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Rafiq M, Hassan N, Rehman M, Hayat M, Nadeem G, Hassan F, Iqbal N, Ali H, Zada S, Kang Y, Sajjad W, Jamal M. Challenges and Approaches of Culturing the Unculturable Archaea. BIOLOGY 2023; 12:1499. [PMID: 38132325 PMCID: PMC10740628 DOI: 10.3390/biology12121499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Affiliation(s)
- Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- FF Institute (Huzhou) Co., Ltd., Huzhou 313000, China
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Maliha Rehman
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Jinan 266101, China
| | - Gullasht Nadeem
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Farwa Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Naveed Iqbal
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Sahib Zada
- Guangzhou Institute of Energy Conservation, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou, Guiyang 550025, China
- Key Laboratory of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan 23200, Pakistan
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Rapid pyritization in the presence of a sulfur/sulfate-reducing bacterial consortium. Sci Rep 2020; 10:8264. [PMID: 32427954 PMCID: PMC7237684 DOI: 10.1038/s41598-020-64990-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 04/06/2020] [Indexed: 11/15/2022] Open
Abstract
Sedimentary pyrite (FeS2) is commonly thought to be a product of microbial sulfate reduction and hence may preserve biosignatures. However, proof that microorganisms are involved in pyrite formation is still lacking as only metastable iron sulfides are usually obtained in laboratory cultures. Here we show the rapid formation of large pyrite spherules through the sulfidation of Fe(III)-phosphate (FP) in the presence of a consortium of sulfur- and sulfate-reducing bacteria (SRB), Desulfovibrio and Sulfurospirillum, enriched from ferruginous and phosphate-rich Lake Pavin water. In biomineralization experiments inoculated with this consortium, pyrite formation occurred within only 3 weeks, likely enhanced by the local enrichment of polysulfides around SRB cells. During this same time frame, abiotic reaction of FP with sulfide led to the formation of vivianite (Fe3(PO4)2·8H2O) and mackinawite (FeS) only. Our results suggest that rates of pyritization vs. vivianite formation are regulated by SRB activity at the cellular scale, which enhances phosphate release into the aqueous phase by increased efficiency of iron sulfide precipitation, and thus that these microorganisms strongly influence biological productivity and Fe, S and P cycles in the environment.
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Jacquemot P, Viennet JC, Bernard S, Le Guillou C, Rigaud B, Delbes L, Georgelin T, Jaber M. The degradation of organic compounds impacts the crystallization of clay minerals and vice versa. Sci Rep 2019; 9:20251. [PMID: 31882914 PMCID: PMC6934458 DOI: 10.1038/s41598-019-56756-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/28/2019] [Indexed: 12/03/2022] Open
Abstract
Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.
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Affiliation(s)
- Pierre Jacquemot
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
| | - Jean-Christophe Viennet
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
| | - Sylvain Bernard
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France.
| | | | | | - Ludovic Delbes
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
| | | | - Maguy Jaber
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
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Alleon J, Flannery DT, Ferralis N, Williford KH, Zhang Y, Schuessler JA, Summons RE. Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments. Sci Rep 2019; 9:16712. [PMID: 31723181 PMCID: PMC6853986 DOI: 10.1038/s41598-019-53272-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/30/2019] [Indexed: 11/27/2022] Open
Abstract
Hydrothermal and metamorphic processes could have abiotically produced organo-mineral associations displaying morphological and isotopic characteristics similar to those of fossilized microorganisms in ancient rocks, thereby leaving false-positive evidence for early life in the geological record. Recent studies revealed that geologically-induced alteration processes do not always completely obliterate all molecular information about the original organic precursors of ancient microfossils. Here, we report the molecular, geochemical, and mineralogical composition of organo-mineral associations in a chert sample from the ca. 3.47 billion-year-old (Ga) Mount Ada Basalt, in the Pilbara Craton, Western Australia. Our observations indicate that the molecular characteristics of carbonaceous matter are consistent with hydrothermally altered biological organics, although significantly distinct from that of organic microfossils discovered in a chert sample from the ca. 3.43 Ga Strelley Pool Formation in the same area. Alternatively, the presence of native metal alloys in the chert, previously believed to be unstable in such hydrothermally influenced environments, indicates strongly reducing conditions that were favorable for the abiotic formation of organic matter. Drawing definitive conclusions about the origin of most Paleoarchean organo-mineral associations therefore requires further characterization of a range of natural samples together with experimental simulations to constrain the molecular composition and geological fate of hydrothermally-generated condensed organics.
