Complete genome sequence of Terriglobus saanensis type strain SP1PR4T, an Acidobacteria from tundra soil

Standards in Genomic Sciences (2012) 7:59-69 DOI:10.4056/sigs.3036810 The Genomic Standards Consortium Complete genome sequence of Terriglobus saanensis type strain SP1PR4T, an Acidobacteria from tundra soil Suman R. Rawat1*, Minna K. Männistö2, Valentin Starovoytov3, Lynne Goodwin5, Matt Nolan6 Lauren Hauser4, Miriam Land4, Karen Walston Davenport5, Tanja Woyke6 and Max M. Häggblom1 1 Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, 08901-8520, 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 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 6 DOE Joint Genome Institute, Walnut Creek, California, USA *Corresponding author: Suman R. Rawat ([email protected]) Keywords: cold adapted, acidophile, tundra soil, Acidobacteria Terriglobus saanensis SP1PR4T is a novel species of the genus Terriglobus. T. saanensis is of ecological interest because it is a representative of the phylum Acidobacteria, which are dominant members of bacterial soil microbiota in Arctic ecosystems. T. saanensis is a coldadapted acidophile and a versatile heterotroph utilizing a suite of simple sugars and complex polysaccharides. The genome contained an abundance of genes assigned to metabolism and transport of carbohydrates including gene modules encoding for carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides. T. saanensis SP1PR4T represents the first member of genus Terriglobus with a completed genome sequence, consisting of a single replicon of 5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer that the physiology and metabolic potential of T. saanensis is adapted to allow for resilience to the nutrientdeficient conditions and fluctuating temperatures of Arctic tundra soils. Introduction Strain SP1PR4T (= DSM 23119 = ATCC BAA1853) is the type strain of Terriglobus saanensis. It is second of two validly ascribed species of the genus Terriglobus, with T. roseus first isolated from agricultural soils in 2007 [1]. T. saanensis SP1PR4T was isolated from Arctic tundra soil collected from a wind exposed site of Saana fjeld, north-western Finland (69°01’N, 20°50’E) [2,3]. The species name saanensis (sa.a.nen' sis. N.L. masc. adj. saanensis) pertains to Mount Saana in Finland. Acidobacteria are found in diverse soil environments and are widely distributed in Arctic and boreal soils [4-8]. However, relatively little is still known about their metabolic potential and ecological roles in these habitats. Despite a large collection of Acidobacteria 16S rRNA gene sequences in databases that represent diverse phylotypes from various habitats, few have been cultivated and described. Acidobacteria represent 26 phylogenetic subdivisions based on 16S rRNA gene phylogeny [9] of which subdivisions 1, 3, 4 and 6 are most commonly detected in soil environments [10]. The abundance of Acidobacteria has been found to correlate with soil pH [2,10,11] and carbon [1,12,13] with subdivision 1 Acidobacteria being most abundant in slightly acidic soils. The phylogenetic diversity, ubiquity and abundance of this group suggest that they play important ecological roles in soils. Terriglobus saanensis type strain SP1PR4T 60 Standards in Genomic Sciences Our previous studies on bacterial community profiling from Arctic alpine tundra soils of northern Finland have shown that Acidobacteria dominate in the acidic tundra heaths [2] and after multiple freeze-thaw cycles [6]. Using selective isolation techniques, including freezing soils at -20°C for 7 days, we have been able to isolate several slow growing and fastidious strains of Acidobacteria. On the basis of phylogenetic, phenotypic and chemotaxonomic data, including 16S rRNA, rpoB gene sequence similarity and DNA–DNA hybridization, strain SP1PR4T was classified as a novel species of the genus Terriglobus [3]. Here, we summarize the physiological features together with the complete genome sequence and annotation of Terriglobus saanensis SP1PR4T. Classification and features Within the genus Terriglobus, two species are ascribed with validly published names, T. saanensis SP1PR4T [3] isolated from Arctic tundra soils and T. roseus KBS 63T (DSM 18391) isolated from agricultural soils (KBS-LTER site) [1]. Searching the NCBI non-redundant nucleotide database for homology to 16S rRNA gene sequence of T. saanensis SP1PR4T identified 10 cultured and 20 uncultured strains that were unclassified, with ≥97% 16S