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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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Li L, Qu L, Li T. The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats. Sci Rep 2023; 13:13134. [PMID: 37573461 PMCID: PMC10423290 DOI: 10.1038/s41598-023-39953-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 08/02/2023] [Indexed: 08/14/2023] Open
Abstract
Selenium (Se) is an important microelement for animal health. However, the knowledge about the effects of Se supplementation on rumen eukaryotic community remains less explored. In this study, the ruminal eukaryotic diversity in three months old Shaanbei white cashmere wether goats, with body weight (26.18 ± 2.71) kg, fed a basal diet [0.016 mg/kg Se dry matter (DM), control group (CG)] were compared to those animals given basal diet supplemented with different levels of organic Se in the form of Selenohomolanthionine (SeHLan), namely low Se group (LSE, 0.3 mg/kg DM), medium Se group (MSE, 0.6 mg/kg Se DM) and high Se group (HSE, 1.2 mg/kg DM) using 18S rRNA amplicon sequencing. Illumina sequencing generated 2,623,541 reads corresponding to 3123 operational taxonomic units (OTUs). Taxonomic analysis revealed that Eukaryota (77.95%) and Fungi (14.10%) were the dominant eukaryotic kingdom in all samples. The predominant rumen eukaryotic phylum was found to be Ciliophora (92.14%), while fungal phyla were dominated by Ascomycota (40.77%), Basidiomycota (23.77%), Mucoromycota (18.32%) and unidentified_Fungi (13.89%). The dominant eukaryotic genera were found to be Entodinium (55.44%), Ophryoscolex (10.51%) and Polyplastron (10.19%), while the fungal genera were dominanted by Mucor (15.39%), Pichia (9.88%), Aspergillu (8.24%), Malassezia (7.73%) and unidentified_Neocallimastigaceae (7.72%). The relative abundance of eukaryotic genera Ophryoscolex, Enoploplastron and fungal genus Mucor were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Spearman correlation analysis revealed that the ciliate protozoa and fungi were negatively correlated with each other. The results of this study provided newer information about the effects of Se on rumen eukaryotic diversity patterns using 18s rRNA high-throughput sequencing technology.
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Affiliation(s)
- Longping Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China
| | - Tuo Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, 719000, China
- College of Life Sciences, Yulin University, Yulin, 719000, China
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Arora J, Kinjo Y, Šobotník J, Buček A, Clitheroe C, Stiblik P, Roisin Y, Žifčáková L, Park YC, Kim KY, Sillam-Dussès D, Hervé V, Lo N, Tokuda G, Brune A, Bourguignon T. The functional evolution of termite gut microbiota. MICROBIOME 2022; 10:78. [PMID: 35624491 PMCID: PMC9137090 DOI: 10.1186/s40168-022-01258-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota. RESULTS We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. CONCLUSIONS Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Aleš Buček
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Crystal Clitheroe
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Lucia Žifčáková
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ki Yoon Kim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - David Sillam-Dussès
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology, LEEC, UR 4443, Villetaneuse, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
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Abstract
High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.
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Affiliation(s)
- Jennifer Pett-Ridge
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
| | - Peter K Weber
- Lawrence Livermore National Lab, Physical and Life Science Directorate, Livermore, CA, USA.
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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Husnik F, Tashyreva D, Boscaro V, George EE, Lukeš J, Keeling PJ. Bacterial and archaeal symbioses with protists. Curr Biol 2021; 31:R862-R877. [PMID: 34256922 DOI: 10.1016/j.cub.2021.05.049] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.
