1
|
Kopejtka K, Tomasch J, Shivaramu S, Saini MK, Kaftan D, Koblížek M. Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica. mSystems 2024; 9:e0070624. [PMID: 39189770 PMCID: PMC11406998 DOI: 10.1128/msystems.00706-24] [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: 05/23/2024] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m-2 s-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m-2 s-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms. IMPORTANCE Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.
Collapse
Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| | - Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| | - Mohit Kumar Saini
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Acad Sci, Třeboň, Czechia
| |
Collapse
|
2
|
Vivenzio VM, Esposito D, Monti SM, De Simone G. Bacterial α-CAs: a biochemical and structural overview. Enzymes 2024; 55:31-63. [PMID: 39222995 DOI: 10.1016/bs.enz.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Carbonic anhydrases belonging to the α-class are widely distributed in bacterial species. These enzymes have been isolated from bacteria with completely different characteristics including both Gram-negative and Gram-positive strains. α-CAs show a considerable similarity when comparing the biochemical, kinetic and structural features, with only small differences which reflect the diverse role these enzymes play in Nature. In this chapter, we provide a comprehensive overview on bacterial α-CA data, with a highlight to their potential biomedical and biotechnological applications.
Collapse
|
3
|
Barbosa ACC, Venceslau SS, Pereira IAC. DsrMKJOP is the terminal reductase complex in anaerobic sulfate respiration. Proc Natl Acad Sci U S A 2024; 121:e2313650121. [PMID: 38285932 PMCID: PMC10861901 DOI: 10.1073/pnas.2313650121] [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: 08/08/2023] [Accepted: 12/20/2023] [Indexed: 01/31/2024] Open
Abstract
Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical sulfur cycle. In spite of its importance to the sulfur and carbon cycles, industrial processes, and human health, it is still not clear how reduction of sulfate to sulfide is coupled to energy conservation. A central step in the pathway is the reduction of sulfite by the DsrAB dissimilatory sulfite reductase, which leads to the production of a DsrC-trisulfide. A membrane-bound complex, DsrMKJOP, is present in most organisms that have DsrAB and DsrC, and its involvement in energy conservation has been inferred from sequence analysis, but its precise function was so far not determined. Here, we present studies revealing that the DsrMKJOP complex of the sulfate reducer Archaeoglobus fulgidus works as a menadiol:DsrC-trisulfide oxidoreductase. Our results reveal a close interaction between the DsrC-trisulfide and the DsrMKJOP complex and show that electrons from the quinone pool reduce consecutively the DsrM hemes b, the DsrK noncubane [4Fe-4S]3+/2+ catalytic center, and finally the DsrC-trisulfide with concomitant release of sulfide. These results clarify the role of this widespread respiratory membrane complex and support the suggestion that DsrMKJOP contributes to energy conservation upon reduction of the DsrC-trisulfide in the last step of DSR.
Collapse
Affiliation(s)
- Ana C. C. Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras2780-156, Portugal
| | - Sofia S. Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras2780-156, Portugal
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras2780-156, Portugal
| |
Collapse
|
4
|
Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [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: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
Collapse
Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
| |
Collapse
|
5
|
Crockford PW, Bar On YM, Ward LM, Milo R, Halevy I. The geologic history of primary productivity. Curr Biol 2023; 33:4741-4750.e5. [PMID: 37827153 DOI: 10.1016/j.cub.2023.09.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
The rate of primary productivity is a keystone variable in driving biogeochemical cycles today and has been throughout Earth's past.1 For example, it plays a critical role in determining nutrient stoichiometry in the oceans,2 the amount of global biomass,3 and the composition of Earth's atmosphere.4 Modern estimates suggest that terrestrial and marine realms contribute near-equal amounts to global gross primary productivity (GPP).5 However, this productivity balance has shifted significantly in both recent times6 and through deep time.7,8 Combining the marine and terrestrial components, modern GPP fixes ≈250 billion tonnes of carbon per year (Gt C year-1).5,9,10,11 A grand challenge in the study of the history of life on Earth has been to constrain the trajectory that connects present-day productivity to the origin of life. Here, we address this gap by piecing together estimates of primary productivity from the origin of life to the present day. We estimate that ∼1011-1012 Gt C has cumulatively been fixed through GPP (≈100 times greater than Earth's entire carbon stock). We further estimate that 1039-1040 cells have occupied the Earth to date, that more autotrophs than heterotrophs have ever existed, and that cyanobacteria likely account for a larger proportion than any other group in terms of the number of cells. We discuss implications for evolutionary trajectories and highlight the early Proterozoic, which encompasses the Great Oxidation Event (GOE), as the time where most uncertainty exists regarding the quantitative census presented here.
Collapse
Affiliation(s)
- Peter W Crockford
- Department of Earth Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada; Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - Yinon M Bar On
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel; Division of Geological Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Luce M Ward
- Department of Geosciences, Smith College, Northampton, MA 01063, USA
| | - Ron Milo
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| |
Collapse
|
6
|
Watanabe Y, Tajika E, Ozaki K. Evolution of iron and oxygen biogeochemical cycles during the Precambrian. GEOBIOLOGY 2023; 21:689-707. [PMID: 37622474 DOI: 10.1111/gbi.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Iron (Fe) is an essential element for life, and its geochemical cycle is intimately linked to the coupled history of life and Earth's environment. The accumulated geologic records indicate that ferruginous waters existed in the Precambrian oceans not only before the first major rise of atmospheric O2 levels (Great Oxidation Event; GOE) during the Paleoproterozoic, but also during the rest of the Proterozoic. However, the interactive evolution of the biogeochemical cycles of O2 and Fe during the Archean-Proterozoic remains ambiguous. Here, we develop a biogeochemical model to investigate the coupled biogeochemical evolution of Fe-O2 -P-C cycles across the GOE. Our model demonstrates that the marine Fe cycle was less sensitive to changes in the production rate of O2 before the GOE (atmospheric pO2 < 10-6 PAL; present atmospheric level). When the P supply rate to the ocean exceeds a certain threshold, the GOE occurs and atmospheric pO2 rises to ~10-3 -10-1 PAL. After the GOE, the marine Fe(II) concentration is highly sensitive to atmospheric pO2 , suggesting that the marine redox landscape during the Proterozoic may have fluctuated between ferruginous conditions and anoxic non-ferruginous conditions with sulfidic water masses around continental margins. At a certain threshold value of atmospheric pO2 of ~0.3% PAL, the primary oxidation pathway of Fe(II) shifts from the activity of Fe(II)-utilizing anoxygenic photoautotrophs in sunlit surface waters to abiotic process in the deep ocean. This is accompanied by a shift in the primary deposition site of Fe(III) hydroxides from the surface ocean to the deep sea, providing a plausible mechanistic explanation for the observed cessation of iron formations during the Proterozoic.
Collapse
Affiliation(s)
- Yasuto Watanabe
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eiichi Tajika
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazumi Ozaki
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Alternative Earths Team, Interdisciplinary Consortia for Astrobiology Research, National Aeronautics and Space Administration, Riverside, California, USA
| |
Collapse
|
7
|
Neukirchen S, Pereira IAC, Sousa FL. Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction. THE ISME JOURNAL 2023; 17:1680-1692. [PMID: 37468676 PMCID: PMC10504309 DOI: 10.1038/s41396-023-01477-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
Microbial dissimilatory sulfur metabolism utilizing dissimilatory sulfite reductases (Dsr) influenced the biochemical sulfur cycle during Earth's history and the Dsr pathway is thought to be an ancient metabolic process. Here we performed comparative genomics, phylogenetic, and synteny analyses of several Dsr proteins involved in or associated with the Dsr pathway across over 195,000 prokaryotic metagenomes. The results point to an archaeal origin of the minimal DsrABCMK(N) protein set, having as primordial function sulfite reduction. The acquisition of additional Dsr proteins (DsrJOPT) increased the Dsr pathway complexity. Archaeoglobus would originally possess the archaeal-type Dsr pathway and the archaeal DsrAB proteins were replaced with the bacterial reductive-type version, possibly at the same time as the acquisition of the QmoABC and DsrD proteins. Further inventions of two Qmo complex types, which are more spread than previously thought, allowed microorganisms to use sulfate as electron acceptor. The ability to use the Dsr pathway for sulfur oxidation evolved at least twice, with Chlorobi and Proteobacteria being extant descendants of these two independent adaptations.
