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Zhang R, Liu P, Wang Y, Roberts AP, Bai J, Liu Y, Zhu K, Du Z, Chen G, Pan Y, Li J. Phylogenetics and biomineralization of a novel magnetotactic Gammaproteobacterium from a freshwater lake in Beijing, China. FEMS Microbiol Ecol 2023; 99:fiad150. [PMID: 37974050 DOI: 10.1093/femsec/fiad150] [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: 07/04/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023] Open
Abstract
Magnetotactic bacteria (MTB) have the remarkable capability of producing intracellularly membrane-enveloped magnetic nanocrystals (i.e. magnetosomes) and swimming along geomagnetic field lines. Despite more than 50 years of research, bacterial diversity and magnetosome biomineralization within MTB are relatively less known in the Gammaproteobacteria class than other groups. This is incompatible with the status of Gammaproteobacteria as the most diverse class of gram-negative bacteria with a number of ecologically important bacteria. Here, we identify a novel MTB strain YYHR-1 affiliated with the Gammaproteobacteria class of the Pseudomonadota phylum from a freshwater lake. In YYHR-1, most magnetosome crystals are organized into a long chain aligned along the cell long axis; unusually, a few small superparamagnetic crystals are located at the side of the chain, off the main chain axis. Micromagnetic simulations indicate that magnetostatic interactions among adjacent crystals within a chain reduce the Gibbs energy to enhance chain stability. Genomic analysis suggests that duplication of magnetosome gene clusters may result in off-chain magnetosomes formation. By integrating available genomic data from Gammaproteobacteria, the phylogenetic position of MTB in this class is reassigned here. Our new findings expand knowledge about MTB diversity and magnetosome biomineralization, and deepen understanding of the phylogenetics of the Gammaproteobacteria.
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Affiliation(s)
- Rongrong Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- Marine College, Shandong University, Weihai 264209, China
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqin Wang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - Jinling Bai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- Marine College, Shandong University, Weihai 264209, China
| | - Yan Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kelei Zhu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519082, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongjun Du
- Marine College, Shandong University, Weihai 264209, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai 264209, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing 100029, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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102
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Rivas-Marin E, Moyano-Palazuelo D, Henriques V, Merino E, Devos DP. Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes. Nat Commun 2023; 14:7224. [PMID: 37940686 PMCID: PMC10632474 DOI: 10.1038/s41467-023-43096-3] [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: 04/15/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023] Open
Abstract
Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
| | - David Moyano-Palazuelo
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Valentina Henriques
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
- Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, University of Lille, Lille, France.
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103
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Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Front Microbiol 2023; 14:1286626. [PMID: 38029103 PMCID: PMC10663253 DOI: 10.3389/fmicb.2023.1286626] [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: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron-sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron-sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.
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Affiliation(s)
- Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Kaustubh Amritkar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael Wolfe
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
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104
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes. Sci Rep 2023; 13:19207. [PMID: 37932283 PMCID: PMC10628120 DOI: 10.1038/s41598-023-44172-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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105
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Barak H, Fuchs N, Liddor-Naim M, Nir I, Sivan A, Kushmaro A. Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data. Front Microbiol 2023; 14:1247119. [PMID: 38029171 PMCID: PMC10656735 DOI: 10.3389/fmicb.2023.1247119] [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: 06/25/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.
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Affiliation(s)
- Hana Barak
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Naomi Fuchs
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Liddor-Naim
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Irit Nir
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alex Sivan
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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106
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Rekadwad BN, Shouche YS, Jangid K. Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis. Arch Microbiol 2023; 205:366. [PMID: 37917352 DOI: 10.1007/s00203-023-03694-7] [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: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India.
- Microbe AI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India.
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India
- Gut Microbiology Research Division, SKAN Research Trust, Bangalore, 560034, Karnataka, India
| | - Kamlesh Jangid
- Bioenergy Group, DST-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, Maharashtra, India
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Kramer AM, Thornlow B, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations. Syst Biol 2023; 72:1039-1051. [PMID: 37232476 PMCID: PMC10627557 DOI: 10.1093/sysbio/syad031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/14/2023] [Accepted: 06/22/2023] [Indexed: 05/27/2023] Open
Abstract
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold. There are currently over 14 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an "online" approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) and pseudo-ML methods may be more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger data sets. Here, we evaluate the performance of de novo and online phylogenetic approaches, as well as ML, pseudo-ML, and MP frameworks for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimization with UShER and matOptimize produces equivalent SARS-CoV-2 phylogenies to some of the most popular ML and pseudo-ML inference tools. MP optimization with UShER and matOptimize is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo inference. Our results therefore suggest that parsimony-based methods like UShER and matOptimize represent an accurate and more practical alternative to established ML implementations for large SARS-CoV-2 phylogenies and could be successfully applied to other similar data sets with particularly dense sampling and short branch lengths.
