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Nie C, Chen L, Zhao B, Wu Z, Zhang M, Yan Y, Li B, Xia Y. Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135074. [PMID: 38954855 DOI: 10.1016/j.jhazmat.2024.135074] [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: 01/27/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.
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Affiliation(s)
- Cailong Nie
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liming Chen
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Wu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxi Yan
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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2
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Hug LA. The ever-changing tree of life. Nat Microbiol 2024:10.1038/s41564-024-01768-w. [PMID: 39095498 DOI: 10.1038/s41564-024-01768-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Affiliation(s)
- Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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3
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Kohtz AJ, Petrosian N, Krukenberg V, Jay ZJ, Pilhofer M, Hatzenpichler R. Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature 2024:10.1038/s41586-024-07631-6. [PMID: 39048824 DOI: 10.1038/s41586-024-07631-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/30/2024] [Indexed: 07/27/2024]
Abstract
Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences1,2. For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialized group of archaea, the Euryarchaeota1. The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are also involved in methanogenesis3-6. Here we cultured Candidatus Methanosuratincola verstraetei strain LCB70, a member of the archaeal class Methanomethylicia (formerly Verstraetearchaeota) within the phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic and transcriptomic analyses demonstrated that this thermophilic archaeon grows by means of methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. verstraetei are coccoid cells with archaella and chemoreceptor arrays, and that they can form intercellular bridges connecting two to three cells with continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. verstraetei suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Nikolai Petrosian
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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4
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Shoemaker A, Maritan A, Cosar S, Nupp S, Menchaca A, Jackson T, Dang A, Baxter BK, Colman DR, Dunham EC, Boyd ES. Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah. FEMS Microbiol Ecol 2024; 100:fiae105. [PMID: 39054286 PMCID: PMC11287216 DOI: 10.1093/femsec/fiae105] [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: 05/08/2024] [Revised: 07/03/2024] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.
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Affiliation(s)
- Anna Shoemaker
- Department of Earth Sciences, Montana State University, P.O. Box 173480, Bozeman, MT 59717, United States
| | - Andrew Maritan
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Su Cosar
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Sylvia Nupp
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Ana Menchaca
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Thomas Jackson
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Aria Dang
- Department of Chemistry and Biochemistry, Montana State University, P.O. Box 173400, Bozeman, MT 59717, United States
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster University, 1840 South 1300 East, Salt Lake City, UT 84105, United States
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric C Dunham
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, United States
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Moody ERR, Álvarez-Carretero S, Mahendrarajah TA, Clark JW, Betts HC, Dombrowski N, Szánthó LL, Boyle RA, Daines S, Chen X, Lane N, Yang Z, Shields GA, Szöllősi GJ, Spang A, Pisani D, Williams TA, Lenton TM, Donoghue PCJ. The nature of the last universal common ancestor and its impact on the early Earth system. Nat Ecol Evol 2024:10.1038/s41559-024-02461-1. [PMID: 38997462 DOI: 10.1038/s41559-024-02461-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/04/2024] [Indexed: 07/14/2024]
Abstract
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA's metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09-4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49-2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
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Affiliation(s)
- Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | | | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - James W Clark
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Holly C Betts
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Lénárd L Szánthó
- Department of Biological Physics, Eötvös University, Budapest, Hungary
- MTA-ELTE 'Lendulet' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, HUN-REN Center for Ecological Research, Budapest, Hungary
| | | | - Stuart Daines
- Global Systems Institute, University of Exeter, Exeter, UK
| | - Xi Chen
- Department of Earth Sciences, University College London, London, UK
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Graham A Shields
- Department of Earth Sciences, University College London, London, UK
| | - Gergely J Szöllősi
- MTA-ELTE 'Lendulet' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, HUN-REN Center for Ecological Research, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK.
| | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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6
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Jimenez N, Norton T, Diadala G, Bell E, Valenti M, Farland LV, Mahnert N, Herbst-Kralovetz MM. Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain. BMC Med 2024; 22:283. [PMID: 38972981 PMCID: PMC11229265 DOI: 10.1186/s12916-024-03500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Chronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient's quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP. METHODS Vaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2. RESULTS Significant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺. CONCLUSIONS Vaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.
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Affiliation(s)
- Nicole Jimenez
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Taylor Norton
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Gurbeen Diadala
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
| | - Emerald Bell
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA
- University of Arizona College of Nursing, Tucson, AZ, USA
| | - Michelle Valenti
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Leslie V Farland
- UA Cancer Center, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
- Department of Obstetrics and Gynecology, College of Medicine Tucson, University of Arizona, Tucson, AZ, USA
| | - Nichole Mahnert
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Obstetrics and Gynecology, Banner University Medical Center Phoenix, Phoenix, AZ, USA
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Building ABC-1, Lab 331E, 425 N. 5 St, Phoenix, AZ, 85004, USA.
- UA Cancer Center, University of Arizona, Tucson, AZ, USA.
