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Pallen MJ. The dynamic history of prokaryotic phyla: discovery, diversity and division. Int J Syst Evol Microbiol 2024; 74. [PMID: 39250184 PMCID: PMC11382960 DOI: 10.1099/ijsem.0.006508] [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: 09/10/2024] Open
Abstract
Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.
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Affiliation(s)
- Mark J Pallen
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
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2
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Vosseberg J, van Hooff JJE, Köstlbacher S, Panagiotou K, Tamarit D, Ettema TJG. The emerging view on the origin and early evolution of eukaryotic cells. Nature 2024; 633:295-305. [PMID: 39261613 DOI: 10.1038/s41586-024-07677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/05/2024] [Indexed: 09/13/2024]
Abstract
The origin of the eukaryotic cell, with its compartmentalized nature and generally large size compared with bacterial and archaeal cells, represents a cornerstone event in the evolution of complex life on Earth. In a process referred to as eukaryogenesis, the eukaryotic cell is believed to have evolved between approximately 1.8 and 2.7 billion years ago from its archaeal ancestors, with a symbiosis with a bacterial (proto-mitochondrial) partner being a key event. In the tree of life, the branch separating the first from the last common ancestor of all eukaryotes is long and lacks evolutionary intermediates. As a result, the timing and driving forces of the emergence of complex eukaryotic features remain poorly understood. During the past decade, environmental and comparative genomic studies have revealed vital details about the identity and nature of the host cell and the proto-mitochondrial endosymbiont, enabling a critical reappraisal of hypotheses underlying the symbiotic origin of the eukaryotic cell. Here we outline our current understanding of the key players and events underlying the emergence of cellular complexity during the prokaryote-to-eukaryote transition and discuss potential avenues of future research that might provide new insights into the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Julian Vosseberg
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jolien J E van Hooff
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kassiani Panagiotou
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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3
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Valentin-Alvarado LE, Appler KE, De Anda V, Schoelmerich MC, West-Roberts J, Kivenson V, Crits-Christoph A, Ly L, Sachdeva R, Greening C, Savage DF, Baker BJ, Banfield JF. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nat Commun 2024; 15:6384. [PMID: 39085194 PMCID: PMC11291895 DOI: 10.1038/s41467-024-49872-z] [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: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kathryn E Appler
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Environmental Systems Sciences; ETH Zürich, Zürich, Switzerland
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexander Crits-Christoph
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Cultivarium, Watertown, MA, USA
| | - Lynn Ly
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Rasmussen AN, Tolar BB, Bargar JR, Boye K, Francis CA. Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 2024; 9:e0031424. [PMID: 38940520 PMCID: PMC11264602 DOI: 10.1128/msystems.00314-24] [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: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024] Open
Abstract
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
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Affiliation(s)
- Anna N. Rasmussen
- Department of Earth System Science, Stanford University, Stanford, California, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Bradley B. Tolar
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - John R. Bargar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin Boye
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher A. Francis
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Oceans Department, Stanford University, Stanford, California, USA
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Nakagawa S, Imachi H, Shimamura S, Yanaka S, Yagi H, Yagi-Utsumi M, Sakai H, Kato S, Ohkuma M, Kato K, Takai K. Characterization of protein glycosylation in an Asgard archaeon. BBA ADVANCES 2024; 6:100118. [PMID: 39081798 PMCID: PMC11284389 DOI: 10.1016/j.bbadva.2024.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Archaeal cells are typically enveloped by glycosylated S-layer proteins. Archaeal protein glycosylation provides valuable insights not only into their adaptation to their niches but also into their evolutionary trajectory. Notably, thermophilic Thermoproteota modify proteins with N-glycans that include two GlcNAc units at the reducing end, resembling the "core structure" preserved across eukaryotes. Recently, Asgard archaea, now classified as members of the phylum Promethearchaeota, have offered unprecedented opportunities for understanding the role of archaea in eukaryogenesis. Despite the presence of genes indicative of protein N-glycosylation in this archaeal group, these have not been experimentally investigated. Here we performed a glycoproteome analysis of the firstly isolated Asgard archaeon Promethearchaeum syntrophicum. Over 700 different proteins were identified through high-resolution LC-MS/MS analysis, however, there was no evidence of either the presence or glycosylation of putative S-layer proteins. Instead, N-glycosylation in this archaeon was primarily observed in an extracellular solute-binding protein, possibly related to chemoreception or transmembrane transport of oligopeptides. The glycan modification occurred on an asparagine residue located within the conserved N-X-S/T sequon, consistent with the pattern found in other archaea, bacteria, and eukaryotes. Unexpectedly, three structurally different N-glycans lacking the conventional core structure were identified in this archaeon, presenting unique compositions that included atypical sugars. Notably, one of these sugars was likely HexNAc modified with a threonine residue, similar to modifications previously observed in mesophilic methanogens within the Methanobacteriati. Our findings advance our understanding of Asgard archaea physiology and evolutionary dynamics.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 273-0061, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 273-0061, Japan
| | - Shigeru Shimamura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 273-0061, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Hirokazu Yagi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Hiroyuki Sakai
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Submarine Resources Research Center, JAMSTEC, Yokosuka 273-0061, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya 467-8603, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 273-0061, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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Tamarit D, Köstlbacher S, Appler KE, Panagiotou K, De Anda V, Rinke C, Baker BJ, Ettema TJG. Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode. Syst Appl Microbiol 2024; 47:126525. [PMID: 38909391 DOI: 10.1016/j.syapm.2024.126525] [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] [Received: 04/19/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024]
Abstract
Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name Asgardarchaeota lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2TS, proposed to serve as the nomenclatural type for the species Asgardarchaeum abyssiTS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that A. abyssi AB3033_2TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for Asgardarchaeota using established Thermoproteota lineages in the GTDB r207 reference tree, we establish a robust classification and propose Asgardarchaeum as the type genus for the family Asgardarchaeaceae (fam. nov)., the order Asgardarchaeales (ord. nov.), the class Asgardarchaeia (class. nov.), and the phylum Asgardarchaeota (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.
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Affiliation(s)
- Daniel Tamarit
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands; Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Kathryn E Appler
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Kassiani Panagiotou
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA; Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Christian Rinke
- Faculty of Biology, Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA; Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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Tran LT, Akıl C, Senju Y, Robinson RC. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol 2024; 7:273. [PMID: 38472392 DOI: 10.1038/s42003-024-05888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.
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Affiliation(s)
- Linh T Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
- Division of Structural Biology, University of Oxford, Oxford, England
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.
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Wenck BR, Vickerman RL, Burkhart BW, Santangelo TJ. Archaeal histone-based chromatin structures regulate transcription elongation rates. Commun Biol 2024; 7:236. [PMID: 38413771 PMCID: PMC10899632 DOI: 10.1038/s42003-024-05928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes. We demonstrate that substitution of histone residues that modify histone-DNA contacts or the three-dimensional chromatin structure result in radically altered transcription elongation rates and pausing patterns. Chromatin-barriers slow and pause RNAP, providing regulatory potential. The modest impacts of TFS on elongation rates through chromatin landscapes is correlated with TFS-dispensability from the archaeon Thermococcus kodakarensis. Our results detail the importance of distinct chromatin structures for archaeal gene expression and provide a unique perspective on the evolution of, and regulatory strategies imposed by, eukaryotic chromatin.
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Affiliation(s)
- Breanna R Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert L Vickerman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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9
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Iqbal S, Begum F, Ullah I, Jalal N, Shaw P. Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities. Crit Rev Microbiol 2024:1-21. [PMID: 38385313 DOI: 10.1080/1040841x.2024.2319669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.
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Affiliation(s)
- Sajid Iqbal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, China
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ihsan Ullah
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Nasir Jalal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
| | - Peter Shaw
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
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10
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Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [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: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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11
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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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12
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Carlton JD, Langwig MV, Gong X, Aguilar-Pine EJ, Vázquez-Rosas-Landa M, Seitz KW, Baker BJ, De Anda V. Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles. ISME COMMUNICATIONS 2023; 3:64. [PMID: 37355707 PMCID: PMC10290634 DOI: 10.1038/s43705-023-00269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.
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Affiliation(s)
- John D Carlton
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Xianzhe Gong
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Emily J Aguilar-Pine
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mirna Vázquez-Rosas-Landa
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Unidad Académica de Ecologia y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Kiley W Seitz
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- EMBL Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
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13
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Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li WJ, Hua ZS, Chen LX, Banfield JF, John ES, Reysenbach AL, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 2023; 618:992-999. [PMID: 37316666 PMCID: PMC10307638 DOI: 10.1038/s41586-023-06186-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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Affiliation(s)
- Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology, Lund University, Lund, Sweden
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - William H Lewis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Felix Homa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan Lombard
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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14
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Oren A, Göker M. Candidatus List. Lists of names of prokaryotic Candidatus phyla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159402 DOI: 10.1099/ijsem.0.005821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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15
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Wells M, Kim M, Akob DM, Basu P, Stolz JF. Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles. Microbiol Spectr 2023; 11:e0414522. [PMID: 36951557 PMCID: PMC10100899 DOI: 10.1128/spectrum.04145-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.
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Affiliation(s)
- Michael Wells
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Denise M. Akob
- United States Geological Survey, Geology, Energy, and Minerals Science Center, Reston, Virginia, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana, USA
| | - John F. Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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16
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Ponlachantra K, Suginta W, Robinson RC, Kitaoku Y. AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea. Bioessays 2023; 45:e2200119. [PMID: 36461738 DOI: 10.1002/bies.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.
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Affiliation(s)
- Khongpon Ponlachantra
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
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17
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Rodrigues-Oliveira T, Wollweber F, Ponce-Toledo RI, Xu J, Rittmann SKMR, Klingl A, Pilhofer M, Schleper C. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 2023; 613:332-339. [PMID: 36544020 PMCID: PMC9834061 DOI: 10.1038/s41586-022-05550-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.
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Affiliation(s)
- Thiago Rodrigues-Oliveira
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Florian Wollweber
- Institute of Molecular Biology & Biophysics, ETH Zürich, Zürich, Switzerland
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Jingwei Xu
- Institute of Molecular Biology & Biophysics, ETH Zürich, Zürich, Switzerland
| | - Simon K-M R Rittmann
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Andreas Klingl
- Plant Development & Electron Microscopy, Biocenter, Ludwig-Maximilans-Universität München, Planegg-Martinsried, Germany
| | - Martin Pilhofer
- Institute of Molecular Biology & Biophysics, ETH Zürich, Zürich, Switzerland.
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria.
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18
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Spang A. Is an archaeon the ancestor of eukaryotes? Environ Microbiol 2022; 25:775-779. [PMID: 36562617 DOI: 10.1111/1462-2920.16323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, AB Den Burg, The Netherlands.,Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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19
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Zhou Z, Liu Y, Anantharaman K, Li M. The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis. MLIFE 2022; 1:374-381. [PMID: 38818484 PMCID: PMC10989744 DOI: 10.1002/mlf2.12048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/13/2022] [Accepted: 11/13/2022] [Indexed: 06/01/2024]
Abstract
The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.