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Affiliation(s)
- Alexander M Kramer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cheng Ye
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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108
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Hassani Y, Aboudharam G, Drancourt M, Grine G. Current knowledge and clinical perspectives for a unique new phylum: Nanaorchaeota. Microbiol Res 2023; 276:127459. [PMID: 37557061 DOI: 10.1016/j.micres.2023.127459] [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: 09/23/2022] [Revised: 05/28/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
Nanoarchaea measuring less than 500 nm and encasing an average 600-kb compact genome have been studied for twenty years, after an estimated 4193-million-year evolution. Comprising only four co-cultured representatives, these symbiotic organisms initially detected in deep-sea hydrothermal vents and geothermal springs, have been further distributed in various environmental ecosystems worldwide. Recent isolation by co-culture of Nanopusillus massiliensis from the unique ecosystem of the human oral cavity, prompted us to review the evolutionary diversity of nanaorchaea resulting in a rapidly evolving taxonomiy. Regardless of their ecological niche, all nanoarchaea share limited metabolic capacities correlating with an obligate ectosymbiotic or parasitic lifestyle; focusing on the dynamics of nanoarchaea-bacteria nanoarchaea-archaea interactions at the morphological and metabolic levels; highlighting proteins involved in nanoarchaea attachment to the hosts, as well metabolic exchanges between both organisms; and highlighting clinical nanoarchaeology, an emerging field of research in the frame of the recent discovery of Candidate Phyla radiation (CPR) in human microbiota. Future studies in clinical nanobiology will expand knowledge of the nanaorchaea repertoire associated with human microbiota and diseases, to improve our understanding of the diversity of these nanoorganims and their intreactions with microbiota and host tissues.
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Affiliation(s)
- Yasmine Hassani
- Aix-Marseille-Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille 13005, France; IHU Méditerranée Infection, Marseille 13005, France
| | - Gérard Aboudharam
- IHU Méditerranée Infection, Marseille 13005, France; Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - Michel Drancourt
- Aix-Marseille-Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille 13005, France; IHU Méditerranée Infection, Marseille 13005, France
| | - Ghiles Grine
- Aix-Marseille-Univ., IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille 13005, France; Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France.
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109
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Foor SD, Brangulis K, Shakya AK, Rana VS, Bista S, Kitsou C, Ronzetti M, Alreja AB, Linden SB, Altieri AS, Baljinnyam B, Akopjana I, Nelson DC, Simeonov A, Herzberg O, Caimano MJ, Pal U. A unique borrelial protein facilitates microbial immune evasion. mBio 2023; 14:e0213523. [PMID: 37830812 PMCID: PMC10653885 DOI: 10.1128/mbio.02135-23] [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: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Lyme disease is a major tick-borne infection caused by a bacterial pathogen called Borrelia burgdorferi, which is transmitted by ticks and affects hundreds of thousands of people every year. These bacterial pathogens are distinct from other genera of microbes because of their distinct features and ability to transmit a multi-system infection to a range of vertebrates, including humans. Progress in understanding the infection biology of Lyme disease, and thus advancements towards its prevention, are hindered by an incomplete understanding of the microbiology of B. burgdorferi, partly due to the occurrence of many unique borrelial proteins that are structurally unrelated to proteins of known functions yet are indispensable for pathogen survival. We herein report the use of diverse technologies to examine the structure and function of a unique B. burgdorferi protein, annotated as BB0238-an essential virulence determinant. We show that the protein is structurally organized into two distinct domains, is involved in multiplex protein-protein interactions, and facilitates tick-to-mouse pathogen transmission by aiding microbial evasion of early host cellular immunity. We believe that our findings will further enrich our understanding of the microbiology of B. burgdorferi, potentially impacting the future development of novel prevention strategies against a widespread tick-transmitted infection.
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Affiliation(s)
- Shelby D. Foor
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Anil K. Shakya
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Vipin S. Rana
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Sandhya Bista
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Chrysoula Kitsou
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Michael Ronzetti
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adit B. Alreja
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Sara B. Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Amanda S. Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Inara Akopjana
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Daniel C. Nelson
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Melissa J. Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Virginia-Maryland College of Veterinary Medicine, College Park, Maryland, USA
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110
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564641. [PMID: 37961710 PMCID: PMC10634959 DOI: 10.1101/2023.10.30.564641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Wilbert
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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111
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Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell 2023; 186:4803-4817.e13. [PMID: 37683634 PMCID: PMC10633639 DOI: 10.1016/j.cell.2023.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.
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Affiliation(s)
- Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Pia A Andrade
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Andi Liu
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Kevin J Cutler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Jeffrey S McLean
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA
| | | | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA; Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA 98195, USA.
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112
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Wiegand S, Sobol M, Schnepp-Pesch LK, Yan G, Iqbal S, Vollmers J, Müller JA, Kaster AK. Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes. Microorganisms 2023; 11:2612. [PMID: 37894270 PMCID: PMC10608941 DOI: 10.3390/microorganisms11102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; (S.W.); (M.S.); (L.K.S.-P.); (G.Y.); (S.I.); (J.V.); (J.A.M.)
