Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria

Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats

Complete genome sequence of Desulfurispirillum indicum strain S5T

Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only includes three other cultured species. Strain S5T is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes

Identification of Anaerobic Selenate-Respiring Bacteria from Aquatic Sediments▿

The diversity population of microorganisms with the capability to use selenate as a terminal electron acceptor, reducing it to selenite and elemental selenium by the process known as dissimilatory selenate reduction, is largely unknown. The overall objective of this study was to gain an in-depth understanding of anaerobic biotransformation of selenium in the environment, particularly anaerobic respiration, and to characterize the microorganisms catalyzing this process. Here, we demonstrate the isolation and characterization of four novel anaerobic dissimilatory selenate-respiring bacteria enriched from a variety of sources, including sediments from three different water bodies in Chennai, India, and a tidal estuary in New Jersey. Strains S5 and S7 from India, strain KM from the Meadowlands, NJ, and strain pn1, categorized as a laboratory contaminant, were all phylogenetically distinct, belonging to various phyla in the bacterial domain. The 16S rRNA gene sequence shows that strain S5 constitutes a new genus belonging to Chrysiogenetes, while strain S7 belongs to the Deferribacteres, with greater than 98% 16S rRNA gene similarity to Geovibrio ferrireducens. Strain KM is related to Malonomonas rubra, Pelobacter acidigallici, and Desulfuromusa spp., with 96 to 97% 16S rRNA gene similarity. Strain pn1 is 99% similar to Pseudomonas stutzeri. Strains S5, S7, and KM are obligately anaerobic selenate-respiring microorganisms, while strain pn1 is facultatively anaerobic. Besides respiring selenate, all these strains also respire nitrate

Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.

We report the draft 3.675-Mbp genome sequence of "Candidatus Halobonum tyrrellensis" strain G22, a novel halophilic archaeon isolated from the surface hypersaline waters of Lake Tyrrell, Australia. The availability of the first genome from the "Candidatus Halobonum" genus provides a new genomic resource for the comparative genomic analysis of halophilic Archaea

Candidatus Halobonum tyrrellensis strain G22, phylogenetic trees

<p>These are the phylogenetic trees associated with this genome annoucement (http://genomea.asm.org/content/1/6/e01001-13.full). The trees shows the placement of Ca. Halobonum tyrrellensis G22 within the Halobacteria</p> <p>- HaloG22_16S_v2, is a phylogenetic tree based on the 16S rRNA gene. Alignment was done using Mafft and tree built using FastTree.</p> <p>- HaloG22_v6, contains a phylogenetic tree based on protein markers. The software PhyloPhlan was used to generate this tree</p> <p> </p> <p></p

Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

<div><p>Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative <i>de novo</i> assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.</p></div

Metabolic connectivity graph showing community distribution of protein family clusters.

<p>Cohesive populations are shown as similarly colored nodes and vectors according to numbers of shared features, based on unsupervised protein family clustering of 12 habitat-specific genomes.</p

Phylogenetic distribution of protein BLAST matches for assembled population genomes and unclassified scaffolds.

<p>Taxonomic distribution of non-self matches versus the Genbank nr database were calculated using the DarkHorse algorithm at a filter threshold setting of 0.05, including only alignments covering at least 70% of both query and target sequences with an e-value of 1e-5 or better.</p