Thomas BC

References (11)

Title : Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis - Crits-Christoph_2018_Nature_558_440
Author(s) : Crits-Christoph A , Diamond S , Butterfield CN , Thomas BC , Banfield JF
Ref : Nature , 558 :440 , 2018
Abstract : In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment(1,2). Most known antibiotics are derived from a few culturable microbial taxa (3) , and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated (4) . Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils(5-7), but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes (5) . We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.
ESTHER : Crits-Christoph_2018_Nature_558_440
PubMedSearch : Crits-Christoph_2018_Nature_558_440
PubMedID: 29899444
Gene_locus related to this paper: 9bact-a0a2v8qcw8

Title : Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments - Hernsdorf_2017_ISME.J_11_1915
Author(s) : Hernsdorf AW , Amano Y , Miyakawa K , Ise K , Suzuki Y , Anantharaman K , Probst A , Burstein D , Thomas BC , Banfield JF
Ref : Isme J , 11 :1915 , 2017
Abstract : Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.
ESTHER : Hernsdorf_2017_ISME.J_11_1915
PubMedSearch : Hernsdorf_2017_ISME.J_11_1915
PubMedID: 28350393
Gene_locus related to this paper: 9eury-a0a2i0pxa9 , 9spir-a0a2n1tka6 , 9firm-a0a2n2bq22 , 9firm-a0a2n2cxr7 , 9prot-a0a2n3dmk3 , 9delt-a0a2n2m1c4 , 9bact-a0a2i0q977 , 9bact-a0a2n1vaz9 , 9bact-a0a2n2vup6 , 9bact-a0a2n2w5u3 , 9bact-a0a2n2wjd9 , 9bact-a0a2n2wss4 , 9bact-a0a2n2xcb2 , 9bact-a0a2n2ylq2 , 9bact-a0a2n2yyx7 , 9bact-a0a2n2z6r2 , 9bact-a0a2n2ziv6 , 9bact-a0a2n3aau1

Title : Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations - Probst_2017_Environ.Microbiol_19_459
Author(s) : Probst AJ , Castelle CJ , Singh A , Brown CT , Anantharaman K , Sharon I , Hug LA , Burstein D , Emerson JB , Thomas BC , Banfield JF
Ref : Environ Microbiol , 19 :459 , 2017
Abstract : As in many deep underground environments, the microbial communities in subsurface high-CO2 ecosystems remain relatively unexplored. Recent investigations based on single-gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO2 -saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high-quality genomes from 150 microbial species affiliated with 46 different phylum-level lineages. Bacteria from two novel phylum-level lineages have the capacity for CO2 fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood-Ljungdahl pathway and the Calvin-Benson-Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO2 -concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H2 is an important inter-species energy currency even under gaseous CO2 -saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO2 saturation.
ESTHER : Probst_2017_Environ.Microbiol_19_459
PubMedSearch : Probst_2017_Environ.Microbiol_19_459
PubMedID: 27112493
Gene_locus related to this paper: 9bact-a0a1j5b1a3 , 9delt-a0a1j5dck5 , 9bact-a0a1j4sae3 , 9bact-a0a1j4vix4 , 9bact-a0a1j5a4q9 , 9bact-a0a1j5acn2 , 9bact-a0a1j5ba31 , 9delt-a0a1j4sq21 , 9bact-a0a1j5fm19 , 9delt-a0a1j5edt4 , 9delt-a0a1j5dgg6 , 9gamm-a0a1j5ij09 , 9prot-a0a1j4y0r0 , 9bact-a0a1j4x4y9

Title : Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs - Hu_2016_MBio_7_e01669
Author(s) : Hu P , Tom L , Singh A , Thomas BC , Baker BJ , Piceno YM , Andersen GL , Banfield JF
Ref : MBio , 7 :e01669 , 2016
Abstract : UNLABELLED: Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27 degrees C) and 2,743 m (80 to 83 degrees C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. IMPORTANCE: The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.
ESTHER : Hu_2016_MBio_7_e01669
PubMedSearch : Hu_2016_MBio_7_e01669
PubMedID: 26787827
Gene_locus related to this paper: 9psed-a0a101db53 , 9gamm-a0a124f6b0