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113
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Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA. Expanded microbiome niches of RAG-deficient patients. Cell Rep Med 2023; 4:101205. [PMID: 37757827 PMCID: PMC10591041 DOI: 10.1016/j.xcrm.2023.101205] [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: 09/13/2022] [Revised: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
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Affiliation(s)
- Ryan A Blaustein
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - ShihQueen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Glenna Banania
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Keisuke Nagao
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Dimana Dimitrova
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jennifer A Kanakry
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Helen Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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114
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Li L, Huang D, Hu Y, Rudling NM, Canniffe DP, Wang F, Wang Y. Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle. Nat Commun 2023; 14:6450. [PMID: 37833297 PMCID: PMC10576062 DOI: 10.1038/s41467-023-42193-7] [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: 02/24/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.
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Affiliation(s)
- Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yaoxun Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Nicola M Rudling
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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115
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Zhang S, Han Y, Schofield W, Nicosia M, Karell PE, Newhall KP, Zhou JY, Musich RJ, Pan S, Valujskikh A, Sangwan N, Dwidar M, Lu Q, Stappenbeck TS. Select symbionts drive high IgA levels in the mouse intestine. Cell Host Microbe 2023; 31:1620-1638.e7. [PMID: 37776865 DOI: 10.1016/j.chom.2023.09.001] [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: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Immunoglobulin A (IgA) is an important factor in maintaining homeostasis at mucosal surfaces, yet luminal IgA levels vary widely. Total IgA levels are thought to be driven by individual immune responses to specific microbes. Here, we found that the prebiotic, pectin oligosaccharide (pec-oligo), induced high IgA levels in the small intestine in a T cell-dependent manner. Surprisingly, this IgA-high phenotype was retained after cessation of pec-oligo treatment, and microbiome transmission either horizontally or vertically was sufficient to retain high IgA levels in the absence of pec-oligo. Interestingly, the bacterial taxa enriched in the overall pec-oligo bacterial community differed from IgA-coated microbes in this same community. Rather, a group of ethanol-resistant microbes, highly enriched for Lachnospiraceae bacterium A2, drove the IgA-high phenotype. These findings support a model of intestinal adaptive immunity in which a limited number of microbes can promote durable changes in IgA directed to many symbionts.
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Affiliation(s)
- Shanshan Zhang
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan 250000, P.R. China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yi Han
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Michael Nicosia
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan J Musich
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Anna Valujskikh
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiuhe Lu
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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116
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Rahlff J, Esser SP, Plewka J, Heinrichs ME, Soares A, Scarchilli C, Grigioni P, Wex H, Giebel HA, Probst AJ. Marine viruses disperse bidirectionally along the natural water cycle. Nat Commun 2023; 14:6354. [PMID: 37816747 PMCID: PMC10564846 DOI: 10.1038/s41467-023-42125-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.
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Affiliation(s)
- Janina Rahlff
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany.
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39231, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743, Jena, Germany.
| | - Sarah P Esser
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Julia Plewka
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - André Soares
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Claudio Scarchilli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123, Rome, Italy
| | - Paolo Grigioni
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123, Rome, Italy
| | - Heike Wex
- Atmospheric Microphysics, Leibniz Institute for Tropospheric Research (TROPOS), 04318, Leipzig, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Center for Marine Sensors (ZfMarS), Carl von Ossietzky University of Oldenburg, 26382, Wilhelmshaven, Germany
| | - Alexander J Probst
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141, Essen, Germany
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117
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Rangel LT, Fournier GP. Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies. Microorganisms 2023; 11:2499. [PMID: 37894157 PMCID: PMC10609509 DOI: 10.3390/microorganisms11102499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The trimming of fast-evolving sites, often known as "slow-fast" analysis, is broadly used in microbial phylogenetic reconstruction under the assumption that fast-evolving sites do not retain an accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here, we show that, contrary to this assumption, even the fastest-evolving sites present in the conserved proteins often used in Tree of Life studies contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site-specific substitution rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we also show that both slow- and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have a substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of the Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.
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Affiliation(s)
- L. Thibério Rangel
- Department of Earth, Atmospheric, & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
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Priest T, von Appen WJ, Oldenburg E, Popa O, Torres-Valdés S, Bienhold C, Metfies K, Boulton W, Mock T, Fuchs BM, Amann R, Boetius A, Wietz M. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. THE ISME JOURNAL 2023; 17:1612-1625. [PMID: 37422598 PMCID: PMC10504371 DOI: 10.1038/s41396-023-01461-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.
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Affiliation(s)
- Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Ellen Oldenburg
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Ovidiu Popa
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Sinhué Torres-Valdés
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - William Boulton
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, 28359, Germany
| | - Matthias Wietz
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany.
