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Zheng R, Cheng X, Gao X, Zhang C, Cheng X, David Waite T. Iron-retrofitted anaerobic baffled reactor system for rural wastewater treatment: Stable performance of nutrients removal with phosphorus recovery and minimal sludge production. BIORESOURCE TECHNOLOGY 2024; 408:131179. [PMID: 39084532 DOI: 10.1016/j.biortech.2024.131179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024]
Abstract
An iron-retrofitted anaerobic baffled reactor (ABR) system was developed for the effective treatment of rural wastewater with reduced maintenance demand and aeration costs. Average removal efficiencies of chemical oxygen demand, total nitrogen and total phosphorus of 99.4%, 62.7% and 92.6% were achieved respectively, when the ABR system was operating at steady state. With effective bioreduction of FeIII in the anaerobic chambers, phosphorus was immobilized in the sludge as vivianite, the sole phosphorus-carrying mineral. The FeIII in the recirculated sludge induced Feammox in the ABR reactor, contributing 14.8% to total nitrogen removal. Biophase separation and enrichment of microorganisms associated with iron and nitrogen transformations were observed in the system after Fe dosing, which enhanced the removal of pollutants. The coupling of Feammox and vivianite crystallization to remove nitrogen and phosphorus in an iron-retrofitted ABR would appear to be a promising technology for rural wastewater treatment.
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Affiliation(s)
- Ruoning Zheng
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - Xiaohui Cheng
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - Xiaozhong Gao
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - Changyong Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Xiang Cheng
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, Beijing 100083, China.
| | - T David Waite
- Water Research Center, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
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2
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Alarcon HV, Mohl JE, Chong GW, Betancourt A, Wang Y, Leng W, White JC, Xu J. Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source. Appl Environ Microbiol 2024; 90:e0086324. [PMID: 38899885 PMCID: PMC11267869 DOI: 10.1128/aem.00863-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures ("py"') demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c- and b-type cytochromes was observed in "py," pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells' photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(-), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet's history.
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Affiliation(s)
- Hugo V. Alarcon
- Environmental Science and Engineering Program, the University of Texas at El Paso, El Paso, Texas, USA
| | - Jonathon E. Mohl
- Department of Mathematical Sciences, the University of Texas at El Paso, El Paso, Texas, USA
- Border Biomedical Research Center, the University of Texas at El Paso, El Paso, Texas, USA
| | - Grace W. Chong
- Department of Earth, Environmental and Resource Sciences, the University of Texas at El Paso, El Paso, Texas, USA
| | - Ana Betancourt
- Border Biomedical Research Center, the University of Texas at El Paso, El Paso, Texas, USA
| | - Yi Wang
- The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Weinan Leng
- The National Center for Earth and Environmental Nanotechnology Infrastructure, Blacksburg, Virginia, USA
| | - Jason C. White
- The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Jie Xu
- Environmental Science and Engineering Program, the University of Texas at El Paso, El Paso, Texas, USA
- Department of Earth, Environmental and Resource Sciences, the University of Texas at El Paso, El Paso, Texas, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
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3
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Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 2024; 627:915-922. [PMID: 38480893 PMCID: PMC10972752 DOI: 10.1038/s41586-024-07180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/08/2024] [Indexed: 04/01/2024]
Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, Waterloo, Ontario, Canada.
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.
| | - N A Shaw
- University of Waterloo, Waterloo, Ontario, Canada
| | - S Nagashima
- Tokyo Metropolitan University, Tokyo, Japan
- Kanagawa University, Yokohama, Japan
| | - J J Venkiteswaran
- University of Waterloo, Waterloo, Ontario, Canada
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - S L Schiff
- University of Waterloo, Waterloo, Ontario, Canada
| | - T Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - M Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - S Hanada
- Tokyo Metropolitan University, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Tank
- Tokyo Metropolitan University, Tokyo, Japan
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - J D Neufeld
- University of Waterloo, Waterloo, Ontario, Canada.
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4
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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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5
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Olmsted CN, Ort R, Tran PQ, McDaniel EA, Roden EE, Bond DR, He S, McMahon KD. Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environ Microbiol 2023; 25:705-720. [PMID: 36529539 DOI: 10.1111/1462-2920.16314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.