Collapse
Affiliation(s)
- Sinje Neukirchen
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipa L Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| |
Collapse
|
8
|
Watanabe Y, Tajika E, Ozaki K. Biogeochemical transformations after the emergence of oxygenic photosynthesis and conditions for the first rise of atmospheric oxygen. GEOBIOLOGY 2023; 21:537-555. [PMID: 36960595 DOI: 10.1111/gbi.12554] [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: 07/15/2022] [Revised: 02/09/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
The advent of oxygenic photosynthesis represents the most prominent biological innovation in the evolutionary history of the Earth. The exact timing of the evolution of oxygenic photoautotrophic bacteria remains elusive, yet these bacteria profoundly altered the redox state of the ocean-atmosphere-biosphere system, ultimately causing the first major rise in atmospheric oxygen (O2 )-the so-called Great Oxidation Event (GOE)-during the Paleoproterozoic (~2.5-2.2 Ga). However, it remains unclear how the coupled atmosphere-marine biosphere system behaved after the emergence of oxygenic photoautotrophs (OP), affected global biogeochemical cycles, and led to the GOE. Here, we employ a coupled atmospheric photochemistry and marine microbial ecosystem model to comprehensively explore the intimate links between the atmosphere and marine biosphere driven by the expansion of OP, and the biogeochemical conditions of the GOE. When the primary productivity of OP sufficiently increases in the ocean, OP suppresses the activity of the anaerobic microbial ecosystem by reducing the availability of electron donors (H2 and CO) in the biosphere and causes climate cooling by reducing the level of atmospheric methane (CH4 ). This can be attributed to the supply of OH radicals from biogenic O2 , which is a primary sink of biogenic CH4 and electron donors in the atmosphere. Our typical result also demonstrates that the GOE is triggered when the net primary production of OP exceeds >~5% of the present oceanic value. A globally frozen snowball Earth event could be triggered if the atmospheric CO2 level was sufficiently small (<~40 present atmospheric level; PAL) because the concentration of CH4 in the atmosphere would decrease faster than the climate mitigation by the carbonate-silicate geochemical cycle. These results support a prolonged anoxic atmosphere after the emergence of OP during the Archean and the occurrence of the GOE and snowball Earth event during the Paleoproterozoic.
Collapse
Affiliation(s)
- Yasuto Watanabe
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eiichi Tajika
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazumi Ozaki
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| |
Collapse
|
9
|
Hesketh-Best PJ, Bosco-Santos A, Garcia SL, O’Beirne MD, Werne JP, Gilhooly WP, Silveira CB. Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:126. [PMID: 38665202 PMCID: PMC11041744 DOI: 10.1038/s43247-023-00796-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/05/2023] [Indexed: 04/28/2024]
Abstract
Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.
Collapse
Affiliation(s)
| | - Alice Bosco-Santos
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Sofia L. Garcia
- Department of Biology, University of Miami, Coral Gables, FL USA
| | - Molly D. O’Beirne
- Department of Geology & Environmental Science, University of Pittsburgh, Pittsburgh, PA USA
| | - Josef P. Werne
- Department of Geology & Environmental Science, University of Pittsburgh, Pittsburgh, PA USA
| | - William P. Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN USA
| | | |
Collapse
|
10
|
Zhang Y, Chen R, Zhang D, Qi S, Liu Y. Metabolite interactions between host and microbiota during health and disease: Which feeds the other? Biomed Pharmacother 2023; 160:114295. [PMID: 36709600 DOI: 10.1016/j.biopha.2023.114295] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Metabolites produced by the host and microbiota play a crucial role in how human bodies develop and remain healthy. Most of these metabolites are produced by microbiota and hosts in the digestive tract. Metabolites in the gut have important roles in energy metabolism, cellular communication, and host immunity, among other physiological activities. Although numerous host metabolites, such as free fatty acids, amino acids, and vitamins, are found in the intestine, metabolites generated by gut microbiota are equally vital for intestinal homeostasis. Furthermore, microbiota in the gut is the sole source of some metabolites, including short-chain fatty acids (SCFAs). Metabolites produced by microbiota, such as neurotransmitters and hormones, may modulate and significantly affect host metabolism. The gut microbiota is becoming recognized as a second endocrine system. A variety of chronic inflammatory disorders have been linked to aberrant host-microbiota interplays, but the precise mechanisms underpinning these disturbances and how they might lead to diseases remain to be fully elucidated. Microbiome-modulated metabolites are promising targets for new drug discovery due to their endocrine function in various complex disorders. In humans, metabolotherapy for the prevention or treatment of various disorders will be possible if we better understand the metabolic preferences of bacteria and the host in specific tissues and organs. Better disease treatments may be possible with the help of novel complementary therapies that target host or bacterial metabolism. The metabolites, their physiological consequences, and functional mechanisms of the host-microbiota interplays will be highlighted, summarized, and discussed in this overview.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Rui Chen
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China.
| | - Shuang Qi
- Department of Anethesiology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand and Foot Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.
| |
Collapse
|
11
|
Timm J, Pike DH, Mancini JA, Tyryshkin AM, Poudel S, Siess JA, Molinaro PM, McCann JJ, Waldie KM, Koder RL, Falkowski PG, Nanda V. Design of a minimal di-nickel hydrogenase peptide. SCIENCE ADVANCES 2023; 9:eabq1990. [PMID: 36897954 PMCID: PMC10005181 DOI: 10.1126/sciadv.abq1990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/07/2023] [Indexed: 06/07/2023]
Abstract
Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.
Collapse
Affiliation(s)
- Jennifer Timm
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Douglas H. Pike
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Joshua A. Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Alexei M. Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Jan A. Siess
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Paul M. Molinaro
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - James J. McCann
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Kate M. Waldie
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| |
Collapse
|
12
|
Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
Collapse
Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| |
Collapse
|
13
|
The Evolution of Nitric Oxide Function: From Reactivity in the Prebiotic Earth to Examples of Biological Roles and Therapeutic Applications. Antioxidants (Basel) 2022; 11:antiox11071222. [PMID: 35883712 PMCID: PMC9311577 DOI: 10.3390/antiox11071222] [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: 05/17/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/01/2022] Open
Abstract
Nitric oxide was once considered to be of marginal interest to the biological sciences and medicine; however, there is now wide recognition, but not yet a comprehensive understanding, of its functions and effects. NO is a reactive, toxic free radical with numerous biological targets, especially metal ions. However, NO and its reaction products also play key roles as reductant and oxidant in biological redox processes, in signal transduction, immunity and infection, as well as other roles. Consequently, it can be sensed, metabolized and modified in biological systems. Here, we present a brief overview of the chemistry and biology of NO—in particular, its origins in geological time and in contemporary biology, its toxic consequences and its critical biological functions. Given that NO, with its intrinsic reactivity, appeared in the early Earth’s atmosphere before the evolution of complex lifeforms, we speculate that the potential for toxicity preceded biological function. To examine this hypothesis, we consider the nature of non-biological and biological targets of NO, the evolution of biological mechanisms for NO detoxification, and how living organisms generate this multifunctional gas.