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119
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Garner RE, Kraemer SA, Onana VE, Fradette M, Varin MP, Huot Y, Walsh DA. A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nat Microbiol 2023; 8:1920-1934. [PMID: 37524802 DOI: 10.1038/s41564-023-01435-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 06/20/2023] [Indexed: 08/02/2023]
Abstract
Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.
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Affiliation(s)
- Rebecca E Garner
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | | | - Vera E Onana
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
| | - Maxime Fradette
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marie-Pierre Varin
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Yannick Huot
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada
- Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.
- Groupe de recherche interuniversitaire en limnologie, Montreal, Quebec, Canada.
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120
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Moreno IJ, Brahamsha B, Donia MS, Palenik B. Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River. MICROBIAL ECOLOGY 2023; 86:1534-1551. [PMID: 36757423 PMCID: PMC10497668 DOI: 10.1007/s00248-023-02186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.
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Affiliation(s)
- Ivan J Moreno
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Bianca Brahamsha
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
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Reyes-Umana VM, Coates JD. A description of the genus Denitromonas nom. rev.: Denitromonas iodatirespirans sp. nov., a novel iodate-reducing bacterium, and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats. Microbiol Spectr 2023; 11:e0091523. [PMID: 37772843 PMCID: PMC10581121 DOI: 10.1128/spectrum.00915-23] [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: 03/03/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three new Denitromonas spp. isolated from tidal mudflats in the San Francisco Bay. We demonstrate that Denitromonas spp. are indeed all facultative denitrifying bacteria that utilize a variety of carbon sources such as acetate, lactate, and succinate. In addition, individual strains also use the esoteric electron acceptors perchlorate, chlorate, and iodate. Both 16S and Rps/Rpl phylogenetic analyses place Denitromonas spp. as a deep branching clade in the family Zoogloeaceae, separate from either Thauera spp., Azoarcus spp., or Aromatoleum spp. Genome sequencing reveals a G + C content ranging from 63.72% to 66.54%, and genome sizes range between 4.39 and 5.18 Mb. Genes for salt tolerance and denitrification are distinguishing features that separate Denitromonas spp. from the closely related Azoarcus and Aromatoleum genera. IMPORTANCE The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three Denitromonas spp., Denitromonas iodatirespirans sp. nov.-a novel iodate-reducing bacterium-and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats.
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Affiliation(s)
- Victor M. Reyes-Umana
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D. Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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122
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Lim Y, Yang SJ, Kang I, Cho JC. Metagenomic data from surface seawater of the east coast of South Korea. Sci Data 2023; 10:647. [PMID: 37737276 PMCID: PMC10517112 DOI: 10.1038/s41597-023-02556-7] [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: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth's oceans, thereby meriting its recognition as a "miniature ocean". The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued. Here, we present a monthly time-series metagenomic dataset spanning a one-year period in 2009, obtained from surface (10 m) seawater samples collected off the coast of the East Sea. The dataset encompasses 12 metagenomes, amounting 195 Gbp, with 14.73-22.52 Gbp per sample. This dataset is accompanied by concurrently measured physicochemical parameters. Our anticipation is that these metagenomes will facilitate extensive investigations aimed at elucidating various aspects of the marine microbial ecosystems in the East Sea.
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Affiliation(s)
- Yeonjung Lim
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea
| | - Seung-Jo Yang
- CJ Bioscience, Inc., Sejong-daero 14, Seoul, 04527, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
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123
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Seong HJ, Kim JJ, Sul WJ. ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool. Brief Bioinform 2023; 24:bbad381. [PMID: 37889119 DOI: 10.1093/bib/bbad381] [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: 06/20/2023] [Revised: 09/16/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.
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Affiliation(s)
- Hoon Je Seong
- Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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Itoh H, Sugisawa Y, Mise K, Xu Z, Kuniyasu M, Ushijima N, Kawano K, Kobayashi E, Shiratori Y, Masuda Y, Senoo K. Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils. Int J Syst Evol Microbiol 2023; 73. [PMID: 37675765 DOI: 10.1099/ijsem.0.006073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T, W786T, Red222T, Red802T, Red803T, and Red804T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T, Red802T, Red803T, and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains. The former four strains shared 97.95-99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix, whereas the latter two strains 94.86-95.49% similarities. The average amino acid identity of strains W79T and W786T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79T, W786T, Red222T, Red803T, and Red804T) except for strain Red802T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota/Holophagae/Holophagales/Holophagaceae, comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yumi Sugisawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Kazumori Mise
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Present address: Marine College, Shandong University, Weihai, Shandong, PR China
| | - Miyu Kuniyasu
- Department of Biotechnology, Hokkaido High-technology College, Hokkaido 061-1396, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Keisuke Kawano
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
- Present address: Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Emiko Kobayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940-0826, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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125
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Zajkowski T, Lee MD, Sharma S, Vallota-Eastman A, Kuska M, Malczewska M, Rothschild LJ. Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins 2023; 91:1298-1315. [PMID: 37519023 DOI: 10.1002/prot.26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27 980 560 proteins scanned, 228 561 were identified as candidate prions (~0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the three domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that a relationship between these functions and candidate prions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.