rRNA sequence identity. Phylogenetic tree based on 16S rRNA gene depicting the position of T. saanensis SP1PR4T relative to the other type strains within the family Acidobacteriaceae is shown in Figure 1. T. saanensis SP1PR4T is distinctly clustered into a separate branch with T. roseus KBS 63T (DQ660892) [1], as its closest described relative (97.1% 16S rRNA sequence identity). Strain SP1PR4T showed ~95% 16S rRNA gene identity to four strains in the genus Granulicella isolated from tundra soils, namely “G. tundricola” (95.9%), “G. sapmiensis” (95.8%), “G. mallensis” (95.5%) and “G. arctica” (94.9%) [3,15] (Figure 1). Strain SP1PR4T grows at pH 4.5-7.5 with an optimum at 6.0 and at temperatures of +4 to +30°C with an optimum of +25°C on R2 medium [3]. On R2 agar, strain SP1PR4T forms small, circular, convex colonies with a diameter of approximately 1 mm. The pigment varies from light beige to light pink depending on the age of the culture. Cells of strains SP1PR4T are Gram-negative, non-sporeforming, non-motile aerobic rods with a length of 1.5– 3.0 µm and a diameter of 0.5–0.7 µm. The cellwall structure in ultrathin sections of electron micrographs of cells of strain SP1PR4T demonstrates numerous outer-membrane vesicles (Table 1, Figure 2). Strain SP1PR4T utilized carbon substrates for growth which include cellobiose, D-fructose, Dgalactose, D-glucose, lactose, D-maltose, Dmannose, D-ribose, sucrose, D-trehalose, D-xylose, D-melezitose, D-raffinose and N-acetyl-Dglucosamine. Strain SP1PR4T hydrolyzed polysaccharides such as starch, pectin, laminarin and aesculin but not gelatin, cellulose, xylan, lichenan, sodium alginate, pullulan, chitosan or chitin. Enzyme activities of strain SP1PR4T include chitobiase, catalase, acid and alkaline phosphatase, leucine arylamidase, naphthol-AS-B1phosphohydrolase, αand β-galactosidase, αand β-glucosidase, β-glucuronidase, N-acetyl-βglucosaminidase, α-mannosidase and α-fucosidase [3,15]. Chemotaxonomy The major cellular fatty acids in T. saanensis SP1PR4T are iso-C15:0 (39.9%), C16:1 ω7c (28.4%), iso-C13:0 (9.8%) and C16:0 (9.8%). The cellular fatty acid compositions of strain SP1PR4T were relatively similar to that of T. roseus DSM 18391T, with higher relative abundance of iso-C13:0 and a corresponding lower abundance of iso-C15:0 in strain SP1PR4T [3]. Genome sequencing and annotation Genome project history Strain SP1PR4T was selected for sequencing in 2009 by the DOE Joint Genome Institute (JGI) community sequencing program. The Quality Draft (QD) assembly and annotation were completed on August 6, 2010. The complete genome was made available on Jan 24, 2011. The genome project is deposited in the Genomes On-Line Database (GOLD) [25] and the complete genome sequence of strain SP1PR4T is deposited in GenBank. Table 2 presents the project information and its association with MIGS version 2.0 [16]. Rawat et al. http://standardsingenomics.org 61 Figure 1. Phylogenetic tree highlighting the position of T. saanensis SP1PR4T relative to the other type strains within the family Acidobacteriaceae. The maximum likelihood tree was inferred from 1,359 aligned positions of the 16S rRNA gene sequences and derived using MEGA version 5 [14]. Bootstrap values (expressed as percentages of 1,000 replicates) of >50 are shown at branch points. Bar: 0.02 substitutions per nucleotide position. The strains (type strain=T) and their corresponding GenBank accession numbers are displayed in parentheses with strain T. saanensis SP1PR4T shown in bold. Bryobacter aggregatus MPL3 (AM162405) was used as outgroup. T. saanensis SP1PR4T and T. roseus KBS 63T (DSM 18391) genome sequences have been revealed. Figure 2. Electron micrograph of cells of T. saanensis strain SP1PR4T (bar 0.5 µm). Terriglobus saanensis type strain SP1PR4T 62 Standards in Genomic Sciences Table 1. Classification and general features of T. saanensis SP1PR4T according to the MIGS recommendations [16]. MIGS ID Property Term Evidence codes Domain Bacteria TAS [17] Phylum Acidobacteria TAS [18,19] Class Acidobacteria TAS [20] Classification Order Acidobacteriales TAS [21,22] Family Acidobacteriaceae TAS [18,23] Genus Terriglobus TAS [1] Species Terriglobus saanensis TAS [3] Type strain: SP1PR4T Gram stain negative TAS [3] Cell shape rod TAS [3] Motility non-motile TAS [3] Sporulation non-spore forming TAS [3] Temperature range 4–30°C TAS [3] Optimum temperature 25°C TAS [3] pH range 4.5-7.5 TAS [3] Optimum pH 6.0 TAS [3] Salinity not reported NAS