Collapse
|
14
|
Grosch M, Stiebritz MT, Bolney R, Winkler M, Jückstock E, Busch H, Peters S, Siegle AF, van Slageren J, Ribbe M, Hu Y, Trapp O, Robl C, Weigand W. Mackinawite supported reduction of C1 substrates into prebiotically relevant precursors. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mario Grosch
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat IAAC GERMANY
| | - Martin T Stiebritz
- UC Irvine: University of California Irvine Department of Molecular Biology and Biochemistry UNITED STATES
| | - Robert Bolney
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat IAAC GERMANY
| | - Mario Winkler
- Universität Stuttgart Fakultät 3 Chemie: Universitat Stuttgart Fakultat 3 Chemie IPC GERMANY
| | - Eric Jückstock
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat IAAC GERMANY
| | - Hannah Busch
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat IAAC GERMANY
| | - Sophia Peters
- Ludwig-Maximilians-Universität München Fakultät für Chemie und Pharmazie: Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Department of Chemistry GERMANY
| | - Alexander F. Siegle
- Ludwig-Maximilians-Universität München Fakultät für Chemie und Pharmazie: Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Department of Chemistry GERMANY
| | - Joris van Slageren
- Universität Stuttgart Fakultät 3 Chemie: Universitat Stuttgart Fakultat 3 Chemie IPC GERMANY
| | - Markus Ribbe
- UC Irvine: University of California Irvine Department of Molecular Biology and Biochemistry GERMANY
| | - Yilin Hu
- UC Irvine: University of California Irvine Department of Molecular Biology and Biochemistry UNITED STATES
| | - Oliver Trapp
- Ludwig-Maximilians-Universität München Fakultät für Geowissenschaften: Ludwig-Maximilians-Universitat Munchen Fakultat fur Geowissenschaften Department of Chemistry UNITED STATES
| | - Christian Robl
- Friedrich Schiller Universitat Jena Chemisch Geowissenschaftliche Fakultat IAAC GERMANY
| | - Wolfgang Weigand
- Institut fuer Anorganische und Analytische Chemie Friedrich-Schiller-Universitaet Jena Humboldtstrasse 8 07743 Jena GERMANY
| |
Collapse
|
15
|
Tanabe TS, Dahl C. HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies. Mol Ecol Resour 2022; 22:2758-2774. [PMID: 35579058 DOI: 10.1111/1755-0998.13642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 05/11/2022] [Indexed: 11/26/2022]
Abstract
Sulfur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulfide and sulfur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulfate, thiosulfate and sulfur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulfur compounds occurring in sulfur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulfur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulfur oxidation as opposed to sulfur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighborhood. The HMMs were validated on an annotated test dataset and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulfur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulfur-rich glacier, and were able to replicate and extend previous reports.
Collapse
Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| |
Collapse
|
16
|
Kandhol N, Aggarwal B, Bansal R, Parveen N, Singh VP, Chauhan DK, Sonah H, Sahi S, Grillo R, Peralta-Videa J, Deshmukh R, Tripathi DK. Nanoparticles as a potential protective agent for arsenic toxicity alleviation in plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118887. [PMID: 35077838 DOI: 10.1016/j.envpol.2022.118887] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/19/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Aggrandized technological and industrial progression in past decades have occasioned immense depreciation in the quality of environment and ecosystem, majorly due to augmentation in the number of obnoxious pollutants incessantly being released in soil, water or air. Arsenic (As) is one such hazardous metalloid contaminating the environment which has the potential to detrimentally affect the life on earth. Even in minute quantity, As is known to cause various critical diseases in humans and toxicity in plants. Recent studies on nanoparticles (NPs) approve of their ability to qualify the criterion of becoming a potent tool for mitigating As-induced phytotoxicity. Nanoparticles are reported to promote plant growth under As-stress by stimulating various alterations at physiological, biochemical, and molecular levels. In this review, we provide an up-to-date compilation of research that has been carried out in comprehending the mechanisms utilized by nanoparticles including controlled As uptake and distribution in plants, maintenance of ROS homeostasis during stress and chelation and vacuolar sequestration of As so as to reduce the severity of toxicity induced by As, and potential areas of research in this field will also be indicated for future perspectives.
Collapse
Affiliation(s)
- Nidhi Kandhol
- Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | - Bharti Aggarwal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Nishat Parveen
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Allahabad, 211002, India
| | - Devendra Kumar Chauhan
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Shivendra Sahi
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, 19104-4495, USA
| | - Renato Grillo
- São Paulo State University (UNESP), Department of Physics and Chemistry, School of Engineering, Ilha Solteira, SP, 15385-000, Brazil
| | - José Peralta-Videa
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Ave., El Paso, TX, 79968, United States
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Durgesh Kumar Tripathi
- Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India.
| |
Collapse
|
17
|
Arthur R, Nicholson A. Selection principles for Gaia. J Theor Biol 2022; 533:110940. [PMID: 34710434 DOI: 10.1016/j.jtbi.2021.110940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
The Gaia hypothesis considers the life-environment coupled system as a single entity that acts to regulate and maintain habitable conditions on Earth. In this paper we discuss three mechanisms which could potentially lead to Gaia: Selection by Survival, Sequential Selection and Entropic Hierarchy. We use the Tangled Nature Model of co-evolution as a common framework for investigating all three, using an extended version of the standard model to elaborate on Gaia as an example of an entropic hierarchy. This idea, which combines sequential selection together with a reservoir of diversity that acts as a 'memory', implies a tendency towards growth and increasing resilience of the Gaian system over time. We then discuss how Gaian memory could be realised in practice via the microbial seed bank, climate refugia and lateral gene transfer and conclude by discussing testable implications of an entropic hierarchy for the study of Earth history and the search for life in the universe. This paper adds to the existing taxonomy of Gaia hypotheses to suggest an "Entropic Gaia" where we argue that increasing biomass, complexity and enhanced habitability over time is a statistically likely feature of a co-evolving system.
Collapse
Affiliation(s)
- Rudy Arthur
- Department of Computer Science, University of Exeter, North Park Road, Exeter EX4 4RN, UK.
| | - Arwen Nicholson
- Department of Physics, University of Exeter, North Park Road, Exeter EX4 4QL, UK
| |
Collapse
|
18
|
Neira G, Vergara E, Cortez D, Holmes DS. A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. Antioxidants (Basel) 2021; 11:antiox11010059. [PMID: 35052563 PMCID: PMC8773360 DOI: 10.3390/antiox11010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.
Collapse
Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Diego Cortez
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago 8420524, Chile
- Correspondence:
| |
Collapse
|
19
|
Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake. NITROGEN 2021. [DOI: 10.3390/nitrogen2040029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium, and organic nitrogen in the deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water body with high concentrations of methane, ferrous iron, and manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to a phytoplankton bloom. The decomposition of the bulk of the organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and is accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimolimnion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrate occurs. Overall, most of the organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.
Collapse
|
20
|
Szeinbaum N, Toporek Y, Reinhard CT, Glass JB. Microbial helpers allow cyanobacteria to thrive in ferruginous waters. GEOBIOLOGY 2021; 19:510-520. [PMID: 33871172 PMCID: PMC8349797 DOI: 10.1111/gbi.12443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/15/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O2 on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe2+ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet, cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe2+ -rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe2+ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with ROS defence mechanisms increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe2+ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations and may expand the upper bound for tolerable Fe2+ concentrations for cyanobacteria.