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Affiliation(s)
- Tomasz Zajkowski
- Universities Space Research Association at NASA Ames Research Center, Mountain View, California, USA
- Polish Astrobiology Society, Warsaw, Poland
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- KBR, NASA Ames Research Center, Mountain View, California, USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Alec Vallota-Eastman
- Department of Earth Science, University of California, Santa Barbara, California, USA
| | - Mikołaj Kuska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Malczewska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California, USA
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126
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Chang H, Bai J, Zhang H, Huang R, Chu H, Wang Q, Liu H, Cheng J, Jiang H. Origin and evolution of the main starch biosynthetic enzymes. Synth Syst Biotechnol 2023; 8:462-468. [PMID: 37692203 PMCID: PMC10485787 DOI: 10.1016/j.synbio.2023.05.006] [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: 04/03/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 09/12/2023] Open
Abstract
Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.
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Affiliation(s)
- Hong Chang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jie Bai
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hejian Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Rong Huang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Huanyu Chu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Qian Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hao Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jian Cheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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Yu T, Hu H, Zeng X, Wang Y, Pan D, Deng L, Liang L, Hou J, Wang F. Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics. MLIFE 2023; 2:272-282. [PMID: 38817817 PMCID: PMC10989822 DOI: 10.1002/mlf2.12082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 06/01/2024]
Abstract
Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia, which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of Bathyarchaeia, named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 (Ca. B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. Ca. B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, mtgB) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the mtgB gene confirmed O-demethylation activity. The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that Bathyarchaeia, capable of O-demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.
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Affiliation(s)
- Tiantian Yu
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Haining Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xianhong Zeng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Donald Pan
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Longhui Deng
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Lewen Liang
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Fengping Wang
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Southern Marine Science and EngineeringGuangdong Laboratory (Zhuhai)ZhuhaiChina
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128
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Pan J, Zhang X, Xu W, Liu Y, Liu L, Luo Z, Li M. Wood-Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history. mSystems 2023; 8:e0030523. [PMID: 37458475 PMCID: PMC10469681 DOI: 10.1128/msystems.00305-23] [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: 03/28/2023] [Accepted: 05/29/2023] [Indexed: 07/22/2023] Open
Abstract
Korarchaeota, due to its rarity in common environments, is one of the archaeal phyla that has received the least attention from researchers. It was previously thought to consist solely of strict thermophiles. However, our study provides genetic evidence for the presence of korarchaeal members in temperate subsurface seawater. Furthermore, a systematic reclassification of the Korarchaeota based on 16S rRNA genes and genomes has revealed three novel marine groups (Kor-6 to Kor-8) at the root of the Korarchaeota branch. Kor-6 contains microbes that are present in moderate temperatures. All three novel marine phyla possess genes for the Wood-Ljungdahl pathway, and Kor-7 and Kor-8 possess fewer genes encoding oxygen resistance traits than other korarchaeal groups, suggesting a distinct lifestyle for these novel phyla. Our results, together with estimations of Korarchaeota divergence times, suggest that oxygen availability may be one of the important factors that have influenced the evolution of Korarchaeota. IMPORTANCE Korarchaeota were previously thought to inhabit exclusively high-temperature environments. However, our study provides genetic evidence for their unexpected presence in temperate marine waters. Through analysis of publicly available korarchaeal reference data, we have systematically reclassified Korarchaeota and identified the existence of three previously unknown marine groups (Kor-6, Kor-7, and Kor-8) at the root of the Korarchaeota branch. Comparative analysis of their gene content revealed that these novel groups exhibit a lifestyle distinct from other Korarchaeota. Specifically, they have the ability to fix carbon exclusively via the Wood-Ljungdahl (WL) pathway, and the genomes within Kor-7 and Kor-8 contain few genes encoding antioxidant enzymes, indicating their strictly anaerobic lifestyle. Further studies suggest that the genes related to methane metabolism and the WL pathway may have been inherited from a common ancestor of the Korarchaeota and that oxygen availability may be one of the important evolutionary factors that shaped the diversification of this archaeal phylum.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, Guangdong, China
| | - Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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129
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Zhao R, Le Moine Bauer S, Babbin AR. " Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces. Appl Environ Microbiol 2023; 89:e0080023. [PMID: 37470485 PMCID: PMC10467342 DOI: 10.1128/aem.00800-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sven Le Moine Bauer
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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130
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Su Z, Liu T, Guo J, Zheng M. Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12557-12570. [PMID: 37589598 PMCID: PMC10470456 DOI: 10.1021/acs.est.3c00636] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing bacteria (NOB). Since NOB were first isolated 130 years ago, the understanding of the phylogenetical and physiological diversities of NOB has been gradually deepened. In recent endeavors of advanced biological nitrogen removal, NOB have been more considered as a troublesome disruptor, and strategies on NOB suppression often fail in practice after long-term operation due to the growth of specific NOB that are able to adapt to even harsh conditions. In line with a review of the history of currently known NOB genera, a phylogenetic tree is constructed to exhibit a wide range of NOB in different phyla. In addition, the growth behavior and metabolic performance of different NOB strains are summarized. These specific features of various NOB (e.g., high oxygen affinity of Nitrospira, tolerance to chemical inhibitors of Nitrobacter and Candidatus Nitrotoga, and preference to high temperature of Nitrolancea) highlight the differentiation of the NOB ecological niche in biological nitrogen processes and potentially support their adaptation to different suppression strategies (e.g., low dissolved oxygen, chemical treatment, and high temperature). This review implicates the acquired physiological characteristics of NOB to their emergence from a genomic and ecological perspective and emphasizes the importance of understanding physiological characterization and genomic information in future wastewater treatment studies.