MIGS-22 Oxygen requirement aerobe TAS [3] Carbon source cellobiose, D-fructose, D-galactose, D-glucose, lactose, D-maltose, D-mannose, D-ribose, sucrose, D-trehalose, D-xylose, D-melezitose, Draffinose, starch, pectin, laminarin and aesculin TAS [3] MIGS-6 Habitat terrestrial TAS [3] MIGS-15 Biotic relationship free-living TAS [3] MIGS-14 Pathogenicity non-pathogen NAS Biosafety level 1 NAS Isolation tundra soil TAS [3] MIGS-4 Geographic location Saana fjeld, Arctic tundra, Finland TAS [3] MIGS-5 Sample collection time 2004-2005 TAS [3] MIGS-4.1 Latitude 69°01’N, TAS [3] MIGS-4.2 Longitude 20°50’E TAS [3] MIGS-4.3 Depth not reported NAS MIGS-4.4 Altitude not reported NAS *Evidence codes - IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [24]. Rawat et al. http://standardsingenomics.org 63 Table 2. Genome sequencing project information. MIGS ID Property Term MIGS 31 Finishing quality Finished MIGS-28 Libraries used Three libraries, an Illumina GAii shotgun library (GSGY), a 454 Titanium standard library (GSXT, GWTA) and a paired end 454 (GSFP) library MIGS 29 Sequencing platforms 454 Titanium standard, 454 Paired End, Illumina MIGS 31.2 Sequencing coverage 39× (454), 180× (Illumina) MIGS 30 Assemblers Newbler, Velvet, Phrap MIGS 32 Gene calling method ProdigaL, GenePRIMP Locud Tag AciPR4 INSDC / RefSeq ID CP002467, NC_014963, GenBank Date of Release October 7, 2011 GOLD ID Gc01604 NCBI project ID 48971 MIGS 13 Source material identifier ATCC BAA-1853, DSM 23119 Project relevance Environmental, Biogeochemical cycling of carbon, Biotechnological, GEBA Growth conditions and genomic DNA extraction Strain SP1PR4T was cultivated in R2 medium as previously described [3]. Genomic DNA (gDNA) of high sequencing quality was isolated using a modified CTAB method and evaluated according to the Quality Control (QC) guidelines provided by the DOE Joint Genome Institute. Genome sequencing and assembly The finished genome of T. saanensis SP1PR4T (JGI ID 4088690) was generated at the DOE Joint genome Institute (JGI) using a combination of Illumina [26] and 454 technologies [27]. For this genome, an Illumina GAii shotgun library which generated 23,685,130 reads totaling 916 Mb, a 454 Titanium standard library which generated 409,633 reads and a paired end 454 library with an average insert size of 10.8 kb which generated 180,451 reads totaling 157 Mb of 454 data, were constructed and sequenced. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website [28]. The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3. Illumina sequencing data was assembled with Velvet, version 0.7.63 [29]. We integrated the 454 Newbler consensus shreds, the Illumina Velvet consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS - 4.24 (High Performance Software, LLC). The software Consed [30,31] was used in the finishing process. Illumina data was used to correct potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished). Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher [32], or sequencing cloned bridging PCR fragments with sub-cloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR (J-F Cheng, unpublished) primer walks. The final assembly is based on 157 Mb of 454 data which provides an average 39× coverage and 916 Mb of Illumina data which provides an average 180× coverage of the genome. Genome annotation Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [34]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, (COGs) [35,36], and InterPro. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscanSE [37], RNAMMer [38], Rfam [39], TMHMM [40], and signalP [41]. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [42]. Terriglobus saanensis type strain SP1PR4T 64 Standards in Genomic Sciences Genome properties The genome consists of one circular chromosome of 5,095,226 bp in size with a GC content of 57.3% and consists of 54 RNA genes (Figure 3, Table 3). Of the 4,333 predicted genes, 4,279 are proteincoding genes (CDSs) and 99 are pseudogenes. Of the total CDSs, 67% represent COG functional categories and 43% consist of signal peptides. The distribution of genes into COG functional categories is presented in Figure 3 and Table 4. Discussion Genome analysis of T. saanensis identified a high abundance of genes assigned to COG functional categories for transport and metabolism carbohydrates (9.5%) and amino acids (7.6%), energy conversion (6.2%), cell envelope biogenesis (9.6%) and transcription (9.2%) [15]. This indicates that the