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7
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Imachi H, Nobu MK, Kato S, Takaki Y, Miyazaki M, Miyata M, Ogawara M, Saito Y, Sakai S, Tahara YO, Takano Y, Tasumi E, Uematsu K, Yoshimura T, Itoh T, Ohkuma M, Takai K. Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov. Int J Syst Evol Microbiol 2024; 74:006435. [PMID: 38967634 PMCID: PMC11316595 DOI: 10.1099/ijsem.0.006435] [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: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1T, was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1T and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1T grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1T showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×106 16S rRNA gene copies ml-1. MK-D1T had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LTT (76.09 %) and Methanothermobacter tenebrarum RMAST (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1T (JCM 39240T and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Masaru K. Nobu
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
- Submarine Resources Research Center, JAMSTEC, Yokosuka, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | | | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Katsuyuki Uematsu
- Department of Marine and Earth Sciences, Marine Work Japan, Yokosuka, Japan
| | | | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, 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), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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8
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Sorokin DY, Merkel AY, Kolganova TV, Bale NJ, Sinninghe Damsté JS. Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria. Syst Appl Microbiol 2024; 47:126519. [PMID: 38759530 DOI: 10.1016/j.syapm.2024.126519] [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: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The genus Natronospira is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, N. proteinivora, the isolates are extremely salt-tolerant obligate alkaliphiles. However, N. proteinivora was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus Natronospira as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (Natronospiraceae) and order (Natronospirales) within the class Gammaproteobacteria. On the basis of distinct phenotypic and genomic properties, strain AB-CW1T (JCM 335396 = UQM 41579) is proposed to be classified as Natronospira elongata sp. nov., and AB-CW4T (JCM 335397 = UQM 41580) as Natronospira bacteriovora sp. nov.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, TU Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana V Kolganova
- Skryabin Insitutute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
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9
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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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10
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Wilson LA, Melville JN, Pedroso MM, Krco S, Hoelzle R, Zaugg J, Southam G, Virdis B, Evans P, Supper J, Harmer JR, Tyson G, Clark A, Schenk G, Bernhardt PV. Kinetic, electrochemical and spectral characterization of bacterial and archaeal rusticyanins; unexpected stability issues and consequences for applications in biotechnology. J Inorg Biochem 2024; 256:112539. [PMID: 38593609 DOI: 10.1016/j.jinorgbio.2024.112539] [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: 01/24/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
Motivated by the ambition to establish an enzyme-driven bioleaching pathway for copper extraction, properties of the Type-1 copper protein rusticyanin from Acidithiobacillus ferrooxidans (AfR) were compared with those from an ancestral form of this enzyme (N0) and an archaeal enzyme identified in Ferroplasma acidiphilum (FaR). While both N0 and FaR show redox potentials similar to that of AfR their electron transport rates were significantly slower. The lack of a correlation between the redox potentials and electron transfer rates indicates that AfR and its associated electron transfer chain evolved to specifically facilitate the efficient conversion of the energy of iron oxidation to ATP formation. In F. acidiphilum this pathway is not as efficient unless it is up-regulated by an as of yet unknown mechanism. In addition, while the electrochemical properties of AfR were consistent with previous data, previously unreported behavior was found leading to a form that is associated with a partially unfolded form of the protein. The cyclic voltammetry (CV) response of AfR immobilized onto an electrode showed limited stability, which may be connected to the presence of the partially unfolded state of this protein. Insights gained in this study may thus inform the engineering of optimized rusticyanin variants for bioleaching processes as well as enzyme-catalyzed solubilization of copper-containing ores such as chalcopyrite.
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Affiliation(s)
- Liam A Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jamie N Melville
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert Hoelzle
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Julian Zaugg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gordon Southam
- School of the Environment, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul Evans
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jenna Supper
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gene Tyson
- Centre for Microbiome Research, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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11
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Liu R, Cai R, Wang M, Zhang J, Zhang H, Li C, Sun C. Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent. ENVIRONMENTAL MICROBIOME 2024; 19:43. [PMID: 38909236 PMCID: PMC11193907 DOI: 10.1186/s40793-024-00585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.
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Affiliation(s)
- Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jing Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaolun Li
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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12
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Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [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: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
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Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
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13
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Di Cesare A, Sathicq MB, Sbaffi T, Sabatino R, Manca D, Breider F, Coudret S, Pinnell LJ, Turner JW, Corno G. Parity in bacterial communities and resistomes: Microplastic and natural organic particles in the Tyrrhenian Sea. MARINE POLLUTION BULLETIN 2024; 203:116495. [PMID: 38759465 DOI: 10.1016/j.marpolbul.2024.116495] [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: 09/28/2023] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/19/2024]
Abstract
Petroleum-based microplastic particles (MPs) are carriers of antimicrobial resistance genes (ARGs) in aquatic environments, influencing the selection and spread of antimicrobial resistance. This research characterized MP and natural organic particle (NOP) bacterial communities and resistomes in the Tyrrhenian Sea, a region impacted by plastic pollution and climate change. MP and NOP bacterial communities were similar but different from the free-living planktonic communities. Likewise, MP and NOP ARG abundances were similar but different (higher) from the planktonic communities. MP and NOP metagenome-assembled genomes contained ARGs associated with mobile genetic elements and exhibited co-occurrence with metal resistance genes. Overall, these findings show that MPs and NOPs harbor potential pathogenic and antimicrobial resistant bacteria, which can aid in the spread of antimicrobial resistance. Further, petroleum-based MPs do not represent novel ecological niches for allochthonous bacteria; rather, they synergize with NOPs, collectively facilitating the spread of antimicrobial resistance in marine ecosystems.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Maria Belen Sathicq
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) CONICET-UNLP, Bv. 120 y 62 n1437, La Plata, Buenos Aires, Argentina
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Dario Manca
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Florian Breider
- Ecole Polytechnique Fédérale de Lausanne EPFL, Central Environmental Laboratory, IIE, ENAC, Station 2, CH-1015 Lausanne, Switzerland
| | - Sylvain Coudret
- Ecole Polytechnique Fédérale de Lausanne EPFL, Central Environmental Laboratory, IIE, ENAC, Station 2, CH-1015 Lausanne, Switzerland
| | - Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, Canyon, TX, USA
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, USA
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy.
