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Zawierucha K, Trzebny A, Buda J, Bagshaw E, Franzetti A, Dabert M, Ambrosini R. Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms. PLoS One 2022; 17:e0262039. [PMID: 35020747 PMCID: PMC8754347 DOI: 10.1371/journal.pone.0262039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.
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Affiliation(s)
- Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznań, Poland
- * E-mail:
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznań, Poland
| | - Elizabeth Bagshaw
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Andrea Franzetti
- Earth and Environmental Sciences Department, University of Milano-Bicocca, Milan, Italy
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
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2
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Potapov AM, Beaulieu F, Birkhofer K, Bluhm SL, Degtyarev MI, Devetter M, Goncharov AA, Gongalsky KB, Klarner B, Korobushkin DI, Liebke DF, Maraun M, Mc Donnell RJ, Pollierer MM, Schaefer I, Shrubovych J, Semenyuk II, Sendra A, Tuma J, Tůmová M, Vassilieva AB, Chen T, Geisen S, Schmidt O, Tiunov AV, Scheu S. Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev Camb Philos Soc 2022; 97:1057-1117. [DOI: 10.1111/brv.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Frédéric Beaulieu
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri‐Food Canada Ottawa ON K1A 0C6 Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Karl‐Wachsmann‐Allee 6 03046 Cottbus Germany
| | - Sarah L. Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Maxim I. Degtyarev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anton A. Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Konstantin B. Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Daniil I. Korobushkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Dana F. Liebke
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Rory J. Mc Donnell
- Department of Crop and Soil Science Oregon State University Corvallis OR 97331 U.S.A
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Julia Shrubovych
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Institute of Systematics and Evolution of Animals PAS Slawkowska 17 Pl 31‐016 Krakow Poland
- State Museum Natural History of NAS of Ukraine Teatralna 18 79008 Lviv Ukraine
| | - Irina I. Semenyuk
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
- Joint Russian‐Vietnamese Tropical Center №3 Street 3 Thang 2, Q10 Ho Chi Minh City Vietnam
| | - Alberto Sendra
- Colecciones Entomológicas Torres‐Sala, Servei de Patrimoni Històric, Ajuntament de València València Spain
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri Universitat de València València Spain
| | - Jiri Tuma
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Biology Centre CAS, Institute of Entomology Branisovska 1160/31 370 05 Ceske Budejovice Czech Republic
| | - Michala Tůmová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anna B. Vassilieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Ting‐Wen Chen
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Stefan Geisen
- Department of Nematology Wageningen University & Research 6700ES Wageningen The Netherlands
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science University College Dublin Belfield Dublin 4 Ireland
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- Centre of Biodiversity and Sustainable Land Use Büsgenweg 1 37077 Göttingen Germany
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3
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Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881984 DOI: 10.1099/ijsem.0.004671] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Pilgrim J, Thongprem P, Davison HR, Siozios S, Baylis M, Zakharov EV, Ratnasingham S, deWaard JR, Macadam CR, Smith MA, Hurst GDD. Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis. Gigascience 2021; 10:6187866. [PMID: 33764469 PMCID: PMC7992394 DOI: 10.1093/gigascience/giab021] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/05/2020] [Accepted: 03/05/2021] [Indexed: 01/25/2023] Open
Abstract
Background Rickettsia are intracellular bacteria best known as the causative agents of human and animal diseases. Although these medically important Rickettsia are often transmitted via haematophagous arthropods, other Rickettsia, such as those in the Torix group, appear to reside exclusively in invertebrates and protists with no secondary vertebrate host. Importantly, little is known about the diversity or host range of Torix group Rickettsia. Results This study describes the serendipitous discovery of Rickettsia amplicons in the Barcode of Life Data System (BOLD), a sequence database specifically designed for the curation of mitochondrial DNA barcodes. Of 184,585 barcode sequences analysed, Rickettsia is observed in ∼0.41% of barcode submissions and is more likely to be found than Wolbachia (0.17%). The Torix group of Rickettsia are shown to account for 95% of all unintended amplifications from the genus. A further targeted PCR screen of 1,612 individuals from 169 terrestrial and aquatic invertebrate species identified mostly Torix strains and supports the “aquatic hot spot” hypothesis for Torix infection. Furthermore, the analysis of 1,341 SRA deposits indicates that Torix infections represent a significant proportion of all Rickettsia symbioses found in arthropod genome projects. Conclusions This study supports a previous hypothesis that suggests that Torix Rickettsia are overrepresented in aquatic insects. In addition, multiple methods reveal further putative hot spots of Torix Rickettsia infection, including in phloem-feeding bugs, parasitoid wasps, spiders, and vectors of disease. The unknown host effects and transmission strategies of these endosymbionts make these newly discovered associations important to inform future directions of investigation involving the understudied Torix Rickettsia.
