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Hou J, Wang Y, Zhu P, Yang N, Liang L, Yu T, Niu M, Konhauser K, Woodcroft BJ, Wang F. Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment. Sci Adv 2023; 9:eadf5069. [PMID: 37406125 DOI: 10.1126/sciadv.adf5069] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth's surface environment.
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Affiliation(s)
- Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Zhu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Na Yang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kurt Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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2
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Moore KR, Daye M, Gong J, Williford K, Konhauser K, Bosak T. A review of microbial-environmental interactions recorded in Proterozoic carbonate-hosted chert. Geobiology 2023; 21:3-27. [PMID: 36268586 PMCID: PMC10092529 DOI: 10.1111/gbi.12527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The record of life during the Proterozoic is preserved by several different lithologies, but two in particular are linked both spatially and temporally: chert and carbonate. These lithologies capture a snapshot of dominantly peritidal environments during the Proterozoic. Early diagenetic chert preserves some of the most exceptional Proterozoic biosignatures in the form of microbial body fossils and mat textures. This fossiliferous and kerogenous chert formed in shallow marine environments, where chert nodules, layers, and lenses are often surrounded by and encased within carbonate deposits that themselves often contain kerogen and evidence of former microbial mats. Here, we review the record of biosignatures preserved in peritidal Proterozoic chert and chert-hosting carbonate and discuss this record in the context of experimental and environmental studies that have begun to shed light on the roles that microbes and organic compounds may have played in the formation of these deposits. Insights gained from these studies suggest temporal trends in microbial-environmental interactions and place new constraints on past environmental conditions, such as the concentration of silica in Proterozoic seawater, interactions among organic compounds and cations in seawater, and the influence of microbial physiology and biochemistry on selective preservation by silicification.
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Affiliation(s)
- Kelsey R. Moore
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Mirna Daye
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Jian Gong
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | - Kurt Konhauser
- Department of Earth and Atmospheric SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Yue T, Hu Y, Alessi DS, Konhauser K, Hao W, Sun W, Xu Z. Correction to "Mechanism of Goethite Precipitation on Magnetite and Maghemite Nanoparticles Studied by Surface Complexation/Precipitation Modeling". Langmuir 2019; 35:10676. [PMID: 31339725 DOI: 10.1021/acs.langmuir.9b01709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Tong Yue
- School of Minerals Processing and Bioengineering , Central South University , Changsha , China 410083
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta , Canada T6G 1H9
| | - Yuehua Hu
- School of Minerals Processing and Bioengineering , Central South University , Changsha , China 410083
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences , University of Alberta , Edmonton , Alberta , Canada T6G 2E3
| | - Kurt Konhauser
- Department of Earth and Atmospheric Sciences , University of Alberta , Edmonton , Alberta , Canada T6G 2E3
| | - Weiduo Hao
- Department of Earth and Atmospheric Sciences , University of Alberta , Edmonton , Alberta , Canada T6G 2E3
| | - Wei Sun
- School of Minerals Processing and Bioengineering , Central South University , Changsha , China 410083
| | - Zhenghe Xu
- Department of Chemical and Materials Engineering , University of Alberta , Edmonton , Alberta , Canada T6G 1H9
- Department of Materials Science and Engineering , Southern University of Science and Technology , Shenzhen , Guangdong 518055 , China
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Playter T, Konhauser K, Owttrim GW, Whitford DS, Warchola T, Hodgson C, Mloszewska AM, Sutherland B, Zonneveld JP, Pemberton SG, Gingras MK. Determination of the Settling Rate of Clay/Cyanobacterial Floccules. J Vis Exp 2018. [PMID: 29939174 DOI: 10.3791/57176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The mechanisms underpinning the deposition of fine-grained, organic-rich sediments are still largely debated. Specifically, the impact of the interaction of clay particles with reactive, planktonic cyanobacterial cells to the sedimentary record is under studied. This interaction is a potentially major contributor to shale depositional models. Within a lab setting, the flocculation and sedimentation rates of these materials can be examined and measured in a controlled environment. Here, we detail a protocol for measuring the sedimentation rate of cyanobacterial/clay mixtures. This methodology is demonstrated through the description of two sample experiments: the first uses kaolin (a dehydrated form of kaolinite) and Synechococcus sp. PCC 7002 (a marine coccoid cyanobacteria), and the second uses kaolin and Synechocystis sp. PCC 6803 (a freshwater coccoid cyanobacteria). Cyanobacterial cultures are mixed with varying amounts of clay within a specially designed tank apparatus optimized to allow continuous, real-time video and photographic recording. The sampling procedures are detailed as well as a post-collection protocol for precise measurement of chlorophyll a from which the concentration of cyanobacterial cells remaining in suspension can be determined. Through experimental replication, a profile is constructed that displays sedimentation rate.