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14
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [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: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - 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, 230026, China.
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15
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Li J, Guo W, Wang J, Feng X, Lin Q, Zheng Y, Zhang F, Mi Y, Zhu X, Jiang E, Xiao Z, Wang J, Feng S. Strong Homology Between Colonizing and Bloodstream Carbapenem-Resistant Acinetobacter Spp.: Implications for Empiric Antibiotic Therapy in Hematological Patients. Infect Drug Resist 2024; 17:1827-1838. [PMID: 38741942 PMCID: PMC11090193 DOI: 10.2147/idr.s458427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
Objective This study aimed to assess the impact of colonization status on the outcomes of Acinetobacter spp. bloodstream infection (BSI) and investigate the homology and within-host evolution between colonizing and bloodstream carbapenem-resistant Acinetobacter spp. (CRA) to inform antibiotic therapeutic decisions. Methods We analyzed clinical outcomes of 46 hematological patients with Acinetobacter spp. BSI and performed whole-genome sequencing on the remaining CRA isolates. Results Among the patients, 39.1% (n=18) had prior Acinetobacter spp. colonization. Colonized patients had higher rates of polymicrobial BSI (50.0% vs 21.4%, P=0.044) and CRA BSI (72.2% vs 17.9%, P<0.001), resulting in elevated inflammatory markers and increased 30-day mortality. Each of the eight pairs of the remaining respiratory colonizing and bloodstream CRA strains belonged to the same genomospecies. Each pair exhibited definitive agreement in at least 21 of the 22 most representative antibiotic susceptibility tests. The minimum spanning tree based on multilocus sequence typing (MLST) and phylogenetic trees based on MLST and single nucleotide polymorphism (SNP) all indicated that each pair shared the same minimum branch. Very few non-synonymous SNPs in genic regions were identified during the transition from respiratory colonization to bloodstream infection, with minimal changes in virulence genes. Homology analysis suggested that CRA BSI originated from colonizing isolates in the respiratory tract. Conclusion Strict infection control measures are needed to manage Acinetobacter spp. colonisation in hematological patients. Appropriate empirical therapy can be administered for suspected CRA BSI based on the antimicrobial minimum inhibitory concentration of CRA colonising the respiratory tract.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Wenjing Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Jieru Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Xiaomeng Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Qingsong Lin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Yizhou Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Fengkui Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Yingchang Mi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
| | - Sizhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People’s Republic of China
- Tianjin Institutes of Health Science, Tianjin, 301600, People’s Republic of China
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Mukhopadhyay B. A reminder-peptidoglycan cell walls indeed occur in the archaeal domain, specifically in the members of Methanobacteria and Methanopyri classes. Front Microbiol 2024; 15:1329047. [PMID: 38784805 PMCID: PMC11111885 DOI: 10.3389/fmicb.2024.1329047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024] Open
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17
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Tian Q, Zhang P, Zhai Y, Wang Y, Zou Q. Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data. Genome Biol Evol 2024; 16:evae102. [PMID: 38748485 PMCID: PMC11135637 DOI: 10.1093/gbe/evae102] [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] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and analyzing the deluge of sequencing data for precise taxonomic classification remains a formidable challenge. Existing classification approaches primarily fall into two categories, database-based methods and machine learning methods, each presenting its own set of challenges and advantages. On this basis, the aim of our study was to conduct a comparative analysis between these two methods while also investigating the merits of integrating multiple database-based methods. Through an in-depth comparative study, we evaluated the performance of both methodological categories in taxonomic classification by utilizing simulated data sets. Our analysis revealed that database-based methods excel in classification accuracy when backed by a rich and comprehensive reference database. Conversely, while machine learning methods show superior performance in scenarios where reference sequences are sparse or lacking, they generally show inferior performance compared with database methods under most conditions. Moreover, our study confirms that integrating multiple database-based methods does, in fact, enhance classification accuracy. These findings shed new light on the taxonomic classification of high-throughput sequencing data and bear substantial implications for the future development of computational biology. For those interested in further exploring our methods, the source code of this study is publicly available on https://github.com/LoadStar822/Genome-Classifier-Performance-Evaluator. Additionally, a dedicated webpage showcasing our collected database, data sets, and various classification software can be found at http://lab.malab.cn/~tqz/project/taxonomic/.