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Affiliation(s)
- Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Emma E George
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Cohen SK, Aschtgen MS, Lynch JB, Koehler S, Chen F, Escrig S, Daraspe J, Ruby EG, Meibom A, McFall-Ngai M. Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging. Cell Microbiol 2021; 22:e13177. [PMID: 32185893 DOI: 10.1111/cmi.13177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/18/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022]
Abstract
Extracellular bacterial symbionts communicate biochemically with their hosts to establish niches that foster the partnership. Using quantitative ion microprobe isotopic imaging (nanoscale secondary ion mass spectrometry [NanoSIMS]), we surveyed localization of 15 N-labelled molecules produced by the bacterium Vibrio fischeri within the cells of the symbiotic organ of its host, the Hawaiian bobtail squid, and compared that with either labelled non-specific species or amino acids. In all cases, two areas of the organ's epithelia were significantly more 15 N enriched: (a) surface ciliated cells, where environmental symbionts are recruited, and (b) the organ's crypts, where the symbiont population resides in the host. Label enrichment in all cases was strongest inside host cell nuclei, preferentially in the euchromatin regions and the nucleoli. This permissiveness demonstrated that uptake of biomolecules is a general mechanism of the epithelia, but the specific responses to V. fischeri cells recruited to the organ's surface are due to some property exclusive to this species. Similarly, in the organ's deeper crypts, the host responds to common bacterial products that only the specific symbiont can present in that location. The application of NanoSIMS allows the discovery of such distinct modes of downstream signalling dependent on location within the host and provides a unique opportunity to study the microbiogeographical patterns of symbiotic dialogue.
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Affiliation(s)
- Stephanie K Cohen
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie-Stéphanie Aschtgen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jonathan B Lynch
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Sabrina Koehler
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Fangmin Chen
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Stéphane Escrig
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, Hawai'i
| | - Anders Meibom
- Laboratory of Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
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Guzman J, Vilcinskas A. Bacteria associated with cockroaches: health risk or biotechnological opportunity? Appl Microbiol Biotechnol 2020; 104:10369-10387. [PMID: 33128616 PMCID: PMC7671988 DOI: 10.1007/s00253-020-10973-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
Abstract Cockroaches have existed for 300 million years and more than 4600 extant species have been described. Throughout their evolution, cockroaches have been associated with bacteria, and today Blattabacterium species flourish within specialized bacteriocytes, recycling nitrogen from host waste products. Cockroaches can disseminate potentially pathogenic bacteria via feces and other deposits, particularly members of the family Enterobacteriaceae, but also Staphylococcus and Mycobacterium species, and thus, they should be cleared from sites where hygiene is essential, such as hospitals and kitchens. On the other hand, cockroaches also carry bacteria that may produce metabolites or proteins with potential industrial applications. For example, an antibiotic-producing Streptomyces strain was isolated from the gut of the American cockroach Periplaneta americana. Other cockroach-associated bacteria, including but not limited to Bacillus, Enterococcus, and Pseudomonas species, can also produce bioactive metabolites that may be suitable for development as pharmaceuticals or plant protection products. Enzymes that degrade industrially relevant substrates, or that convert biomasses into useful chemical precursors, are also expressed in cockroach-derived bacteria and could be deployed for use in the food/feed, paper, oil, or cosmetics industries. The analysis of cockroach gut microbiomes has revealed a number of lesser-studied bacteria that may form the basis of novel taxonomic groups. Bacteria associated with cockroaches can therefore be dangerous or useful, and this review explores the bacterial clades that may provide opportunities for biotechnological exploitation. Key points • Members of the Enterobacteriaceae are the most frequently cultivated bacteria from cockroaches. • Cultivation-independent studies have revealed a diverse community, led by the phyla Bacteroidetes and Firmicutes. • Although cockroaches may carry pathogenic bacteria, most strains are innocuous and may be useful for biotechnological applications. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-10973-6.
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany.