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Affiliation(s)
- Tiffany Playter
- Department of Earth and Atmospheric Sciences, University of Alberta;
| | - Kurt Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta
| | | | | | - Tyler Warchola
- Department of Earth and Atmospheric Sciences, University of Alberta
| | - Cheryl Hodgson
- Department of Earth and Atmospheric Sciences, University of Alberta; Department of Earth Sciences, Simon Fraser University
| | | | - Bruce Sutherland
- Department of Earth and Atmospheric Sciences, University of Alberta
| | - J-P Zonneveld
- Department of Earth and Atmospheric Sciences, University of Alberta
| | | | - Murray K Gingras
- Department of Earth and Atmospheric Sciences, University of Alberta
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Sanchez DF, Simionovici AS, Lemelle L, Cuartero V, Mathon O, Pascarelli S, Bonnin A, Shapiro R, Konhauser K, Grolimund D, Bleuet P. 2D/3D Microanalysis by Energy Dispersive X-ray Absorption Spectroscopy Tomography. Sci Rep 2017; 7:16453. [PMID: 29184091 PMCID: PMC5705590 DOI: 10.1038/s41598-017-16345-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
X-ray spectroscopic techniques have proven to be particularly useful in elucidating the molecular and electronic structural information of chemically heterogeneous and complex micro- and nano-structured materials. However, spatially resolved chemical characterization at the micrometre scale remains a challenge. Here, we report the novel hyperspectral technique of micro Energy Dispersive X-ray Absorption Spectroscopy (μED-XAS) tomography which can resolve in both 2D and 3D the spatial distribution of chemical species through the reconstruction of XANES spectra. To document the capability of the technique in resolving chemical species, we first analyse a sample containing 2-30 μm grains of various ferrous- and ferric-iron containing minerals, including hypersthene, magnetite and hematite, distributed in a light matrix of a resin. We accurately obtain the XANES spectra at the Fe K-edge of these four standards, with spatial resolution of 3 μm. Subsequently, a sample of ~1.9 billion-year-old microfossil from the Gunflint Formation in Canada is investigated, and for the first time ever, we are able to locally identify the oxidation state of iron compounds encrusting the 5 to 10 μm microfossils. Our results highlight the potential for attaining new insights into Precambrian ecosystems and the composition of Earth's earliest life forms.
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Affiliation(s)
| | - Alexandre S Simionovici
- ISTerre, UGA, CNRS, Observatoire des Sciences de l'Univers, CS 40700, 38058, Grenoble, France
| | - Laurence Lemelle
- LGL-TPE, Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS UMR5276, F-69342, Lyon, France
| | - Vera Cuartero
- ESRF-The European Synchrotron, 71, Avenue des Martyrs, Grenoble, France
| | - Olivier Mathon
- ESRF-The European Synchrotron, 71, Avenue des Martyrs, Grenoble, France
| | - Sakura Pascarelli
- ESRF-The European Synchrotron, 71, Avenue des Martyrs, Grenoble, France
| | - Anne Bonnin
- Paul Scherrer Institut, CH-5232, Villigen PSI, Switzerland
| | - Russell Shapiro
- Geological and Environmental Sciences Department, CSU Chico, Chico, CA, USA
| | - Kurt Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Pierre Bleuet
- University Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
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Gauger T, Konhauser K, Kappler A. Protection of Nitrate-Reducing Fe(II)-Oxidizing Bacteria from UV Radiation by Biogenic Fe(III) Minerals. Astrobiology 2016; 16:301-310. [PMID: 27027418 DOI: 10.1089/ast.2015.1365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Due to the lack of an ozone layer in the Archean, ultraviolet radiation (UVR) reached early Earth's surface almost unattenuated; as a consequence, a terrestrial biosphere in the form of biological soil crusts would have been highly susceptible to lethal doses of irradiation. However, a self-produced external screen in the form of nanoparticular Fe(III) minerals could have effectively protected those early microorganisms. In this study, we use viability studies by quantifying colony-forming units (CFUs), as well as Fe(II) oxidation and nitrate reduction rates, to show that encrustation in biogenic and abiogenic Fe(III) minerals can protect a common soil bacteria such as the nitrate-reducing Fe(II)-oxidizing microorganisms Acidovorax sp. strain BoFeN1 and strain 2AN from harmful UVC radiation. Analysis of DNA damage by quantifying cyclobutane pyrimidine dimers (CPD) confirmed the protecting effect by Fe(III) minerals. This study suggests that Fe(II)-oxidizing microorganisms, as would have grown in association with mafic and ultramafic soils/outcrops, would have been able to produce their own UV screen, enabling them to live in terrestrial habitats on early Earth.
