Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

<p>Abstract</p> <p>Background</p> <p>The phylum <it>Verrucomicrobia </it>is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the <it>Verrucomicrobia</it>, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.</p> <p>Results</p> <p>We report the complete genome sequence of strain V4, the first one from a representative of the <it>Verrucomicrobia</it>. Isolate V4, initially named "<it>Methylokorus infernorum</it>" (and recently renamed <it>Methylacidiphilum infernorum</it>) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of <it>M. infernorum </it>was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C₁-utilization pathways compared to other known methylotrophs. The <it>M. infernorum </it>genome does not encode tubulin, which was previously discovered in bacteria of the genus <it>Prosthecobacter</it>, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping <it>Planctomycetes</it>, <it>Verrucomicrobia </it>and <it>Chlamydiae </it>into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the <it>M. infernorum </it>lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of <it>M. infernorum </it>shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.</p> <p>Conclusion</p> <p>The results of genome analysis of <it>M. infernorum </it>support the monophyly of the PVC superphylum. <it>M. infernorum </it>possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways <it>via </it>horizontal gene transfer, in particular, from <it>Proteobacteria</it>.</p> <p>Reviewers</p> <p>This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.</p

Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles

Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai‘i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500–800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (&lt;400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network “hubs” (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies

Metabolic versatility of Caldarchaeales from geothermal features of Hawai’i and Chile as revealed by five metagenome-assembled genomes

Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai‘i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai‘i are high quality bins with completeness &gt;95% and contamination &lt;1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota

Draft Genome Sequence of Streptomyces sp. Strain ventii, Isolated from a Microbial Mat near Hydrothermal Vents within the Axial Seamount in the Pacific Ocean, and Resequencing of the Type Strains Streptomyces lonarensis NCL 716 and Streptomyces bohaiensis 11A07

The draft genome of Streptomyces sp. strain ventii, an environmental isolate recovered from deep-sea hydrothermal vents in the Pacific Ocean, is presented along with the resequenced draft genomes of the type strains Streptomyces bohaiensis 11A07 and Streptomyces lonarensis NCL 716

Assembling the Marine Metagenome, One Cell at a Time

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa

Polyphasic characterization of an epilithic biofilm from a lava cave in Kīlauea Caldera, Hawaiʻi

Ph.D. University of Hawaii at Manoa 2012.Includes bibliographical references.The microbial community in an epilithic biofilm on an lava cave wall in Kīlauea Caldera, Hawaiʻi, was characterized by a polyphasic approach. Ribosomal-pyrotag and metagenomic sequencing revealed phylogenetic diversity rivaling that in a Guerrero Negro hypersaline microbial mat. Targeted cultivations led to the isolation, characterization, and genome sequencing of a deeply divergent novel cyanobacterium. Diverse Bacteria and Archaea lineages were detected. The most abundant sequences, representing ~24% of the metagenomic reads analyzed, affiliated with Burkholderia. Comparative metagenomic analyses revealed community composition and function most similar to those in soils. Two novel cyanobacteria detected in metagenomic data were cultivated; JS1 is related to Gloeobacter violaceus PCC 7421T , the only cultivated Gloeobacter species. JS2 may represent a new genus in the Oscillatoriales since it shares <95% 16S rRNA gene sequence identity with its nearest neighbor, a Leptolyngbya sp. A third cultivated cyanobacterium (JS3) not detected in clone libraries, ribosomal-pyrotag or metagenomic data sets, belongs in the true-branching filamentous Stigonematales; JS3 shares 98.1% 16S rRNA gene sequence identity with Fischerella muscicola PCC 7414, and may be a new Fischerella sp. Comparing the complete genome sequence of JS1 with that of G. violaceus PCC 7421T revealed JS1 represents a new species, despite sharing 98.7% 16S rRNA gene sequence identity with PCC7421T . The name Candidatus Gloeobacter kilaueaensis is proposed, with JS1T the Type strain. Maximum likelihood phylogenetic trees based on 16S rRNA gene sequences and 43 concatenated ribosomal proteins showed Candidatus Gloeobacter kilaueaensis JS1T places in the deep-branching Gloeobacter clade, but is less basal than G. violaceus. Divergence times based on Bayesian analyses suggested these Gloeobacter species diverged 150-300 MYA. The isolation, characterization, and genome sequencing of a deeply divergent novel Gloeobacter is significant given that for forty years we have known only one species in the entire order. Of broader significance is confirmation that by integrating molecular and cultivation methods we can target for cultivation specific Bacteria and or Archaea only detected in molecular analyses; a range of scripts was also developed to analyze and visualize sequence data

TYGS classification of three bacterial isolate genomes

TYGS classification of three bacterial isolates.</p

The archaeal legacy of eukaryotes : A phylogenomic perspective

The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explainedbyinvokingacellular fusionatthe rootofthe eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to re-evaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling ofarchaeal genomes in this super-phylum will certainly providea better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.</p