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Affiliation(s)
- Jack Pilgrim
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Panupong Thongprem
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Helen R Davison
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Matthew Baylis
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK.,Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Craig R Macadam
- Buglife - The Invertebrate Conservation Trust, Balallan House, 24 Allan Park, Stirling FK8 2QG, UK
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph, Ontario N1G 2W1, Canada
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
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5
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Zeibich L, Guhl J, Drake HL. Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris. FEMS MICROBES 2020. [DOI: 10.1093/femsmc/xtaa002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTMany higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.
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Affiliation(s)
- Lydia Zeibich
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
| | - Jennifer Guhl
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch Strasse 1-3, 95440 Bayreuth, Germany
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6
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Takeuchi M, Kuwahara H, Murakami T, Takahashi K, Kajitani R, Toyoda A, Itoh T, Ohkuma M, Hongoh Y. Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut. THE ISME JOURNAL 2020; 14:2288-2301. [PMID: 32483307 PMCID: PMC7608387 DOI: 10.1038/s41396-020-0688-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
Several Trichonympha protist species in the termite gut have independently acquired Desulfovibrio ectosymbionts in apparently different stages of symbiosis. Here, we obtained the near-complete genome sequence of Desulfovibrio phylotype ZnDsv-02, which attaches to the surface of Trichonympha collaris cells, and compared it with a previously obtained genome sequence of 'Candidatus Desulfovibrio trichonymphae' phylotype Rs-N31, which is almost completely embedded in the cytoplasm of Trichonympha agilis. Single-nucleotide polymorphism analysis indicated that although Rs-N31 is almost clonal, the ZnDsv-02 population on a single host cell is heterogeneous. Despite these differences, the genome of ZnDsv-02 has been reduced to 1.6 Mb, which is comparable to that of Rs-N31 (1.4 Mb), but unlike other known ectosymbionts of protists with a genome similar in size to their free-living relatives. Except for the presence of a lactate utilization pathway, cell-adhesion components and anti-phage defense systems in ZnDsv-02, the overall gene-loss pattern between the two genomes is very similar, including the loss of genes responsive to environmental changes. Our study suggests that genome reduction can occur in ectosymbionts, even when they can be transmitted horizontally and obtain genes via lateral transfer, and that the symbiont genome size depends heavily on their role in the symbiotic system.
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Affiliation(s)
- Mariko Takeuchi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Hirokazu Kuwahara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Takumi Murakami
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- Department of Informatics, National Institute of Genetics, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, 411-8540, Japan
| | - Kazuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, 411-8540, Japan
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, Japan.
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7
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Pankratov TA, Grouzdev DS, Patutina EO, Kolganova TV, Berestovskaya JJ, Ashikhmin AA. Lichenicoccus roseus gen. nov., sp. nov., the first bacteriochlorophyll a-containing, psychrophilic and acidophilic Acetobacteraceae bacteriobiont of lichen Cladonia species. Int J Syst Evol Microbiol 2020; 70:4591-4601. [PMID: 32658637 DOI: 10.1099/ijsem.0.004318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll a-containing bacterial strains, KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152, were isolated from the thalli of Cladonia arbuscula and Cladonia stellaris lichens. Cells from the strains were coccoid and reproduced by binary division. They were motile at the early stages of growth and utilized sugars and alcohols. All strains were psychrophilic and acidophilic, capable of growth between pH 3.5 and 7.5 (optimum, pH 5.5), and at 4-30 °C (optimum, 10-15 °C). The major fatty acids were C18 : 1 ω7c and C18 : 0; the lipids were phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, phosphatidylglycerol, glycolipids, diphosphatidylglycerol and polar lipids with an unknown structure. The quinone was Q-10. The DNA G+C content was 67.8 mol%. Comparative 16S rRNA gene analysis together with other data, supported that the strains, KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152 belonged to the same species. Whole genome analysis of the strain KEBCLARHB70RT and average amino acid identity values confirmed its distinctive phylogenetic position within the family Acetobacteraceae. Phenotypic, ecological and genomic characteristics distinguished strains KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152 from all genera in the family Acetobacteraceae. Therefore, we propose a novel genus and a novel species, Lichenicoccus roseus gen. nov., sp. nov., for these novel Acetobacteraceae members. Strain KEBCLARHB70RT (=KCTC 72321T=VKM B-3305T) has been designated as the type strain.