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany.,Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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9
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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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10
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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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11
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Bar-Shmuel N, Behar A, Segoli M. What do we know about biological nitrogen fixation in insects? Evidence and implications for the insect and the ecosystem. INSECT SCIENCE 2020; 27:392-403. [PMID: 31207108 DOI: 10.1111/1744-7917.12697] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/22/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Many insects feed on a low-nitrogen diet, and the origin of their nitrogen supply is poorly understood. It has been hypothesized that some insects rely on nitrogen-fixing bacteria (diazotrophs) to supplement their diets. Nitrogen fixation by diazotrophs has been extensively studied and convincingly demonstrated in termites, while evidence for the occurrence and role of nitrogen fixation in the diet of other insects is less conclusive. Here, we summarize the methods to detect nitrogen fixation in insects and review the available evidence for its occurrence (focusing on insects other than termites). We distinguish between three aspects of nitrogen fixation investigations: (i) detecting the presence of potential diazotrophs; (ii) detecting the activity of the nitrogen-fixing enzyme; and (iii) detecting the assimilation of fixed nitrogen into the insect tissues. We show that although evidence from investigations of the first aspect reveals ample opportunities for interactions with potential diazotrophs in a variety of insects, demonstrations of actual biological nitrogen fixation and the assimilation of fixed nitrogen are restricted to very few insect groups, including wood-feeding beetles, fruit flies, leafcutter ants, and a wood wasp. We then discuss potential implications for the insect's fitness and for the ecosystem as a whole. We suggest that combining these multiple approaches is crucial for the study of nitrogen fixation in insects, and argue that further demonstrations are desperately needed in order to determine the relative importance of diazotrophs for insect diet and fitness, as well as to evaluate their overall impact on the ecosystem.
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Affiliation(s)
- Nitsan Bar-Shmuel
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Adi Behar
- Kimron Veterinary Institute, Department of Parasitology, Bet Dagan, Israel
| | - Michal Segoli
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
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12
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Stephens ME, Gage DJ. Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host. PLoS One 2020; 15:e0233065. [PMID: 32413056 PMCID: PMC7228121 DOI: 10.1371/journal.pone.0233065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
The hindgut protists of wood-feeding termites are usually colonized by prokaryotic symbionts. Many of the hurdles that have prevented a better understanding of these symbionts arise from variation among protist and termite host species and the inability to maintain prominent community members in culture. These issues have made it difficult to study the fidelity, acquisition, and differences in colonization of protists by bacterial symbionts. In this study, we use high throughput amplicon sequencing of the V4 region of 16S rRNA genes to determine the composition of bacterial communities associated with single protist cells of six protist species, from the genera Pyrsonympha, Dinenympha, and Trichonympha that are present in the hindgut of the termite Reticulitermes flavipes. By analyzing amplicon sequence variants (ASVs), the diversity and distribution of protist-associated bacteria was compared within and across these six different protist species. ASV analysis showed that, in general, each protist genus associated with a distinct community of bacterial symbionts which were conserved across different termite colonies. However, some ASVs corresponding to ectosymbionts (Spirochaetes) were shared between different Dinenympha species and to a lesser extent with Pyrsonympha and Trichonympha hosts. This suggested that certain bacterial symbionts may be cosmopolitan to some degree and perhaps acquired by horizontal transmission. Using a fluorescence-based cell assay, we could observe the horizontal acquisition of surface-bound bacteria. This acquisition was shown to be time-dependent, involve active processes, and was non-random with respect to binding locations on some protists.
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Affiliation(s)
- Michael E. Stephens
- Department of Entomology, Cornell University, Ithaca NY, United States of America
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States of America
| | - Daniel J. Gage
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States of America
- * E-mail:
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13
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Nalepa CA. Origin of Mutualism Between Termites and Flagellated Gut Protists: Transition From Horizontal to Vertical Transmission. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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14
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Treitli SC, Kolisko M, Husník F, Keeling PJ, Hampl V. Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics. Proc Natl Acad Sci U S A 2019; 116:19675-19684. [PMID: 31492817 PMCID: PMC6765251 DOI: 10.1073/pnas.1910793116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lower termites harbor in their hindgut complex microbial communities that are involved in the digestion of cellulose. Among these are protists, which are usually associated with specific bacterial symbionts found on their surface or inside their cells. While these form the foundations of a classic system in symbiosis research, we still know little about the functional basis for most of these relationships. Here, we describe the complex functional relationship between one protist, the oxymonad Streblomastix strix, and its ectosymbiotic bacterial community using single-cell genomics. We generated partial assemblies of the host S. strix genome and Candidatus Ordinivivax streblomastigis, as well as a complex metagenome assembly of at least 8 other Bacteroidetes bacteria confirmed by ribosomal (r)RNA fluorescence in situ hybridization (FISH) to be associated with S. strix. Our data suggest that S. strix is probably not involved in the cellulose digestion, but the bacterial community on its surface secretes a complex array of glycosyl hydrolases, providing them with the ability to degrade cellulose to monomers and fueling the metabolism of S. strix In addition, some of the bacteria can fix nitrogen and can theoretically provide S. strix with essential amino acids and cofactors, which the protist cannot synthesize. On the contrary, most of the bacterial symbionts lack the essential glycolytic enzyme enolase, which may be overcome by the exchange of intermediates with S. strix This study demonstrates the value of the combined single-cell (meta)genomic and FISH approach for studies of complicated symbiotic systems.
