To elucidate how geothermal irregularities affect the sustainability of high-temperature microbiomes we studied the synecological dynamics of a geothermal microbial mat community (GMMC) vis-à-vis fluctuations in its environment. Spatiotemporally-discrete editions of a photosynthetic GMMC colonizing the travertine mound of a circum-neutral hot spring cluster served as the model-system. In 2010 a strong geyser atop the mound discharged mineral-rich hot water, which nourished a GMMC continuum from the proximal channels (PC) upto the slope environment (SE) along the mound’s western face. In 2011 that geyser extinguished and consequently the erstwhile mats disappeared. Nevertheless, two relatively-weaker vents erupted in the southern slope and their mineral-poor outflow supported a small GMMC patch in the SE. Comparative metagenomics showed that this mat was a relic of the 2010 community, conserved via population dispersal from erstwhile PC as well as SE niches. Subsequently in 2012, as hydrothermal activity augmented in the southern slope, ecological niches widened and the physiologically-heterogeneous components of the 2011 “seed-community” split into PC and SE meta-communities, thereby reclaiming either end of the thermal gradient. Resilience of incumbent populations, and the community’s receptiveness towards immigrants, were the key qualities that ensured the GMMC’s sustenance amidst habitat degradation and dispersal to discrete environments.

The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.Sulfur chemoautotrophy is an ancient metabolism (7). However, ecologically and taxonomically diverse prokaryotes have, over billions of years of evolution, developed myriad mechanisms for inorganic sulfur compound oxidation (4). Tetrathiobacter kashmirensis (reclassified as Advenella kashmirensis), a chemolithoautotrophic betaproteobacterium belonging to the family Alcaligenaceae (3, 5), oxidizes thiosulfate by a poorly understood mechanism called the tetrathionate intermediate (S 4 I) pathway (2-4). Again, though Alcaligenaceae is a monophyletic group of closely related genera (3), its members show extensive ecophysiological diversity and range from soil-dwelling xenobiotic degraders (e.g., Alcaligenes, Achromobacter, etc.) to pathogens of various animal groups (e.g., Bordetella, Taylorella, etc.). As such, the whole-genome shotgun sequence of T. kashmirensis strain WT 001T presented here has two academic uses: (i) in providing a molecular understanding of the S 4 I pathway and (ii) in elucidating the genomic evolution of nonpathogenic Alcaligenaceae vis-à-vis their pathogenic relatives.Whole-genome sequencing was performed with the SOLiD 4 system (Applied Biosystems, Foster City, CA). A total of 33,854,957 mate-paired 50-bp-long reads were utilized for assembly by using a combination of the SOLiD system de novo accessory tools 2.0 software (SOLiD Software) and the CAP3 sequence assembly program (6). The genome was annotated by compiling results obtained from the RAST (Rapid Annotation using Subsystem Technology) server (1) with those derived from manual analyses. In the estimated 4,427,252-bp genome of WT 001 T , 4,563 potential coding sequences (CDSs) were identified, of which 1,029 had no homolog in the nonredundant database. One copy each of the 16S, 23S, and 5S rRNA genes, clustered in a single operon, were identified together with 38 tRNA genes distributed over the genome. The GϩC content of the genome was found to be 54%. During SOLiD-based deep sequencing and contig assembly, a 49,652-bp plasmid, pWTk445, was also identified on the basis of its 99% similarity with the IncP plasmid pBTK445, which was partially sequenced earlier from strain WGT of T. kashmirensis (EU585932). No pathogenicity island (or for that matter, genes associated with virulence or disease, cellular invasion, and/or intracellular resistance) was detected, nor were any genes for motility or chemotaxis, production of toxins or superantigens, quorum sensing, or biofilm formation or adhesion. However, 6 intact or truncated transposase-like genes, 12 phage-related genes, and 63 genes responsible for re...

Understanding the role of visceral fat accumulation in the occurrence and progression of metabolic syndrome is of considerable interest. In order to understand the difference between visceral tissue biology of healthy and unhealthy obese individuals, we have used microarray profiling to compare genome-wide expression differences between visceral adipose tissue biopsies obtained from obese diabetics, and those from age and body mass index (BMI) matched normal glucose tolerance subjects. Whereas genes upregulated in diabetics showed enrichment of natural killer cell mediated cytotoxicity, the downregulated genes showed enrichment of biosynthesis of unsaturated fatty acids. Given the known inhibitory effect of unsaturated fatty acids on inflammation and natural killer cell number or activity, our results suggest that visceral inflammation resulting from decreased levels of unsaturated fatty acids may underlie progression of diabetes in obese individuals.

The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (MTCC 7265) belongs to the family Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers valuable insight into the adaptive specializations and evolution of free-living soil bacteria that are phylogenetically closely related to symbiotic and invasive rhizobacteria.T axonomically diverse bacteria can use sulfur as an inorganic substrate (lithotrophy) by apparently distinct biochemical pathways (5). This mechanistic multiplicity notwithstanding, sox (sulfur oxidation) genes are omnipresent in members of the domain Bacteria (4, 6). However, functional essentiality of the Sox complex is proven only in facultatively lithotrophic alphaproteobacteria (5). The soildwelling alphaproteobacterium Pseudaminobacter salicylatoxidans KCT001 (family Phyllobacteriaceae, order Rhizobiales [2]) is a wellstudied Sox model (9, 10), but unlike the prototypical Paracoccus pantotrophus (4), it can utilize tetrathionate as a substrate (10) and produces distinct 34 S fractionation during thiosulfate oxidation (M. Alam et al., unpublished data). Evidently, there is more to sulfur lithotrophy even within members of the class Alphaproteobacteria than what is explained by the Sox system alone. As such, whole-genome information on strain KCT001 would not only help us understand sulfur lithotrophy better but would also help in elucidating adaptations and evolution of free-living soil bacteria vis-à-vis their symbiotic and invasive relatives.Genome sequencing was performed on the Ion PGM sequencer (12) using a 316 chip. MIRA 3.4.0 was used to assemble 1,640,570 reads (mean length of 226 nucleotides) into 53 contigs at 66ϫ overall coverage. The genome was annotated by compiling results obtained from the RAST server (1) with those derived from manual analyses. In the estimated 4,612,407-bp genome of P. salicylatoxidans KCT001, 4,553 potential coding sequences (CDSs) could be identified, out of which ϳ800 were hypothetical genes. The GϩC content of the genome was 62.8%. One copy each of the 16S, 23S, and 5S rRNA genes were identified together with 48 tRNA genes. Though the rRNA operon was distributed over five contigs, careful scrutiny revealed 200-to 250-nucleotide overlaps among them (viz., PROY_52, PROY_44, reverse complementary [RC] of PROY_45, RC of PROY_50 and PROY_46, in that order), thereby suggesting their merger into one. Again, the 125,589-bp contig PROY_16 could be part of a large plasmid, since it harbored a repABC operon alongside a parB gene, four integrases/recombinases, and 11 transposon/IS-related genes. Notably, the putative chromosome replicating and partitioning genes were found located elsewhere.Corroborating the phylogenetic proximity of the KCT001 strain with the nodule-forming and nitrogen-fixing mesorhizobia, its genome revealed at least one homolog each of nodB (involved in nodulation signal synthesis) (7) and of nodF and nodE (which define the host range of rhizobia) (3). Additionall...

This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001T was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001T, respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001T genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001T genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001T. So, while WT001T relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement.