1
|
Kawano K, Awano T, Yoshinaga A, Sugiyama J, Sawayama S, Nakagawa S. Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus. Int J Syst Evol Microbiol 2024; 74:006530. [PMID: 39325648 PMCID: PMC11426391 DOI: 10.1099/ijsem.0.006530] [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: 02/26/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.
Collapse
Affiliation(s)
- Keisuke Kawano
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tatsuya Awano
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Arata Yoshinaga
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Junji Sugiyama
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki 444-8787, Japan
| |
Collapse
|
2
|
Rey-Velasco X, Lucena T, Belda A, Gasol JM, Sánchez O, Arahal DR, Pujalte MJ. Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean. Front Microbiol 2024; 15:1407904. [PMID: 38863746 PMCID: PMC11165706 DOI: 10.3389/fmicb.2024.1407904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.
Collapse
Affiliation(s)
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Ana Belda
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| |
Collapse
|
3
|
Kanbe H, Sano Y, Mise K, Kanie S, Ushijima N, Kawano K, Kihara M, Itoh H. Lysinibacillus piscis sp. nov. isolated from the gut of mottled spinefoot Siganus fuscescens. Arch Microbiol 2024; 206:228. [PMID: 38643446 DOI: 10.1007/s00203-024-03937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 04/22/2024]
Abstract
A novel Lysinibacillus strain, designated KH24T, was isolated from the gut of Siganus fuscescens, a herbivorous fish, which was captured off the coast of Okinawa, Japan. Strain KH24T is a rod-shaped, Gram-stain-positive, spore-forming, and motile bacterium that forms off-white colonies. The 16S rRNA gene sequence of strain KH24T showed the highest similarity (97.4%) with Lysinibacillus pakistanensis JCM 18776T and L. irui IRB4-01T. Genomic similarities between strain KH24T and Lysinibacillus type strains, based on average nucleotide identity, digital DNA-DNA hybridization (genome-to-genome distance calculation), and average amino acid identity were 70.4-77.7%, 17.1-24.4%, and 69.2-81.2%, respectively, which were lower than species delineation thresholds. Strain KH24T growth occurred at pH values of 5.5-8.5, temperatures of 20-40 °C, and NaCl concentrations of 0-4.0%, and optimally at pH 7.0, 30 °C, and 0%, respectively. Unlike related Lysinibacillus type strains, strain KH24T could assimilate D-glucose, D-fructose, N-acetyl-glucosamine, amygdalin, arbutin, esculin, ferric citrate, salicin, D-cellobiose, D-maltose, D-sucrose, and gentiobiose. Major fatty acids included iso-C15:0 (45.8%), anteiso-C15:0 (15.1%), iso-C17:0 (12.6%), and anteiso-C17:0 (10.9%). Menaquinone-7 was the predominant quinone, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and lysophosphatidylethanolamine. Based on its genetic and phenotypic properties, strain KH24T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus piscis sp. nov. is proposed. The type strain is KH24T (= JCM 36611 T = KCTC 43676 T).
Collapse
Affiliation(s)
- Hiyu Kanbe
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-Ku, Sapporo, 005-8601, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Shizuoka, Mishima, 411-8540, Japan
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Yuki Sano
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-Ku, Sapporo, 005-8601, Japan
- Research Center, JAPAN NUTRITION Co., Ltd., Nasu-shiobara, Tochigi, 325-0103, Japan
| | - Kazumori Mise
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Shusei Kanie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, 060-8586, Japan
| | - Keisuke Kawano
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-Ku, Sapporo, 005-8601, Japan
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Minoru Kihara
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-Ku, Sapporo, 005-8601, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-Ku, Sapporo, 062-8517, Japan.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Burbick CR, Munson E, Lawhon SD, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [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] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
Collapse
Affiliation(s)
- Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
6
|
Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of
Anaeromyxobacter
species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of
Anaeromyxobacter
,
Anaeromyxobacter dehalogenans
2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in
A. dehalogenans
2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.