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Affiliation(s)
- Qinzhong Tian
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Pinglu Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Yixiao Zhai
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
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18
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Boden JS, Zhong J, Anderson RE, Stüeken EE. Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics. Nat Commun 2024; 15:3703. [PMID: 38697988 PMCID: PMC11066067 DOI: 10.1038/s41467-024-47914-0] [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: 08/20/2023] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life's origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS; <1 µM) appeared around the same time or in the Mesoarchean depending on the reconstruction method. Most enzymatic pathways for metabolising reduced phosphorus emerged and expanded across the tree of life later. This includes phosphonate-catabolising CP-lyases, phosphite-oxidising pathways and hypophosphite-oxidising pathways. CP-lyases are particularly abundant in dissolved phosphate concentrations below 0.1 µM. Our results thus indicate at least local regions of declining phosphate levels through the Archean, possibly linked to phosphate-scavenging Fe(III), which may have limited productivity. However, reduced phosphorus species did not become widely used until after the Paleoproterozoic Great Oxidation Event (2.3 Ga), possibly linked to expansion of the biosphere at that time.
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Affiliation(s)
- Joanne S Boden
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom.
| | - Juntao Zhong
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Rika E Anderson
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, Bute Building, Queen's terrace, St. Andrews, Fife, United Kingdom
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19
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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [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: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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20
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Zhou Y, Yan A, Yang J, He W, Guo S, Li Y, Wu J, Dai Y, Pan X, Cui D, Pereira O, Teng W, Bi R, Chen S, Fan L, Wang P, Liao Y, Qin W, Sui SF, Zhu Y, Zhang C, Liu Z. Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans. Front Microbiol 2024; 15:1367658. [PMID: 38737410 PMCID: PMC11082331 DOI: 10.3389/fmicb.2024.1367658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions. Methods In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria. Results and Discussion Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.
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Affiliation(s)
- Yangkai Zhou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - An Yan
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jiawen Yang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shuai Guo
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yifan Li
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jing Wu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yanchao Dai
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Xijiang Pan
- Shanghai NanoPort, Thermo Fisher Scientific Inc., Shanghai, China
| | - Dongyu Cui
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Olivier Pereira
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, China
| | - Wenkai Teng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ran Bi
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Peiyi Wang
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yan Liao
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Wei Qin
- School of Biological Sciences and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Sen-Fang Sui
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
- Advanced Institute for Ocean Research, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zheng Liu
- Cryo-Electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiol Spectr 2024; 12:e0359023. [PMID: 38451230 PMCID: PMC10986573 DOI: 10.1128/spectrum.03590-23] [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: 10/07/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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22
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, origin, and evolution of the ESCRT systems. mBio 2024; 15:e0033524. [PMID: 38380930 PMCID: PMC10936438 DOI: 10.1128/mbio.00335-24] [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: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.IMPORTANCEAll eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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23
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Sorokin DY, Elcheninov AG, Bale NJ, Sinninghe Damsté JS, Kublanov IV. Natronoglomus mannanivorans gen. nov., sp. nov., beta-1,4-mannan utilizing natronoarchaea from hypersaline soda lakes. Front Microbiol 2024; 15:1364606. [PMID: 38533326 PMCID: PMC10963439 DOI: 10.3389/fmicb.2024.1364606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/14/2024] [Indexed: 03/28/2024] Open
Abstract
Beta-mannans are insoluble plant polysaccharides with beta-1,4-linked mannose as the backbone. We used three forms of this polysaccharide, namely, pure mannan, glucomannan, and galactomannan, to enrich haloarchaea, which have the ability to utilize mannans for growth. Four mannan-utilizing strains obtained in pure cultures were closely related to each other on the level of the same species. Furthermore, another strain selected from the same habitats with a soluble beta-1,4-glucan (xyloglucan) was also able to grow with mannan. The phylogenomic analysis placed the isolates into a separate lineage of the new genus level within the family Natrialbaceae of the class Halobacteria. The strains are moderate alkaliphiles, extremely halophilic, and aerobic saccharolytics. In addition to the three beta-mannan forms, they can also grow with cellulose, xylan, and xyloglucan. Functional genome analysis of two representative strains demonstrated the presence of several genes coding for extracellular endo-beta-1,4-mannanase from the GH5_7 and 5_8 subfamilies and the GH26 family of glycosyl hydrolases. Furthermore, a large spectrum of genes encoding other glycoside hydrolases that were potentially involved in the hydrolysis of cellulose and xylan were also identified in the genomes. A comparative genomics analysis also showed the presence of similar endo-beta-1,4-mannanase homologs in the cellulotrophic genera Natronobiforma and Halococcoides. Based on the unique physiological properties and the results of phylogenomic analysis, the novel mannan-utilizing halolarchaea are proposed to be classified into a new genus and species Natronoglomus mannanivorans gen. nov., sp. nov. with the type strain AArc-m2/3/4 (=JCM 34861=UQM 41565).
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J. Bale
- NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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24
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Yi X, Brandt KK, Xue S, Peng J, Wang Y, Li M, Deng Y, Duan G. Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China. ENVIRONMENTAL MICROBIOME 2024; 19:13. [PMID: 38429752 PMCID: PMC10908009 DOI: 10.1186/s40793-024-00555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70-80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.