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Affiliation(s)
- Zhichao Zhou
- Department of BacteriologyUniversity of Wisconsin–MadisonMadisonWisconsinUSA
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | | | - Meng Li
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
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20
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Brinkmeier J, Coelho S, de Massy B, Bourbon HM. Evolution and Diversity of the TopoVI and TopoVI-like Subunits With Extensive Divergence of the TOPOVIBL subunit. Mol Biol Evol 2022; 39:msac227. [PMID: 36256608 PMCID: PMC9665070 DOI: 10.1093/molbev/msac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identified in some eukaryotes, and a global view is lacking to understand its evolutionary pattern. In addition, in eukaryotes, the two TopoVI subunits (TopoVIA and TopoVIB) have been duplicated and have evolved to give rise to Spo11 and TopoVIBL, forming TopoVI-like (TopoVIL), a complex essential for generating DNA breaks that initiate homologous recombination during meiosis. TopoVIL is essential for sexual reproduction. How the TopoVI subunits have evolved to ensure this meiotic function is unclear. Here, we investigated the phylogenetic conservation of TopoVI and TopoVIL. We demonstrate that BIN4 and RHL1, potentially interacting with TopoVIB, have co-evolved with TopoVI. Based on model structures, this observation supports the hypothesis for a role of TopoVI in decatenation of replicated chromatids and predicts that in eukaryotes the TopoVI catalytic complex includes BIN4 and RHL1. For TopoVIL, the phylogenetic analysis of Spo11, which is highly conserved among Eukarya, highlighted a eukaryal-specific N-terminal domain that may be important for its regulation. Conversely, TopoVIBL was poorly conserved, giving rise to ATP hydrolysis-mutated or -truncated protein variants, or was undetected in some species. This remarkable plasticity of TopoVIBL provides important information for the activity and function of TopoVIL during meiosis.
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Affiliation(s)
- Julia Brinkmeier
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Susana Coelho
- Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier 34396, France
| | - Henri-Marc Bourbon
- Centre de Biologie Intégrative, CNRS, Université de Toulouse, Toulouse 31400, France
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21
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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22
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Medvedeva S, Sun J, Yutin N, Koonin EV, Nunoura T, Rinke C, Krupovic M. Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nat Microbiol 2022; 7:962-973. [PMID: 35760839 PMCID: PMC11165672 DOI: 10.1038/s41564-022-01144-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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23
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Abstract
Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.
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24
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere. Genome Biol Evol 2022; 14:evac034. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Courtney W Stairs
- Department of Biology, Microbiology research group, Lund University, Lund, Sweden
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25
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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26
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Xie R, Wang Y, Huang D, Hou J, Li L, Hu H, Zhao X, Wang F. Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. SCIENCE CHINA. LIFE SCIENCES 2022; 65:818-829. [PMID: 34378142 DOI: 10.1007/s11427-021-1969-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.
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Affiliation(s)
- Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haining Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoxiao Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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27
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Da Cunha V, Gaïa M, Forterre P. The expanding Asgard archaea and their elusive relationships with Eukarya. MLIFE 2022; 1:3-12. [PMID: 38818326 PMCID: PMC10989751 DOI: 10.1002/mlf2.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 06/01/2024]
Abstract
The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.