Title : Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system - Anantharaman_2016_Nat.Commun_7_13219
Author(s) : Anantharaman K , Brown CT , Hug LA , Sharon I , Castelle CJ , Probst AJ , Thomas BC , Singh A , Wilkins MJ , Karaoz U , Brodie EL , Williams KH , Hubbard SS , Banfield JF
Ref : Nat Commun , 7 :13219 , 2016
Abstract : The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
ESTHER : Anantharaman_2016_Nat.Commun_7_13219
PubMedSearch : Anantharaman_2016_Nat.Commun_7_13219
PubMedID: 27774985
Gene_locus related to this paper: 9actn-a0a1f2wnf2 , 9prot-a0a1f2zxa9 , 9prot-a0a1f3a341 , 9burk-a0a1f4gq83 , 9burk-a0a1f4jft0 , 9burk-a0a1f4jgv2 , 9bact-a0a1f5uhh6 , 9chlr-a0a1f8pce2 , 9chlr-a0a1f8rbl5 , 9delt-a0a1f9a0t4 , 9delt-a0a1f9a2c0 , 9delt-a0a1f9ae10 , 9delt-a0a1f9af25 , 9delt-a0a1f9af82 , 9delt-a0a1f9amj5 , 9delt-a0a1f9an51 , 9delt-a0a1f9at34 , 9delt-a0a1f9aty2 , 9caul-a0a1g2wqt0 , 9bact-a0a1f3b975 , 9bact-a0a1f3bcf0 , 9bact-a0a1f3d7d6 , 9bact-a0a1f3dc76 , 9bact-a0a1f3dlp4 , 9bact-a0a1f3m0t6 , 9bact-a0a1f5ubz9 , 9bact-a0a1f5v0j4.1 , 9bact-a0a1f6csp4 , 9delt-a0a1f9m8k9 , 9bact-a0a1f9ws57 , 9bact-a0a1f9x2j2 , 9bact-a0a1f9y7k0 , 9bact-a0a1g0xkp9 , 9bact-a0a1g0y206 , 9bact-a0a1g0y3r8 , 9bact-a0a1g0yvr9 , 9bact-a0a1g0z8g9 , 9bact-a0a1g0z8w0 , 9bact-a0a1g0z924 , 9bact-a0a1g0z9w2 , 9bact-a0a1g0zh38 , 9bact-a0a1g0zsq4 , 9bact-a0a1g0zvp5 , 9bact-a0a1g0zw10 , 9bact-a0a1g1a6y3 , 9bact-a0a1g1bui0 , 9bact-a0a1g1byx9 , 9bact-a0a1g1c1n8 , 9bact-a0a1g1ccx9 , 9bact-a0a1g1ch43 , 9bact-a0a1g2y1z2 , 9bact-a0a1g2y3s3 , 9bact-a0a1g2y920 , 9bact-a0a1g2ym98 , 9bact-a0a1g2zgd9 , 9bact-a0a1g2zs85 , 9bact-a0a1g2zvy6 , 9bact-a0a1g2zxp8 , 9bact-a0a1g2zyx8 , 9bact-a0a1g3acf7 , 9bact-a0a1g3acp7 , 9spir-a0a1g3rsi6 , 9bact-a0a1g3zm42 , 9bact-a0a1g3zy77 , 9burk-a0a1f4h3a4 , 9bact-a0a1f5are5 , 9delt-a0a1f9chr0 , 9delt-a0a1f9lyx9 , 9delt-a0a1f9q9b7 , 9spir-a0a1g3m944 , 9prot-a0a1f2xrk8 , 9burk-a0a1f4g492 , 9bact-a0a1f5s6a1 , 9prot-a0a1f6gqf1 , 9bact-a0a1f6kk86 , 9bact-a0a1f7l112 , 9delt-a0a1f9fcx8 , 9bact-a0a1g0xqk6 , 9bact-a0a1g0y1x8 , 9gamm-a0a1g0z1y7 , 9bact-a0a1g0zgb1 , 9bact-a0a1g0zr85 , 9bact-a0a1g1a966 , 9bact-a0a1g1p2l4 , 9bact-a0a1g2z2x3 , 9bact-a0a1g2zfe6 , 9gamm-a0a1g3d8a5 , 9sphn-a0a1g3jwd2 , 9spir-a0a1g3ql42 , 9spir-a0a1g3ql48 , 9sphn-a0a1g3k9z6 , 9prot-a0a1f3axs2 , 9prot-a0a1f4a0e8 , 9burk-a0a1f8vhq0 , 9gamm-a0a1g0e773 , 9delt-a0a1f8xkx8 , 9delt-a0a1f9a855 , 9delt-a0a1f9kky5 , 9delt-a0a1f9b9l8 , 9burk-a0a1f4g8f2 , 9chlr-a0a1f8s5g8 , 9prot-a0a1g3ijf7 , 9prot-a0a1f3asi7 , 9prot-a0a1f2xim9 , 9rhob-a0a1g3g7x8 , 9prot-a0a1f8iqy5 , 9caul-a0a1g2wlx3 , 9prot-a0a1f2z9z6 , 9prot-a0a1f3ana3 , 9prot-a0a1f2z5b6 , 9prot-a0a1f2zii4 , 9delt-a0a1f9lda2 , 9delt-a0a1f9cme4 , 9delt-a0a1f9ncr4 , 9bact-a0a1g3a740 , 9bact-a0a1g2z8g2 , 9prot-a0a1g3igl9 , 9bact-a0a1f3e9w0 , 9bact-a0a1f3eds7 , 9bact-a0a1f3ggm4 , 9bact-a0a1f3in43 , 9bact-a0a1f3itl2 , 9bact-a0a1f3ivf6 , 9bact-a0a1f3k5y3 , 9bact-a0a1f3kde1 , 9bact-a0a1f3lf60 , 9bact-a0a1f3lx44 , 9bact-a0a1f3mgp8 , 9bact-a0a1f3mh02 , 9bact-a0a1f3psq9 , 9bact-a0a1f3q8b1 , 9bact-a0a1f5au09 , 9bact-a0a1g0bdg2 , 9bact-a0a1g0pi16 , 9bact-a0a1g0r9q4 , 9bact-a0a1g0rzj9 , 9bact-a0a1g0vh13

