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Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
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Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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2
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Diet Influences the Gut Microbial Diversity and Olfactory Preference of the German Cockroach Blattella germanica. Curr Microbiol 2022; 80:23. [PMID: 36460931 DOI: 10.1007/s00284-022-03123-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
The gut microbiota of insects has been proven to play a role in the host's nutrition and foraging. The German cockroach, Blattella germanica, is an important vector of various pathogens and causes severe allergic reactions in humans. Food bait is an effective and frequently used method of controlling this omnivorous insect. Thus, understanding the relationships among diet, gut microbiota, and olfactory preferences could be useful for optimizing this management strategy. In this study, B. germanica was exposed to different foods, i.e., high-fat diet, high-protein diet, high-starch diet, and dog food (as control). Then their gut microbial and olfactory responses were investigated. 16S rRNA gene sequencing confirmed that the gut microbiota significantly differed across the four treatments, especially in relation to bacteria associated with the metabolism and digestion of essential components. Behavioral tests and the antenna electrophysiological responses showed that insects had a greater preference for other types of diets compared with their long-term domesticated diet. Moreover, continuously providing a single-type diet could change almost all the OR genes' expression of B. germanica, especially BgORco, which was significantly repressed compared to control. These results indicate that diet can shape the gut microbiota diversity and drive the olfactory preference of B. germanica. The association between gut microbiota profiles and diets can be utilized in managing B. germanica according to their olfactory preference.
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3
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Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses. Microbiol Spectr 2022; 10:e0277922. [PMID: 36094208 PMCID: PMC9603385 DOI: 10.1128/spectrum.02779-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of "collaborative pathways" for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems. IMPORTANCE The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as "collaborative pathways". To date, collaborative pathways have only been reported from sap-feeding insects. Here, we examined metabolic interactions between cockroaches, a group of detritivorous insects, and their obligate endosymbiont, Blattabacterium, and only found evidence of collaborative pathways for arginine biosynthesis. The rarity of collaborative pathways in cockroaches and Blattabacterium contrasts with their prevalence in insect hosts feeding on phloem-sap. Our results suggest that host diet is a factor affecting metabolic integration in obligate symbiotic systems.
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4
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Manthey JD, Girón JC, Hruska JP. Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts. Ecol Evol 2022; 12:e9026. [PMID: 35795355 PMCID: PMC9251289 DOI: 10.1002/ece3.9026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures.
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Affiliation(s)
- Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - Jennifer C. Girón
- Department of EntomologyPurdue UniversityWest LafayetteIndianaUSA
- Natural Science Research LaboratoryMuseum of Texas Tech UniversityLubbockTexasUSA
| | - Jack P. Hruska
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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5
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Of Cockroaches and Symbionts: Recent Advances in the Characterization of the Relationship between Blattella germanica and Its Dual Symbiotic System. Life (Basel) 2022; 12:life12020290. [PMID: 35207577 PMCID: PMC8878154 DOI: 10.3390/life12020290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Mutualistic stable symbioses are widespread in all groups of eukaryotes, especially in insects, where symbionts have played an essential role in their evolution. Many insects live in obligate relationship with different ecto- and endosymbiotic bacteria, which are needed to maintain their hosts’ fitness in their natural environment, to the point of even relying on them for survival. The case of cockroaches (Blattodea) is paradigmatic, as both symbiotic systems coexist in the same organism in two separated compartments: an intracellular endosymbiont (Blattabacterium) inside bacteriocytes located in the fat body, and a rich and complex microbiota in the hindgut. The German cockroach Blattella germanica is a good model for the study of symbiotic interactions, as it can be maintained in the laboratory in controlled populations, allowing the perturbations of the two symbiotic systems in order to study the communication and integration of the tripartite organization of the host–endosymbiont–microbiota, and to evaluate the role of symbiotic antimicrobial peptides (AMPs) in host control over their symbionts. The importance of cockroaches as reservoirs and transmission vectors of antibiotic resistance sequences, and their putative interest to search for AMPs to deal with the problem, is also discussed.
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6
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Kinjo Y, Lo N, Martín PV, Tokuda G, Pigolotti S, Bourguignon T. Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont. Mol Biol Evol 2021; 38:3820-3831. [PMID: 34426845 PMCID: PMC8382890 DOI: 10.1093/molbev/msab159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.