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Affiliation(s)
- Timofey A Pankratov
- S.N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Ekaterina O Patutina
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Tatiana V Kolganova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Julia J Berestovskaya
- S.N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center, Pushchino Scientific Center for Biological Research of Russian Academy of Sciences, Pushchino 142290, Russia
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Murakami T, Onouchi S, Igai K, Ohkuma M, Hongoh Y. Ectosymbiotic bacterial microbiota densely colonize the surface of thelastomatid nematodes in the gut of the wood-feeding cockroach Panesthia angustipennis. FEMS Microbiol Ecol 2019; 95:5250881. [PMID: 30561598 DOI: 10.1093/femsec/fiy238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/14/2018] [Indexed: 12/30/2022] Open
Abstract
Cockroaches generally harbor thelastomatid nematodes (pinworms) in their gut. In this study, we discovered that the surfaces of two undescribed thelastomatid species in the hindgut of the wood-feeding cockroach Panesthia angustipennis were consistently and densely colonized by bacteria. Epifluorescence microscopy using 4',6-diamidino-2-phenylindole and transmission electron microscopy revealed that several distinct morphotypes of bacteria covered almost the entire body surface of the nematodes in single or multiple layers. Sequencing analysis of 16S rRNA amplicons of either entire nematodes or sections of nematode body surfaces indicated that the associated bacterial microbiota consisted of several dominant phylotypes belonging to either Dysgonomonadaceae (Bacteroidales termite cluster V), Rikennellaceae or Ruminococcaceae. These phylotypes formed clades with sequences previously obtained from cockroach and/or termite guts. Comparisons of the bacterial community structure of the entire cockroach hindgut microbiota vs the nematode-associated microbiota suggested that these dominant bacterial phylotypes preferentially colonized the nematode surface. The two nematode species shared most of the dominant bacterial phylotypes, but the bacterial community structures differed significantly. Colonization by five predominant phylotypes was confirmed by fluorescence in situ hybridization analysis using phylotype-specific probes. Our study provides fundamental information on this previously unknown ectosymbiosis between gut bacteria and thelastomatid pinworms.
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Affiliation(s)
- Takumi Murakami
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-W3-48 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Shu Onouchi
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-W3-48 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Katsura Igai
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-W3-48 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyada, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1-W3-48 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyada, Tsukuba, Ibaraki 305-0074, Japan
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9
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Ren Z, Martyniuk N, Oleksy IA, Swain A, Hotaling S. Ecological Stoichiometry of the Mountain Cryosphere. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00360] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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10
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Shen L, Liu Y, Wang N, Adhikari NP. Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment. Microorganisms 2019; 7:E211. [PMID: 31336655 PMCID: PMC6680632 DOI: 10.3390/microorganisms7070211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/04/2019] [Accepted: 07/18/2019] [Indexed: 12/26/2022] Open
Abstract
Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier.
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Affiliation(s)
- Liang Shen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Ninglian Wang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Urban and Environmental Science, Northwest University, Xian 710069, China
| | - Namita Paudel Adhikari
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
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11
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Zeibich L, Schmidt O, Drake HL. Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem. Environ Microbiol 2019; 21:1436-1451. [DOI: 10.1111/1462-2920.14556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Lydia Zeibich
- Department of Ecological MicrobiologyUniversity of Bayreuth 95440 Bayreuth Germany
| | - Oliver Schmidt
- Department of Ecological MicrobiologyUniversity of Bayreuth 95440 Bayreuth Germany
| | - Harold L. Drake
- Department of Ecological MicrobiologyUniversity of Bayreuth 95440 Bayreuth Germany
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12
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Murakami T, Segawa T, Takeuchi N, Barcaza Sepúlveda G, Labarca P, Kohshima S, Hongoh Y. Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community. Environ Microbiol 2018; 20:4170-4183. [PMID: 30246365 DOI: 10.1111/1462-2920.14420] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022]
Abstract
The glacier stonefly Andiperla willinki is the largest metazoan inhabiting the Patagonian glaciers. In this study, we analysed the gut microbiome of the aquatic nymphs by 16S rRNA gene amplicon and metagenomic sequencing. The bacterial gut community was consistently dominated by taxa typical of animal digestive tracts, such as Dysgonomonadaceae and Lachnospiraceae, as well as those generally indigenous to glacier environments, such as Polaromonas. Interestingly, the dominant Polaromonas phylotypes detected in the stonefly gut were almost never detected in the glacier surface habitat. Fluorescence in situ hybridization analysis revealed that the bacterial lineages typical of animal guts colonized the gut wall in a co-aggregated form, while Polaromonas cells were not included in the aggregates. Draft genomes of several dominant bacterial lineages were reconstructed from metagenomic datasets and indicated that the predominant Dysgonomonadaceae bacterium is capable of degrading various polysaccharides derived from host-ingested food, such as algae, and that other dominant bacterial lineages ferment saccharides liberated by the polysaccharide degradation. Our results suggest that the gut bacteria-host association in the glacier stonefly contributes to host nutrition as well as material cycles in the glacier environment.
