Mercury Methylation by Metabolically Versatile and Cosmopolitan Marine Bacteria
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Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. -
Prokaryotic Community Structure and Activity of Sulfate Reducers in Production Water from High-Temperature Oil Reservoirs with and Without Nitrate Treatment
Prokaryotic community structure and activity of sulfate reducers in production water from high-temperature oil reservoirs with and without nitrate treatment Dr. Antje Gittel Dept. of Biological Sciences, Aarhus University ISMOS 2 Aarhus 2009 Introduction Hypothesis Results Conclusions Offshore oil production systems Separation Oil Gas Water Production Injection ~80 degC 50-60 degC Reservoir ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Characteristics of the study sites Norway Halfdan • Injection of sulfate-rich seawater Denmark • High loads of organic carbon compounds in the reservoir Dan Enrichment of sulfate -reducing prokaryotes Danish Underground Consortium, Maersk Oil (SRP ) that produce H 2S Souring, plugging, biocorrosion, toxicity, ..... • Strategy to control SRP activity at Halfdan: Addition of nitrate to the injection water ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Principles of SRP inhibition by nitrate addition (i) Stimulation of heterothrophic nitrate- reducing bacteria (hNRB ) that hNRB outcompete SRP for electron donors (ii) Activity of nitrate -reducing, sulfide - oxidizing bacteria (NR-SOB ) resulting in SRP NR-SOB a decreasing net production of H2S (iii) Increase in redox potential by the production of nitrite and nitrous oxides and thereby and inhibition of SRP ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Compared to an untreated oil field (Dan), nitrate addition to the injection water at Halfdan stimulates the growth of hNRB and/or NR-SOB , resulting in: 1) A general change in the prokaryotic community composition, i.e. • Presence of competitive hNRB and NR-SOB and/or • Presence of SRP that are able to reduce nitrate instead of sulfate 2) A decrease in SRP abundance and activity and 3) A reduced net sulfide production. -
1 Strong Purifying Selection Is Associated with Genome
1 Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared to the mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G+C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that genomes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment. -
Microbial Diversity Under Extreme Euxinia: Mahoney Lake, Canada V
Geobiology (2012), 10, 223–235 DOI: 10.1111/j.1472-4669.2012.00317.x Microbial diversity under extreme euxinia: Mahoney Lake, Canada V. KLEPAC-CERAJ,1,2 C. A. HAYES,3 W. P. GILHOOLY,4 T. W. LYONS,5 R. KOLTER2 AND A. PEARSON3 1Department of Molecular Genetics, Forsyth Institute, Cambridge, MA, USA 2Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA 3Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 4Department of Earth and Planetary Sciences, Washington University, Saint Louis, MO, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA ABSTRACT Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and ⁄ or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distribu- tions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteo- bacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomi- crobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion. -
Diversity and Community Structure of Marine Microbes Around the Benham Rise Underwater Plateau, Northeastern Philippines
Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines Andrian P. Gajigan1,2, Aletta T. Yñiguez1, Cesar L. Villanoy1, Maria Lourdes San Diego-McGlone1, Gil S. Jacinto1 and Cecilia Conaco1 1 Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines 2 Current affiliation: Department of Oceanography, University of Hawaii at Manoa, USA ABSTRACT Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Corre- spondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide Submitted 8 January 2018 foundational information on the diversity of marine microbes in Philippine waters. -
Tree Scale: 1 D Bacteria P Desulfobacterota C Jdfr-97 O Jdfr-97 F Jdfr-97 G Jdfr-97 S Jdfr-97 Sp002010915 WGS ID MTPG01