Collapse
Affiliation(s)
- Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Yael Toporek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | | | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA
| |
Collapse
|
21
|
Miralles-Robledillo JM, Bernabeu E, Giani M, Martínez-Serna E, Martínez-Espinosa RM, Pire C. Distribution of Denitrification among Haloarchaea: A Comprehensive Study. Microorganisms 2021; 9:1669. [PMID: 34442748 PMCID: PMC8400030 DOI: 10.3390/microorganisms9081669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
Microorganisms from the Halobacteria class, also known as haloarchaea, inhabit a wide range of ecosystems of which the main characteristic is the presence of high salt concentration. These environments together with their microbial communities are not well characterized, but some of the common features that they share are high sun radiation and low availability of oxygen. To overcome these stressful conditions, and more particularly to deal with oxygen limitation, some microorganisms drive alternative respiratory pathways such as denitrification. In this paper, denitrification in haloarchaea has been studied from a phylogenetic point of view. It has been demonstrated that the presence of denitrification enzymes is a quite common characteristic in Halobacteria class, being nitrite reductase and nitric oxide reductase the enzymes with higher co-occurrence, maybe due to their possible role not only in denitrification, but also in detoxification. Moreover, copper-nitrite reductase (NirK) is the only class of respiratory nitrite reductase detected in these microorganisms up to date. The distribution of this alternative respiratory pathway and their enzymes among the families of haloarchaea has also been discussed and related with the environment in which they constitute the major populations. Complete denitrification phenotype is more common in some families like Haloarculaceae and Haloferacaceae, whilst less common in families such as Natrialbaceae and Halorubraceae.
Collapse
Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Elena Martínez-Serna
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (J.M.M.-R.); (E.B.); (M.G.); (E.M.-S.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Cyanobacteria and biogeochemical cycles through Earth history. Trends Microbiol 2021; 30:143-157. [PMID: 34229911 DOI: 10.1016/j.tim.2021.05.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]
Abstract
Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.
Collapse
|
24
|
Krissansen-Totton J, Kipp MA, Catling DC. Carbon cycle inverse modeling suggests large changes in fractional organic burial are consistent with the carbon isotope record and may have contributed to the rise of oxygen. GEOBIOLOGY 2021; 19:342-363. [PMID: 33764615 PMCID: PMC8359855 DOI: 10.1111/gbi.12440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 05/23/2023]
Abstract
Abundant geologic evidence shows that atmospheric oxygen levels were negligible until the Great Oxidation Event (GOE) at 2.4-2.1 Ga. The burial of organic matter is balanced by the release of oxygen, and if the release rate exceeds efficient oxygen sinks, atmospheric oxygen can accumulate until limited by oxidative weathering. The organic burial rate relative to the total carbon burial rate can be inferred from the carbon isotope record in sedimentary carbonates and organic matter, which provides a proxy for the oxygen source flux through time. Because there are no large secular trends in the carbon isotope record over time, it is commonly assumed that the oxygen source flux changed only modestly. Therefore, declines in oxygen sinks have been used to explain the GOE. However, the average isotopic value of carbon fluxes into the atmosphere-ocean system can evolve due to changing proportions of weathering and outgassing inputs. If so, large secular changes in organic burial would be possible despite unchanging carbon isotope values in sedimentary rocks. Here, we present an inverse analysis using a self-consistent carbon cycle model to determine the maximum change in organic burial since ~4 Ga allowed by the carbon isotope record and other geological proxies. We find that fractional organic burial may have increased by 2-5 times since the Archean. This happens because O2 -dependent continental weathering of 13 C-depleted organics changes carbon isotope inputs to the atmosphere-ocean system. This increase in relative organic burial is consistent with an anoxic-to-oxic atmospheric transition around 2.4 Ga without declining oxygen sinks, although these likely contributed. Moreover, our inverse analysis suggests that the Archean absolute organic burial flux was comparable to modern, implying high organic burial efficiency and ruling out very low Archean primary productivity.
Collapse
Affiliation(s)
- Joshua Krissansen-Totton
- Department of Earth and Space Sciences/Astrobiology Program, University of Washington, Seattle, WA, USA
- Virtual Planetary Laboratory, NASA Nexus for Exoplanet System Science, Seattle, WA, USA
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA, USA
| | - Michael A Kipp
- Department of Earth and Space Sciences/Astrobiology Program, University of Washington, Seattle, WA, USA
- Virtual Planetary Laboratory, NASA Nexus for Exoplanet System Science, Seattle, WA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David C Catling
- Department of Earth and Space Sciences/Astrobiology Program, University of Washington, Seattle, WA, USA
- Virtual Planetary Laboratory, NASA Nexus for Exoplanet System Science, Seattle, WA, USA
| |
Collapse
|
25
|
Rego ES, Busigny V, Lalonde SV, Philippot P, Bouyon A, Rossignol C, Babinski M, de Cássia Zapparoli A. Anoxygenic photosynthesis linked to Neoarchean iron formations in Carajás (Brazil). GEOBIOLOGY 2021; 19:326-341. [PMID: 33660904 DOI: 10.1111/gbi.12438] [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: 10/14/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
Microbial activity is often invoked as a direct or indirect contributor to the precipitation of ancient chemical sedimentary rocks such as Precambrian iron formations (IFs). Determining a specific metabolic pathway from the geological record remains a challenge, however, due to a lack of constraints on the initial conditions and microbially induced redox reactions involved in the formation of iron oxides. Thus, there is ongoing debate concerning the role of photoferrotrophy, that is the process by which inorganic carbon is fixed into organic matter using light as an energy source and Fe(II) as an electron donor, in the deposition of IFs. Here, we examine ~2.74-Ga-old Neoarchean IFs and associated carbonates from the Carajás Mineral Province, Brazil, to reconstruct redox conditions and to infer the oxidizing mechanism that allowed one of the world's largest iron deposits to form. The absence of cerium (Ce) anomalies reveals that conditions were pervasively anoxic during IF deposition, while unprecedented europium (Eu) anomalies imply that Fe was supplied by intense hydrothermal activity. A positive and homogeneous Fe isotopic signal in space and time in these IFs indicates a low degree of partial oxidation of Fe(II), which, combined with the presence of 13 C-depleted organic matter, points to a photoautotrophic metabolic driver. Collectively, our results argue in favor of reducing conditions during IF deposition and suggest anoxygenic photosynthesis as the most plausible mechanism responsible for Fe oxidation in the Carajás Basin.