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Affiliation(s)
- Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Morgan Gaïa
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRSUniv. Evry, Université Paris‐SaclayEvryFrance
| | - Patrick Forterre
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
- Département de Microbiologie, Institut PasteurParisFrance
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28
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Liu H, Hu Z, Zhou M, Zhang H, Zhang X, Yue Y, Yao X, Wang J, Xi C, Zheng P, Xu X, Hu B. PM 2.5 drives bacterial functions for carbon, nitrogen, and sulfur cycles in the atmosphere. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118715. [PMID: 34933062 DOI: 10.1016/j.envpol.2021.118715] [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: 10/10/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Airborne bacteria may absorb the substance from the atmospheric particles and play a role in biogeochemical cycling. However, these studies focused on a few culturable bacteria and the samples were usually collected from one site. The metabolic potential of a majority of airborne bacteria on a regional scale and their driving factors remain unknown. In this study, we collected particulates with aerodynamic diameter ≤2.5 μm (PM2.5) from 8 cities that represent different regions across China and analyzed the samples via high-throughput sequencing of 16S rRNA genes, quantitative polymerase chain reaction (qPCR) analysis, and functional database prediction. Based on the FAPROTAX database, 326 (80.69%), 191 (47.28%) and 45 (11.14%) bacterial genera are possible to conduct the pathways of carbon, nitrogen, and sulfur cycles, respectively. The pathway analysis indicated that airborne bacteria may lead to the decrease in organic carbon while the increase in ammonium and sulfate in PM2.5 samples, all of which are the important components of PM2.5. Among the 19 environmental factors studied including air pollutants, meteorological factors, and geographical conditions, PM2.5 concentration manifested the strongest correlations with the functional genes for the transformation of ammonium and sulfate. Moreover, the PM2.5 concentration rather than the sampling site will drive the distribution of functional genera. Thus, a bi-directional relationship between PM2.5 and bacterial metabolism is suggested. Our findings shed light on the potential bacterial pathway for the biogeochemical cycling in the atmosphere and the important role of PM2.5, offering a new perspective for atmospheric ecology and pollution control.
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Affiliation(s)
- Huan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; School of Civil Engineering, Chongqing University, Chongqing, 400044, China
| | - Zhichao Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Ping Zheng
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Xu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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29
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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30
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Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ. Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 2022; 7:200-212. [PMID: 35027677 PMCID: PMC8813620 DOI: 10.1038/s41564-021-01039-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022]
Abstract
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.
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Affiliation(s)
- Fabai Wu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alon Philosof
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Aditi Narayanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Igor A Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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31
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Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, " Candidatus Sysuiplasmatales". Appl Environ Microbiol 2021; 87:e0106521. [PMID: 34524897 DOI: 10.1128/aem.01065-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order ("Candidatus Sysuiplasmatales") in the class Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea, which typically show obligately anaerobic metabolisms. Notably, "Ca. Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders Methanomassiliicoccales and "Candidatus Gimiplasmatales," "Ca. Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that "Ca. Sysuiplasmatales," the closely related orders Methanomassiliicoccales and "Ca. Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H4F Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. IMPORTANCE A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales, and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, "Ca. Sysuiplasmatales," within Thermoplasmata in extremely acidic mine environments. "Ca. Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between "Ca. Sysuiplasmatales" and closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.
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Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. THE ISME JOURNAL 2021; 15:3005-3018. [PMID: 33953361 PMCID: PMC8443620 DOI: 10.1038/s41396-021-00935-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/07/2021] [Accepted: 02/10/2021] [Indexed: 02/03/2023]
Abstract
Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Peng-Fei Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, PR China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, PR China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China.
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Tahon G, Patricia Geesink, Ettema TJG. Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. Annu Rev Microbiol 2021; 75:359-381. [PMID: 34351791 DOI: 10.1146/annurev-micro-040921-050212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
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A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol 2021; 6:946-959. [PMID: 34155373 DOI: 10.1038/s41564-021-00918-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.
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Osman JR, Viedma P, Mendoza J, Fernandes G, DuBow MS, Cotoras D. Prokaryotic diversity and biogeochemical characteristics of field living and laboratory cultured stromatolites from the hypersaline Laguna Interna, Salar de Atacama (Chile). Extremophiles 2021; 25:327-342. [PMID: 33993356 DOI: 10.1007/s00792-021-01232-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Stromatolites are organo-sedimentary structures found principally in seas and saline lakes that contain sheets of sediments and minerals formed by layers of microbial communities, which trap sediments and induce the precipitation of minerals.A living stromatolite from the alkaline Laguna Interna in the Salar de Atacama was collected and one of the fragments was deposited in an experimental aquarium for 18 months. We used Illumina sequencing of PCR-amplified V4 regions of 16S rRNA genes from total extracted DNA to identify the microbial populations. The chemical structure was studied using X-Ray Diffraction (XRD) and bench chemical methods. We found that members belonging to the Proteobacteria, Planctomycetes, Chloroflexi and Bacteroidetes phyla dominated the bacterial communities of the living and aquarium cultured samples. The potential metabolic functionality of the prokaryotic community reveals that sulfur, nitrogen, methane and carbon fixation metabolism functions are present in the samples. This study is the first to provide new insights into the prokaryotic community composition from this unusual aquatic desert site. Further studies will be helpful to obtain a better understanding of the biotic and abiotic mechanisms residing in stromatolites from Laguna Interna, as well as to have better knowledge about the formation of these biosignatures.
