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Novel Prosthecate Bacteria from the Candidate Phylum Acetothermia
The ISME Journal https://doi.org/10.1038/s41396-018-0187-9 ARTICLE Novel prosthecate bacteria from the candidate phylum Acetothermia 1 1 1 1 Liping Hao ● Simon Jon McIlroy ● Rasmus Hansen Kirkegaard ● Søren Michael Karst ● 1 2 2 1 Warnakulasuriya Eustace Yrosh Fernando ● Hüsnü Aslan ● Rikke Louise Meyer ● Mads Albertsen ● 1 1 Per Halkjær Nielsen ● Morten Simonsen Dueholm Received: 21 November 2017 / Revised: 9 February 2018 / Accepted: 20 March 2018 © The Author(s) 2018. This article is published with open access Abstract Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic 1234567890();,: 1234567890();,: lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy, and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions. Introduction many bacterial lineages lack cultivated representatives, and the bacteria affiliated to these candidate lineages are often Microorganisms drive the major biogeochemical nutrient poorly described [6–8]. -
Supplemental Materials Adaptations of Atribacteria to Life In
1 Supplemental Materials 2 Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life 3 Authors: Jennifer B. Glass1*, Piyush Ranjan2*, Cecilia B. Kretz1#, Brook L. Nunn3, Abigail M. Johnson1, James McManus4, Frank J. Stewart2 4 Affiliations: 5 1School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA 6 2School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA 7 3Department of Genome Sciences, University of Washington, Seattle, WA 8 4Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA 9 10 #Now at: Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 11 Atlanta, Georgia, USA 12 *Correspondence to: [email protected] 13 Dedication: To Katrina Edwards 14 1 15 Table S1. Additional geochemical data for ODP Site 1244 at Hydrate Ridge drilled on IODP Leg 204. 16 See Fig. 1 for methane, sulfate, manganese, iron, and iodide concentrations. 17 Depth reactive reactive Hole (mbsf) %TC %TN %TS %TIC %TOC C:N %CaCO3 Fe (%) Mn (%) C1H2 1.95/2.25 2.07 0.2 0.42 0.17 1.9 11.05 1.46 0.38 0.002 C1H3 3.45/3.75 1.88 0.14 0.55 0.70 1.2 9.85 5.81 0.45 0.004 F2H4 8.6 1.54 0.17 0.39 0.44 1.1 7.55 3.66 0.57 0.005 F3H4 18.1 1.55 0.24 0.64 0.08 1.5 7.14 0.68 0.80 0.004 C3H4 20.69 1.22 0.18 0.22 0.08 1.1 7.40 0.65 1.10 0.004 E10H5 68.55 1.71 0.22 0.42 0.13 1.6 8.38 1.08 0.51 0.003 E19H5 138.89 1.42 0.20 0.07 0.51 0.9 5.32 4.23 1.41 0.012 18 2 19 Table S2. -
Atribacteria Reproducing Over Millions of Years in the Atlantic Abyssal Subseafloor
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.198200; this version posted July 11, 2020. 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 4.0 International license. Atribacteria reproducing over millions of years in the Atlantic abyssal subseafloor. Aurèle Vuillemin1, Sergio Vargas1, Ömer K. Coskun1, Robert Pockalny3, Richard W. Murray4, David C. Smith3, Steven D’Hondt3 and William D. Orsi1,2,* 1 Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians- Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany. 2 GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany. 3 Graduate School of Oceanography, University of Rhode Island, 02882 Narragansett, USA 4 Woods Hole Oceanographic Institution, Woods Hole, MA 02543. * Corresponding author: William D. Orsi - [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.198200; this version posted July 11, 2020. 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 4.0 International license. Abstract How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a five million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. -
Downloaded from NCBI Genbank (MT066494–MT067558)
microorganisms Article Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka Camille Thomas 1,* , Alexander Francke 2, Hendrik Vogel 3, Bernd Wagner 4 and Daniel Ariztegui 1 1 Department of Earth Sciences, University of Geneva, 1205 Geneva, Switzerland; [email protected] 2 Department of Earth Sciences, University of Adelaide, 5005 Adelaide, Australia; [email protected] 3 Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, 3012 Bern, Switzerland; [email protected] 4 Institute of Geology and Mineralogy, University of Cologne, 50674 Cologne, Germany; [email protected] * Correspondence: [email protected] Received: 13 October 2020; Accepted: 3 November 2020; Published: 5 November 2020 Abstract: Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. -