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Affiliation(s)
- Xingyun Yi
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Sino-Danish Center (SDC), 101408, Beijing, China
| | - Shudan Xue
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, 10093, Beijing, China
| | - Yifei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, Guangdong, China
| | - Ye Deng
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, 100085, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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25
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Cui HL, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR, Minegishi H, Montalvo-Rodriguez R, Oren A, Sanchez-Porro C, Ventosa A, Vreeland RH. Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 2024; 74:006290. [PMID: 38456846 PMCID: PMC10999741 DOI: 10.1099/ijsem.0.006290] [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: 12/26/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024] Open
Abstract
Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Mohammad Ali Amoozegar
- Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran
| | - Mike L. Dyall-Smith
- Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, 3010, Australia
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe, Japan
| | | | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Cristina Sanchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Russell H. Vreeland
- Eastern Shore Microbes, 15397 Merry Cat Lane, Post Office Box 216, Belle Haven, VA 23306, USA
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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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Xu S, Huang H, Chen S, Muhammad ZUA, Wei W, Xie W, Jiang H, Hou S. Recovery of 1887 metagenome-assembled genomes from the South China Sea. Sci Data 2024; 11:197. [PMID: 38351104 PMCID: PMC10864278 DOI: 10.1038/s41597-024-03050-4] [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: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
The South China Sea (SCS) is a marginal sea characterized by strong land-sea biogeochemical interactions. SCS has a distinctive landscape with a multitude of seamounts in its basin. Seamounts create "seamount effects" that influence the diversity and distribution of planktonic microorganisms in the surrounding oligotrophic waters. Although the vertical distribution and community structure of marine microorganisms have been explored in certain regions of the global ocean, there is a lack of comprehensive microbial genomic surveys for uncultured microorganisms in SCS, particularly in the seamount regions. Here, we employed a metagenomic approach to study the uncultured microbial communities sampled from the Xianbei seamount region to the North Coast waters of SCS. A total of 1887 non-redundant prokaryotic metagenome-assembled genomes (MAGs) were reconstructed, of which, 153 MAGs were classified as high-quality MAGs based on the MIMAG standards. The community structure and genomic information provided by this dataset could be used to analyze microbial distribution and metabolism in the SCS.
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Affiliation(s)
- Shuaishuai Xu
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Songze Chen
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen, 518049, China
| | - Zain Ul Arifeen Muhammad
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenya Wei
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510632, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510632, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Shengwei Hou
- Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, Origin and Evolution of the ESCRT Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579148. [PMID: 38903064 PMCID: PMC11188069 DOI: 10.1101/2024.02.06.579148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Endosomal Sorting Complexes Required for Transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold, using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The Last Archaeal Common Ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Fan L, Xu B, Chen S, Liu Y, Li F, Xie W, Prabhu A, Zou D, Wan R, Li H, Liu H, Liu Y, Kao SJ, Chen J, Zhu Y, Rinke C, Li M, Zhu M, Zhang C. Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth. PNAS NEXUS 2024; 3:pgae057. [PMID: 38380056 PMCID: PMC10877094 DOI: 10.1093/pnasnexus/pgae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
Abstract
Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.
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Affiliation(s)
- Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Bu Xu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI 96822, USA
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519082, China
| | - Apoorva Prabhu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Ru Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Haodong Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yuhang Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai 200062, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Maoyan Zhu
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
- Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
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Ghaly TM, Focardi A, Elbourne LDH, Sutcliffe B, Humphreys WF, Jaschke PR, Tetu SG, Paulsen IT. Exploring virus-host-environment interactions in a chemotrophic-based underground estuary. ENVIRONMENTAL MICROBIOME 2024; 19:9. [PMID: 38291480 PMCID: PMC10829341 DOI: 10.1186/s40793-024-00549-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions. RESULTS Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water. CONCLUSION This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such 'dark', low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels.
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Affiliation(s)
- Timothy M Ghaly
- School of Natural Sciences, Macquarie University, Sydney, Australia.
| | - Amaranta Focardi
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Liam D H Elbourne
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | | | - William F Humphreys
- School of Biological Sciences, University of Western Australia, Perth, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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31
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Wetzel S, Müller A, Kohnert E, Mehrbarzin N, Huber R, Häcker G, Kreutz C, Lederer AK, Badr MT. Longitudinal dynamics of gut bacteriome and mycobiome interactions pre- and post-visceral surgery in Crohn's disease. Front Cell Infect Microbiol 2024; 13:1275405. [PMID: 38287975 PMCID: PMC10822897 DOI: 10.3389/fcimb.2023.1275405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Alterations of the gut microbiome are involved in the pathogenesis of Crohn's disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients' outcome. Methods We report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day. Results No significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers. Conclusions Our findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.