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Affiliation(s)
- Zicheng Su
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Tao Liu
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Min Zheng
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
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131
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Mak L, Meleshko D, Danko DC, Barakzai WN, Maharjan S, Belchikov N, Hajirasouliha I. Ariadne: synthetic long read deconvolution using assembly graphs. Genome Biol 2023; 24:197. [PMID: 37641111 PMCID: PMC10463629 DOI: 10.1186/s13059-023-03033-5] [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: 03/24/2022] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
Synthetic long read sequencing techniques such as UST's TELL-Seq and Loop Genomics' LoopSeq combine 3[Formula: see text] barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3[Formula: see text] unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.
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Affiliation(s)
- Lauren Mak
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - Dmitry Meleshko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - David C. Danko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, USA
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | | | - Salil Maharjan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
| | - Natan Belchikov
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine of Cornell University, New York, USA
| | - Iman Hajirasouliha
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, USA
- Englander Institute for Precision Medicine, The Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, USA
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132
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van den Elzen A, Helena-Bueno K, Brown CR, Chan LI, Melnikov S. Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA. Nucleic Acids Res 2023; 51:8048-8059. [PMID: 37395434 PMCID: PMC10450194 DOI: 10.1093/nar/gkad560] [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: 09/09/2022] [Revised: 05/29/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Ribosomal genes are widely used as 'molecular clocks' to infer evolutionary relationships between species. However, their utility as 'molecular thermometers' for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.
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Affiliation(s)
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lewis I Chan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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133
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Vigneron A, Vincent WF, Lovejoy C. Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog. ISME COMMUNICATIONS 2023; 3:82. [PMID: 37596370 PMCID: PMC10439189 DOI: 10.1038/s43705-023-00287-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/20/2023]
Abstract
Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
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134
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Teichman S, Lee MD, Willis AD. Analyzing microbial evolution through gene and genome phylogenies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553440. [PMID: 37645842 PMCID: PMC10462103 DOI: 10.1101/2023.08.15.553440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories. To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies. We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects. We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets. Our method is available as an open-source R package, and assists with estimating, visualizing and interacting with a collection of bacterial gene phylogenies. dimension reduction, microbiome, non-Euclidean, statistical genetics, visualization.
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Affiliation(s)
| | - Michael D Lee
- NASA Ames Research Center and Blue Marble Space Institute of Science
| | - Amy D Willis
- Department of Biostatistics, University of Washington
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135
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Bissett A, Mamet SD, Lamb EG, Siciliano SD. Linking niche size and phylogenetic signals to predict future soil microbial relative abundances. Front Microbiol 2023; 14:1097909. [PMID: 37645222 PMCID: PMC10461061 DOI: 10.3389/fmicb.2023.1097909] [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: 11/14/2022] [Accepted: 07/10/2023] [Indexed: 08/31/2023] Open
Abstract
Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.
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Affiliation(s)
| | | | - Eric G. Lamb
- University of Saskatchewan, Saskatoon, SK, Canada
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136
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Caetano-Anollés G, Claverie JM, Nasir A. A critical analysis of the current state of virus taxonomy. Front Microbiol 2023; 14:1240993. [PMID: 37601376 PMCID: PMC10435761 DOI: 10.3389/fmicb.2023.1240993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), IM2B, IOM, Aix Marseille University, CNRS, Marseille, France
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137
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Green SJ, Torok T, Allen JE, Eloe-Fadrosh E, Jackson SA, Jiang SC, Levine SS, Levy S, Schriml LM, Thomas WK, Wood JM, Tighe SW. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. ASTROBIOLOGY 2023; 23:897-907. [PMID: 37102710 PMCID: PMC10457625 DOI: 10.1089/ast.2022.0044] [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: 04/10/2022] [Accepted: 01/23/2023] [Indexed: 06/19/2023]
Abstract
Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.