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Affiliation(s)
- Tina Gauger
- 1 Geomicrobiology, Center for Applied Geosciences, University of Tübingen , Tübingen, Germany
| | - Kurt Konhauser
- 2 Department of Earth and Atmospheric Sciences, University of Alberta , Edmonton, Canada
| | - Andreas Kappler
- 1 Geomicrobiology, Center for Applied Geosciences, University of Tübingen , Tübingen, Germany
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Kolo K, Konhauser K, Krumbein WE, Ingelgem YV, Hubin A, Claeys P. Microbial dissolution of hematite and associated cellular fossilization by reduced iron phases: a study of ancient microbe-mineral surface interactions. Astrobiology 2009; 9:777-796. [PMID: 19845448 DOI: 10.1089/ast.2008.0263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report here on magnetite- and wustite-encrusted and geometrically oriented microbial-like structures (MLS) attached to the surfaces of hematite (alpha-Fe(2)O(3)) crystals in a banded iron formation. Field emission scanning electron microscope (FE-SEM) and scanning electron microscope (SEM) imaging showed a 3-D network of MLS arranged in 1 microm x approximately 20 microm coccoidal-like chains (CLC) of various geometrical shapes: dichotomous and budding-like protrusions, parallel, intersecting, triangular, or sinusoidal. Individual spheroidal forms ( approximately 1 mum in diameter), some displaying what appears to be division, were also abundant. In addition to their size, morphology, and preferred orientations, a microbial origin of these chains and single spheroidal forms is inferred by the presence of material that resembles extracellular polymeric substances (EPS) extending from the base of the chains along the mineral surface: the attachment sites show circular dissolution pits of about 100 nm diameter. Other thin structures protruding from the CLC are reminiscent of bacterial "nanowires." We were, however, unable to find any extant cells, organic carbon, or even recover DNA from the MLS, which suggests that they, if microbial, are possibly mineralogically replaced casts or mineral encrustations of cells. It is further speculated that, given the nature of the substrate upon which the forms are attached and their preferential orientations, it seems plausible that the "original cells" may have been Fe(III)-reducing bacteria that exploited structural imperfections in the crystal lattice. Importantly, the preservation of the ancient microbial shapes in mineral casts of magnetite, wustite, or both may be an overlooked means by which cellular features in the rock record are retained.
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Affiliation(s)
- Kamal Kolo
- Earth System Science, Department Materials and Chemistry, Vrije Universiteit Brussel, Brussels, Belgium.
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Abstract
Magnetite crystals precipitated as a consequence of Fe(III) reduction by Shewanella algae BrY after 265 h incubation and 5-year anaerobic storage were investigated with transmission electron microscopy, Mössbauer spectroscopy and X-ray diffraction. The magnetite crystals were typically superparamagnetic with an approximate size of 13 nm. The lattice constants of the 265 h and 5-year crystals are 8.4164A and 8.3774A, respectively. The Mössbauer spectra indicated that the 265 h magnetite had excess Fe(II) in its crystal-chemistry (Fe(3+) (1.990)Fe(2+) (1.015)O(4)) but the 5-year magnetite was Fe(II)-deficient in stoichiometry (Fe(3+) (2.388)Fe(2+) (0.419)O(4)). Such crystal-chemical changes may be indicative of the degeneration of superparamagnetic magnetite through the aqueous oxidization of Fe(II) anaerobically, and the concomitant oxidation of the organic phases (fatty acid methyl esters) that were present during the initial formation of the magnetite. The observation of a corona structure on the aged magnetite corroborates the anaerobic oxidation of Fe(II) on the outer layers of magnetite crystals. These results suggest that there may be a possible link between the enzymatic activity of the bacteria and the stability of Fe(II)-excess magnetite, which may help explain why stable nano-magnetite grains are seldom preserved in natural environments.
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Affiliation(s)
- Y-L Li
- Department of Earth Sciences and School of Biological Sciences, The University of Hong Kong, Hong Kong.
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