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Affiliation(s)
- Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Paula Villa Martín
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Simone Pigolotti
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
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7
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Cao Y, Dietrich CH. Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for Auchenorrhyncha phylogeny. Cladistics 2021; 38:38-58. [DOI: 10.1111/cla.12474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yanghui Cao
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL61820USA
| | - Christopher H. Dietrich
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL61820USA
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8
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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9
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Arab DA, Lo N. Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts. J Mol Evol 2021; 89:238-248. [PMID: 33730185 DOI: 10.1007/s00239-021-10001-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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10
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Noda T, Okude G, Meng XY, Koga R, Moriyama M, Fukatsu T. Bacteriocytes and Blattabacterium Endosymbionts of the German Cockroach Blattella germanica, the Forest Cockroach Blattella nipponica, and Other Cockroach Species. Zoolog Sci 2020; 37:399-410. [PMID: 32972080 DOI: 10.2108/zs200054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/30/2020] [Indexed: 11/17/2022]
Abstract
Cockroaches are commonly found in human residences and notorious as hygienic and nuisance pests. Notably, however, no more than 30 cockroach species are regarded as pests, while the majority of 4,500 cockroaches in the world are living in forest environments with little relevance to human life. Why some cockroaches have exceptionally adapted to anthropic environments and established pest status is of interest. Here we investigated the German cockroach Blattella germanica, which is a cosmopolitan pest species, and the forest cockroach Blattella nipponica, which is a wild species closely related to B. germanica. In contrast to easy rearing of B. germanica, laboratory rearing of B. nipponica was challenging-several trials enabled us to keep the insects for up to three months. We particularly focused on the distribution patterns of specialized cells, bacteriocytes, for harboring endosymbiotic Blattabacterium, which has been suggested to contribute to host's nitrogen metabolism and recycling, during the postembryonic development of the insects. The bacteriocytes were consistently localized to visceral fat bodies filling the abdominal body cavity, where a number of single bacteriocytes were scattered among the adipocytes, throughout the developmental stages in both females and males. The distribution patterns of the bacteriocytes were quite similar between B. germanica and B. nipponica, and also among other diverse cockroach species, plausibly reflecting the highly conserved cockroach-Blattabacterium symbiotic association over evolutionary time. Our study lays a foundation to experimentally investigate the origin and the processes of urban pest evolution, on account of possible involvement of microbial associates.
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Affiliation(s)
- Tomohito Noda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Genta Okude
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Xian-Ying Meng
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Ryuichi Koga
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Minoru Moriyama
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Takema Fukatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan,
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11
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Kashkouli M, Castelli M, Floriano AM, Bandi C, Epis S, Fathipour Y, Mehrabadi M, Sassera D. Characterization of a novel Pantoea symbiont allows inference of a pattern of convergent genome reduction in bacteria associated with Pentatomidae. Environ Microbiol 2020; 23:36-50. [PMID: 32686279 DOI: 10.1111/1462-2920.15169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022]
Abstract
Phytophagous stink bugs typically harbor nutritional symbiotic bacteria in their midgut, to integrate their unbalanced diet. In the Pentatomidae, most symbionts are affiliated to the genus Pantoea, and are polyphyletic. This suggests a scenario of an ancestral establishment of symbiosis, followed by multiple symbiont replacement events by akin environmental bacteria in different host lineages. In this study, a novel Pantoeaspecies ('CandidatusPantoea persica') was characterized from the gut of the pentatomid Acrosternum arabicum, and shown to be highly abundant in a specific portion of the gut and necessary for the host development. The genome of the symbiont (2.9 Mb), while presenting putative host-supportive metabolic pathways, including those for amino acids and vitamin synthesis, showed a high level of pseudogenization, indicating ongoing genome reduction. Comparative analyses with other free-living and symbiotic Pantoea highlighted a convergent pattern of genome reduction in symbionts of pentatomids, putatively following the typical phases modelized in obligate nutritional symbionts of insects. Additionally, this system has distinctive traits, as hosts are closely related, and symbionts originated multiple independent times from closely related free-living bacteria, displaying convergent and independent conspicuous genome reduction. Due to such peculiarities, this may become an ideal model to study genome evolutionary processes in insect symbionts.