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Affiliation(s)
- Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Müller
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roman Huber
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann-Kathrin Lederer
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of General, Visceral and Transplant Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Aufdecken gemeinsamer Prinzipien immunvermittelter Erkrankungen: von der Grundlagenwissenschaft zu neuen Therapien (IMM-PACT)-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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32
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Benito Merino D, Lipp JS, Borrel G, Boetius A, Wegener G. Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin. THE ISME JOURNAL 2024; 18:wrad004. [PMID: 38365230 PMCID: PMC10811742 DOI: 10.1093/ismejo/wrad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood-Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Straße 2, 428359, Bremen, Germany
| | - Julius S Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
| | - Guillaume Borrel
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
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Zhao D, Zhang S, Chen J, Zhao J, An P, Xiang H. Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea. THE ISME JOURNAL 2024; 18:wrad033. [PMID: 38366248 PMCID: PMC10873845 DOI: 10.1093/ismejo/wrad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 02/18/2024]
Abstract
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Sichuan Normal University, Sichuan 610068, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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34
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Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Res 2024; 52:D777-D783. [PMID: 37897342 PMCID: PMC10767986 DOI: 10.1093/nar/gkad943] [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: 08/18/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Meta'omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to data type, study or sampled microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering a wide array of microbial environments and augmented with manually-curated contextual data. Across a total metagenomic assembly of 16 Tbp, SPIRE comprises 35 billion predicted protein sequences and 1.16 million newly constructed metagenome-assembled genomes (MAGs) of medium or high quality. Beyond mapping to the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 novel species-level clusters, the majority of which are unclassified at species level using current tools. SPIRE enables taxonomic profiling of these species clusters via an updated, custom mOTUs database (https://motu-tool.org/) and includes several layers of functional annotation, as well as crosslinks to several (micro-)biological databases. The resource is accessible, searchable and browsable via http://spire.embl.de.
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Affiliation(s)
- Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Pamela Ferretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Askarbek Orakov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Oleksandr M Maistrenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Hans-Joachim Ruscheweyh
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr. 142, 69117 Heidelberg, Germany
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Thea Van Rossum
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Daniel R Mende
- Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Robert D Finn
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Bioinformatics, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
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Xie X, Deng X, Chen J, Chen L, Yuan J, Chen H, Wei C, Liu X, Qiu G. Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter. ISME COMMUNICATIONS 2024; 4:ycae049. [PMID: 38808122 PMCID: PMC11131965 DOI: 10.1093/ismeco/ycae049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024]
Abstract
Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.
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Affiliation(s)
- Xiaojing Xie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jinling Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
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Hu Y, Ma X, Li XX, Tan S, Cheng M, Hou J, Cui HL. Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern. Int J Syst Evol Microbiol 2024; 74. [PMID: 38197785 DOI: 10.1099/ijsem.0.006231] [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: 01/11/2024] Open
Abstract
Two extremely halophilic archaeal strains, GSLN9T and XZYJT29T, were isolated from the saline soil in different regions of western China. Both strains GSLN9T and XZYJT29T have two 16S rRNA genes with similarities of 95.1 and 94.8 %, respectively. Strain GSLN9T was mostly related to the genus Halomicrococcus based on 16S rRNA (showing 91.0-96.0 % identities) and rpoB' genes (showing 92.0 % identity). Strain XZYJT29T showed 92.1-97.6 % (16S rRNA gene) and 91.4-93.1 % (rpoB' gene) sequence similarities to its relatives in the genus Halosimplex, respectively. The polar lipid profile of strain GSLN9T included phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate (PGS), sulphated mannosyl glucosyl diether (S-DGD-1) and sulphated galactosyl mannosyl glucosyl diether (S-TGD-1), mostly similar to that of Halomicrococcus hydrotolerans H22T. PA, PG, PGP-Me, S-DGD-1 (S-DGD-PA), S2-DGD, S-TGD-1 and an unidentified glycolipid were detected in strain XZYJT29T; this polar lipid composition is similar to those of members of the genus Halosimplex. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between these two strains and their relatives of the genera Halomicrococcus and Halosimplex were no more than 82, 27 and 80 %, respectively, much lower than the thresholds for species demarcation. Other phenotypic characterization results indicated that strains GSLN9T and XZYJT29T can be differentiated from the current species of the genera Halomicrococcus and Halosimplex, respectively. These results revealed that strains GSLN9T (=CGMCC 1.15215T=JCM 30842T) and XZYJT29T (=CGMCC 1.15828T=JCM 31853T) represent novel species of Halomicrococcus and Halosimplex, for which the names Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov. are proposed.
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Affiliation(s)
- Yao Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue Ma
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shun Tan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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37
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McGuinness AJ, Stinson LF, Snelson M, Loughman A, Stringer A, Hannan AJ, Cowan CSM, Jama HA, Caparros-Martin JA, West ML, Wardill HR. From hype to hope: Considerations in conducting robust microbiome science. Brain Behav Immun 2024; 115:120-130. [PMID: 37806533 DOI: 10.1016/j.bbi.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/14/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome science has been one of the most exciting and rapidly evolving research fields in the past two decades. Breakthroughs in technologies including DNA sequencing have meant that the trillions of microbes (particularly bacteria) inhabiting human biological niches (particularly the gut) can be profiled and analysed in exquisite detail. This microbiome profiling has profound impacts across many fields of research, especially biomedical science, with implications for how we understand and ultimately treat a wide range of human disorders. However, like many great scientific frontiers in human history, the pioneering nature of microbiome research comes with a multitude of challenges and potential pitfalls. These include the reproducibility and robustness of microbiome science, especially in its applications to human health outcomes. In this article, we address the enormous promise of microbiome science and its many challenges, proposing constructive solutions to enhance the reproducibility and robustness of research in this nascent field. The optimisation of microbiome science spans research design, implementation and analysis, and we discuss specific aspects such as the importance of ecological principals and functionality, challenges with microbiome-modulating therapies and the consideration of confounding, alternative options for microbiome sequencing, and the potential of machine learning and computational science to advance the field. The power of microbiome science promises to revolutionise our understanding of many diseases and provide new approaches to prevention, early diagnosis, and treatment.