Title : Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone - Butterfield_2016_PeerJ_4_e2687
Author(s) : Butterfield CN , Li Z , Andeer PF , Spaulding S , Thomas BC , Singh A , Hettich RL , Suttle KB , Probst AJ , Tringe SG , Northen T , Pan C , Banfield JF
Ref : PeerJ , 4 :e2687 , 2016
Abstract : Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.
ESTHER : Butterfield_2016_PeerJ_4_e2687
PubMedSearch : Butterfield_2016_PeerJ_4_e2687
PubMedID: 27843720
Gene_locus related to this paper: 9gamm-a0a1q6wqt1 , 9bact-a0a1q6y4g7 , 9prot-a0a1q7tw10 , 9bact-a0a1q6xg26 , 9actn-a0a1q7axs7 , 9actn-a0a1q7vz10

Title : Measurement of bacterial replication rates in microbial communities - Brown_2016_Nat.Biotechnol_34_1256
Author(s) : Brown CT , Olm MR , Thomas BC , Banfield JF
Ref : Nat Biotechnol , 34 :1256 , 2016
Abstract : Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies.
ESTHER : Brown_2016_Nat.Biotechnol_34_1256
PubMedSearch : Brown_2016_Nat.Biotechnol_34_1256
PubMedID: 27819664
Gene_locus related to this paper: 9prot-a0a1q6t442 , 9prot-a0a1q6u8x3 , 9bace-a0a1q6gjr4 , 9bace-a0a1q6hct0 , 9bact-a0a1q6ink8 , 9bact-a0a1u7l8f4

