T 72 Standards in Genomic Sciences Rawat et al. T Table 1. Classification and general features of G. mallensis strain MP5ACTX8 according to the MIGS recommendations [32] MIGS ID Property Term Evidence codea Classification Domain Bacteria TAS [33] Phylum Acidobacteria TAS [34,35] Class Acidobacteria TAS [36,37] Order Acidobacteriales TAS [36,38] Family Acidobacteriaceae TAS [34 (...truncated)