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Affiliation(s)
- Amelia J McGuinness
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Matthew Snelson
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia.
| | - Amy Loughman
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Andrea Stringer
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | | | - Hamdi A Jama
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia
| | | | - Madeline L West
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Hannah R Wardill
- Supportive Oncology Research Group, Precision Medicine (Cancer), South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, Adelaide, South Australia, Australia
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38
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Dragone NB, Hoffert M, Strickland MS, Fierer N. Taxonomic and genomic attributes of oligotrophic soil bacteria. ISME COMMUNICATIONS 2024; 4:ycae081. [PMID: 38988701 PMCID: PMC11234899 DOI: 10.1093/ismeco/ycae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum-from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the "slow lane." However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils.
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Affiliation(s)
- Nicholas B Dragone
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Michael Hoffert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, United States
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39
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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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40
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Trouche B, Schauberger C, Bouderka F, Auguet JC, Belser C, Poulain J, Thamdrup B, Wincker P, Arnaud-Haond S, Glud RN, Maignien L. Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments. ISME COMMUNICATIONS 2023; 3:133. [PMID: 38135695 PMCID: PMC10746724 DOI: 10.1038/s43705-023-00341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.
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Affiliation(s)
- Blandine Trouche
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280, Plouzané, France.
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark.
| | - Clemens Schauberger
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Feriel Bouderka
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280, Plouzané, France
| | | | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Évry, Université Paris-Saclay, 91057, Evry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Évry, Université Paris-Saclay, 91057, Evry, France
| | - Bo Thamdrup
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Évry, Université Paris-Saclay, 91057, Evry, France
| | | | - Ronnie N Glud
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Loïs Maignien
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280, Plouzané, France.
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, USA.
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41
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [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] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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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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O'Brien PA, Tan S, Frade PR, Robbins SJ, Engelberts JP, Bell SC, Vanwonterghem I, Miller DJ, Webster NS, Zhang G, Bourne DG. Validation of key sponge symbiont pathways using genome-centric metatranscriptomics. Environ Microbiol 2023; 25:3207-3224. [PMID: 37732569 DOI: 10.1111/1462-2920.16509] [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: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Microbiome Research, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, Tasmania, Australia
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology and Women's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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Gondhalekar R, Kempes CP, McGlynn SE. Scaling of Protein Function across the Tree of Life. Genome Biol Evol 2023; 15:evad214. [PMID: 38007693 PMCID: PMC10715193 DOI: 10.1093/gbe/evad214] [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: 03/27/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/28/2023] Open
Abstract
Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal nontrivial generalities as genomes change in size. The abundance of functional categories across genomes has previously been found to show power law scaling with respect to the total number of functional categories, suggesting that universal constraints shape genomic category abundance. Here, we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3,726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genome-encoded protein annotations increase or decrease. Furthermore, we find that scaling varies between phyletic groups at both the domain and phyla levels and is less universal than previously thought. This variability in functional scaling is not related to taxonomic phylogeny resolved at the phyla level, suggesting that differences in cell plan or physiology outweigh broad patterns of taxonomic evolution. Since genomes are maintained and replicated by the functional proteins encoded by them, these results point to functional degeneracy between taxonomic groups and unique evolutionary trajectories toward these. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Together, our results reveal unique shifts in functions across the tree of life and highlight that as genomes grow or shrink, proteins of various functions may be added or lost.