Collapse
Affiliation(s)
- Eric Siciliano Rego
- Instituto de Geociências, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris cedex 05, France
- Géosciences Montpellier, Université de Montpellier, CNRS, Université des Antilles, Montpellier, France
| | - Vincent Busigny
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris cedex 05, France
| | - Stefan V Lalonde
- Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, CNRS, Plouzané, France
| | - Pascal Philippot
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris cedex 05, France
- Géosciences Montpellier, Université de Montpellier, CNRS, Université des Antilles, Montpellier, France
- Departamento de Geofísica, Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil
| | - Amaury Bouyon
- Géosciences Montpellier, Université de Montpellier, CNRS, Université des Antilles, Montpellier, France
| | - Camille Rossignol
- Institut de Physique du Globe de Paris, Université de Paris, CNRS, Paris cedex 05, France
- Departamento de Geofísica, Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil
| | - Marly Babinski
- Instituto de Geociências, Universidade de São Paulo, Cidade Universitária, São Paulo, Brazil
| | | |
Collapse
|
26
|
Koemets E, Fedotenko T, Khandarkhaeva S, Bykov M, Bykova E, Thielmann M, Chariton S, Aprilis G, Koemets I, Glazyrin K, Liermann H, Hanfland M, Ohtani E, Dubrovinskaia N, McCammon C, Dubrovinsky L. Chemical Stability of FeOOH at High Pressure and Temperature, and Oxygen Recycling in Early Earth History**. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100274] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Egor Koemets
- Bayerisches Geoinstitut University of Bayreuth 95440 Bayreuth Germany
- Institut Charles Gerhardt Montpellier (UMR CNRS 5253) Université de Montpellier 34095 Montpellier Cedex 5 France
| | - Timofey Fedotenko
- Material Physics and Technology at Extreme Conditions Laboratory of Crystallography Universität Bayreuth 95440 Bayreuth Germany
| | | | - Maxim Bykov
- Bayerisches Geoinstitut University of Bayreuth 95440 Bayreuth Germany
- Photon Science Deutsches Elektronen-Synchrotron 22607 Hamburg Germany
| | - Elena Bykova
- Photon Science Deutsches Elektronen-Synchrotron 22607 Hamburg Germany
| | - Marcel Thielmann
- Bayerisches Geoinstitut University of Bayreuth 95440 Bayreuth Germany
| | - Stella Chariton
- Bayerisches Geoinstitut University of Bayreuth 95440 Bayreuth Germany
| | - Georgios Aprilis
- Material Physics and Technology at Extreme Conditions Laboratory of Crystallography Universität Bayreuth 95440 Bayreuth Germany
| | - Iuliia Koemets
- Bayerisches Geoinstitut University of Bayreuth 95440 Bayreuth Germany
| | | | | | - Michael Hanfland
- ESRF-The European Synchrotron CS40220 38043 Grenoble Cedex 9 France
| | - Eiji Ohtani
- Department of Earth Science Graduate School of Science Tohoku University Sendai 980-8578 Japan
| | - Natalia Dubrovinskaia
- Material Physics and Technology at Extreme Conditions Laboratory of Crystallography Universität Bayreuth 95440 Bayreuth Germany
| | | | | |
Collapse
|
27
|
Friese A, Bauer K, Glombitza C, Ordoñez L, Ariztegui D, Heuer VB, Vuillemin A, Henny C, Nomosatryo S, Simister R, Wagner D, Bijaksana S, Vogel H, Melles M, Russell JM, Crowe SA, Kallmeyer J. Organic matter mineralization in modern and ancient ferruginous sediments. Nat Commun 2021; 12:2216. [PMID: 33850127 PMCID: PMC8044167 DOI: 10.1038/s41467-021-22453-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023] Open
Abstract
Deposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite highly abundant reactive ferric iron phases like goethite that persist throughout the sediment. Ferric iron can thus be buried over geologic timescales even in the presence of labile organic carbon. Coexistence of ferric iron with millimolar concentrations of methane further demonstrates lack of iron-dependent methane oxidation. With negligible methane oxidation, methane diffuses from the sediment into overlying waters where it can be oxidized with oxygen or escape to the atmosphere. In low-oxygen ferruginous Archaean and Proterozoic oceans, therefore, sedimentary methane production was likely favored with strong potential to influence Earth's early climate.
Collapse
Affiliation(s)
- André Friese
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Kohen Bauer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Clemens Glombitza
- ETH Zürich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, Switzerland
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Luis Ordoñez
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Daniel Ariztegui
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Sulung Nomosatryo
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Research Center for Limnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor, West Java, Indonesia
| | - Rachel Simister
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Jawa Barat, Indonesia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Martin Melles
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - James M Russell
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI, USA
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
| |
Collapse
|
28
|
Chacon-Baca E, Santos A, Sarmiento AM, Luís AT, Santisteban M, Fortes JC, Dávila JM, Diaz-Curiel JM, Grande JA. Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain. ASTROBIOLOGY 2021; 21:443-463. [PMID: 33351707 DOI: 10.1089/ast.2019.2164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.
Collapse
Affiliation(s)
- Elizabeth Chacon-Baca
- Departamento de Geología, Facultad de Ciencias de la Tierra, Universidad Autónoma de Nuevo Léon (UANL), Linares, México
| | - Ana Santos
- Department of Applied Geosciences, CCTH-Science and Technology Research Centre, University of Huelva, Huelva, Spain
- Applied Geosciences Research Group (RNM276), Departamento de Ciencias de la Tierra, Facultad de Ciencias Experimentales, Universidad de Huelva, Huelva, Spain
| | - Aguasanta Miguel Sarmiento
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Ana Teresa Luís
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- GeoBioTec Research Unit, Department of Geosciences, University of Aveiro, Aveiro, Portugal
| | - Maria Santisteban
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Juan Carlos Fortes
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - José Miguel Dávila
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Jesus M Diaz-Curiel
- Departamento de Geología, Escuela Técnica Superior de Ingenieros de Minas, Madrid, Spain
| | - Jose Antonio Grande
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| |
Collapse
|
29
|
Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria. mBio 2021; 13:e0290421. [PMID: 35100867 PMCID: PMC8805035 DOI: 10.1128/mbio.02904-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.
Collapse
|
30
|
Ward LM, Shih PM. Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer. PLoS One 2021; 16:e0239248. [PMID: 33507911 PMCID: PMC7842958 DOI: 10.1371/journal.pone.0239248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/29/2020] [Indexed: 11/19/2022] Open
Abstract
Photosynthesis-both oxygenic and more ancient anoxygenic forms-has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic "Granick hypothesis" for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.
Collapse
Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
| |
Collapse
|
31
|
Roland FAE, Borges AV, Darchambeau F, Llirós M, Descy JP, Morana C. The possible occurrence of iron-dependent anaerobic methane oxidation in an Archean Ocean analogue. Sci Rep 2021; 11:1597. [PMID: 33452366 PMCID: PMC7810693 DOI: 10.1038/s41598-021-81210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 11/24/2022] Open
Abstract
In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L-1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L-1 d-1, respectively, were put in evidence. In the Fe oxidation-reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.
Collapse
Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, Liège, Belgium.
| | | | | | - Marc Llirós
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Girona Biomedical Research Institute, Salt, Catalunya, Spain
| | | | - Cédric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| |
Collapse
|
32
|
Gupta D, Guzman MS, Bose A. Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications. ACTA ACUST UNITED AC 2020; 47:863-876. [DOI: 10.1007/s10295-020-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Abstract
Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
Collapse
Affiliation(s)
- Dinesh Gupta
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| | - Michael S Guzman
- grid.250008.f 0000 0001 2160 9702 Biosciences and Biotechnology Division Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA USA
| | - Arpita Bose
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| |
Collapse
|
33
|
Liu W, Hao J, Elzinga EJ, Piotrowiak P, Nanda V, Yee N, Falkowski PG. Anoxic photogeochemical oxidation of manganese carbonate yields manganese oxide. Proc Natl Acad Sci U S A 2020; 117:22698-22704. [PMID: 32868429 PMCID: PMC7502741 DOI: 10.1073/pnas.2002175117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The oxidation states of manganese minerals in the geological record have been interpreted as proxies for the evolution of molecular oxygen in the Archean eon. Here we report that an Archean manganese mineral, rhodochrosite (MnCO3), can be photochemically oxidized by light under anoxic, abiotic conditions. Rhodochrosite has a calculated bandgap of about 5.4 eV, corresponding to light energy centering around 230 nm. Light at that wavelength would have been present on Earth's surface in the Archean, prior to the formation of stratospheric ozone. We show experimentally that the photooxidation of rhodochrosite in suspension with light centered at 230 nm produced H2 gas and manganite (γ-MnOOH) with an apparent quantum yield of 1.37 × 10-3 moles hydrogen per moles incident photons. Our results suggest that manganese oxides could have formed abiotically on the surface in shallow waters and on continents during the Archean eon in the absence of molecular oxygen.
