101
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Krauze P, Kämpf H, Horn F, Liu Q, Voropaev A, Wagner D, Alawi M. Microbiological and Geochemical Survey of CO 2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic. Front Microbiol 2017; 8:2446. [PMID: 29321765 PMCID: PMC5732176 DOI: 10.3389/fmicb.2017.02446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/24/2017] [Indexed: 02/01/2023] Open
Abstract
The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.
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Affiliation(s)
- Patryk Krauze
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Horst Kämpf
- GFZ German Research Centre for Geosciences, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Qi Liu
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | | | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany.,Institute for Earth and Environmental Sciences, University of Potsdam, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
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102
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Ham B, Choi BY, Chae GT, Kirk MF, Kwon MJ. Geochemical Influence on Microbial Communities at CO 2-Leakage Analog Sites. Front Microbiol 2017; 8:2203. [PMID: 29170659 PMCID: PMC5684959 DOI: 10.3389/fmicb.2017.02203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/26/2017] [Indexed: 01/22/2023] Open
Abstract
Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites.
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Affiliation(s)
- Baknoon Ham
- KU-KIST Green School, Korea University, Seoul, South Korea
| | - Byoung-Young Choi
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Gi-Tak Chae
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS, United States
| | - Man Jae Kwon
- KU-KIST Green School, Korea University, Seoul, South Korea.,Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
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103
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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104
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Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill. Proc Natl Acad Sci U S A 2017; 114:E8950-E8952. [PMID: 29073089 DOI: 10.1073/pnas.1712466114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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105
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Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ. Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. MICROBIOME 2017; 5:112. [PMID: 28865481 PMCID: PMC5581439 DOI: 10.1186/s40168-017-0331-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. RESULTS Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. CONCLUSIONS CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life.
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Affiliation(s)
- R E Danczak
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M D Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - C Kenah
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - M Slattery
- Ohio Environmental Protection Agency, Columbus, OH, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - M J Wilkins
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- School of Earth Sciences, The Ohio State University, Columbus, OH, USA.
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106
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Finstad KM, Probst AJ, Thomas BC, Andersen GL, Demergasso C, Echeverría A, Amundson RG, Banfield JF. Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. Front Microbiol 2017; 8:1435. [PMID: 28804480 PMCID: PMC5532433 DOI: 10.3389/fmicb.2017.01435] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.
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Affiliation(s)
- Kari M. Finstad
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
| | - Alexander J. Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
| | - Brian C. Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States
| | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del NorteAntofagasta, Chile
| | - Alex Echeverría
- Centro de Biotecnología, Universidad Católica del NorteAntofagasta, Chile
| | - Ronald G. Amundson
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
| | - Jillian F. Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, BerkeleyCA, United States
- Department of Earth and Planetary Sciences, University of California, Berkeley, BerkeleyCA, United States
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107
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Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME JOURNAL 2017; 11:2864-2868. [PMID: 28742071 DOI: 10.1038/ismej.2017.126] [Citation(s) in RCA: 1042] [Impact Index Per Article: 148.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/18/2017] [Accepted: 06/05/2017] [Indexed: 01/17/2023]
Abstract
The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively compare large genome sets, but they are not accurate with draft-quality genomes. Here we present dRep, a program that reduces the computational time for pairwise genome comparisons by sequentially applying a fast, inaccurate estimation of genome distance, and a slow, accurate measure of average nucleotide identity. dRep achieves a 28 × increase in speed with perfect recall and precision when benchmarked against previously developed algorithms. We demonstrate the use of dRep for genome recovery from time-series datasets. Each metagenome was assembled separately, and dRep was used to identify groups of essentially identical genomes and select the best genome from each replicate set. This resulted in recovery of significantly more and higher-quality genomes compared to the set recovered using co-assembly.
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Affiliation(s)
- Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.,Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
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108
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Sánchez-Osuna M, Barbé J, Erill I. Comparative genomics of the DNA damage-inducible network in the Patescibacteria. Environ Microbiol 2017; 19:3465-3474. [DOI: 10.1111/1462-2920.13826] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/09/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia; Universitat Autònoma de Barcelona; Spain
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia; Universitat Autònoma de Barcelona; Spain
| | - Ivan Erill
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland USA
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109
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Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A 2017; 114:7432-7437. [PMID: 28652349 DOI: 10.1073/pnas.1703424114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.