Title Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere Through Submarine Mud Volcanoes Author
Atribacteria from the Subseafloor Sedimentary Biosphere Title Disperse to the Hydrosphere through Submarine Mud Volcanoes Hoshino, Tatsuhiko; Toki, Tomohiro; Ijiri, Akira; Morono, Author(s) Yuki; Machiyama, Hideaki; Ashi, Juichiro; Okamura, Kei; Inagaki, Fumio Citation Frontiers in Microbiology, 8: 1135 Issue Date 2017-06-20 URL http://hdl.handle.net/20.500.12000/37630 This Document is Protected by copyright and was first Rights published by Frontiers. All rights reserved. it is reproduced with permission. fmicb-08-01135 June 17, 2017 Time: 14:58 # 1 ORIGINAL RESEARCH published: 20 June 2017 doi: 10.3389/fmicb.2017.01135 Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes Tatsuhiko Hoshino1,2*, Tomohiro Toki3, Akira Ijiri1,2, Yuki Morono1,2, Hideaki Machiyama2, Juichiro Ashi4, Kei Okamura5 and Fumio Inagaki1,2,6 1 Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science Technology, Nankoku, Japan, 2 Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science Technology, Nankoku, Japan, 3 Faculty of Science, University of the Ryukyus, Nishihara, Japan, 4 Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan, 5 Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan, 6 Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science Technology, Yokohama, Japan Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by Edited by: the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into Jennifer F. -
Genomic Analysis of Uncultured Microbes in Marine Sediments
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2017 Singled Out: Genomic analysis of uncultured microbes in marine sediments Jordan Toby Bird University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Bird, Jordan Toby, "Singled Out: Genomic analysis of uncultured microbes in marine sediments. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4829 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jordan Toby Bird entitled "Singled Out: Genomic analysis of uncultured microbes in marine sediments." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Karen G. Lloyd, Major Professor We have read this dissertation and recommend its acceptance: Mircea Podar, Andrew D. Steen, Erik R. Zinser Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Singled Out: Genomic analysis of uncultured microbes in marine sediments A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jordan Toby Bird December 2017 Copyright © 2017 by Jordan Bird All rights reserved. -
Global Diversity of Microbial Communities in Marine Sediment
Global diversity of microbial communities in marine sediment Tatsuhiko Hoshinoa,1, Hideyuki Doib,1, Go-Ichiro Uramotoa,2, Lars Wörmerc,d, Rishi R. Adhikaric,d, Nan Xiaoa,e, Yuki Moronoa, Steven D’Hondtf, Kai-Uwe Hinrichsc,d, and Fumio Inagakia,e,1 aKochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, 783-8502 Kochi, Japan; bGraduate School of Simulation Studies, University of Hyogo, Kobe, 650-0047 Hyogo, Japan; cMARUM-Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, 28359 Bremen, Germany; dDepartment of Geosciences, University of Bremen, 28359 Bremen, Germany; eMantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering, JAMSTEC, Yokohama, Kanagawa 236-0001, Japan; and fGraduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882 Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 4, 2020 (received for review November 17, 2019) Microbial life in marine sediment contributes substantially to biomass, even from 2-km-deep anoxic Miocene sediment (9–12) global biomass and is a crucial component of the Earth system. and 101.5-Ma oxic sediment. Subseafloor sediment includes both aerobic and anaerobic micro- Factors that may limit the deep sedimentary biosphere are not bial ecosystems, which persist on very low fluxes of bioavailable restricted to scarcity of nutrients and scarcity of energy-yielding energy over geologic time. However, the taxonomic diversity of substrates. Limiting factors may also include temperature, pres- the marine sedimentary microbial biome and the spatial distribu- sure, pH, salinity, water availability, sediment porosity, or per- tion of that diversity have been poorly constrained on a global meability. -