Collapse
Affiliation(s)
- Winnie Liu
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854
| | - Jihua Hao
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Evert J Elzinga
- Department of Earth and Environmental Sciences, Rutgers University-Newark, Newark, NJ 07102
| | - Piotr Piotrowiak
- Department of Chemistry, Rutgers University-Newark, Newark, NJ 07102
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854
| | - Nathan Yee
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854
| | - Paul G Falkowski
- Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854;
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901
| |
Collapse
|
34
|
Chernyh NA, Neukirchen S, Frolov EN, Sousa FL, Miroshnichenko ML, Merkel AY, Pimenov NV, Sorokin DY, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Lebedinsky AV, Cardoso Pereira IA, Bonch-Osmolovskaya EA. Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism. Nat Microbiol 2020; 5:1428-1438. [DOI: 10.1038/s41564-020-0776-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/16/2020] [Indexed: 02/07/2023]
|
35
|
Mantle data imply a decline of oxidizable volcanic gases could have triggered the Great Oxidation. Nat Commun 2020; 11:2774. [PMID: 32487988 PMCID: PMC7265485 DOI: 10.1038/s41467-020-16493-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 11/18/2022] Open
Abstract
Aerobic lifeforms, including humans, thrive because of abundant atmospheric O2, but for much of Earth history O2 levels were low. Even after evidence for oxygenic photosynthesis appeared, the atmosphere remained anoxic for hundreds of millions of years until the ~2.4 Ga Great Oxidation Event. The delay of atmospheric oxygenation and its timing remain poorly understood. Two recent studies reveal that the mantle gradually oxidized from the Archean onwards, leading to speculation that such oxidation enabled atmospheric oxygenation. But whether this mechanism works has not been quantitatively examined. Here, we show that these data imply that reducing Archean volcanic gases could have prevented atmospheric O2 from accumulating until ~2.5 Ga with ≥95% probability. For two decades, mantle oxidation has been dismissed as a key driver of the evolution of O2 and aerobic life. Our findings warrant a reconsideration for Earth and Earth-like exoplanets. The early Earth’s atmosphere had very low oxygen levels for hundreds of millions of years, until the 2.4 Ga Great Oxidation Event, which remains poorly understood. Here, the authors show that reducing Archean volcanic gases could have prevented atmospheric O2 from accumulating, and therefore mantle oxidation was likely very important in setting the evolution of O2 and aerobic life.
Collapse
|
36
|
Abiotic hydrogen (H 2) sources and sinks near the Mid-Ocean Ridge (MOR) with implications for the subseafloor biosphere. Proc Natl Acad Sci U S A 2020; 117:13283-13293. [PMID: 32482880 DOI: 10.1073/pnas.2002619117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Free hydrogen (H2) is a basal energy source underlying chemosynthetic activity within igneous ocean crust. In an attempt to systematically account for all H2 within young oceanic lithosphere (<10 Ma) near the Mid-Ocean Ridge (MOR), we construct a box model of this environment. Within this control volume, we assess abiotic H2 sources (∼6 × 1012 mol H2/y) and sinks (∼4 × 1012 mol H2/y) and then attribute the net difference (∼2 × 1012 mol H2/y) to microbial consumption in order to balance the H2 budget. Despite poorly constrained details and large uncertainties, our analytical framework allows us to synthesize a vast body of pertinent but currently disparate information in order to propose an initial global estimate for microbial H2 consumption within young ocean crust that is tractable and can be iteratively improved upon as new data and studies become available. Our preliminary investigation suggests that microbes beneath the MOR may be consuming a sizeable portion (at least ∼30%) of all produced H2, supporting the widely held notion that subseafloor microbes voraciously consume H2 and play a fundamental role in the geochemistry of Earth's ocean-atmosphere system.
Collapse
|
37
|
When is Chemical Disequilibrium in Earth-like Planetary Atmospheres a Biosignature versus an Anti-biosignature? Disequilibria from Dead to Living Worlds. ACTA ACUST UNITED AC 2020. [DOI: 10.3847/1538-4357/ab7b81] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
38
|
Catling DC, Zahnle KJ. The Archean atmosphere. SCIENCE ADVANCES 2020; 6:eaax1420. [PMID: 32133393 PMCID: PMC7043912 DOI: 10.1126/sciadv.aax1420] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/10/2019] [Indexed: 05/05/2023]
Abstract
The atmosphere of the Archean eon-one-third of Earth's history-is important for understanding the evolution of our planet and Earth-like exoplanets. New geological proxies combined with models constrain atmospheric composition. They imply surface O2 levels <10-6 times present, N2 levels that were similar to today or possibly a few times lower, and CO2 and CH4 levels ranging ~10 to 2500 and 102 to 104 times modern amounts, respectively. The greenhouse gas concentrations were sufficient to offset a fainter Sun. Climate moderation by the carbon cycle suggests average surface temperatures between 0° and 40°C, consistent with occasional glaciations. Isotopic mass fractionation of atmospheric xenon through the Archean until atmospheric oxygenation is best explained by drag of xenon ions by hydrogen escaping rapidly into space. These data imply that substantial loss of hydrogen oxidized the Earth. Despite these advances, detailed understanding of the coevolving solid Earth, biosphere, and atmosphere remains elusive, however.
Collapse
Affiliation(s)
- David C. Catling
- Department of Earth and Space Sciences and cross-campus Astrobiology Program, Box 351310, University of Washington, Seattle, WA 98195, USA
| | - Kevin J. Zahnle
- Space Sciences Division, NASA Ames Research Center, MS 245-3, Moffett Field, CA 94035, USA
| |
Collapse
|
39
|
Lueder U, Jørgensen BB, Kappler A, Schmidt C. Photochemistry of iron in aquatic environments. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:12-24. [PMID: 31904051 DOI: 10.1039/c9em00415g] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Light energy is a driver for many biogeochemical element cycles in aquatic systems. The sunlight-induced photochemical reduction of ferric iron (Fe(iii) photoreduction) to ferrous iron (Fe(ii)) by either direct ligand-to-metal charge transfer or by photochemically produced radicals can be an important source of dissolved Feaq2+ in aqueous and sedimentary environments. Reactive oxygen species (ROS) are formed by a variety of light-dependent reactions. Those ROS can oxidize Fe(ii) or reduce Fe(iii), and due to their high reactivity they are key oxidants in aquatic systems where they influence many other biogeochemical cycles. In oxic waters with circumneutral pH, the produced Fe(ii) reaches nanomolar concentrations and serves as a nutrient, whereas in acidic waters, freshwater and marine sediments, which are rich in Fe(ii), the photochemically formed Fe(ii) can reach concentrations of up to 100 micromolar and be used as additional electron donor for acidophilic aerobic, microaerophilic, phototrophic and, if nitrate is present, for nitrate-reducing Fe(ii)-oxidizing bacteria. Therefore, Fe(iii) photoreduction may not only control the primary productivity in the oceans but has a tremendous impact on Fe cycling in the littoral zone of freshwater and marine environments. In this review, we summarize photochemical reactions involving Fe, discuss the role of ROS in Fe cycling, and highlight the importance of photoreductive processes in the environment.
Collapse
Affiliation(s)
- Ulf Lueder
- Geomicrobiology Group, Center for Applied Geoscience (ZAG), University of Tuebingen, Sigwartstrasse 10, D-72076 Tuebingen, Germany.