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Affiliation(s)
- Charles N Olmsted
- Department of Molecular and Environmental Toxicology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Roger Ort
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Daniel R Bond
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
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6
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Roux S, Fischer MG, Hackl T, Katz LA, Schulz F, Yutin N. Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 2023; 13:204. [PMID: 36830574 PMCID: PMC9952930 DOI: 10.3390/biom13020204] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthias G. Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Xiao R, Kuang B, Hu Y, Wang Y, Bai J, Zhang L, Wang C, Wei Z, Zhang K, Jorquera MA, Campos M, Acuña JJ, Pan W. Ecological risk assessment of glyphosate and its possible effect on bacterial community in surface sediments of a typical shallow Lake, northern China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114445. [PMID: 38321664 DOI: 10.1016/j.ecoenv.2022.114445] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 02/08/2024]
Abstract
Glyphosate is a widely used herbicide worldwide and its prevalent presence in aquatic ecosystems poses a threat to living organisms. This study evaluated potential ecological risk of glyphosate to sediment-dwelling organisms and assessed the probable effect of glyphosate on structure and predicated function of sediment-attached bacterial communities from a large shallow lake in northern China based on 16S rRNA high-throughput sequencing. Results suggested that glyphosate showed a medium to high concentration (up to 8.63 mg/kg) and chronic risk to sediment-dwelling organisms (10% samples exhibiting medium to high risk quotient), especially in sites nearby farmland and residential areas in August. Bacterial community identification based on 16S rRNA sequence indicated some species of dominant phylum Proteobacteria and Campilobacterota (e.g., Steroidobacteraceae, Thiobacillus, Gallionellaceae, Sulfurimonadaceae) were stimulated while some species of dominant phylum Actinobacteriota, Acidobacteriota and Firmicutes (e.g., Nocardioidaceae, Microtrichales, Vicinamibacteraceae, Paenisporosarcina) were inhibited by glyphosate accumulation. The stimulating species were related to sulfur-oxidizing, sulfate-, iron-, or nitrate-reducing bacteria; The inhibiting species were related to plant bacterial endophytes, polyphosphate-accumulating organisms (PAOs) and denitrifers. Correspondingly, promoted bacterial metabolic functions of "sulfite respiration", "nitrogen respiration", "aromatic compound degradation" and "nitrification" but suppressed "cellulolysis", "manganese oxidation", "anoxygenic photoautotrophy S oxidizing" and "nitrate denitrification" were predicated on functional annotation of prokaryotic taxa. Although these results could only partly suggest the impacts of glyphosate on the bacterial communities due to the lack of actual results from control experiments, the identified Steroidobacteraceae could be thought as a bioindicator in the future mechanism study for the ecological effect and bioremediation of glyphosate. This work intends to arise the concern about the depletion of biodiversity and bacterial metabolic functions with contribution of glyphosate in part in eutrophic lakes.
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Affiliation(s)
- Rong Xiao
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Bo Kuang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yanping Hu
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yaping Wang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Chen Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zhuoqun Wei
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Kegang Zhang
- Department of Environmental Science and Engineering, North China Electric Power University, Baoding 071003, China
| | - Milko A Jorquera
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Marco Campos
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Jacquelinne J Acuña
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Wenbin Pan
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
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8
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Barnum TP, Coates JD. Chlorine redox chemistry is widespread in microbiology. THE ISME JOURNAL 2023; 17:70-83. [PMID: 36202926 PMCID: PMC9751292 DOI: 10.1038/s41396-022-01317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.