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Affiliation(s)
- Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42 Vestec, Czech Republic
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Filip Husník
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42 Vestec, Czech Republic;
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15
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16
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Kinjo Y, Bourguignon T, Tong KJ, Kuwahara H, Lim SJ, Yoon KB, Shigenobu S, Park YC, Nalepa CA, Hongoh Y, Ohkuma M, Lo N, Tokuda G. Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches. Genome Biol Evol 2018; 10:1622-1630. [PMID: 29860278 PMCID: PMC6022663 DOI: 10.1093/gbe/evy110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 12/23/2022] Open
Abstract
Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti. On the basis of genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of ∼630 kbp, with the exception of the termite Mastotermes darwiniensis (∼590 kbp) and Cryptocercus punctulatus (∼614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from three species of Cryptocercus in order to shed light on the genomic evolution of Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived Blattabacterium genomes were reduced (∼614 kbp), except for that associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic analysis of these genomes and their content indicates that Blattabacterium experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly due to similar selective forces. We found evidence of ongoing genome reduction in Blattabacterium from three lineages of the C. punctulatus species complex, which independently lost one cysteine biosynthetic gene. We also sequenced the genome of the Blattabacterium associated with Salganea taiwanensis, a subsocial xylophagous cockroach that does not vertically transmit gut symbionts via proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial cockroaches. Overall, our results show that genome reduction occurred on multiple occasions in Blattabacterium, and is still ongoing, possibly because of new associations with gut symbionts in some lineages.
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Affiliation(s)
- Yukihiro Kinjo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Kwei Jun Tong
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Hirokazu Kuwahara
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Sang Jin Lim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Shuji Shigenobu
- National Institute for Basic Biology, NIBB Core Research Facilities, Okazaki, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Christine A Nalepa
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, USA
| | - Yuichi Hongoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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17
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Levy B, Jami E. Exploring the Prokaryotic Community Associated With the Rumen Ciliate Protozoa Population. Front Microbiol 2018; 9:2526. [PMID: 30420841 PMCID: PMC6217230 DOI: 10.3389/fmicb.2018.02526] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/03/2018] [Indexed: 11/13/2022] Open
Abstract
Ciliate protozoa are an integral part of the rumen microbiome and were found to exert a large effect on the rumen ecosystem itself as well as their host animal physiology. Part of these effects have been attributed to their ability to harbor a diverse ecto- and endo-symbiotic community of prokaryotic cells. Studies on the relationship between the protozoa population and their associated prokaryotic community in the rumen mainly focused on the methanogens, revealing that protozoa play a major role in enhancing methanogenesis potential. In contrast, little is known about the composition and function of the bacteria associated with rumen protozoa and the extent of this association. In this study, we characterize the prokaryotic communities associated with different protozoa populations and compare their structure to the free-living prokaryotic population residing in the cow rumen. We show that the overall protozoa associated prokaryotic community structure differs significantly compared to the free-living community in terms of richness and composition. The methanogens proportion was significantly higher in all protozoa populations compared to the free-living fraction, while the Lachnospiraceae was the most prevalent bacterial family in the protozoa associated bacterial communities. Several taxa not detected or detected in extremely low abundance in the free-living community were enriched in the protozoa associated bacterial community. These include members of the Endomicrobia class, previously identified as protozoa symbionts in the termite gut. Our results show that rumen protozoa harbor prokaryotic communities that are compositionally different from their surroundings, which may be the result of specific tropism between the prokaryotic community and protozoa.