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Affiliation(s)
- Jorge R Osman
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile. .,Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile.
| | - Pabla Viedma
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
| | - Jorge Mendoza
- Laboratorio de Química de Suelos, Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Gustavo Fernandes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay Campus CNRS, Bâtiment 21, Avenue de la Terasse, 91190, Gif-sur-Yvette, France
| | - Davor Cotoras
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
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Knopp M, Stockhorst S, van der Giezen M, Garg SG, Gould SB. The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3. Genome Biol Evol 2021; 13:6248096. [PMID: 33892498 PMCID: PMC8220308 DOI: 10.1093/gbe/evab085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
The identification of the asgard archaea has fueled speculations regarding the nature of the archaeal host in eukaryogenesis and its level of complexity prior to endosymbiosis. Here, we analyzed the coding capacity of 150 eukaryotes, 1,000 bacteria, and 226 archaea, including the only cultured member of the asgard archaea. Clustering methods that consistently recover endosymbiotic contributions to eukaryotic genomes recover an asgard archaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that this group's diversity rivals that of all other archaea combined. The number of homologs shared exclusively between asgard archaea and eukaryotes is only 27 on average. This tiny asgard archaeal-unique contribution to the root of eukaryotic protein families questions claims that archaea evolved complexity prior to eukaryogenesis. Genomic and cellular complexity remains a eukaryote-specific feature and is best understood as the archaeal host's solution to housing an endosymbiont.
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Affiliation(s)
- Michael Knopp
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | - Simon Stockhorst
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | | | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
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Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy). Microorganisms 2021; 9:microorganisms9040859. [PMID: 33923677 PMCID: PMC8072921 DOI: 10.3390/microorganisms9040859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022] Open
Abstract
Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.
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Russum S, Lam KJK, Wong NA, Iddamsetty V, Hendargo KJ, Wang J, Dubey A, Zhang Y, Medrano-Soto A, Saier MH. Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PLoS One 2021; 16:e0247806. [PMID: 33770091 PMCID: PMC7997004 DOI: 10.1371/journal.pone.0247806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.
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Affiliation(s)
- Steven Russum
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Katie Jing Kay Lam
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Nicholas Alan Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Vasu Iddamsetty
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Kevin J. Hendargo
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Jianing Wang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Aditi Dubey
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Yichi Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Arturo Medrano-Soto
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
| | - Milton H. Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
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Yin X, Cai M, Liu Y, Zhou G, Richter-Heitmann T, Aromokeye DA, Kulkarni AC, Nimzyk R, Cullhed H, Zhou Z, Pan J, Yang Y, Gu JD, Elvert M, Li M, Friedrich MW. Subgroup level differences of physiological activities in marine Lokiarchaeota. THE ISME JOURNAL 2021; 15:848-861. [PMID: 33149207 PMCID: PMC8027215 DOI: 10.1038/s41396-020-00818-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/12/2022]
Abstract
Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.
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Affiliation(s)
- Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Guowei Zhou
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | | | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Henrik Cullhed
- International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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40
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Zhang JW, Dong HP, Hou LJ, Liu Y, Ou YF, Zheng YL, Han P, Liang X, Yin GY, Wu DM, Liu M, Li M. Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. ISME JOURNAL 2021; 15:1826-1843. [PMID: 33452484 PMCID: PMC8163825 DOI: 10.1038/s41396-020-00890-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023]
Abstract
Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.