d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermodesulfobacterium s Thermodesulfobacterium commune WGS ID JQLF01 d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermosulfurimonas s Thermosulfurimonas dismutans WGS ID LWLG01 d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f DG-60 g DG-60 s DG-60 sp001304365 WGS ID LJNA01 ID WGS sp001304365 DG-60 s DG-60 g DG-60 f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f Desulfofervidaceae g Desulfofervidus s Desulfofervidus auxilii RS GCF 001577525 1 001577525 GCF RS auxilii Desulfofervidus s Desulfofervidus g Desulfofervidaceae f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfatatoraceae g Thermodesulfatator s Thermodesulfatator atlanticus WGS ID ATXH01 d Bacteria p Desulfobacterota c Desulfobacteria o Desulfatiglandales f NaphS2 g 4484-190-2 s 4484-190-2 sp002050025 WGS ID MVDB01 ID WGS sp002050025 4484-190-2 s 4484-190-2 g NaphS2 f Desulfatiglandales o Desulfobacteria c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g QOAM01 s QOAM01 sp003978075 WGS ID QOAM01 d Bacteria p Desulfobacterota c BSN033 o UBA8473 f UBA8473 g UBA8473 s UBA8473 sp002782605 WGS -
Vertically Distinct Microbial Communities in the Mariana and Kermadec Trenches
RESEARCH ARTICLE Vertically distinct microbial communities in the Mariana and Kermadec trenches Logan M. Peoples1, Sierra Donaldson1, Oladayo Osuntokun1, Qing Xia1,2, Alex Nelson3, Jessica Blanton1, Eric E. Allen1, Matthew J. Church3,4, Douglas H. Bartlett1* 1 Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America, 2 Department of Soil Science, North Carolina State University, Raleigh, NC, United States of America, 3 Center for Microbial Oceanography: Research and Education, C- MORE Hale, University of Hawai`i at Mānoa, Honolulu, HI, United States of America, 4 Flathead Lake Biological Station, University of Montana, Polson, MT, United States of America a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct micro- bial communities compared to those at shallower depths due to high hydrostatic pressures, OPEN ACCESS topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of Citation: Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, et al. (2018) Vertically the communities present in the bottom waters of the Kermadec and Mariana trenches. Esti- distinct microbial communities in the Mariana and mates of microbial protein production indicate active populations under in situ hydrostatic Kermadec trenches. PLoS ONE 13(4): e0195102. pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and https://doi.org/10.1371/journal.pone.0195102 size fraction are important drivers of microbial community structure. Many putative hadal Editor: Hauke Smidt, Wageningen University, bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodos- NETHERLANDS pirilliceae, and Aquibacter, are similar to members identified in other trenches. -
Reclassification of Desulfobacterium Phenolicum As Desulfobacula Phenolica Comb. Nov. and Description of Strain Saxt As Desulfot
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 171–177 Printed in Great Britain Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov., sp. nov. Jan Kuever,1 Martin Ko$ nneke,1 Alexander Galushko2 and Oliver Drzyzga3 Author for correspondence: Jan Kuever. Tel: j49 421 2028 734. Fax: j49 421 2028 580. e-mail: jkuever!mpi-bremen.de 1 Max-Planck-Institute for A mesophilic, sulfate-reducing bacterium (strain SaxT) was isolated from Marine Microbiology, marine coastal sediment in the Baltic Sea and originally described as a Department of Microbiology, ‘Desulfoarculus’ sp. It used a large variety of substrates, ranging from simple Celsiusstrasse 1, D-28359 organic compounds and fatty acids to aromatic compounds as electron donors. Bremen, Germany Autotrophic growth was possible with H2,CO2 and formate in the presence of 2 Fakulta$ tfu$ r Biologie, sulfate. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur Universita$ t Konstanz, and nitrate were not reduced. Fermentative growth was obtained with Postfach 5560, D-78457 Konstanz, Germany pyruvate, but not with fumarate or malate. Substrate oxidation was usually complete leading to CO , but at high substrate concentrations acetate 3 University of Bremen, 2 Center for Environmental accumulated. CO dehydrogenase activity was observed, indicating the Research and Technology operation of the CO dehydrogenase pathway (reverse Wood pathway) for CO2 (UFT), Department of fixation and complete oxidation of acetyl-CoA. The rod-shaped cells were Marine Microbiology, Leobener Strasse, D-28359 08–10 µm wide and 15–25 µm long. Spores were not produced and cells Bremen, Germany stained Gram-negative. -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Hydrothermal Vent Plume at the Mid-Atlantic Ridge