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Affiliation(s)
- Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Emiley Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Sunny C. Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA
| | - Stuart S. Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jason M. Wood
- Research Informatics Core, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Scott W. Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, Vermont, USA
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138
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Amorín de Hegedüs R, Conesa A, Foster JS. Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems. Front Microbiol 2023; 14:1174685. [PMID: 37577445 PMCID: PMC10416242 DOI: 10.3389/fmicb.2023.1174685] [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: 02/26/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Microbes continually shape Earth's biochemical and physical landscapes by inhabiting diverse metabolic niches. Despite the important role microbes play in ecosystem functioning, most microbial species remain unknown highlighting a gap in our understanding of structured complex ecosystems. To elucidate the relevance of these unknown taxa, often referred to as "microbial dark matter," the integration of multiple high throughput sequencing technologies was used to evaluate the co-occurrence and connectivity of all microbes within the community. Since there are no standard methodologies for multi-omics integration of microbiome data, we evaluated the abundance of "microbial dark matter" in microbialite-forming communities using different types meta-omic datasets: amplicon, metagenomic, and metatranscriptomic sequencing previously generated for this ecosystem. Our goal was to compare the community structure and abundances of unknown taxa within the different data types rather than to perform a functional characterization of the data. Metagenomic and metatranscriptomic data were input into SortMeRNA to extract 16S rRNA gene reads. The output, as well as amplicon sequences, were processed through QIIME2 for taxonomy analysis. The R package mdmnets was utilized to build co-occurrence networks. Most hubs presented unknown classifications, even at the phyla level. Comparisons of the highest scoring hubs of each data type using sequence similarity networks allowed the identification of the most relevant hubs within the microbialite-forming communities. This work highlights the importance of unknown taxa in community structure and proposes that ecosystem network construction can be used on several types of data to identify keystone taxa and their potential function within microbial ecosystems.
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Affiliation(s)
- Rocío Amorín de Hegedüs
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Department of Microbiology and Cell Sciences, Space Life Sciences Lab, University of Florida, Merritt Island, FL, United States
| | - Ana Conesa
- Spanish National Research Council, Institute for Integrative Systems Biology, Valencia, Spain
| | - Jamie S. Foster
- Department of Microbiology and Cell Sciences, Space Life Sciences Lab, University of Florida, Merritt Island, FL, United States
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Maatouk M, Merhej V, Pontarotti P, Ibrahim A, Rolain JM, Bittar F. Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality. Microorganisms 2023; 11:1933. [PMID: 37630493 PMCID: PMC10459063 DOI: 10.3390/microorganisms11081933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
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Affiliation(s)
- Mohamad Maatouk
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Vicky Merhej
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Pierre Pontarotti
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Ahmad Ibrahim
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
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140
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Santana-Pereira ALR, Moen FS, Severance B, Liles MR. Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment. Front Microbiol 2023; 14:1114548. [PMID: 37577441 PMCID: PMC10413278 DOI: 10.3389/fmicb.2023.1114548] [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: 12/02/2022] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.
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Affiliation(s)
| | | | | | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
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141
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Kordiš D, Turk V. Origin and Early Diversification of the Papain Family of Cysteine Peptidases. Int J Mol Sci 2023; 24:11761. [PMID: 37511529 PMCID: PMC10380794 DOI: 10.3390/ijms241411761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.
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Affiliation(s)
- Dušan Kordiš
- Department of Molecular and Biomedical Sciences, J. Stefan Institute, 1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry, Molecular and Structural Biology, J. Stefan Institute, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
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142
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Leng H, Wang Y, Zhao W, Sievert SM, Xiao X. Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution. Nat Commun 2023; 14:4354. [PMID: 37468486 DOI: 10.1038/s41467-023-39960-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
It has been proposed that early bacteria, or even the last universal common ancestor of all cells, were thermophilic. However, research on the origin and evolution of thermophily is hampered by the difficulties associated with the isolation of deep-branching thermophilic microorganisms in pure culture. Here, we isolate a deep-branching thermophilic bacterium from a deep-sea hydrothermal vent, using a two-step cultivation strategy ("Subtraction-Suboptimal", StS) designed to isolate rare organisms. The bacterium, which we name Zhurongbacter thermophilus 3DAC, is a sulfur-reducing heterotroph that is phylogenetically related to Coprothermobacterota and other thermophilic bacterial groups, forming a clade that seems to represent a major, early-diverging bacterial lineage. The ancestor of this clade might be a thermophilic, strictly anaerobic, motile, hydrogen-dependent, and mixotrophic bacterium. Thus, our study provides insights into the early evolution of thermophilic bacteria.
