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Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

View Article: PubMed Central - PubMed

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Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

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Phylogenetic tree based comparisons between 16S rRNA gene sequences from strain HIMB624, strain HTCC2181, type strains of related species within the family Methylophilaceae, and more distantly related Betaproteobacteria. Several Gammaproteobacteria and Alphaproteobacteria strains were used as outgroups. Sequence selection and alignment improvements were carried out using the ‘All-Species Living Tree’ project database [14] and the ARB software package [15]. The tree was inferred from 1,223 alignment positions using the RAxML maximum likelihood method [16]. Bootstrap support values, determined by RAxML [17], are displayed above branches if larger than 60% from 1000 replicates. The scale bar indicates substitutions per site.
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f1: Phylogenetic tree based comparisons between 16S rRNA gene sequences from strain HIMB624, strain HTCC2181, type strains of related species within the family Methylophilaceae, and more distantly related Betaproteobacteria. Several Gammaproteobacteria and Alphaproteobacteria strains were used as outgroups. Sequence selection and alignment improvements were carried out using the ‘All-Species Living Tree’ project database [14] and the ARB software package [15]. The tree was inferred from 1,223 alignment positions using the RAxML maximum likelihood method [16]. Bootstrap support values, determined by RAxML [17], are displayed above branches if larger than 60% from 1000 replicates. The scale bar indicates substitutions per site.

Mentions: Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed strain HIMB624 to be closely related to a large number of environmental gene clones obtained predominantly from seawater. Alignment of the HIMB624 16S rRNA gene sequence with the Silva release 104 reference database containing only high quality, aligned 16S rRNA sequences with a minimum length of 1,200 bases for Bacteria released in October 2010 (n=512,037 entries) [13], revealed 350 entries that belong to the same phylogenetic lineage within the Betaproteobacteria. Of these, only the entries from HTCC2181, HIMB624 and one other strain (AB022337) originated from cultivated isolates and all entries in the lineage were derived either from seawater, freshwater, or the marine environment. In phylogenetic analyses with taxonomically described members of the Betaproteobacteria, strains HIMB624 and HTCC2181 formed a monophyletic lineage within the family Methylophilaceae (Figure 1; 96.5% sequence similarity). The 16S rRNA gene of strain HIMB624 was most similar to the type strains of Methylophilus luteus strain Mim (94.4%) and Methylophilus flavus strain Ship (94.3%), both isolated from plants [18]; Methylophilus methylotrophus strain NCIMB 10515 (93.7%), isolated from activated sludge [19]; Methylotenera mobilis strain JLW8 (93.7%), isolated from freshwater sediment [20]; Methylobacillus flagellatus strain KT (93.5%) isolated from sewage [21]; Methylovorus mays strain C isolated from maize phyllosphere (92.5%) [22]; and Methylobacillus pratensis strain F31 (91.8%), isolated from meadow grass [23].


Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria.

Huggett MJ, Hayakawa DH, Rappé MS - Stand Genomic Sci (2012)

Phylogenetic tree based comparisons between 16S rRNA gene sequences from strain HIMB624, strain HTCC2181, type strains of related species within the family Methylophilaceae, and more distantly related Betaproteobacteria. Several Gammaproteobacteria and Alphaproteobacteria strains were used as outgroups. Sequence selection and alignment improvements were carried out using the ‘All-Species Living Tree’ project database [14] and the ARB software package [15]. The tree was inferred from 1,223 alignment positions using the RAxML maximum likelihood method [16]. Bootstrap support values, determined by RAxML [17], are displayed above branches if larger than 60% from 1000 replicates. The scale bar indicates substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368401&req=5