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Affiliation(s)
- Bar Levy
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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18
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Overlapping Community Compositions of Gut and Fecal Microbiomes in Lab-Reared and Field-Collected German Cockroaches. Appl Environ Microbiol 2018; 84:AEM.01037-18. [PMID: 29959246 PMCID: PMC6102980 DOI: 10.1128/aem.01037-18] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023] Open
Abstract
German cockroaches, Blattella germanica (Blattodea: Ectobiidae), are human commensals that move freely between food and waste, disseminating bacteria, including potential pathogens, through their feces. However, the relationship between the microbial communities of the cockroach gut and feces is poorly understood. We analyzed the V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene by next-generation sequencing (NGS) to compare the bacterial and protist diversities in guts versus feces and males versus females, as well as assess variation across cockroach populations. Cockroaches harbored a diverse array of bacteria, and 80 to 90% of the operational taxonomic units (OTUs) were shared between the feces and gut. Lab-reared and field-collected cockroaches had distinct microbiota, and whereas lab-reared cockroaches had relatively conserved communities, considerable variation was observed in the microbial community composition of cockroaches collected in different apartments. Nonetheless, cockroaches from all locations shared some core bacterial taxa. The eukaryotic community in the feces of field-collected cockroaches was found to be more diverse than that in lab-reared cockroaches. These results demonstrate that cockroaches disseminate their gut microbiome in their feces, and they underscore the important contribution of the cockroach fecal microbiome to the microbial diversity of cockroach-infested homes.IMPORTANCE The German cockroach infests diverse human-built structures, including homes and hospitals. It produces potent allergens that trigger asthma and disseminates opportunistic pathogens in its feces. A comprehensive understanding of gut and fecal microbial communities of cockroaches is essential not only to understand their contribution to the biology of the cockroach, but also for exploring their clinical relevance. In this study, we compare the diversity of bacteria and eukaryotes in the cockroach gut and feces and assess the variation in the gut microbiota across cockroach populations.
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19
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Farming, slaving and enslavement: histories of endosymbioses during kinetoplastid evolution. Parasitology 2018; 145:1311-1323. [PMID: 29895336 DOI: 10.1017/s0031182018000781] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Parasitic trypanosomatids diverged from free-living kinetoplastid ancestors several hundred million years ago. These parasites are relatively well known, due in part to several unusual cell biological and molecular traits and in part to the significance of a few - pathogenic Leishmania and Trypanosoma species - as aetiological agents of serious neglected tropical diseases. However, the majority of trypanosomatid biodiversity is represented by osmotrophic monoxenous parasites of insects. In two lineages, novymonads and strigomonads, osmotrophic lifestyles are supported by cytoplasmic endosymbionts, providing hosts with macromolecular precursors and vitamins. Here we discuss the two independent origins of endosymbiosis within trypanosomatids and subsequently different evolutionary trajectories that see entrainment vs tolerance of symbiont cell divisions cycles within those of the host. With the potential to inform on the transition to obligate parasitism in the trypanosomatids, interest in the biology and ecology of free-living, phagotrophic kinetoplastids is beginning to enjoy a renaissance. Thus, we take the opportunity to additionally consider the wider relevance of endosymbiosis during kinetoplastid evolution, including the indulged lifestyle and reductive evolution of basal kinetoplastid Perkinsela.