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Affiliation(s)
- Riddhi Gondhalekar
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Shawn Erin McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [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: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 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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Protasov E, Nonoh JO, Kästle Silva JM, Mies US, Hervé V, Dietrich C, Lang K, Mikulski L, Platt K, Poehlein A, Köhler-Ramm T, Miambi E, Boga HI, Feldewert C, Ngugi DK, Plarre R, Sillam-Dussès D, Šobotník J, Daniel R, Brune A. Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Front Microbiol 2023; 14:1281628. [PMID: 38033561 PMCID: PMC10684969 DOI: 10.3389/fmicb.2023.1281628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
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Affiliation(s)
- Evgenii Protasov
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - James O. Nonoh
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Joana M. Kästle Silva
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lena Mikulski
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Tim Köhler-Ramm
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Edouard Miambi
- Evolutionary Ecology Department, Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), University of Paris-Est Créteil (UPEC), Créteil, France
| | - Hamadi I. Boga
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David K. Ngugi
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), UR 4443, Université Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Li J, Feng X, Wang J, Lin Q, Zheng Y, Zhang F, Mi Y, Zhu X, Jiang E, Xiao Z, Wang J, Feng S. Acinetobacter spp. bloodstream infection in hematological patients: a 10-year single-center study. BMC Infect Dis 2023; 23:796. [PMID: 37964192 PMCID: PMC10648370 DOI: 10.1186/s12879-023-08789-6] [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: 07/19/2023] [Accepted: 11/04/2023] [Indexed: 11/16/2023] Open
Abstract
PURPOSE This study investigated the clinical and antimicrobial characteristics of Acinetobacter spp. bloodstream infection (BSI) in hematological patients. Risk factors for 30-day mortality and carbapenem-resistant Acinetobacter spp. (CRA) BSI acquisition were also identified. METHODS We reviewed forty hematological patients with Acinetobacter spp. BSI in a large Chinese blood disease hospital between 2013 and 2022. The remaining CRA isolates were subjected to whole-genome sequencing. RESULTS The 30-day mortality rate was high at 35%. Hematological patients with Acinetobacter spp. BSI often presented with severe conditions and co-infections at multiple sites. All strains were colistin-susceptible and 40.0% were CR. Multivariate analysis identified several risk factors associated with CRA BSI acquisition, including previous exposure to carbapenems within 30 days and CRA colonization. Very severe aplastic anaemia, tetracycline-resistant Acinetobacter spp. BSI, and unresolved neutropenia after infection were closely associated with 30-day mortality. Non-survivors often presented with higher median PCT and CRP levels and severe complications, such as intracranial infection, cardiac dysfunction, respiratory failure, and severe sepsis or septic shock. Our study also identified inappropriate empirical antibiotic therapy as an independent predictor of 30-day mortality (OR: 11.234, 95% CI: 1.261-20.086, P = 0.030). This study was the first to report A. oleivorans as a human pathogen, and to identify its unique oxacillinase, OXA-325. CONCLUSION An environment-originated non-pathogenic species can become pathogenic when the body's immunity is compromised. Our results also highlighted the importance of improving neutropenia after infection, treating severe organ dysfunction, and administering appropriate empirical antibiotic therapy to reduce mortality in this patient population.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xiaomeng Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jieru Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Qingsong Lin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yizhou Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Fengkui Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yingchang Mi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Sizhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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Gavriilidou A, Avcı B, Galani A, Schorn MA, Ingham CJ, Ettema TJG, Smidt H, Sipkema D. Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle. THE ISME JOURNAL 2023; 17:1808-1818. [PMID: 37587369 PMCID: PMC10579324 DOI: 10.1038/s41396-023-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 08/18/2023]
Abstract
Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| | - Burak Avcı
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Anastasia Galani
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine BV, Verenigingstraat 36, 3515GJ, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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Zadjelovic V, Wright RJ, Borsetto C, Quartey J, Cairns TN, Langille MGI, Wellington EMH, Christie-Oleza JA. Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere. MICROBIOME 2023; 11:225. [PMID: 37908022 PMCID: PMC10619285 DOI: 10.1186/s40168-023-01662-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicrobial Resistance Genes (ARG). In- and ex-situ incubations were used to characterise the riverine plastisphere taxonomically and functionally in order to determine whether antibiotics within the water influenced the ARG profiles in these microbiomes and how these compared to those on natural surfaces such as wood and their planktonic counterparts. RESULTS We show that plastics support a taxonomically distinct microbiome containing potential pathogens and ARGs. While the plastisphere was similar to those biofilms that grew on wood, they were distinct from the surrounding water microbiome. Hence, whilst potential opportunistic pathogens (i.e. Pseudomonas aeruginosa, Acinetobacter and Aeromonas) and ARG subtypes (i.e. those that confer resistance to macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents and glycopeptides) were predominant in all surface-related microbiomes, especially on weathered plastics, a completely different set of potential pathogens (i.e. Escherichia, Salmonella, Klebsiella and Streptococcus) and ARGs (i.e. aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone and fosfomycin) dominated in the planktonic compartment. Our genome-centric analysis allowed the assembly of 215 Metagenome Assembled Genomes (MAGs), linking ARGs and other virulence-related genes to their host. Interestingly, a MAG belonging to Escherichia -that clearly predominated in water- harboured more ARGs and virulence factors than any other MAG, emphasising the potential virulent nature of these pathogenic-related groups. Finally, ex-situ incubations using environmentally-relevant concentrations of antibiotics increased the prevalence of their corresponding ARGs, but different riverine compartments -including plastispheres- were affected differently by each antibiotic. CONCLUSIONS Our results provide insights into the capacity of the riverine plastisphere to harbour a distinct set of potentially pathogenic bacteria and function as a reservoir of ARGs. The environmental impact that plastics pose if they act as a reservoir for either pathogenic bacteria or ARGs is aggravated by the persistence of plastics in the environment due to their recalcitrance and buoyancy. Nevertheless, the high similarities with microbiomes growing on natural co-occurring materials and even more worrisome microbiome observed in the surrounding water highlights the urgent need to integrate the analysis of all environmental compartments when assessing risks and exposure to pathogens and ARGs in anthropogenically-impacted ecosystems. Video Abstract.
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Affiliation(s)
- Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Present address: Centro de Bioinnovación de Antofagasta (CBIA), Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, 1271155, Antofagasta, Chile.
| | - Robyn J Wright
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jeannelle Quartey
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tyler N Cairns
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Morgan G I Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | | | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Biology, University of the Balearic Islands, 07122, Palma, Spain.
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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