Deep-Sea Shipwrecks Represent Island-Like Ecosystems for Marine Microbiomes
The ISME Journal (2021) 15:2883–2891 https://doi.org/10.1038/s41396-021-00978-y ARTICLE Deep-sea shipwrecks represent island-like ecosystems for marine microbiomes 1 1 1 1 1 Leila J. Hamdan ● Justyna J. Hampel ● Rachel D. Moseley ● Rachel. L. Mugge ● Anirban Ray ● 2 3 Jennifer L. Salerno ● Melanie Damour Received: 11 November 2020 / Revised: 19 March 2021 / Accepted: 6 April 2021 / Published online: 22 April 2021 © The Author(s) 2021. This article is published with open access Abstract Biogeography of macro- and micro-organisms in the deep sea is, in part, shaped by naturally occurring heterogeneous habitat features of geological and biological origin such as seeps, vents, seamounts, whale and wood-falls. Artificial features including shipwrecks and energy infrastructure shape the biogeographic patterns of macro-organisms; how they influence microorganisms is unclear. Shipwrecks may function as islands of biodiversity for microbiomes, creating a patchwork of habitats with influence radiating out into the seabed. Here we show microbiome richness and diversity increase as a function of proximity to the historic deep-sea shipwreck Anona in the Gulf of Mexico. Diversity and richness extinction plots provide 1234567890();,: 1234567890();,: evidence of an island effect on microbiomes. A halo of core taxa on the seabed was observed up to 200 m away from the wreck indicative of the transition zone from shipwreck habitat to the surrounding environment. Transition zones around natural habitat features are often small in area compared to what was observed at Anona indicating shipwrecks may exert a large sphere of influence on seabed microbiomes. Historic shipwrecks are abundant, isolated habitats with global distribution, providing a means to explore contemporary processes shaping biogeography on the seafloor. -
Inoculum Source Determines Acetate and Lactate Production During Anaerobic Digestion of Sewage Sludge and Food Waste
bioengineering Article Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste Jan Moestedt 1,2, Maria Westerholm 3, Simon Isaksson 3 and Anna Schnürer 1,3,* 1 Department of Thematic Studies–Environmental Change, Linköping University, SE 581 83 Linköping, Sweden; [email protected] 2 Department R&D, Tekniska verken i Linköping AB, SE 581 15 Linköping, Sweden 3 Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCenter, SE 750 07 Uppsala, Sweden; [email protected] (M.W.); [email protected] (S.I.) * Correspondence: [email protected] Received: 15 November 2019; Accepted: 18 December 2019; Published: 23 December 2019 Abstract: Acetate production from food waste or sewage sludge was evaluated in four semi-continuous anaerobic digestion processes. To examine the importance of inoculum and substrate for acid production, two different inoculum sources (a wastewater treatment plant (WWTP) and a co-digestion plant treating food and industry waste) and two common substrates (sewage sludge and food waste) were used in process operations. The processes were evaluated with regard to the efficiency of hydrolysis, acidogenesis, acetogenesis, and methanogenesis and the microbial community structure was determined. Feeding sewage sludge led to mixed acid fermentation and low total acid yield, whereas feeding food waste resulted in the production of high acetate and lactate yields. Inoculum from WWTP with sewage sludge substrate resulted in maintained methane production, despite a low hydraulic retention time. For food waste, the process using inoculum from WWTP produced high levels of lactate (30 g/L) and acetate (10 g/L), while the process initiated with inoculum from the co-digestion plant had higher acetate (25 g/L) and lower lactate (15 g/L) levels. -