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Affiliation(s)
- Jia-Wei Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.,School of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Guo-Yu Yin
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Dian-Ming Wu
- Key Laboratory of Geographic Information Science, Ministry of Education, 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
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
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Abstract
Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.
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Affiliation(s)
- Brett J Baker
- Department of Marine Science and Marine Science Institute, University of Texas at Austin, Port Aransas, Texas 78373, USA;
| | - Kathryn E Appler
- Department of Marine Science and Marine Science Institute, University of Texas at Austin, Port Aransas, Texas 78373, USA;
| | - Xianzhe Gong
- Department of Marine Science and Marine Science Institute, University of Texas at Austin, Port Aransas, Texas 78373, USA;
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China;
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42
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Yu X, Zhou J, Song W, Xu M, He Q, Peng Y, Tian Y, Wang C, Shu L, Wang S, Yan Q, Liu J, Tu Q, He Z. SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways. Mol Ecol Resour 2020. [DOI: 10.1111/1755-0998.13306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiaoli Yu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Jiayin Zhou
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Wen Song
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Mengzhao Xu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Qiang He
- Department of Civil and Environmental Engineering The University of Tennessee Knoxville TN USA
| | - Yisheng Peng
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems School of Life Sciences Xiamen University Xiamen China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Shanquan Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Jihua Liu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Qichao Tu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
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43
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Hu W, Pan J, Wang B, Guo J, Li M, Xu M. Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order (Candidatus Gimiplasmatales). Environ Microbiol 2020; 23:3695-3709. [PMID: 33295091 DOI: 10.1111/1462-2920.15349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023]
Abstract
Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.
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Affiliation(s)
- Wenzhe Hu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jie Pan
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Li
- Shenzhen key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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44
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Zinke LA, Evans PN, Santos-Medellín C, Schroeder AL, Parks DH, Varner RK, Rich VI, Tyson GW, Emerson JB. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environ Microbiol 2020; 23:340-357. [PMID: 33185945 DOI: 10.1111/1462-2920.15316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022]
Abstract
Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.
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Affiliation(s)
- Laura A Zinke
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | | | - Alena L Schroeder
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Donovan H Parks
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ruth K Varner
- Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.,Department of Earth Sciences, University of New Hampshire, Durham, NH, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, Qld, 4102, Australia
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA
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45
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Akıl C, Kitaoku Y, Tran LT, Liebl D, Choe H, Muengsaen D, Suginta W, Schulte A, Robinson RC. Mythical origins of the actin cytoskeleton. Curr Opin Cell Biol 2020; 68:55-63. [PMID: 33049465 DOI: 10.1016/j.ceb.2020.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
The origin of the eukaryotic cell is one of the greatest mysteries in modern biology. Eukaryotic-wide specific biological processes arose in the lost ancestors of eukaryotes. These distinctive features, such as the actin cytoskeleton, define what it is to be a eukaryote. Recent sequencing, characterization, and isolation of Asgard archaea have opened an intriguing window into the pre-eukaryotic cell. Firstly, sequencing of anaerobic sediments identified a group of uncultured organisms, Asgard archaea, which contain genes with homology to eukaryotic signature genes. Secondly, characterization of the products of these genes at the protein level demonstrated that Asgard archaea have related biological processes to eukaryotes. Finally, the isolation of an Asgard archaeon has produced a model organism in which the morphological consequences of the eukaryotic-like processes can be studied. Here, we consider the consequences for the Asgard actin cytoskeleton and for the evolution of a regulated actin system in the archaea-to-eukaryotic transition.