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20
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Cui L, Yang K, Li HZ, Zhang H, Su JQ, Paraskevaidi M, Martin FL, Ren B, Zhu YG. Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N 2 Labeling. Anal Chem 2018; 90:5082-5089. [PMID: 29557648 DOI: 10.1021/acs.analchem.7b05080] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nitrogen (N) fixation is the conversion of inert nitrogen gas (N2) to bioavailable N essential for all forms of life. N2-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15N2 stable isotope probing (SIP) was developed to discern N2-fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N2-fixing bacteria), along with a marked 15N2-induced Cyt c band shift, generated a highly distinguishable biomarker for N2 fixation. 15N2-induced shift was consistent well with 15N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N2-fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus 15N2 percentage allowed quantification of N2 fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.
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Affiliation(s)
- Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Han Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences , University of Central Lancashire , Preston PR1 2HE , U.K
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences , University of Central Lancashire , Preston PR1 2HE , U.K
| | - Bin Ren
- Department of Chemistry , Xiamen University , Xiamen 361005 , China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
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21
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Nalepa CA. What Kills the Hindgut Flagellates of Lower Termites during the Host Molting Cycle? Microorganisms 2017; 5:E82. [PMID: 29258251 PMCID: PMC5748591 DOI: 10.3390/microorganisms5040082] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 11/17/2022] Open
Abstract
Subsocial wood feeding cockroaches in the genus Cryptocercus, the sister group of termites, retain their symbiotic gut flagellates during the host molting cycle, but in lower termites, closely related flagellates die prior to host ecdysis. Although the prevalent view is that termite flagellates die because of conditions of starvation and desiccation in the gut during the host molting cycle, the work of L.R. Cleveland in the 1930s through the 1960s provides a strong alternate hypothesis: it was the changed hormonal environment associated with the origin of eusociality and its concomitant shift in termite developmental ontogeny that instigates the death of the flagellates in termites. Although the research on termite gut microbial communities has exploded since the advent of modern molecular techniques, the role of the host hormonal environment on the life cycle of its gut flagellates has been neglected. Here Cleveland's studies are revisited to provide a basis for re-examination of the problem, and the results framed in the context of two alternate hypotheses: the flagellate symbionts are victims of the change in host social status, or the flagellates have become incorporated into the life cycle of the eusocial termite colony. Recent work on parasitic protists suggests clear paths for exploring these hypotheses and for resolving long standing issues regarding sexual-encystment cycles in flagellates of the Cryptocercus-termite lineage using molecular methodologies, bringing the problem into the modern era.
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Affiliation(s)
- Christine A Nalepa
- Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA.
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22
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Vera-Ponce de León A, Ormeño-Orrillo E, Ramírez-Puebla ST, Rosenblueth M, Degli Esposti M, Martínez-Romero J, Martínez-Romero E. Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae). Genome Biol Evol 2017; 9:2237-2250. [PMID: 30605507 PMCID: PMC5604089 DOI: 10.1093/gbe/evx156] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.
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Affiliation(s)
- Arturo Vera-Ponce de León
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ernesto Ormeño-Orrillo
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de
Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Shamayim T Ramírez-Puebla
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mauro Degli Esposti
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Julio Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
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Laczny CC, Kiefer C, Galata V, Fehlmann T, Backes C, Keller A. BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res 2017; 45:W171-W179. [PMID: 28472498 PMCID: PMC5570254 DOI: 10.1093/nar/gkx348] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/11/2017] [Accepted: 04/21/2017] [Indexed: 12/20/2022] Open
Abstract
Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.