https://doi.org/10.5194/bg-2019-189 Preprint. Discussion started: 20 June 2019 c Author(s) 2019. CC BY 4.0 License. 1 Successional patterns of (trace) metals and microorganisms in the Rainbow 2 hydrothermal vent plume at the Mid-Atlantic Ridge 3 Sabine Haalboom1,*, David M. Price1,*,#, Furu Mienis1, Judith D.L van Bleijswijk1, Henko C. de 4 Stigter1, Harry J. Witte1, Gert-Jan Reichart1,2, Gerard C.A. Duineveld1 5 1 NIOZ Royal Netherlands Institute for Sea Research, department of Ocean Systems, and Utrecht University, PO Box 59, 6 1790 AB Den Burg, Texel, The Netherlands 7 2 Utrecht University, Faculty of Geosciences, 3584 CD Utrecht, The Netherlands 8 * These authors contributed equally to this work 9 # Current address: University of Southampton, Waterfront Campus, European Way, Southampton, UK, 10 SO14 3ZH. 11 [email protected]; [email protected] 12 13 Keywords: Rainbow vent; Epsilonproteobacteria; Hydrothermal vent plume; Deep-sea mining; Rare 14 earth elements; Seafloor massive sulfides 15 16 Abstract 17 Hydrothermal vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally 18 buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being 19 explored as possible new mining sites for (trace) metals and rare earth elements (REE). It has been 20 suggested that during mining activities large amounts of suspended matter will appear in the water column 21 due to excavation processes, and due to discharge of mining waste from the surface vessel. Understanding 22 how natural hydrothermal plumes evolve as they spread away from their source and how they affect their 23 surrounding environment may provide some analogies for the behaviour of the dilute distal part of 24 chemically enriched mining plumes. -
Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. -
Supporting Information
Supporting Information Bergauer et al. 10.1073/pnas.1708779115 SI Materials and Methods (www.vicbioinformatics.com/software.velvetoptimiser.shtml), were Study Site and Sampling. To study the genomic and proteomic 49 for the dataset of GEO_1 and 51 for the remaining meta- properties of microbial assemblages, water samples were col- genomic datasets (Table S3). The MetaVelvet parameters were lected from the following: the lower euphotic layer at 100-m as follows: ins_length, 220 (GEO); ins_length, 300 (MOCA); depth, the oxygen minimum layer (O2-min), the Labrador Sea- -cov_cutoff, 4; and min_contig_lgth, 1,000 (GEO and MOCA). water (LSW), the Antarctic Intermediate Water (AAIW), the Functional annotation of metagenomic contigs was conducted North Atlantic Deep Water (NADW), the Iceland–Scotland using Prokka v1.11 software tool (4) with an e-value cutoff of 1 × − Overflow Water (ISOW), the South Atlantic Central Water 10 8. To predict the location of ribosomal RNA genes on the (SACW), and the Antarctic Bottom Water (AABW). Seawater contigs, Barrnap 0.6 (www.vicbioinformatics.com/software.barrnap. was sequentially filtered through a 0.8-μm ATTP polycarbonate shtml) was implemented in the Prokka software package, and the filter (142-mm filter diameter; Millipore) and a 0.2-μm Pall SILVA-SSU database was used as data source for HMM models. Supor polyethersulfone or polycarbonate filter (142-mm filter Further assignments into higher-resolution functional prop- diameter; Millipore). Filtration of the samples was accomplished erties were based on protein domains, predicted and character- within 2.5–3 h after recovery of the conductivity, temperature, ized with the database Pfam-A 28.0 (5), where each of the protein and depth (CTD) rosette sampler.