Literature DB >> 32201928

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation.

Mingwei Cai1,2, Yang Liu1, Xiuran Yin3,4, Zhichao Zhou1,5, Michael W Friedrich3,4, Tim Richter-Heitmann3, Rolf Nimzyk6, Ajinkya Kulkarni3, Xiaowen Wang1,2, Wenjin Li1, Jie Pan1, Yuchun Yang5, Ji-Dong Gu5, Meng Li7.   

Abstract

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

Entities:  

Keywords:  Asgard archaea; Gerdarchaeota; coastal sediment; metagenome; metatranscriptome

Mesh:

Substances:

Year:  2020        PMID: 32201928     DOI: 10.1007/s11427-020-1679-1

Source DB:  PubMed          Journal:  Sci China Life Sci        ISSN: 1674-7305            Impact factor:   6.038


  67 in total

1.  SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Authors:  Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A Gurevich; Mikhail Dvorkin; Alexander S Kulikov; Valery M Lesin; Sergey I Nikolenko; Son Pham; Andrey D Prjibelski; Alexey V Pyshkin; Alexander V Sirotkin; Nikolay Vyahhi; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner
Journal:  J Comput Biol       Date:  2012-04-16       Impact factor: 1.479

2.  Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets?

Authors:  David J Burdige
Journal:  Chem Rev       Date:  2007-01-24       Impact factor: 60.622

Review 3.  The physiology of growth arrest: uniting molecular and environmental microbiology.

Authors:  Megan Bergkessel; David W Basta; Dianne K Newman
Journal:  Nat Rev Microbiol       Date:  2016-08-11       Impact factor: 60.633

4.  Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic.

Authors:  John A Burns; Alexandros A Pittis; Eunsoo Kim
Journal:  Nat Ecol Evol       Date:  2018-02-19       Impact factor: 15.460

5.  Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.

Authors:  Jennifer F Biddle; Julius S Lipp; Mark A Lever; Karen G Lloyd; Ketil B Sørensen; Rika Anderson; Helen F Fredricks; Marcus Elvert; Timothy J Kelly; Daniel P Schrag; Mitchell L Sogin; Jean E Brenchley; Andreas Teske; Christopher H House; Kai-Uwe Hinrichs
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

6.  Prediction of signal peptides in archaea.

Authors:  P G Bagos; K D Tsirigos; S K Plessas; T D Liakopoulos; S J Hamodrakas
Journal:  Protein Eng Des Sel       Date:  2008-11-06       Impact factor: 1.650

7.  Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche.

Authors:  Paul-Adrian Bulzu; Adrian-Ştefan Andrei; Michaela M Salcher; Maliheh Mehrshad; Keiichi Inoue; Hideki Kandori; Oded Beja; Rohit Ghai; Horia L Banciu
Journal:  Nat Microbiol       Date:  2019-04-01       Impact factor: 17.745

8.  BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments.

Authors:  Alexis Criscuolo; Simonetta Gribaldo
Journal:  BMC Evol Biol       Date:  2010-07-13       Impact factor: 3.260

9.  Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes.

Authors:  Violette Da Cunha; Morgan Gaia; Daniele Gadelle; Arshan Nasir; Patrick Forterre
Journal:  PLoS Genet       Date:  2017-06-12       Impact factor: 5.917

10.  The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Authors:  Ron Caspi; Hartmut Foerster; Carol A Fulcher; Pallavi Kaipa; Markus Krummenacker; Mario Latendresse; Suzanne Paley; Seung Y Rhee; Alexander G Shearer; Christophe Tissier; Thomas C Walk; Peifen Zhang; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2007-10-27       Impact factor: 16.971

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  17 in total

1.  Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.

Authors:  Ruize Xie; Yinzhao Wang; Danyue Huang; Jialin Hou; Liuyang Li; Haining Hu; Xiaoxiao Zhao; Fengping Wang
Journal:  Sci China Life Sci       Date:  2021-08-06       Impact factor: 6.038

2.  Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.

Authors:  Sofia Medvedeva; Jiarui Sun; Natalya Yutin; Eugene V Koonin; Takuro Nunoura; Christian Rinke; Mart Krupovic
Journal:  Nat Microbiol       Date:  2022-06-27       Impact factor: 30.964

Review 3.  Asgard archaea in saline environments.

Authors:  Horia L Banciu; Ionuț M Gridan; Adrian V Zety; Andreea Baricz
Journal:  Extremophiles       Date:  2022-06-28       Impact factor: 3.035

4.  Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem.

Authors:  Mingwei Cai; Changhai Duan; Xinxu Zhang; Jie Pan; Yang Liu; Cuijing Zhang; Meng Li
Journal:  Sci China Life Sci       Date:  2021-10-14       Impact factor: 10.372

5.  Expanded diversity of Asgard archaea and their relationships with eukaryotes.

Authors:  Yang Liu; Kira S Makarova; Wen-Cong Huang; Yuri I Wolf; Anastasia N Nikolskaya; Xinxu Zhang; Mingwei Cai; Cui-Jing Zhang; Wei Xu; Zhuhua Luo; Lei Cheng; Eugene V Koonin; Meng Li
Journal:  Nature       Date:  2021-04-28       Impact factor: 49.962

6.  Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.

Authors:  Jia-Wei Zhang; Hong-Po Dong; Li-Jun Hou; Yang Liu; Ya-Fei Ou; Yan-Ling Zheng; Ping Han; Xia Liang; Guo-Yu Yin; Dian-Ming Wu; Min Liu; Meng Li
Journal:  ISME J       Date:  2021-01-15       Impact factor: 10.302

7.  High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments.

Authors:  Zhi-Feng Zhang; Yue-Ping Pan; Yue Liu; Meng Li
Journal:  Appl Environ Microbiol       Date:  2021-08-11       Impact factor: 4.792

Review 8.  Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Authors:  Anja Spang; Tara A Mahendrarajah; Pierre Offre; Courtney W Stairs
Journal:  Genome Biol Evol       Date:  2022-05-31       Impact factor: 4.065

9.  Genomic insights into versatile lifestyle of three new bacterial candidate phyla.

Authors:  Xinxu Zhang; Zongbao Liu; Wei Xu; Jie Pan; Yuhan Huang; Mingwei Cai; Zhuhua Luo; Meng Li
Journal:  Sci China Life Sci       Date:  2022-01-13       Impact factor: 10.372

10.  Subgroup level differences of physiological activities in marine Lokiarchaeota.

Authors:  Xiuran Yin; Mingwei Cai; Yang Liu; Guowei Zhou; Tim Richter-Heitmann; David A Aromokeye; Ajinkya C Kulkarni; Rolf Nimzyk; Henrik Cullhed; Zhichao Zhou; Jie Pan; Yuchun Yang; Ji-Dong Gu; Marcus Elvert; Meng Li; Michael W Friedrich
Journal:  ISME J       Date:  2020-11-04       Impact factor: 10.302

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