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Affiliation(s)
- Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan.,Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Takahiro Segawa
- Center of Life Science Research, University of Yamanashi, Yamanashi, Japan.,National Institute of Polar Research, Tokyo, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Chiba University, Chiba, Japan
| | | | | | - Shiro Kohshima
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan
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13
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Lang SA, Shain DH. Atypical Evolution of the F 1F o Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus). Evol Bioinform Online 2018; 14:1176934318788076. [PMID: 30022808 PMCID: PMC6047255 DOI: 10.1177/1176934318788076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.
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Affiliation(s)
- Shirley A Lang
- Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Daniel H Shain
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, USA
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14
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May M, Brown DR. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Mollicutes. Minutes of the closed meeting, 3rd July 2016, Brisbane, Australia. Int J Syst Evol Microbiol 2017; 67:2482-2484. [PMID: 28693682 DOI: 10.1099/ijsem.0.001818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford, Maine, USA
| | - Daniel R Brown
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA
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15
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Murakami T, Segawa T, Dial R, Takeuchi N, Kohshima S, Hongoh Y. Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages. Microbes Environ 2017; 32:32-39. [PMID: 28302989 PMCID: PMC5371072 DOI: 10.1264/jsme2.me16158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages.
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Affiliation(s)
- Takumi Murakami
- Department of Biological Sciences, Tokyo Institute of Technology
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16
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17
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Larsen T, Ventura M, Maraldo K, Triadó-Margarit X, Casamayor EO, Wang YV, Andersen N, O'Brien DM. The dominant detritus-feeding invertebrate in Arctic peat soils derives its essential amino acids from gut symbionts. J Anim Ecol 2016; 85:1275-85. [PMID: 27322934 DOI: 10.1111/1365-2656.12563] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 06/09/2016] [Indexed: 02/04/2023]
Abstract
Supplementation of nutrients by symbionts enables consumers to thrive on resources that might otherwise be insufficient to meet nutritional demands. Such nutritional subsidies by intracellular symbionts have been well studied; however, supplementation of de novo synthesized nutrients to hosts by extracellular gut symbionts is poorly documented, especially for generalists with relatively undifferentiated intestinal tracts. Although gut symbionts facilitate degradation of resources that would otherwise remain inaccessible to the host, such digestive actions alone cannot make up for dietary insufficiencies of macronutrients such as essential amino acids (EAA). Documenting whether gut symbionts also function as partners for symbiotic EAA supplementation is important because the question of how some detritivores are able to subsist on nutritionally insufficient diets has remained unresolved. To answer this poorly understood nutritional aspect of symbiont-host interactions, we studied the enchytraeid worm, a bulk soil feeder that thrives in Arctic peatlands. In a combined field and laboratory study, we employed stable isotope fingerprinting of amino acids to identify the biosynthetic origins of amino acids to bacteria, fungi and plants in enchytraeids. Enchytraeids collected from Arctic peatlands derived more than 80% of their EAA from bacteria. In a controlled feeding study with the enchytraeid Enchytraeus crypticus, EAA derived almost exclusively from gut bacteria when the worms fed on higher fibre diets, whereas most of the enchytraeids' EAA derived from dietary sources when fed on lower fibre diets. Our gene sequencing results of gut microbiota showed that the worms harbour several taxa in their gut lumen absent from their diets and substrates. Almost all gut taxa are candidates for EAA supplementation because almost all belong to clades capable of biosynthesizing EAA. Our study provides the first evidence of extensive symbiotic supplementation of EAA by microbial gut symbionts and demonstrates that symbiotic bacteria in the gut lumen appear to function as partners both for symbiotic EAA supplementation and for digestion of insoluble plant fibres.
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Affiliation(s)
- Thomas Larsen
- Department of Agroecology, Faculty of Sciences and Technology, Aarhus University, Blichers Allé, Postbox 50, 8830, Tjele, Denmark.,Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Marc Ventura
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Kristine Maraldo
- Department of Agroecology, Faculty of Sciences and Technology, Aarhus University, Blichers Allé, Postbox 50, 8830, Tjele, Denmark
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Yiming V Wang
- Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Nils Andersen
- Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Diane M O'Brien
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
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