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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Guo H, Hu B, Si HR, Zhu Y, Zhang W, Li B, Li A, Geng R, Lin HF, Yang XL, Zhou P, Shi ZL. Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. Emerg Microbes Infect 2021; 10:1507-1514. [PMID: 34263709 PMCID: PMC8344244 DOI: 10.1080/22221751.2021.1956373] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the Sarbecovirus phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from Rhinolophus affinis, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.
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Affiliation(s)
- Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Hao-Rui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Wei Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Ang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Rong Geng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Peng Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People’s Republic of China
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Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T. Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. Microorganisms 2020; 8:microorganisms8091373. [PMID: 32906802 PMCID: PMC7564735 DOI: 10.3390/microorganisms8091373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 01/28/2023] Open
Abstract
Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.
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Affiliation(s)
- Ryosuke Nakai
- Microbial Ecology and Technology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo 062-8517, Japan
- Correspondence:
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan;
| | - Nozomi Tazato
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
| | - Sho Morohoshi
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
| | - Tomomi Koide
- Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan; (N.T.); (S.M.); (T.K.)
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Ali MR, Alam ASMRU, Amin MA, Siddique MA, Sultana M, Hossain MA. Emergence of novel lineage of foot-and-mouth disease virus serotype Asia1 BD-18 (G-IX) in Bangladesh. Transbound Emerg Dis 2019; 67:486-493. [PMID: 31587524 DOI: 10.1111/tbed.13381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/18/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023]
Abstract
Foot-and-mouth disease virus (FMDV) is a highly evolutionary divergent pathogen causing great economic havoc in many countries. Among its seven existing serotypes, Asia1 is the least divergent with a single topotype both genetically and antigenically. It is reported sporadically in Indian subcontinent and was classified under lineage G-VIII. In 2018, serotype Asia1 re-emerged in Bangladesh after 2013, along with circulation of a novel serotype Asia1 BD-18 (G-IX) lineage. VP1 phylogeny and sequence variation clearly demonstrated the novel strains which was estimated to have at least >5% nucleotide divergence with distinct clade formation. Also, the Bayesian phylogeographic inferences traced back to the origin time of lineage G-IX in early 2017 and a possible origin in Bangladesh. Mutational analysis considering established eight lineages revealed that the virus strains belonged to lineage G-IX contained a unique mutation at 44 position in the B-C loop region of VP1. Inappropriate vaccination and inefficient outbreak surveillance possibly contributed to the current episode of emergence. Therefore, active surveillance and continued vigilance are essential to assess and timely detect the occurrence, extent and distribution of this novel Asia1 strains in Bangladesh and the neighbouring countries.
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Affiliation(s)
- M Rahmat Ali
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Ministry of Foreign Affairs, Dhaka, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Microbiology, Jashore University of Science & Technology, Jashore, Bangladesh
| | - Md Al Amin
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Department of Livestock Services, Savar, Bangladesh
| | - Mohammad Anwar Siddique
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Jashore University of Science & Technology, Jashore, Bangladesh
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Abstract
We characterized the complete genome of a putative novel Usutu virus (USUV) strain (Usutu-BONN) detected in a dead blackbird from Germany. Genomic analysis revealed several unique amino acid substitutions among the polyprotein gene. Phylogenetic analyses demonstrated that Usutu-BONN constitutes a putative novel African USUV lineage, which was probably recently introduced to central Europe.
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