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Affiliation(s)
- Marzieh Kashkouli
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Michele Castelli
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy.,Department of Biology and Biotechnology, University of Pavia, 27100, Italy
| | - Anna M Floriano
- Department of Biology and Biotechnology, University of Pavia, 27100, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy
| | - Yaghoub Fathipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, 27100, Italy
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12
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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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13
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Arab DA, Bourguignon T, Wang Z, Ho SYW, Lo N. Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes. Biol Lett 2020; 16:20190702. [PMID: 31910734 DOI: 10.1098/rsbl.2019.0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.,Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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14
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The power of neuropeptide precursor sequences to reveal phylogenetic relationships in insects: A case study on Blattodea. Mol Phylogenet Evol 2019; 143:106686. [PMID: 31740335 DOI: 10.1016/j.ympev.2019.106686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 11/20/2022]
Abstract
Recent state-of-the-art analyses in insect phylogeny have exclusively used very large datasets to elucidate higher-level phylogenies. We have tested an alternative and novel approach by evaluating the potential phylogenetic signals of identified and relatively short neuropeptide precursor sequences with highly conserved functional units. For that purpose, we examined available transcriptomes of 40 blattodean species for the translated amino acid sequences of 17 neuropeptide precursors. Recently proposed intra-ordinal relationships of Blattodea, based on the analysis of 2370 protein-coding nuclear single-copy genes (Evangelista et al., 2019), were corroborated with maximum support. The functionally different precursor units were analyzed separately for their phylogenetic information. Although the degree of information was different in the different sequence motifs, all precursor units contained phylogenetic informative data at the ordinal level, and their separate analysis did not reveal contradictory topologies. This study is the first comprehensive exploitation of complete neuropeptide precursor sequences of arthropods in such a context and demonstrates the applicability of these rather short but conserved sequences for an alternative, fast and simple analysis of phylogenetic relationships.
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15
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Evangelista DA, Wipfler B, Béthoux O, Donath A, Fujita M, Kohli MK, Legendre F, Liu S, Machida R, Misof B, Peters RS, Podsiadlowski L, Rust J, Schuette K, Tollenaar W, Ware JL, Wappler T, Zhou X, Meusemann K, Simon S. An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea). Proc Biol Sci 2019; 286:20182076. [PMID: 30963947 PMCID: PMC6364590 DOI: 10.1098/rspb.2018.2076] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/04/2019] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.
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Affiliation(s)
- Dominic A. Evangelista
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Dabney Hall, 1416 Circle Dr., Knoxville, TN 37996, USA
| | - Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller Universität Jena, Vor dem Neutor 1, 07743 Jena, Germany
- Center for Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Olivier Béthoux
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, Paris, France
- Muséum national d'Histoire naturelle, 57 rue Cuvier, CP38, 75005 Paris, France
| | - Alexander Donath
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Manpreet K. Kohli
- Federated Department of Biological Sciences, Rutgers, The State University of New Jersey and NJIT, 195 University Ave, Newark, NJ 07102, USA
| | - Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Ralph S. Peters
- Center for Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Jes Rust
- Steinmann-Institute, Institute for Paleontology, University of Bonn, Nussallee 8, 53115 Bonn, Germany
| | - Kai Schuette
- Animal Ecology and Conservation, Zoological Institute, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ward Tollenaar
- Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jessica L. Ware
- Federated Department of Biological Sciences, Rutgers, The State University of New Jersey and NJIT, 195 University Ave, Newark, NJ 07102, USA
| | - Torsten Wappler
- Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Karen Meusemann
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, Australian Capital Territory, Australia
- Evolutionary Biology and Ecology, Institute for Biology I, University of Freiburg, Hauptstr. 1, 79104 Freiburg (Brsg.), Germany
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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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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Alleman A, Hertweck KL, Kambhampati S. Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome. Sci Rep 2018; 8:13427. [PMID: 30194350 PMCID: PMC6128925 DOI: 10.1038/s41598-018-31796-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/21/2018] [Indexed: 01/30/2023] Open
Abstract
Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.
