Evaluation of the use of multilocus sequence analysis (MLSA) to resolve taxonomic conflicts within the genus Marichromatium

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.

Salinicoccus amylolyticus sp. nov., isolated from a saltern

A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).

Strategies to avoid wrongly labelled genomes using as example the detected wrong taxonomic affiliation for aeromonas genomes in the GenBank database

Around 27,000 prokaryote genomes are presently deposited in the Genome database of GenBank at the National Center for Biotechnology Information (NCBI) and this number is exponentially growing. However, it is not known how many of these genomes correspond correctly to their designated taxon. The taxonomic affiliation of 44 Aeromonas genomes (only five of these are type strains) deposited at the NCBI was determined by a multilocus phylogenetic analysis (MLPA) and by pairwise average nucleotide identity (ANI). Discordant results in relation to taxa assignation were found for 14 (35.9%) of the 39 non-type strain genomes on the basis of both the MLPA and ANI results. Data presented in this study also demonstrated that if the genome of the type strain is not available, a genome of the same species correctly identified can be used as a reference for ANI calculations. Of the three ANI calculating tools compared (ANI calculator, EzGenome and JSpecies), EzGenome and JSpecies provided very similar results. However, the ANI calculator provided higher intra- and inter-species values than the other two tools (differences within the ranges 0.06–0.82% and 0.92–3.38%, respectively). Nevertheless each of these tools produced the same species classification for the studied Aeromonas genomes. To avoid possible misinterpretations with the ANI calculator, particularly when values are at the borderline of the 95% cutoff, one of the other calculation tools (EzGenome or JSpecies) should be used in combination. It is recommended that once a genome sequence is obtained the correct taxonomic affiliation is verified using ANI or a MLPA before it is submitted to the NCBI and that researchers should amend the existing taxonomic errors present in databases.

MLSA barcoding of Marichromatium spp. and reclassification of Marichromatium fluminis (Sucharita et al., 2010) as Phaeochromatium fluminis gen. nov. comb. nov

Thirty-one members of the genus Marichromatium were analysed based on multilocus sequence analysis (MLSA) of four concatenated protein-coding genes (fusA, pufM, dnaK, recA) along with the internal transcribed spacer (ITS; 16S-23S rRNA) region and 16S rRNA gene. The restriction patterns obtained from the in silico analysis of the concatenated sequences were good barcodes for the identification of Marichromatium spp. Distinct phenotypic, chemotaxonomic and molecular differences allowed the separation of Marichromatium fluminis JA418(T) into a new genus in the family Chromatiaceae, for which we propose the name Phaeochromatium fluminis gen. nov. comb. nov.

Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis

It was recently reported that Micromonospora inhabits the intracellular tissues of nitrogen fixing nodules of the wild legume Lupinus angustifolius. To determine if Micromonospora populations are also present in nitrogen fixing nodules of cultivated legumes such as Pisum sativum, we carried out the isolation of this actinobacterium from P. sativum plants collected in two man-managed fields in the region of Castilla and León (Spain). In this work, we describe the isolation of 93 Micromonospora strains recovered from nitrogen fixing nodules and the rhizosphere of P. sativum. The genomic diversity of the strains was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). Forty-six isolates and 34 reference strains were further analyzed using a multilocus sequence analysis scheme developed to address the phylogeny of the genus Micromonospora and to evaluate the species distribution in the two studied habitats. The MLSA results were evaluated by DNA-DNA hybridization to determine their usefulness for the delineation of Micromonospora at the species level. In most cases, DDH values below 70% were obtained with strains that shared a sequence similarity of 98.5% or less. Thus, MLSA studies clearly supported the established taxonomy of the genus Micromonospora and indicated that genomic species could be delineated as groups of strains that share > 98.5% sequence similarity based on the 5 genes selected. The species diversity of the strains isolated from both the rhizosphere and nodules was very high and in many cases the new strains could not be related to any of the currently described species.

Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus

Streptomyces hygroscopicus and related species are the most well known candidate producers of antibiotics and many other industrially and agronomically important secondary metabolites in the genus Streptomyces. Multilocus sequence analysis (MLSA) has shown to be a powerful and pragmatic molecular method for unraveling streptomycete diversities. In this investigation, a multilocus phylogeny of 58 representatives of the S. hygroscopicus 16S rRNA gene clade including S. violaceusniger and related species was examined. The result demonstrated that the MLSA data were helpful in defining members of the S. hygroscopicus clade, providing further evidence that the MLSA scheme of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is a valuable alternative for creating and maintaining operational protocols for the Streptomyces species assignment. DNA-DNA hybridization (DDH) between strains with representative MLSA evolutionary distances, combined with previous data from S. griseus and S. albidoflavus clades, revealed a high correlation between MLSA and DDH, and sustains that the five-gene nucleotide sequence distance of 0.007 could be considered as the species cut-off for the whole genus. This significant correlation thus makes the MLSA scheme applicable to construction of a theory-based taxonomy for both ecology and bioprospecting of streptomycetes. Based on the MLSA and DDH data, as well as phenotypic characteristics, 10 species and three subspecies of the S. hygroscopicus clade are considered to be later heterotypic synonyms of eight genomic species, and Streptomyces glebosus sp. nov., comb. nov. (type strain CGMCC 4.1873(T)=LMG 19950(T)=DSM 40823(T)) and Streptomyces ossamyceticus sp. nov., comb. nov. (type strain CGMCC 4.1866(T)=LMG 19951(T)=DSM 40824(T)) are also proposed.

Blastochloris gulmargensis sp. nov., isolated from an epilithic phototrophic biofilm

A novel Gram-negative, motile, bacteriochlorophyll b-containing purple non-sulfur bacterium, strain JA248T, was isolated from phototrophic enrichments of a yellow–green epilithic biofilm sample collected from Gulmarg, India. The genomic DNA G+C content of strain JA248T was 63.8 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain JA248T had highest similarity to members of the genus Blastochloris and was closely related to Blastochloris sulfoviridis DSM 729T (98.5 % sequence similarity) and Blastochloris viridis DSM 133T (98.4 %) of the class Alphaproteobacteria. Strain JA248T was characterized based on polyphasic taxonomy, and distinct phenotypic and molecular differences based on DNA–DNA hybridization (relatedness of <46.5 % with the two species of the genus Blastochloris), multilocus sequence analysis, and phenotypic and chemotaxonomic evidence separated strain JA248T from other species of the genus Blastochloris. Strain JA248T therefore represents a novel species in the genus Blastochloris, for which the name Blastochloris gulmargensis sp. nov. is proposed. The type strain is JA248T ( = JCM 14795T  = DSM 19786T).