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Building 1540, 8000 Aarhus, Denmark
| | - Andreas Kappler
- Geomicrobiology Group, Center for Applied Geoscience (ZAG), University of Tuebingen, Sigwartstrasse 10, D-72076 Tuebingen, Germany. and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Building 1540, 8000 Aarhus, Denmark
| | - Caroline Schmidt
- Geomicrobiology Group, Center for Applied Geoscience (ZAG), University of Tuebingen, Sigwartstrasse 10, D-72076 Tuebingen, Germany.
| |
Collapse
|
40
|
Gupta D, Sutherland MC, Rengasamy K, Meacham JM, Kranz RG, Bose A. Photoferrotrophs Produce a PioAB Electron Conduit for Extracellular Electron Uptake. mBio 2019; 10:e02668-19. [PMID: 31690680 PMCID: PMC6831781 DOI: 10.1128/mbio.02668-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 11/20/2022] Open
Abstract
Photoferrotrophy is a form of anoxygenic photosynthesis whereby bacteria utilize soluble or insoluble forms of ferrous iron as an electron donor to fix carbon dioxide using light energy. They can also use poised electrodes as their electron donor via phototrophic extracellular electron uptake (phototrophic EEU). The electron uptake mechanisms underlying these processes are not well understood. Using Rhodopseudomonas palustris TIE-1 as a model, we show that a single periplasmic decaheme cytochrome c, PioA, and an outer membrane porin, PioB, form a complex allowing extracellular electron uptake across the outer membrane from both soluble iron and poised electrodes. We observe that PioA undergoes postsecretory proteolysis of its N terminus to produce a shorter heme-attached PioA (holo-PioAC, where PioAC represents the C terminus of PioA), which can exist both freely in the periplasm and in a complex with PioB. The extended N-terminal peptide controls heme attachment, and its processing is required to produce wild-type levels of holo-PioAC and holo-PioACB complex. It is also conserved in PioA homologs from other phototrophs. The presence of PioAB in these organisms correlate with their ability to perform photoferrotrophy and phototrophic EEU.IMPORTANCE Some anoxygenic phototrophs use soluble iron, insoluble iron minerals (such as rust), or their proxies (poised electrodes) as electron donors for photosynthesis. However, the underlying electron uptake mechanisms are not well established. Here, we show that these phototrophs use a protein complex made of an outer membrane porin and a periplasmic decaheme cytochrome (electron transfer protein) to harvest electrons from both soluble iron and poised electrodes. This complex has two unique characteristics: (i) it lacks an extracellular cytochrome c, and (ii) the periplasmic decaheme cytochrome c undergoes proteolytic cleavage to produce a functional electron transfer protein. These characteristics are conserved in phototrophs harboring homologous proteins.
Collapse
Affiliation(s)
- Dinesh Gupta
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Molly C Sutherland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - J Mark Meacham
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri, USA
- Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Robert G Kranz
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Arpita Bose
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
41
|
Thompson KJ, Kenward PA, Bauer KW, Warchola T, Gauger T, Martinez R, Simister RL, Michiels CC, Llirós M, Reinhard CT, Kappler A, Konhauser KO, Crowe SA. Photoferrotrophy, deposition of banded iron formations, and methane production in Archean oceans. SCIENCE ADVANCES 2019; 5:eaav2869. [PMID: 31807693 PMCID: PMC6881150 DOI: 10.1126/sciadv.aav2869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Banded iron formation (BIF) deposition was the likely result of oxidation of ferrous iron in seawater by either oxygenic photosynthesis or iron-dependent anoxygenic photosynthesis-photoferrotrophy. BIF deposition, however, remains enigmatic because the photosynthetic biomass produced during iron oxidation is conspicuously absent from BIFs. We have addressed this enigma through experiments with photosynthetic bacteria and modeling of biogeochemical cycling in the Archean oceans. Our experiments reveal that, in the presence of silica, photoferrotroph cell surfaces repel iron (oxyhydr)oxides. In silica-rich Precambrian seawater, this repulsion would separate biomass from ferric iron and would lead to large-scale deposition of BIFs lean in organic matter. Excess biomass not deposited with BIF would have deposited in coastal sediments, formed organic-rich shales, and fueled microbial methanogenesis. As a result, the deposition of BIFs by photoferrotrophs would have contributed fluxes of methane to the atmosphere and thus helped to stabilize Earth's climate under a dim early Sun.
Collapse
Affiliation(s)
- Katharine J. Thompson
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul A. Kenward
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kohen W. Bauer
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tyler Warchola
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Tina Gauger
- Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Raul Martinez
- Institut für Geo- und Umweltnaturwissenschaften, Albert-Ludwigs-Universität, Mineralogie-Geochemie, 79104 Freiburg, Germany
| | - Rachel L. Simister
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Céline C. Michiels
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc Llirós
- Department of Genetics and Microbiology, BioSciences Faculty, Universitat Autònoma de Barcelona, Catalunya, Spain
| | | | - Andreas Kappler
- Center for Applied Geosciences, University of Tuebingen, 72076 Tuebingen, Germany
| | - Kurt O. Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Sean A. Crowe
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
42
|
Van Treuren W, Dodd D. Microbial Contribution to the Human Metabolome: Implications for Health and Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2019; 15:345-369. [PMID: 31622559 DOI: 10.1146/annurev-pathol-020117-043559] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human gastrointestinal tract is home to an incredibly dense population of microbes. These microbes employ unique strategies to capture energy in this largely anaerobic environment. In the process of breaking down dietary- and host-derived substrates, the gut microbiota produce a broad range of metabolic products that accumulate to high levels in the gut. Increasingly, studies are revealing that these chemicals impact host biology, either by acting on cells within the gastrointestinal tract or entering circulation and exerting their effects at distal sites within the body. Given the high level of functional diversity in the gut microbiome and the varied diets that we consume, the repertoire of microbiota-derived molecules within our bodies varies dramatically across individuals. Thus, the microbes in our gut and the metabolic end products they produce represent a phenotypic lever that we can potentially control to develop new therapeutics for personalized medicine. Here, we review current understanding of how microbes in the gastrointestinal tract contribute to the molecules within our gut and those that circulate within our bodies. We also highlight examples of how these molecules affect host physiology and discuss potential strategies for controlling their production to promote human health and to treat disease.
Collapse
Affiliation(s)
- William Van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA;
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA; .,Department of Pathology, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
43
|
Fakhraee M, Katsev S. Organic sulfur was integral to the Archean sulfur cycle. Nat Commun 2019; 10:4556. [PMID: 31591394 PMCID: PMC6779745 DOI: 10.1038/s41467-019-12396-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/06/2019] [Indexed: 11/09/2022] Open
Abstract
The chemistry of the Early Earth is widely inferred from the elemental and isotopic compositions of sulfidic sedimentary rocks, which are presumed to have formed globally through the reduction of seawater sulfate or locally from hydrothermally supplied sulfide. Here we argue that, in the anoxic Archean oceans, pyrite could form in the absence of ambient sulfate from organic sulfur contained within living cells. Sulfides could be produced through mineralization of reduced sulfur compounds or reduction of organic-sourced sulfite. Reactive transport modeling suggests that, for sulfate concentrations up to tens of micromolar, organic sulfur would have supported 20 to 100% of sedimentary pyrite precipitation and up to 75% of microbial sulfur reduction. The results offer an alternative explanation for the low range of δ34S in Archean sulfides, and raise a possibility that sulfate scarcity delayed the evolution of dissimilatory sulfate reduction until the initial ocean oxygenation around 2.7 Ga.
Collapse
Affiliation(s)
- Mojtaba Fakhraee
- Large Lakes Observatory, University of Minnesota Duluth, 2205 E. 5th St., Duluth, MN, 55812, USA.
| | - Sergei Katsev
- Large Lakes Observatory, University of Minnesota Duluth, 2205 E. 5th St., Duluth, MN, 55812, USA.