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Affiliation(s)
- Austin Alleman
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Kate L Hertweck
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
| | - Srini Kambhampati
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
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18
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Vicente CSL, Mondal SI, Akter A, Ozawa S, Kikuchi T, Hasegawa K. Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PLoS One 2018; 13:e0200512. [PMID: 29990378 PMCID: PMC6039017 DOI: 10.1371/journal.pone.0200512] [Citation(s) in RCA: 9] [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: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022] Open
Abstract
The successful adaptation of cockroaches is, in part, dependent of the activity of their obligatory endosymbionts, Blattabacterium spp., which are involved in uric acid degradation, nitrogen assimilation and nutrient provisioning. Their strategic localization, within bacteriocytes in the proximities of uric acid storage cells (urocytes), highlights their importance in the recycling of nitrogen from urea and ammonia, end-products not secreted by their host insects. In this study, we present the complete genome sequence of two new Blattabacterium spp. from Periplaneta fuliginosa (BPfu) and P. japonica (BPja), and detailed comparison with other Blattabacterium strains from different cockroach species. The genomes of BPfu and BPja show a high degree of stability as showed with for other Blattabacterium representatives, only presenting a 19-kb fragment inversion between BPja and BPfu. In fact, the phylogenomics showed BPja as an ancestor species of BPfu, BPLAN (P. americana) and BBor (Blatta orientalis), in congruence with their host cockroach phylogeny. Their functional profile is similar and closest to the omnivorous strain BBge (Blattella germanica). Interesting, BPja possesses the complete set of enzymes involved sulfate assimilatory pathway only found in BBge and BMda (Mastotermes darwiniensis). The newly sequenced genomes of BPja and BPfu emphasise the remarkable stability of Blattabacterium genomes supported by their long-term coevolution and obligatory lifestyle in their host insect.
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Affiliation(s)
- Cláudia S. L. Vicente
- NemaLab/ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Shakhinur Islam Mondal
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Arzuba Akter
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Sota Ozawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Tasei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koichi Hasegawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
- * E-mail:
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19
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Evangelista D, Thouzé F, Kohli MK, Lopez P, Legendre F. Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny. Mol Phylogenet Evol 2018; 128:112-122. [PMID: 29969656 DOI: 10.1016/j.ympev.2018.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 11/18/2022]
Abstract
Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.
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Affiliation(s)
- Dominic Evangelista
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - France Thouzé
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Manpreet Kaur Kohli
- Department of Biological Sciences, Rutgers, The State University of New Jersey, 195 University Ave., Newark, NJ 07102, United States.
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
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20
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Magnabosco C, Moore KR, Wolfe JM, Fournier GP. Dating phototrophic microbial lineages with reticulate gene histories. GEOBIOLOGY 2018; 16:179-189. [PMID: 29384268 PMCID: PMC5873394 DOI: 10.1111/gbi.12273] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/23/2017] [Indexed: 05/19/2023]
Abstract
Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non-sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non-sulfur bacteria, prior to the GOE. Together, these results indicate that HGT-constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.
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Affiliation(s)
- C. Magnabosco
- Flatiron Institute Center for Computational BiologySimons FoundationNew York, NYUSA
| | - K. R. Moore
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - J. M. Wolfe
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - G. P. Fournier
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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21
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Taerum SJ, De Martini F, Liebig J, Gile GH. Incomplete Co-cladogenesis Between Zootermopsis Termites and Their Associated Protists. ENVIRONMENTAL ENTOMOLOGY 2018; 47:184-195. [PMID: 29325010 DOI: 10.1093/ee/nvx193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Coevolution is a major driver of speciation in many host-associated symbionts. In the termite-protist digestive symbiosis, the protists are vertically inherited by anal feeding among nest mates. Lower termites (all termite families except Termitidae) and their symbionts have broadly co-diversified over ~170 million yr. However, this inference is based mainly on the restricted distribution of certain protist genera to certain termite families. With the exception of one study, which demonstrated congruent phylogenies for the protist Pseudotrichonympha and its Rhinotermitidae hosts, coevolution in this symbiosis has not been investigated with molecular methods. Here we have characterized the hindgut symbiotic protists (Phylum Parabasalia) across the genus Zootermopsis (Archotermopsidae) using single cell isolation, molecular phylogenetics, and high-throughput amplicon sequencing. We report that the deepest divergence in the Zootermopsis phylogeny (Zootermopsis laticeps [Banks; Isoptera: Termopsidae]) corresponds with a divergence in three of the hindgut protist species. However, the crown Zootermopsis taxa (Zootermopsis angusticollis [Hagen; Isoptera: Termopsidae], Z. nevadensis nevadensis [Hagen; Isoptera: Termopsidae], and Z. nevadensis nuttingi [Haverty & Thorne; Isoptera: Termopsidae]) share the same protist species, with no evidence of co-speciation under our methods. We interpret this pattern as incomplete co-cladogenesis, though the possibility of symbiont exchange cannot be entirely ruled out. This is the first molecular evidence that identical communities of termite-associated protist species can inhabit multiple distinct host species.
