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Takahashi K, Kuwahara H, Horikawa Y, Izawa K, Kato D, Inagaki T, Yuki M, Ohkuma M, Hongoh Y. Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade. THE ISME JOURNAL 2023; 17:1895-1906. [PMID: 37653056 PMCID: PMC10579323 DOI: 10.1038/s41396-023-01502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.
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Affiliation(s)
- Kazuki Takahashi
- 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
| | - Yutaro Horikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kazuki Izawa
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Daiki Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Tatsuya Inagaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, 305-0074, 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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Kashinskaya EN, Simonov EP, Vlasenko PG, Markevich GN, Shokurova AV, Andree KB, Solovyev MM. The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia). J Nematol 2021; 53:e2021-106. [PMID: 34957411 PMCID: PMC8672423 DOI: 10.21307/jofnem-2021-106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.
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Affiliation(s)
- E N Kashinskaya
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,University of Tyumen, Institute of Environmental and Agricultural Biology (X-BIO), 25 Lenina St., Tyumen, 625003, Russia
| | - P G Vlasenko
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | | | - A V Shokurova
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - K B Andree
- Instituto de Investigación y Tecnología Agroalimentarias; Cultius Aquàtics; San Carlos de la Rapita, Tarragona, ES 08140, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,Tomsk State University; Institute of Biology, Ecology, Soil Science, Agriculture, and Forestry; 36 Lenin Ave, Tomsk, 634050, Russia
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Arango RA, Schoville SD, Currie CR, Carlos-Shanley C. Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar). Front Microbiol 2021; 12:632715. [PMID: 34079527 PMCID: PMC8166220 DOI: 10.3389/fmicb.2021.632715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/15/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding the effects of environmental disturbances on insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts are known to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. In this study, subterranean termites [Reticulitermes flavipes (Kollar)] were exposed to three different temperature treatments characterized as low (15°C), medium (27°C), and high (35°C). Results suggested that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites also showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termite's physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.
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Affiliation(s)
- Rachel A. Arango
- USDA Forest Service, Forest Products Laboratory, Madison, WI, United States
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
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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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Jahnes BC, Sabree ZL. Nutritional symbiosis and ecology of host-gut microbe systems in the Blattodea. CURRENT OPINION IN INSECT SCIENCE 2020; 39:35-41. [PMID: 32109859 DOI: 10.1016/j.cois.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/31/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Cockroaches and termites (Order: Blattodea) have been the subject of substantial research attention for over a century due, in part, to a subset of them having a strong propensity to cohabitate with humans and their structures. Recent research has led to numerous insights into their behavior, physiology, and ecology, as well as their ability to harbor taxonomically diverse microbial communities within their digestive systems, which include taxa that contribute to host growth and development. Further, recent investigations into the physiological and behavioral adaptations that enable recalcitrant polysaccharide digestion and the maintenance of microbial symbionts in cockroaches and termites suggests that symbionts contribute significantly to nutrient provisioning and processing.
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Affiliation(s)
- Benjamin C Jahnes
- Department of Microbiology, Ohio State University, 105 Biological Sciences Building, 484 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Zakee L Sabree
- Department of Microbiology, Ohio State University, 105 Biological Sciences Building, 484 W. 12th Avenue, Columbus, OH, 43210, USA; Department of Evolution, Ecology and Organismal Biology, Ohio State University, 300 Aronoff Laboratory, 318 W. 12th Avenue, Columbus OH, 43210, USA.
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Lampert N, Mikaelyan A, Brune A. Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches. BMC Microbiol 2019; 19:238. [PMID: 31666028 PMCID: PMC6864750 DOI: 10.1186/s12866-019-1601-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/20/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. RESULTS The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. CONCLUSION Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.
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Affiliation(s)
- Niclas Lampert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Aram Mikaelyan
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,Present Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27607, USA
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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