One-Step Production of C6–C8 Carboxylates by Mixed Culture Solely Grown on CO
He et al. Biotechnol Biofuels (2018) 11:4 https://doi.org/10.1186/s13068-017-1005-8 Biotechnology for Biofuels RESEARCH Open Access One‑step production of C6–C8 carboxylates by mixed culture solely grown on CO Pinjing He1,2,3, Wenhao Han1, Liming Shao2,3 and Fan Lü1,2,4* Abstract Background: This study aimed at producing C6–C8 medium-chain carboxylates (MCCAs) directly from gaseous CO using mixed culture. The yield and C2–C8 product composition were investigated when CO was continuously fed with gradually increasing partial pressure. Results: The maximal concentrations of n-caproate, n-heptylate, and n-caprylate were 1.892, 1.635, and 1 1 1 1.033 mmol L− , which were achieved at the maximal production rates of 0.276, 0.442, and 0.112 mmol L− day− , respectively. Microbial analysis revealed that long-term acclimation and high CO partial pressure were important to establish a CO-tolerant and CO-utilizing chain-elongating microbiome, rich in Acinetobacter, Alcaligenes, and Rhodo- bacteraceae and capable of forming MCCAs solely from CO. Conclusions: These results demonstrated that carboxylate and syngas platform could be integrated in a shared growth vessel, and could be a promising one-step technique to convert gaseous syngas to preferable liquid biochem- icals, thereby avoiding the necessity to coordinate syngas fermentation to short-chain carboxylates and short-to- medium-chain elongation. Thus, this method could provide an alternative solution for the utilization of waste-derived syngas and expand the resource of promising biofuels. Keywords: Syngas fermentation, Chain elongation, Carboxylates, One-step production, Mixed culture Background the thermal treatment of biowaste or artifcial polymers In recent times, conversion of waste to biochemicals [3–5]. -
PDF (Chapter 2)
32 Chapter2 CHARACTERIZATION OF MICROBIAL ASSOCIATIONS WITH METHANOTROPHIC ARCHAEA AND SULFATE-REDUCING BACTERIA THROUGH STATISTICAL COMPARISON OF NESTED MAGNETO-FISH ENRICHMENTS 33 Abstract Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to a consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly -
Fossil Pigments and Sedimentary DNA at Laguna Potrok Aike, Argentina Title Page Abstract Introduction A
Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 12, 18345–18388, 2015 www.biogeosciences-discuss.net/12/18345/2015/ doi:10.5194/bgd-12-18345-2015 BGD © Author(s) 2015. CC Attribution 3.0 License. 12, 18345–18388, 2015 This discussion paper is/has been under review for the journal Biogeosciences (BG). Fossil pigments and Please refer to the corresponding final paper in BG if available. sedimentary DNA at Laguna Potrok Aike Recording of climate and diagenesis A. Vuillemin et al. through fossil pigments and sedimentary DNA at Laguna Potrok Aike, Argentina Title Page Abstract Introduction A. Vuillemin1, D. Ariztegui2, P. R. Leavitt3,4, L. Bunting3, and the PASADO Conclusions References Science Team5,6 Tables Figures 1GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Sect. 4.5 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany 2Department of Earth Sciences, University of Geneva, rue des Maraîchers 13, 1205 Geneva, J I Switzerland J I 3Limnology Laboratory, Department of Biology, University of Regina, Regina, Saskatchewan, Canada Back Close 4Institute of Environmental Change and Society, University of Regina, Regina, Saskatchewan, Canada Full Screen / Esc 5GEOPOLAR, Institute of Geography, University of Bremen, Celsiusstr. FVG-M, 28359 Bremen, Germany Printer-friendly Version 6GEOTOP Research Centre, Montréal, Canada Interactive Discussion 18345 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Received: 12 October 2015 – Accepted: 2 November 2015 – Published: 16 November 2015 Correspondence to: A. Vuillemin ([email protected]) BGD Published by Copernicus Publications on behalf of the European Geosciences Union. 12, 18345–18388, 2015 Fossil pigments and sedimentary DNA at Laguna Potrok Aike A.