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Affiliation(s)
| | | | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Tempe, AZ
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22
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Bourguignon T, Tang Q, Ho SYW, Juna F, Wang Z, Arab DA, Cameron SL, Walker J, Rentz D, Evans TA, Lo N. Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics. Mol Biol Evol 2018; 35:970-983. [DOI: 10.1093/molbev/msy013] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Frantisek Juna
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - James Walker
- Department of Agriculture and Water Resources, Cairns, QLD, Australia
| | - David Rentz
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia
| | - Theodore A Evans
- School of Animal Biology, University of Western Australia, Perth, WA, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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23
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Rosas T, García-Ferris C, Domínguez-Santos R, Llop P, Latorre A, Moya A. Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota. FEMS Microbiol Ecol 2018; 94:4794938. [DOI: 10.1093/femsec/fiy002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/08/2018] [Indexed: 02/04/2023] Open
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24
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Gil R, Vargas-Chavez C, López-Madrigal S, Santos-García D, Latorre A, Moya A. Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. THE ISME JOURNAL 2018; 12:124-135. [PMID: 28914880 PMCID: PMC5739004 DOI: 10.1038/ismej.2017.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/31/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.
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Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Institute for Integrative Systems Biology, Universitat de València/CSIC, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. E-mail:
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
| | - Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Diego Santos-García
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
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25
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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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Engl T, Eberl N, Gorse C, Krüger T, Schmidt THP, Plarre R, Adler C, Kaltenpoth M. Ancient symbiosis confers desiccation resistance to stored grain pest beetles. Mol Ecol 2017; 27:2095-2108. [PMID: 29117633 DOI: 10.1111/mec.14418] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 12/12/2022]
Abstract
Microbial symbionts of insects provide a range of ecological traits to their hosts that are beneficial in the context of biotic interactions. However, little is known about insect symbiont-mediated adaptation to the abiotic environment, for example, temperature and humidity. Here, we report on an ancient clade of intracellular, bacteriome-located Bacteroidetes symbionts that are associated with grain and wood pest beetles of the phylogenetically distant families Silvanidae and Bostrichidae. In the saw-toothed grain beetle Oryzaephilus surinamensis, we demonstrate that the symbionts affect cuticle thickness, melanization and hydrocarbon profile, enhancing desiccation resistance and thereby strongly improving fitness under dry conditions. Together with earlier observations on symbiont contributions to cuticle biosynthesis in weevils, our findings indicate that convergent acquisitions of bacterial mutualists represented key adaptations enabling diverse pest beetle groups to survive and proliferate under the low ambient humidity that characterizes dry grain storage facilities.
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Affiliation(s)
- Tobias Engl
- Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Nadia Eberl
- Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Carla Gorse
- Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Theresa Krüger
- Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Thorsten H P Schmidt
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Rudy Plarre
- Federal Institute for Material Research and Testing, Berlin, Germany
| | - Cornel Adler
- Federal Research Centre for Cultivated Plants, Julius-Kühn-Institute, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Martin Kaltenpoth
- Research Group Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
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27
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Xu TT, Chen J, Jiang LY, Qiao GX. Historical and cospeciating associations between Cerataphidini aphids (Hemiptera: Aphididae: Hormaphidinae) and their primary endosymbiont Buchnera aphidicola. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ting-Ting Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, P.R. China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
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28
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Hörnig MK, Haug JT, Haug C. An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans. PeerJ 2017; 5:e3605. [PMID: 28761789 PMCID: PMC5527957 DOI: 10.7717/peerj.3605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 07/01/2017] [Indexed: 01/27/2023] Open
Abstract
Mantodeans or praying mantises are flying insects and well known for their raptorial behaviour, mainly performed by their first pair of thoracic appendages. We describe here a new, exceptionally preserved specimen of the early mantodean Santanmantis axelrodi Grimaldi, 2003 from the famous 110 million years old Crato Formation, Brazil. The incomplete specimen preserves important morphological details, which were not known in this specific form before for this species or any other representative of Mantodea. Unlike in modern representatives or other fossil forms of Mantodea not only the first pair of thoracic appendages shows adaptations for predation. The femora of the second pair of thoracic appendages bear numerous strong, erect spines which appear to have a sharp tip, with this strongly resembling the spines of the first pair of thoracic appendages. This indicates that individuals of S. axelrodi likely used at least two pairs of thoracic appendages to catch prey. This demonstrates that the prey-catching behaviour was more diverse in early forms of praying mantises than anticipated.