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Affiliation(s)
- Caner Akıl
- Institute of Molecular and Cell Biology, A∗STAR (Agency for Science, Technology and Research), Biopolis, 138673, Singapore; Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Linh T Tran
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - David Liebl
- A∗STAR Microscopy Platform, Research Support Center, A∗STAR, Biopolis 138673, Singapore
| | - Han Choe
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea
| | - Duangkamon Muengsaen
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A∗STAR (Agency for Science, Technology and Research), Biopolis, 138673, Singapore; Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
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46
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Gionfriddo CM, Wymore AM, Jones DS, Wilpiszeski RL, Lynes MM, Christensen GA, Soren A, Gilmour CC, Podar M, Elias DA. An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature. Front Microbiol 2020; 11:541554. [PMID: 33123100 PMCID: PMC7573106 DOI: 10.3389/fmicb.2020.541554] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/25/2020] [Indexed: 01/27/2023] Open
Abstract
The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broad-range primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hg-methylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Combined with high-throughput amplicon specific sequencing, the new primer set also indentified novel hgcAB sequences similar to Lentisphaerae, Bacteroidetes, Atribacteria, and candidate phyla WOR-3 and KSB1 bacteria. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature.
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Affiliation(s)
- Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ann M Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel S Jones
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Department of Earth Sciences, Minneapolis, MN, United States
| | - Regina L Wilpiszeski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mackenzie M Lynes
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Geoff A Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ally Soren
- Smithsonian Environmental Research Center, Edgewater, MD, United States
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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47
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Wenck BR, Santangelo TJ. Archaeal transcription. Transcription 2020; 11:199-210. [PMID: 33112729 PMCID: PMC7714419 DOI: 10.1080/21541264.2020.1838865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.
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Affiliation(s)
- Breanna R. Wenck
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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48
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Wong HL, MacLeod FI, White RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. MICROBIOME 2020; 8:135. [PMID: 32938503 PMCID: PMC7495880 DOI: 10.1186/s40168-020-00910-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/19/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as 'microbial dark matter' (MDM), are hypothesised to play key roles in modern microbial mats. RESULTS We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. CONCLUSIONS This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems. Video Abstract.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- RAW Molecular Systems LLC, Spokane, WA, USA
- Department of Bioinformatics and Genomics, The University of North Carolina, Charlotte, NC, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- Department of Marine Sciences, University of Connecticut, Mansfield, USA
- Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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49
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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50
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Liu H, Hu Z, Zhou M, Zhang H, Li Z, Zhang H, Hu J, Yao X, Lou L, Xi C, Zhu L, Xu X, Zheng P, Hu B. Airborne microorganisms exacerbate the formation of atmospheric ammonium and sulfate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114293. [PMID: 32208227 DOI: 10.1016/j.envpol.2020.114293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/10/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Haze pollution is inseparable from the transformation of air pollutants especially the ammonium and sulfate. Chemical and physical processes play important roles in this transformation. However, the role of microbial processes has rarely been studied. In this report, we applied the cultivation-independent metagenomic approach to study airborne microorganisms, investigating the potential microbial-catalyzed transformation of ammonium and sulfate in PM2.5 samples. Functional genes predict that airborne microorganisms have the potential to catalyze ammonium formation but not ammonium oxidation since no ammoxidation genes were identified. We also found that the frequency of sulfate-forming genes was 1.56 times of those for sulfate-reducing genes. It was speculated that microbial metabolisms in the atmosphere could contribute to the accumulation of ammonium and sulfate. With the increase of PM2.5 concentration, the frequency of functional genes and the relative abundance of genera which involved in nitrogen and sulfur metabolisms increased. That suggested air pollution was conducive to the microbial-mediated formation of ammonium and sulfate. Overall, our results provided evidence for the possible role of microbial processes in the air pollutant transformation and brought a new perspective for studying the formation of secondary air pollutants.
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Affiliation(s)
- Huan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhichao Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huihui Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zheng Li
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiajie Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liping Lou
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lizhong Zhu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Xu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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