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Affiliation(s)
- Hao Leng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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143
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Zhong S, Zhou S, Liu S, Wang J, Dang C, Chen Q, Hu J, Yang S, Deng C, Li W, Liu J, Borthwick AGL, Ni J. May microbial ecological baseline exist in continental groundwater? MICROBIOME 2023; 11:152. [PMID: 37468948 PMCID: PMC10355068 DOI: 10.1186/s40168-023-01572-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/13/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental reference with less human interference has been investigated in surface ecosystems such as soils, rivers, and ocean, but the existence of groundwater microbial ecological baseline (GMEB) is still an open question so far. RESULTS Based on high-throughput sequencing information derived from national monitoring of 733 newly constructed wells, we find that bacterial communities in pristine groundwater exhibit a significant lateral diversity gradient and gradually approach the topsoil microbial latitudinal diversity gradient with decreasing burial depth of phreatic water. Among 74 phyla dominated by Proteobacteria in groundwater, Patescibacteria act as keystone taxa that harmonize microbes in shallower aquifers and accelerate decline in bacterial diversity with increasing well-depth. Decreasing habitat niche breadth with increasing well-depth suggests a general change in the relationship among key microbes from closer cooperation in shallow to stronger competition in deep groundwater. Unlike surface-water microbes, microbial communities in pristine groundwater are predominantly shaped by deterministic processes, potentially associated with nutrient sequestration under dark and anoxic environments in aquifers. CONCLUSIONS By unveiling the biogeographic patterns and mechanisms controlling the community assembly of microbes in pristine groundwater throughout China, we firstly confirm the existence of GMEB in shallower aquifers and propose Groundwater Microbial Community Index (GMCI) to evaluate anthropogenic impact, which highlights the importance of GMEB in groundwater water security and health diagnosis. Video Abstract.
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Affiliation(s)
- Sining Zhong
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shungui Zhou
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chenyuan Dang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Jinyun Hu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chunfang Deng
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, People's Republic of China
| | - Juan Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Alistair G L Borthwick
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL8 4AA, UK
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China.
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China.
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144
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Zhang R, Aris-Brosou S, Storck V, Liu J, Abdelhafiz MA, Feng X, Meng B, Poulain AJ. Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation. ISME COMMUNICATIONS 2023; 3:74. [PMID: 37454192 PMCID: PMC10349881 DOI: 10.1038/s43705-023-00277-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21-513 mg kg-1 dry wt. soil; MeHg: 1.21-6.82 ng g-1 dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria.
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Affiliation(s)
- Rui Zhang
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Veronika Storck
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC, H3C 3A7, Canada
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Mahmoud A Abdelhafiz
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China.
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145
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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146
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station. RESEARCH SQUARE 2023:rs.3.rs-3126314. [PMID: 37461605 PMCID: PMC10350232 DOI: 10.21203/rs.3.rs-3126314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS). Results The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Conclusions Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D. Rekha
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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147
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Abstract
Gravity is a fundamental interaction that permeates throughout our Universe. On Earth, gravity gives weight to physical objects, and has been a constant presence throughout terrestrial biological evolution. Thus, gravity has shaped all biological functions, some examples include the growth of plants (e.g., gravitropism), the structure and morphology of biological parts in multicellular organisms, to its effects on our physiological function when humans travel into space. Moreover, from an evolutionary perspective, gravity has been a constant force on biology, and life, to our understanding, should have no reason to not experience the effects of gravity. Interestingly, there appear to be specific biological mechanisms that activate in the absence of gravity, with the space environment the only location to study the effects of a lack of gravity on biological systems. Thus, in this perspective piece, biological adaptations from the cellular to the whole organism levels to the presence and absence of gravity will be organized and described, as well as outlining future areas of research for gravitational biological investigations to address. Up to now, we have observed and shown how gravity effects biology at different levels, with a few examples including genetic (e.g., cell cycle, metabolism, signal transduction associated pathways, etc.), biochemically (e.g., cytoskeleton, NADPH oxidase, Yes-associated protein, etc.), and functionally (e.g., astronauts experiencing musculoskeletal and cardiovascular deconditioning, immune dysfunction, etc., when traveling into space). Based from these observations, there appear to be gravity-sensitive and specific pathways across biological organisms, though knowledge gaps of the effects of gravity on biology remain, such as similarities and differences across species, reproduction, development, and evolutionary adaptations, sex-differences, etc. Thus, here an overview of the literature is provided for context of gravitational biology research to-date and consideration for future studies, as we prepare for long-term occupation of low-Earth Orbit and cis-Lunar space, and missions to the Moon and Mars, experiencing the effects of Lunar and Martian gravity on biology, respectively, through our Artemis program.
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148
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Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
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149
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Zeng J, Pan Y, Hu R, Liu F, Gu H, Ding J, Liu S, Liu S, Yang X, Peng Y, Tian Y, He Q, Wu Y, Yan Q, Shu L, He Z, Wang C. The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131974. [PMID: 37406521 DOI: 10.1016/j.jhazmat.2023.131974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.
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Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Jijuan Ding
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN, USA
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510530, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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150
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Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol 2023; 5:acmi000558.v3. [PMID: 37424544 PMCID: PMC10323806 DOI: 10.1099/acmi.0.000558.v3] [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: 01/09/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Background The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva. Results Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts. Conclusions Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mina E. Adam
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Bhaskar Kumar
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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