Title : Unusual biology across a group comprising more than 15\% of domain Bacteria - Brown_2015_Nature_523_208
Author(s) : Brown CT , Hug LA , Thomas BC , Sharon I , Castelle CJ , Singh A , Wilkins MJ , Wrighton KC , Williams KH , Banfield JF
Ref : Nature , 523 :208 , 2015
Abstract : A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.
ESTHER : Brown_2015_Nature_523_208
PubMedSearch : Brown_2015_Nature_523_208
PubMedID: 26083755
Gene_locus related to this paper: 9bact-a0a0f9xu71 , 9bact-a0a0g0gp54 , 9bact-a0a0g0gs51 , 9bact-a0a0g0xj38 , 9bact-a0a0g1hul2

Title : Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics - Kantor_2015_Environ.Microbiol_17_4929
Author(s) : Kantor RS , van Zyl AW , van Hille RP , Thomas BC , Harrison ST , Banfield JF
Ref : Environ Microbiol , 17 :4929 , 2015
Abstract : Gold ore processing uses cyanide (CN(-) ), which often results in large volumes of thiocyanate- (SCN(-) ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN(-) and CN(-) , but little is known about their membership and metabolic potential. Microbial-based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN(-) and CN(-) into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN(-) and CN(-) degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN(-) degradation. Genome-based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN(-) degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.
ESTHER : Kantor_2015_Environ.Microbiol_17_4929
PubMedSearch : Kantor_2015_Environ.Microbiol_17_4929
PubMedID: 26031303
Gene_locus related to this paper: 9caul-a0a1d2tqz4 , 9caul-a0a1e4gzy2 , 9bact-a0a1e3ync8 , 9rhiz-a0a1e3ylc0 , 9bact-a0a1e4b8y1 , 9bact-a0a1e4b9g4 , 9caul-a0a1e4gyx0 , 9gamm-a0a1e4h6l7 , 9sphn-a0a1e4jga9 , 9gamm-a0a1e4kb00 , 9sphn-a0a1e4md43 , 9gamm-a0a1e4mlb4 , 9prot-a0a1e4pmm4 , 9bact-a0a1e4b938 , 9bact-a0a1e4hnf4 , 9pseu-a0a1e4hu48 , 9sphn-a0a1e4mug8 , 9pseu-a0a1e4ph68 , 9rhiz-a0a1e4fd43 , 9sphn-a0a1e4n749 , 9sphn-a0a1e4jgg3 , 9caul-a0a1e4gst4 , 9gamm-a0a1e4hig1

Title : Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla - Wrighton_2012_Science_337_1661
Author(s) : Wrighton KC , Thomas BC , Sharon I , Miller CS , Castelle CJ , VerBerkmoes NC , Wilkins MJ , Hettich RL , Lipton MS , Williams KH , Long PE , Banfield JF
Ref : Science , 337 :1661 , 2012
Abstract : BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type II/III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO(2) fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.
ESTHER : Wrighton_2012_Science_337_1661
PubMedSearch : Wrighton_2012_Science_337_1661
PubMedID: 23019650
Gene_locus related to this paper: acijo-d0s8f2 , 9bact-k2eq93 , 9bact-k1ymn0 , 9bact-k2ehy0 , 9gamm-n9p1u1 , 9bact-k2cj78 , 9bact-k2dnl8 , 9bact-k2f369 , 9bact-k2f264 , 9bact-k2gak8 , 9bact-k2age0 , 9bact-k2fcq4 , 9bact-k2fvb3 , 9zzzz-k2eg80 , 9bact-k1yi15

Title : Community-wide analysis of microbial genome sequence signatures - Dick_2009_Genome.Biol_10_R85
Author(s) : Dick GJ , Andersson AF , Baker BJ , Simmons SL , Thomas BC , Yelton AP , Banfield JF
Ref : Genome Biol , 10 :R85 , 2009
Abstract : BACKGROUND: Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them.
RESULTS: We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH approximately 5) versus extracellular (pH approximately 1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases.
CONCLUSIONS: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.
ESTHER : Dick_2009_Genome.Biol_10_R85
PubMedSearch : Dick_2009_Genome.Biol_10_R85
PubMedID: 19698104
Gene_locus related to this paper: 9eury-c7dfz3 , 9eury-c7dg61 , 9eury-c7dge3 , 9eury-c7dhl2 , 9eury-c7dhn0