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN, 55812, USA.
| |
Collapse
|
44
|
Finke N, Simister RL, O'Neil AH, Nomosatryo S, Henny C, MacLean LC, Canfield DE, Konhauser K, Lalonde SV, Fowle DA, Crowe SA. Mesophilic microorganisms build terrestrial mats analogous to Precambrian microbial jungles. Nat Commun 2019; 10:4323. [PMID: 31541087 PMCID: PMC6754388 DOI: 10.1038/s41467-019-11541-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 07/03/2019] [Indexed: 12/02/2022] Open
Abstract
Development of Archean paleosols and patterns of Precambrian rock weathering suggest colonization of continents by subaerial microbial mats long before evolution of land plants in the Phanerozoic Eon. Modern analogues for such mats, however, have not been reported, and possible biogeochemical roles of these mats in the past remain largely conceptual. We show that photosynthetic, subaerial microbial mats from Indonesia grow on mafic bedrocks at ambient temperatures and form distinct layers with features similar to Precambrian mats and paleosols. Such subaerial mats could have supported a substantial aerobic biosphere, including nitrification and methanotrophy, and promoted methane emissions and oxidative weathering under ostensibly anoxic Precambrian atmospheres. High C-turnover rates and cell abundances would have made these mats prime locations for early microbial diversification. Growth of landmass in the late Archean to early Proterozoic Eons could have reorganized biogeochemical cycles between land and sea impacting atmospheric chemistry and climate.
Collapse
Affiliation(s)
- N Finke
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Nordic center for earth evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - R L Simister
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | | | - S Nomosatryo
- Research center for Limnology, Indonesian Institute of Sciences (LIPI), Jawa Barat, Indonesia
- GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - C Henny
- Research center for Limnology, Indonesian Institute of Sciences (LIPI), Jawa Barat, Indonesia
| | | | - D E Canfield
- Nordic center for earth evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - K Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - S V Lalonde
- European Institute for Marine Studies, Technopôle Brest-Iroise, Plouzané, France
| | - D A Fowle
- Department of Geology, University of Kansas, Lawrence, KS, USA
| | - S A Crowe
- Departments of Microbiology and Immunology and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
45
|
Edgar JA. L-ascorbic acid and the evolution of multicellular eukaryotes. J Theor Biol 2019; 476:62-73. [DOI: 10.1016/j.jtbi.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/10/2019] [Accepted: 06/02/2019] [Indexed: 12/26/2022]
|
46
|
Ward LM, Shih PM. The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time. Free Radic Biol Med 2019; 140:188-199. [PMID: 30790657 DOI: 10.1016/j.freeradbiomed.2019.01.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/12/2019] [Accepted: 01/31/2019] [Indexed: 12/25/2022]
Abstract
The fixation of inorganic carbon species like CO2 to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O2 in our atmosphere-first during the Great Oxygenation Event at ∼2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O2 into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.
Collapse
Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, United States; Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| |
Collapse
|
47
|
Tosca NJ, Jiang CZ, Rasmussen B, Muhling J. Products of the iron cycle on the early Earth. Free Radic Biol Med 2019; 140:138-153. [PMID: 31071438 DOI: 10.1016/j.freeradbiomed.2019.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/18/2019] [Accepted: 05/02/2019] [Indexed: 11/30/2022]
Abstract
Traditional models for pre-GOE oceans commonly view iron as a critical link to multiple biogeochemical cycles, and an important source of electrons to primary producers. However, an accurate and detailed understanding of the ancient iron cycle has been limited by: (1) our ability to constrain primary depositional processes through observations of the ancient sedimentary rock record, and (2) a quantitative understanding of the aqueous geochemistry of ferrous iron. Recent advances in high resolution petrography and experimental geochemistry, however, have contributed to a new understanding of certain aspects of the early Fe cycle. Most importantly, high resolution petrographic studies of late Archean/early Paleoproterozoic iron formation have documented the prolific deposition of Fe(II)-silicate-rich chemical muds from a dominantly anoxic ocean. At the same time, recent experimental work has shed new light on processes likely to have controlled steady state Fe concentrations in Archean oceans. These studies suggest that spontaneous precipitation of Fe(II)-carbonate was probably rare in Archean oceans, and that Fe(II)-carbonate would have more commonly precipitated on the surfaces of suitable mineral substrates within clastic and chemical sediments, consistent with petrographic observations. In addition, although experimental investigations suggest that maximum Fe concentrations in Archean oceans would have been limited by authigenic Fe(II)-silicate production (rather than Fe(II)-carbonate), the rock record indicates that this process was rarely operative. Instead, sedimentology, stratigraphy, and geochemical modelling suggest that much of the precursor sediment to late Archean iron formation was produced as hydrothermal effluent interacted with seawater in close proximity to seafloor vents. Together, these observations help define a new topology for the ancient Fe cycle. In this view, hydrothermal effluent-seawater mixing would have strongly attenuated the flux of dissolved Fe2+ to Archean oceans, and early diagenetic siderite formation may have balanced globally averaged riverine and hydrothermal Fe2+ input fluxes. In contrast to previous models, this emerging picture of the early Fe cycle suggests that Fe played only a negligible role in supporting anoxygenic phototrophs, reinforcing the concept that electron donors were in comparatively limited supply before the advent of oxygenic photosynthesis.
Collapse
Affiliation(s)
- Nicholas J Tosca
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK.
| | - Clancy Zhijian Jiang
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, OX1 3AN, UK
| | - Birger Rasmussen
- School of Earth Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Janet Muhling
- School of Earth Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| |
Collapse
|
48
|
Ward LM, Idei A, Nakagawa M, Ueno Y, Fischer WW, McGlynn SE. Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs. Microbes Environ 2019; 34:278-292. [PMID: 31413226 PMCID: PMC6759342 DOI: 10.1264/jsme2.me19017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.
Collapse
Affiliation(s)
- Lewis M Ward
- Department of Earth and Planetary Sciences, Harvard University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Division of Geological and Planetary Sciences, California Institute of Technology
| | - Airi Idei
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Tokyo Institute of Technology.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology
| | | |
Collapse
|
49
|
Microbial communities involved in the methane cycle in the near-bottom water layer and sediments of the meromictic subarctic Lake Svetloe. Antonie van Leeuwenhoek 2019; 112:1801-1814. [PMID: 31372944 DOI: 10.1007/s10482-019-01308-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Although arctic and subarctic lakes are important sources of methane, the emission of which will increase due to the melting of permafrost, the processes related to the methane cycle in such environments are far from being comprehensively understood. Here we studied the microbial communities in the near-bottom water layer and sediments of the meromictic subarctic Lake Svetloe using high-throughput sequencing of the 16S rRNA and methyl coenzyme M reductase subunit A genes. Hydrogenotrophic methanogens of the order Methanomicrobiales were abundant, both in the water column and in sediments, while the share of acetoclastic Methanosaetaceae decreased with the depth of sediments. Members of the Methanomassiliicoccales order were absent in the water but abundant in the deep sediments. Archaea known to perform anaerobic oxidation of methane were not found. The bacterial component of the microbial community in the bottom water layer included oxygenic (Cyanobacteria) and anoxygenic (Chlorobi) phototrophs, aerobic Type I methanotrophs, methylotrophs, syntrophs, and various organotrophs. In deeper sediments the diversity of the microbial community decreased, and it became dominated by methanogenic archaea and the members of the Bathyarchaeota, Chloroflexi and Deltaproteobacteria. This study shows that the sediments of a subarctic meromictic lake contain a taxonomically and metabolically diverse community potentially capable of complete mineralization of organic matter.
Collapse
|
50
|
Ward LM, Cardona T, Holland-Moritz H. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 2019; 10:1658. [PMID: 31396180 PMCID: PMC6664022 DOI: 10.3389/fmicb.2019.01658] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 12/15/2022] Open
Abstract
Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.
Collapse
Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hannah Holland-Moritz
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| |
Collapse
|