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110
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Freedman AJ, Tan B, Thompson JR. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir. Environ Microbiol 2017; 19:2228-2245. [PMID: 28229521 PMCID: PMC5518199 DOI: 10.1111/1462-2920.13706] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 02/17/2017] [Indexed: 11/30/2022]
Abstract
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.
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Affiliation(s)
- Adam J.E. Freedman
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - BoonFei Tan
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Janelle R. Thompson
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Environmental Sensing and ModelingSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
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111
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Abstract
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNACys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“Candidatus Parcubacteria” and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNACys species with cysteine in vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes. Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.
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112
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Wurzbacher C, Nilsson RH, Rautio M, Peura S. Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds. ISME JOURNAL 2017; 11:1938-1941. [PMID: 28430187 DOI: 10.1038/ismej.2017.54] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/16/2017] [Accepted: 03/03/2017] [Indexed: 11/09/2022]
Abstract
In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
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Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Milla Rautio
- Département des sciences fondamentales and Centre for Northern Studies (CEN), Université du Québec á Chicoutimi, Chicoutimi, QC, Canada
| | - Sari Peura
- Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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113
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Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF. Potential for microbial H 2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME JOURNAL 2017; 11:1915-1929. [PMID: 28350393 PMCID: PMC5520028 DOI: 10.1038/ismej.2017.39] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/02/2017] [Accepted: 02/05/2017] [Indexed: 01/24/2023]
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.
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Affiliation(s)
- Alex W Hernsdorf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.,Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency, Horonobe, Hokkaido, Japan
| | - Kotaro Ise
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Yohey Suzuki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | | | - David Burstein
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
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114
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Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature 2016; 542:237-241. [PMID: 28005056 PMCID: PMC5300952 DOI: 10.1038/nature21059] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA1,2. Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences3,4. The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research5. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms6,7. Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.
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Affiliation(s)
- David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Steven C Strutt
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA
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115
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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. Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 2016; 4:e2687. [PMID: 27843720 PMCID: PMC5103831 DOI: 10.7717/peerj.2687] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 01/03/2023] Open
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.
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Affiliation(s)
- Cristina N Butterfield
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Zhou Li
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Peter F Andeer
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Susan Spaulding
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Andrea Singh
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Kenwyn B Suttle
- Department of Ecology and Evolutionary Biology, University of California , Santa Cruz , CA , United States
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California , Berkeley , CA , United States
| | | | - Trent Northen
- Lawrence Berkeley National Laboratory , Berkeley , CA , United States
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN , Unites States
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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116
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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. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219. [PMID: 27774985 PMCID: PMC5079060 DOI: 10.1038/ncomms13219] [Citation(s) in RCA: 594] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
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.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Christopher T. Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Alexander J. Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Michael J. Wilkins
- School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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117
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Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd KG. Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. Front Microbiol 2016; 7:1221. [PMID: 27547202 PMCID: PMC4975002 DOI: 10.3389/fmicb.2016.01221] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/22/2016] [Indexed: 02/01/2023] Open
Abstract
The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, USA, we sequenced a single cell amplified genome (SAG), WOR_SM1_SCG, and used it to identify and refine two high-quality genomes from metagenomes, WOR_SM1_79 and WOR_SM1_86-2, from the same site. These three genomic reconstructions form a monophyletic group, which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, caused the protein to be encoded as two subunits at non-adjacent loci. Consistent with the terrestrial spring clades, our estuarine genomes contained a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identified two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which was more widespread, diverse, and not associated with visible mats. The core Alti-1 genome suggested Alti-1 is adapted for the stream environment with lipopolysaccharide production capacity and extracellular hami structures. The core Alti-2 genome suggested members of this clade are free-living with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These data suggested that the hamus structures found in Candidatus Altiarchaeum hamiconexum are not present outside of stream-adapted Altiarchaeales. Homologs to a Na(+) transporter and membrane bound coenzyme A disulfide reductase that were unique to the brackish sediment Alti-2 genomes, could indicate adaptations to the estuarine, sulfur-rich environment.
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Affiliation(s)
- Jordan T Bird
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville TN, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas TX, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley CA, USA
| | - Mircea Podar
- Department of Microbiology, University of Tennessee at Knoxville, KnoxvilleTN, USA; Biosciences Division, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville TN, USA
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