T. saanensis genome encodes for functions involved in transport and utilization of nutrients, mainly carbohydrates and amino acids for energy production and cell biogenesis to maintain cell integrity in cold tundra soils. Further genome analysis revealed an abundance of gene modules for glycoside hydrolases, glycosyl transferases, polysaccharide lyases, carbohydrate esterases, and non-catalytic carbohydrate-binding modules within the carbohydrateactive enzymes (CAZy [43]) family involved in breakdown, utilization and biosynthesis of carbohydrates [15]. T. saanensis hydrolyzed complex carbon polymers, including pectin, laminarin, and starch, and utilized sugars such as cellobiose, D-mannose, D-xylose, D-trehalose and laminarin. This parallels genome predictions for CDSs encoding for enzymes such as pectinases, chitinases, alginate lyases, trehalase and amylases. T. saanensis was unable to hydrolyze carboxymethyl cellulose (CMC) on plate assays and lacked CDSs encoding for cellulases involved in cellulose hydrolysis. However, the T. saanensis genome contained a BcsZ gene encoding for an endocellulase (GH8) as part of a bacterial cellulose synthesis (bcs) operon involved in cellulose biosynthesis in several species. This operon consists of clusters of genes in close proximity to the BcsZ gene which includes a cellulose synthase gene (bcsAB), a cellulose synthase operon protein (bcsC) and a cellulose synthase operon protein (yhj) [15]. In addition, the T. saanensis genome encoded for a large number of gene modules representing glycosyl transferases (GTs) involved in carbohydrate biosynthesis which include cellulose synthase (UDPforming), α-trehalose phosphate synthase [UDPforming], starch glucosyl transferase, ceramide βglucosyltransferase involved in biosynthesis of cellulose, trehalose, starch, hopanoid, and capsular/free exopolysaccharide (EPS) [15]. This suggests that T. saanensis is involved in hydrolysis of lignocellulosic soil organic matter, utilization of stored carbohydrates and biosynthesis of exopolysaccharides. Therefore, we surmise that T. saanensis may be central to carbon cycling processes in Arctic and boreal soil ecosystems. Table 3. Genome statistics Attribute Value % of Total Genome size (bp) 5,095,226 100% DNA coding (bp) 4,578,206 89.9% DNA G+C (bp) 2,921,371 57.3% Number of replicons 1 100% Total genes 4,334 100% RNA genes 54 1.3% rRNA operons 1 - Protein coding genes 4,180 98.8% Pseudo genes 99 2.3% Genes with function prediction 3,203 73.9% Genes in paralog clusters 2,220 51.2% Genes assigned to COGs 3,170 73.2% Genes with Pfam domains 3,108 71.7% Genes with signal peptides 1,867 43.1% Genes with transmembrane helices 1,082 25% CRISPR repeats 0 - Rawat et al. http://standardsingenomics.org 65 Figure 3. Graphical representation of circular map of the chromosome of T. saanensis strain SP1PR4T displaying relevant genome features. From outside to center: Genes on forward strand (color by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. Terriglobus saanensis type strain SP1PR4T 66 Standards in Genomic Sciences Table 4. Number of genes associated with general COG functional categories. Code Value %age Description J 163.0 4.6 Translation, ribosomal structure and biogenesis A 2.0 0.1 RNA processing and modificatin K 293.0 8.3 Transcription L 142.0 4.0 Replication, recombination and repair B 0.0 0.0 Chromatin structure and dynamics D 24.0 0.7 Cell cycle control, Cell division, chromosome partitioning Y 0.0 0.0 Nuclear structure V 98.0 2.8 Defense mechanisms T 174.0 4.9 Signal transduction mechanisms M 307.0 8.7 Cell wall/membrane biogenesis N 56.0 1.6 Cell motility Z 2.0 0.1 Cytoskeleton W 0.0 0.0 Extracellular structures U 113.0 3.2 Intracellular trafficking and secretion O 122.0 3.4 Posttranslational modification, protein turnover, chaperones C 196.0 5.5 Energy production and conversion G 303.0 8.6 Carbohydrate transport and metabolism E 243.0 6.9 Amino acid transport and metabolism F 69.0 2.0 Nucleotide transport and metabolism H 134.0 3.8 Coenzyme transport and metabolism I 116.0 3.3 Lipid transport and metabolism P 134.0 3.8 Inorganic ion transport and metabolism Q 85.0 2.4 Secondary metabolites biosynthesis, transport and catabolism R 443.0 12.5 General function prediction only S 323.0 9.1 Function unknown - 1163. 0 26.8 Not in COGs Acknowledgements The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy Under Contract No. DE-AC02-05CH11231. 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