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Affiliation(s)
- Cedric C. Laczny
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Christina Kiefer
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
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24
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Smith CC, Srygley RB, Healy F, Swaminath K, Mueller UG. Spatial Structure of the Mormon Cricket Gut Microbiome and its Predicted Contribution to Nutrition and Immune Function. Front Microbiol 2017; 8:801. [PMID: 28553263 PMCID: PMC5427142 DOI: 10.3389/fmicb.2017.00801] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/19/2017] [Indexed: 01/24/2023] Open
Abstract
The gut microbiome of insects plays an important role in their ecology and evolution, participating in nutrient acquisition, immunity, and behavior. Microbial community structure within the gut is heavily influenced by differences among gut regions in morphology and physiology, which determine the niches available for microbes to colonize. We present a high-resolution analysis of the structure of the gut microbiome in the Mormon cricket Anabrus simplex, an insect known for its periodic outbreaks in the western United States and nutrition-dependent mating system. The Mormon cricket microbiome was dominated by 11 taxa from the Lactobacillaceae, Enterobacteriaceae, and Streptococcaceae. While most of these were represented in all gut regions, there were marked differences in their relative abundance, with lactic-acid bacteria (Lactobacillaceae) more common in the foregut and midgut and enteric (Enterobacteriaceae) bacteria more common in the hindgut. Differences in community structure were driven by variation in the relative prevalence of three groups: a Lactobacillus in the foregut, Pediococcus lactic-acid bacteria in the midgut, and Pantoea agglomerans, an enteric bacterium, in the hindgut. These taxa have been shown to have beneficial effects on their hosts in insects and other animals by improving nutrition, increasing resistance to pathogens, and modulating social behavior. Using PICRUSt to predict gene content from our 16S rRNA sequences, we found enzymes that participate in carbohydrate metabolism and pathogen defense in other orthopterans. These were predominately represented in the hindgut and midgut, the most important sites for nutrition and pathogen defense. Phylogenetic analysis of 16S rRNA sequences from cultured isolates indicated low levels of divergence from sequences derived from plants and other insects, suggesting that these bacteria are likely to be exchanged between Mormon crickets and the environment. Our study shows strong spatial variation in microbiome community structure, which influences predicted gene content and thus the potential of the microbiome to influence host function.
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Affiliation(s)
- Chad C Smith
- Department of Integrative Biology, University of Texas at Austin, AustinTX, USA
| | - Robert B Srygley
- Northern Plains Agricultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, SidneyMT, USA
| | - Frank Healy
- Department of Biology, Trinity University, San AntonioTX, USA
| | | | - Ulrich G Mueller
- Department of Integrative Biology, University of Texas at Austin, AustinTX, USA
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25
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Nalepa CA, Shimada K, Maekawa K, Luykx P. Distribution of Karyotypes of the Cryptocercus punctulatus Species Complex (Blattodea: Cryptocercidae) in Great Smoky Mountains National Park. JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:3793261. [PMID: 28475683 PMCID: PMC5416888 DOI: 10.1093/jisesa/iex045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Indexed: 06/07/2023]
Abstract
During the period between 1999 and 2006, wood-feeding cockroaches in the Cryptocercus punctulatus Scudder species complex were collected throughout Great Smoky Mountains National Park, USA. The chromosome numbers of insects from 59 sites were determined, and phylogenetic analyses were performed based on mitochondrial COII and nuclear ITS2 DNA. The distribution of the three male karyotypes found in the park (2n = 37, 39, and 45) is mapped and discussed in relation to recent disturbances and glacial history. Clades of the three karyotype groups meet near the ridgeline separating North Carolina from Tennessee in the center of the park, suggesting that these may have originated from separate lower elevation refugia after the last glacial maximum. The timing of divergence and a significant correlation between elevation difference and genetic distance in two of the clades supports this hypothesis. The ecological role of the cockroaches in the park is discussed.
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Affiliation(s)
- Christine A Nalepa
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA
| | - Keisuke Shimada
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan ( ; )
- Current address: Ishikawa Museum of Natural History, Ri-441 Choshi-machi, Kanazawa, Ishikawa 920-1147, Japan
| | - Kiyoto Maekawa
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan (; )
| | - Peter Luykx
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
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26
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Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol 2016; 41:114-121. [PMID: 27419912 DOI: 10.1016/j.copbio.2016.06.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/09/2016] [Accepted: 06/23/2016] [Indexed: 12/29/2022]
Abstract
The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where used to track exchanges of isotopically labelled molecules between organisms. We highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont-host nutrient sharing.
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Affiliation(s)
- Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kilian Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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