Collapse
|
7
|
Yang SH, Oh HM, Park MJ, Jang D, Kwon KK. Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea. J Microbiol 2021; 60:11-17. [PMID: 34964941 DOI: 10.1007/s12275-022-1468-6] [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: 09/08/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped (0.3-0.5 × 1.0-1.9 µm), non-motile marine bacterium designated as ALE3EIT was isolated from a saline volcanic rock aquifer (lava sea-water) on Jeju Island, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain ALE3EIT showed high similarity to 'Altibacter lentus' JLT2010T (97.2%), followed by Marixanthomonas ophiurae KMM 3046T (94.5%). Growth was observed at 10-41°C (optimum, 30°C), at pH 6.0-8.5 (optimum, pH 7.5) and at 0.5-8% (optimum, 4.0%) NaCl. The predominant cellular fatty acids were iso-C15:0 (23.5%), iso-C16:0 (10.2%), iso-C16:0 3OH (10.5%), and iso-C17:0 3OH (16.8%). The DNA G + C contents was 40.4 mol%. The major respiratory quinone was MK-6. The major polar lipids were determined to be phosphatidylethanolamine, two unidentified glycolipids, and two unidentified aminolipids. Several phenotypic characteristics such as production of acetoin, activities of arginine dihydrolase and acid phosphatase, and utilization pattern of carbon sources differentiate strain ALE3EIT from 'A. lentus' JLT2010T. Activities of the lipase, trypsin, α-chymotrypsin and gelatinase and utilization pattern of carbon sources differentiate strain ALE3EIT from M. ophiurae KMM 3046T. The genome of strain ALE3EIT is 3.0 Mbp long and its ANI and AAI values against 'A. lentus' JLT2010T were 76.58 and 72.76, respectively, however, AAI values against members in other genera were lower than 72%. The phylogenomic tree inferred by PhyloPhlAn clearly differentiated the strain ALE3EIT together with strain JLT2010T from other genera in the Falvobacteriaceae. This polyphasic taxonomic data indicates that strain ALE3EIT should be identified as a novel species in the genus 'Altibacter', however, the name has not been validated. Therefore, the strain is classified as a novel genus and is proposed as Constantimarinum furrinae gen. nov., sp. nov. The type strain is ALE3EIT (= KCCM 43303T = JCM 33022T).
Collapse
Affiliation(s)
- Sung-Hyun Yang
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea
| | - Hyun-Myung Oh
- Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea
| | - Mi-Jeong Park
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea.,KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Dongil Jang
- Cotde Inc., Cheonan, 31252, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea. .,KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
8
|
Shimoji H, Itoh H, Matsuura Y, Yamashita R, Hori T, Hojo MK, Kikuchi Y. Worker-dependent gut symbiosis in an ant. ISME COMMUNICATIONS 2021; 1:60. [PMID: 37938661 PMCID: PMC9723695 DOI: 10.1038/s43705-021-00061-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/24/2021] [Accepted: 10/04/2021] [Indexed: 04/27/2023]
Abstract
The hallmark of eusocial insects, honeybees, ants, and termites, is division of labor between reproductive and non-reproductive worker castes. In addition, environmental adaption and ecological dominance are also underpinned by symbiotic associations with beneficial microorganisms. Microbial symbionts are generally considered to be maintained in an insect colony in two alternative ways: shared among all colony members or inherited only by a specific caste. Especially in ants, the reproductive caste plays a crucial role in transmission of the symbionts shared among colony members over generations. Here, we report an exceptional case, the worker-dependent microbiota in an ant, Diacamma cf. indicum from Japan. By collecting almost all the individuals from 22 colonies in the field, we revealed that microbiota of workers is characterized by a single dominant bacterium localized at the hindgut. The bacterium belonging to an unclassified member within the phylum Firmicutes, which is scarce or mostly absent in the reproductive castes. Furthermore, we show that the gut symbiont is acquired at the adult stage. Collectively, our findings strongly suggest that the specific symbiont is maintained by only workers, demonstrating a novel pattern of ant-associated bacterial symbiosis, and thus further our understanding of host-microbe interactions in the light of sociobiology.
Collapse
Affiliation(s)
- Hiroyuki Shimoji
- Shool of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo Hyogo, 669-1337, Japan.
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, 062-8517, Japan.
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan.
| | - Rio Yamashita
- Shool of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo Hyogo, 669-1337, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced IndustrialScience and Technology (AIST) Tsukuba West, Tsukuba, Ibaraki, 305-8569, Japan
| | - Masaru K Hojo
- Shool of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo Hyogo, 669-1337, Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, 062-8517, Japan.
| |
Collapse
|
9
|
Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H. Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol 2021; 12:737531. [PMID: 34659166 PMCID: PMC8516083 DOI: 10.3389/fmicb.2021.737531] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.
Collapse
Affiliation(s)
- Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Xueding Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan
| | | | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Hokkaido, Japan
| |
Collapse
|
10
|
Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo K. Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int J Syst Evol Microbiol 2020; 71. [PMID: 33295856 DOI: 10.1099/ijsem.0.004607] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae. Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas, were 96.3-98.5 %. The genome-related indexes, average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, among the three strains and G. oryzae S43T were 74.7-86.8 %, 21.2-33.3 % and 70.4-89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas, for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.
Collapse
Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 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
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Chie Hayakawa
- School of Agriculture, Utsunomiya University, Tochigi 321-8505, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940-0826, Japan
| | - Keishi Senoo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|