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Affiliation(s)
- Julien Alleon
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
- Now at Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland.
| | - David T Flannery
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nicola Ferralis
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kenneth H Williford
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Yong Zhang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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5
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Javaux EJ. Challenges in evidencing the earliest traces of life. Nature 2019; 572:451-460. [PMID: 31435057 DOI: 10.1038/s41586-019-1436-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 06/21/2019] [Indexed: 11/09/2022]
Abstract
Earth has been habitable for 4.3 billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4 billion years ago-and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond.
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Affiliation(s)
- Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, Department of Geology, University of Liège, Liège, Belgium.
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6
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Alleon J, Summons RE. Organic geochemical approaches to understanding early life. Free Radic Biol Med 2019; 140:103-112. [PMID: 30858060 DOI: 10.1016/j.freeradbiomed.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/02/2019] [Accepted: 03/05/2019] [Indexed: 11/25/2022]
Abstract
Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.
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Affiliation(s)
- Julien Alleon
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Le Guillou C, Bernard S, De la Pena F, Le Brech Y. XANES-Based Quantification of Carbon Functional Group Concentrations. Anal Chem 2018; 90:8379-8386. [DOI: 10.1021/acs.analchem.8b00689] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Corentin Le Guillou
- Unité Matériaux et Transformations (UMET) MR-CNRS 8207, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Sylvain Bernard
- Muséum National d’Histoire Naturelle, Sorbonne Université, CNRS UMR 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, 75005 Paris, France
| | - Francisco De la Pena
- Unité Matériaux et Transformations (UMET) MR-CNRS 8207, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Yann Le Brech
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, UMR 7274, 54001 Nancy, France
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Price A, Pearson VK, Schwenzer SP, Miot J, Olsson-Francis K. Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism. Front Microbiol 2018; 9:513. [PMID: 29616015 PMCID: PMC5869265 DOI: 10.3389/fmicb.2018.00513] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
This work considers the hypothetical viability of microbial nitrate-dependent Fe2+ oxidation (NDFO) for supporting simple life in the context of the early Mars environment. This draws on knowledge built up over several decades of remote and in situ observation, as well as recent discoveries that have shaped current understanding of early Mars. Our current understanding is that certain early martian environments fulfill several of the key requirements for microbes with NDFO metabolism. First, abundant Fe2+ has been identified on Mars and provides evidence of an accessible electron donor; evidence of anoxia suggests that abiotic Fe2+ oxidation by molecular oxygen would not have interfered and competed with microbial iron metabolism in these environments. Second, nitrate, which can be used by some iron oxidizing microorganisms as an electron acceptor, has also been confirmed in modern aeolian and ancient sediment deposits on Mars. In addition to redox substrates, reservoirs of both organic and inorganic carbon are available for biosynthesis, and geochemical evidence suggests that lacustrine systems during the hydrologically active Noachian period (4.1-3.7 Ga) match the circumneutral pH requirements of nitrate-dependent iron-oxidizing microorganisms. As well as potentially acting as a primary producer in early martian lakes and fluvial systems, the light-independent nature of NDFO suggests that such microbes could have persisted in sub-surface aquifers long after the desiccation of the surface, provided that adequate carbon and nitrates sources were prevalent. Traces of NDFO microorganisms may be preserved in the rock record by biomineralization and cellular encrustation in zones of high Fe2+ concentrations. These processes could produce morphological biosignatures, preserve distinctive Fe-isotope variation patterns, and enhance preservation of biological organic compounds. Such biosignatures could be detectable by future missions to Mars with appropriate instrumentation.
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Affiliation(s)
- Alex Price
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K. Pearson
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P. Schwenzer
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Jennyfer Miot
- CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, UMR 7590, Paris, France
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
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