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Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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9
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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10
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Liu K, Schiff SL, Wu L, Molot LA, Venkiteswaran JJ, Paterson MJ, Elgood RJ, Tsuji JM, Neufeld JD. Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14840-14851. [PMID: 36162065 DOI: 10.1021/acs.est.2c04247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable Fe isotopes have only recently been measured in freshwater systems, mainly in meromictic lakes. Here we report the δ56Fe of dissolved, particulate, and sediment Fe in two small dimictic boreal shield headwater lakes: manipulated eutrophic Lake 227, with annual cyanobacterial blooms, and unmanipulated oligotrophic Lake 442. Within the lakes, the range in δ56Fe is large (ca. -0.9 to +1.8‰), spanning more than half the entire range of natural Earth surface samples. Two layers in the water column with distinctive δ56Fe of dissolved (dis) and particulate (spm) Fe were observed, despite differences in trophic states. In the epilimnia of both lakes, a large Δ56Fedis-spm fractionation of 0.4-1‰ between dissolved and particulate Fe was only observed during cyanobacterial blooms in Lake 227, possibly regulated by selective biological uptake of isotopically light Fe by cyanobacteria. In the anoxic layers in both lakes, upward flux from sediments dominates the dissolved Fe pool with an apparent Δ56Fedis-spm fractionation of -2.2 to -0.6‰. Large Δ56Fedis-spm and previously published metagenome sequence data suggest active Fe cycling processes in anoxic layers, such as microaerophilic Fe(II) oxidation or photoferrotrophy, could regulate biogeochemical cycling. Large fractionation of stable Fe isotopes in these lakes provides a potential tool to probe Fe cycling and the acquisition of Fe by cyanobacteria, with relevance for understanding biogeochemical cycling of Earth's early ferruginous oceans.
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Affiliation(s)
- Kai Liu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Sherry L Schiff
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lingling Wu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lewis A Molot
- Faculty of Environmental and Urban Change, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jason J Venkiteswaran
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | | | - Richard J Elgood
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Josh D Neufeld
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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11
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Grouzdev D, Gaisin V, Lunina O, Krutkina M, Krasnova E, Voronov D, Baslerov R, Sigalevich P, Savvichev A, Gorlenko V. Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota. FEMS Microbiol Ecol 2022; 98:6693937. [PMID: 36073352 DOI: 10.1093/femsec/fiac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022] Open
Abstract
Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.
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Affiliation(s)
- Denis Grouzdev
- SciBear OU, 10115 Tallinn, Estonia.,School of Marine and Atmospheric Sciences, Stony Brook University, 11794, Stony Brook, USA
| | - Vasil Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Current affiliation: Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Olga Lunina
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | | | - Elena Krasnova
- Pertsov White Sea Biological Station, 184042, Republic Karelia, Russia
| | - Dmitry Voronov
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia
| | - Roman Baslerov
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Pavel Sigalevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alexander Savvichev
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Vladimir Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
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12
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Ward LM, Shih PM. Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen. PLoS One 2022; 17:e0270187. [PMID: 35913911 PMCID: PMC9342728 DOI: 10.1371/journal.pone.0270187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, for much of Earth history it is thought that anoxygenic photosynthesis-using compounds like ferrous iron or sulfide as electron donors-drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere during late Archean and early Paleoproterozoic time before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.
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Affiliation(s)
- L. M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Geosciences, Smith College, Northampton, Massachusetts, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
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13
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Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov. Microorganisms 2022; 10:microorganisms10071312. [PMID: 35889031 PMCID: PMC9318685 DOI: 10.3390/microorganisms10071312] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.
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14
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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15
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Lambrecht N, Stevenson Z, Sheik CS, Pronschinske MA, Tong H, Swanner ED. " Candidatus Chlorobium masyuteum," a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake. Front Microbiol 2021; 12:695260. [PMID: 34305861 PMCID: PMC8302410 DOI: 10.3389/fmicb.2021.695260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. "Candidatus Chlorobium masyuteum" grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe "Candidatus Pseudopelobacter ferreus" is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While "Ca. C. masyuteum" is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day-1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.
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Affiliation(s)
- Nicholas Lambrecht
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Zackry Stevenson
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Cody S. Sheik
- Department of Biology, University of Minnesota Duluth, Duluth, MN, United States
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, United States
| | - Matthew A. Pronschinske
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
| | - Hui Tong
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Institute of Eco-environmental Science and Technology, Guangdong Academy of Sciences, Guangzhou, China
| | - Elizabeth D. Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, United States
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16
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Garcia SL, Mehrshad M, Buck M, Tsuji JM, Neufeld JD, McMahon KD, Bertilsson S, Greening C, Peura S. Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations. mSystems 2021; 6:e01196-20. [PMID: 33975970 PMCID: PMC8125076 DOI: 10.1128/msystems.01196-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/09/2021] [Indexed: 01/15/2023] Open
Abstract
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.
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Affiliation(s)
- Sarahi L Garcia
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Moritz Buck
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
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