1
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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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2
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Ding J, Liu F, Zeng J, Gu H, Zhang D, Yang X, Wu B, Shu L, He Z, Wang C. Homologous recombination and gene-specific selection co-shape the vertical nucleotide diversity of mangrove sediment microbial populations. Ecol Evol 2024; 14:e70040. [PMID: 39021733 PMCID: PMC11254452 DOI: 10.1002/ece3.70040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
Mangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high-frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0-100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome-wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045-0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non-synonymous mutation ratio between 0-20 and 20-100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene-specific selection, finally resulting in the stratified differentiation occurring between 0-20 and 20-100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems.
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Affiliation(s)
- Jijuan Ding
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Fei Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Jiaxiong Zeng
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Hang Gu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Dandan Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Xueqin Yang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Bo Wu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for BiocontrolSun Yat‐Sen UniversityGuangzhouChina
- Key Laboratory of Watershed Earth Surface Processes and Ecological SecurityZhejiang Normal UniversityJinhuaChina
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3
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Zhang CJ, Liu YR, Cha G, Liu Y, Zhou XQ, Lu Z, Pan J, Cai M, Li M. Potential for mercury methylation by Asgard archaea in mangrove sediments. THE ISME JOURNAL 2023; 17:478-485. [PMID: 36639538 PMCID: PMC9938162 DOI: 10.1038/s41396-023-01360-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Abstract
Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.
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Affiliation(s)
- Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guihong Cha
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Xin-Quan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Chemical Biology Institute, Shenzhen Bay Laboratory, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
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4
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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] [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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5
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Coleine C, Delgado-Baquerizo M. Unearthing terrestrial extreme microbiomes for searching terrestrial-like life in the Solar System. Trends Microbiol 2022; 30:1101-1115. [PMID: 35568658 DOI: 10.1016/j.tim.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023]
Abstract
The possibility of life elsewhere in the universe has fascinated humankind for ages. To the best of our knowledge, life, as we know it, is limited to planet Earth; yet current investigation suggests that life might be more common than previously thought. In this review, we explore extreme terrestrial analogue environments in the search for some notable examples of extreme organisms, including overlooked microbial groups such as viruses, fungi, and protists, associated with limits of life on Earth. This knowledge is integral to provide the foundational principles needed to predict what sort of Earth-like organisms we might find in the Solar System and beyond, and to understand the future and origins of life on Earth.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain.
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6
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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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7
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Cai M, Duan C, Zhang X, Pan J, Liu Y, Zhang C, Li M. Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1222-1234. [PMID: 34668130 DOI: 10.1007/s11427-021-1996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
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Affiliation(s)
- Mingwei Cai
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Changhai Duan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China
| | - Xinxu Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Li
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China.
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8
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Busi SB, Bourquin M, Fodelianakis S, Michoud G, Kohler TJ, Peter H, Pramateftaki P, Styllas M, Tolosano M, De Staercke V, Schön M, de Nies L, Marasco R, Daffonchio D, Ezzat L, Wilmes P, Battin TJ. Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams. Nat Commun 2022; 13:2168. [PMID: 35444202 PMCID: PMC9021309 DOI: 10.1038/s41467-022-29914-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/07/2022] [Indexed: 11/09/2022] Open
Abstract
In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.
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Affiliation(s)
- Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Massimo Bourquin
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tyler J Kohler
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michail Styllas
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Tolosano
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent De Staercke
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Martina Schön
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Leïla Ezzat
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg. .,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Tom J Battin
- River Ecosystems Laboratory, Center for Alpine and Polar Environmental Research (ALPOLE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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9
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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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10
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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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