f1: Phylogenetic tree based comparisons between 16S rRNA gene sequences from strain HIMB624, strain HTCC2181, type strains of related species within the family Methylophilaceae, and more distantly related Betaproteobacteria. Several Gammaproteobacteria and Alphaproteobacteria strains were used as outgroups. Sequence selection and alignment improvements were carried out using the ‘All-Species Living Tree’ project database [14] and the ARB software package [15]. The tree was inferred from 1,223 alignment positions using the RAxML maximum likelihood method [16]. Bootstrap support values, determined by RAxML [17], are displayed above branches if larger than 60% from 1000 replicates. The scale bar indicates substitutions per site.
Mentions: Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed strain HIMB624 to be closely related to a large number of environmental gene clones obtained predominantly from seawater. Alignment of the HIMB624 16S rRNA gene sequence with the Silva release 104 reference database containing only high quality, aligned 16S rRNA sequences with a minimum length of 1,200 bases for Bacteria released in October 2010 (n=512,037 entries) [13], revealed 350 entries that belong to the same phylogenetic lineage within the Betaproteobacteria. Of these, only the entries from HTCC2181, HIMB624 and one other strain (AB022337) originated from cultivated isolates and all entries in the lineage were derived either from seawater, freshwater, or the marine environment. In phylogenetic analyses with taxonomically described members of the Betaproteobacteria, strains HIMB624 and HTCC2181 formed a monophyletic lineage within the family Methylophilaceae (Figure 1; 96.5% sequence similarity). The 16S rRNA gene of strain HIMB624 was most similar to the type strains of Methylophilus luteus strain Mim (94.4%) and Methylophilus flavus strain Ship (94.3%), both isolated from plants [18]; Methylophilus methylotrophus strain NCIMB 10515 (93.7%), isolated from activated sludge [19]; Methylotenera mobilis strain JLW8 (93.7%), isolated from freshwater sediment [20]; Methylobacillus flagellatus strain KT (93.5%) isolated from sewage [21]; Methylovorus mays strain C isolated from maize phyllosphere (92.5%) [22]; and Methylobacillus pratensis strain F31 (91.8%), isolated from meadow grass [23].

View Article: PubMed Central - PubMed

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Please rate it.

Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii... This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43... Strain HIMB624 was isolated from surface seawater of Kaneohe Bay, a subtropical bay on the northeastern shore of Oahu, Hawaii, via dilution to extinction culturing methods... This strain is of interest because it belongs to a globally ubiquitous clade of aquatic bacterioplankton known as OM43, within the obligately methylotrophic family Methylophilaceae of the class Betaproteobacteria... The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases... The tRNAScanSE tool was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer... The genomes of HIMB624 and HTCC2181 were compared to two closely related species within the family Methylophilaceae whose whole genomes are publicly available: Methylotenera mobilis (NC_012968) and Methylovorus glucosotrophus SIP3-4 (NC_012969, NC_012970, NC_012972)... For this comparison only, the four strains were automatically annotated using the RAST annotation server and protein sequences were compared using the sequence based analysis tool in order to identify all shared and unique gene combinations (Figure 4)... Strain HIMB624 contains one gene for a Type 4 fimbrial assembly/ATPase PilB that shares 43.44% protein identity with a gene located on one of the plasmids of Methylovorus glucosotrophus SIP3-4, and strain HTCC2181 contains a single DNA methylase gene that shares 31.1% protein identity with the same plasmid... Other than these, all genes located on the plasmids are exclusive to Methylovorus glucosotrophus SIP3-4, and the large majority of the genes on the plasmids are hypothetical proteins... The genomes of Methylotenera mobilis and Methylovorus glucosotrophus SIP3-4 share over 100 genes associated with motility (twitching, flagella related, pili), along with 13 genes for chemotaxis and 13 genes for secretion that are absent from the genomes of HIMB624 and HTCC2181, while the two smaller genomes have a higher percentage of their genomes (9.13% and 9.19%) dedicated to amino acid transport and metabolism than Methylovorus glucosotrophus SIP3-4 (6.76%) and Methylotenera mobilis (5.81%); and a higher percentage of translation, ribosomal structure and biogenesis genes (11.08% and 11.47%) than Methylovorus glucosotrophus SIP3-4 (6.12%) and Methylotenera mobilis (7.16%)... Due to the small size of the two OM43 lineage genomes, the higher percentages result in a similar total number of genes between all genomes in these categories, at approximately 120 genes for amino acid transport and metabolism and approximately 140 genes for translation, ribosomal structure and biogenesis... The general distribution of genes in all other predicted COG categories are comparable between the four strains, resulting in smaller numbers of total genes in each COG category for the two members of the OM43 lineage due to their comparatively smaller genome sizes.

No MeSH data available.


Related in: MedlinePlus