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Affiliation(s)
- Marie K Hörnig
- Zoological Institute and Museum, Cytology and Evolutionary Biology, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Joachim T Haug
- Biocenter, Department of Biology II and GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carolin Haug
- Biocenter, Department of Biology II and GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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29
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Fujita M, Machida R. Embryonic development of Eucorydia yasumatsui Asahina, with special reference to external morphology (Insecta: Blattodea, Corydiidae). J Morphol 2017; 278:1469-1489. [PMID: 28707769 DOI: 10.1002/jmor.20725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/31/2017] [Accepted: 06/20/2017] [Indexed: 11/10/2022]
Abstract
As the first step in the comparative embryological study of Blattodea, with the aim of reconstructing the groundplan and phylogeny of Dictyoptera and Polyneoptera, the embryonic development of a corydiid was examined and described in detail using Eucorydia yasumatsui. Ten to fifteen micropyles are localized on the ventral side of the egg, and aggregated symbiont bacterial "mycetomes" are found in the egg. The embryo is formed by the fusion of paired blastodermal regions, with higher cellular density on the ventral side of the egg. This type of embryo formation, regarded as one of the embryological autapomorphies of Polyneoptera, was first demonstrated for "Blattaria" in the present study. The embryo undergoes embryogenesis of the short germ band type, and elongates to its full length on the ventral side of the egg. The embryo undergoes katatrepsis and dorsal closure, and then finally, it acquires its definitive form, keeping its original position on the ventral side of the egg, with its anteroposterior axis never reversed throughout development. The information obtained was compared with that of previous studies on other insects. "Micropyles grouped on the ventral side of the egg" is thought to be a part of the groundplan of Dictyoptera, and "possession of bacteria in the form of mycetomes" to be an apomorphic groundplan of Blattodea. Corydiid embryos were revealed to perform blastokinesis of the "non-reversion type (N)", as reported in blaberoid cockroaches other than Corydiidae ("Ectobiidae," Blaberidae, etc.) and in Mantodea; the embryos of blattoid cockroaches (Blattidae and Cryptocercidae) and Isoptera undergo blastokinesis of the "reversion type (R)," in which the anteroposterior axis of the embryo is reversed during blastokinesis. Dictyopteran blastokinesis types can be summarized as "Mantodea (N) + Blattodea [= Blaberoidea (N) + Blattoidea (R) + Isoptera (R)]".
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Affiliation(s)
- Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda Nagano, 386-2204, Japan
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda Nagano, 386-2204, Japan
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30
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Wang Z, Shi Y, Qiu Z, Che Y, Lo N. Reconstructing the phylogeny of Blattodea: robust support for interfamilial relationships and major clades. Sci Rep 2017; 7:3903. [PMID: 28634362 PMCID: PMC5478607 DOI: 10.1038/s41598-017-04243-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/11/2017] [Indexed: 11/09/2022] Open
Abstract
Cockroaches are among the most recognizable of all insects. In addition to their role as pests, they play a key ecological role as decomposers. Despite numerous studies of cockroach phylogeny in recent decades, relationships among most major lineages are yet to be resolved. Here we examine phylogenetic relationships among cockroaches based on five genes (mitochondrial 12S rRNA, 16S rRNA, COII; nuclear 28S rRNA and histone H3), and infer divergence times on the basis of 8 fossils. We included in our analyses sequences from 52 new species collected in China, representing 7 families. These were combined with data from a recent study that examined these same genes from 49 species, resulting in a significant increase in taxa analysed. Three major lineages, Corydioidea, Blaberoidea, and Blattoidea were recovered, the latter comprising Blattidae, Tryonicidae, Lamproblattidae, Anaplectidae, Cryptocercidae and Isoptera. The estimated age of the split between Mantodea and Blattodea ranged from 204.3 Ma to 289.1 Ma. Corydioidea was estimated to have diverged 209.7 Ma (180.5-244.3 Ma 95% confidence interval [CI]) from the remaining Blattodea. The clade Blattoidea diverged from their sister group, Blaberoidea, around 198.3 Ma (173.1-229.1 Ma). The addition of the extra taxa in this study has resulted in significantly higher levels of support for a number of previously recognized groupings.
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Affiliation(s)
- Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Yan Shi
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Zhiwei Qiu
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
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31
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Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PLoS One 2017; 12:e0177189. [PMID: 28545131 PMCID: PMC5436645 DOI: 10.1371/journal.pone.0177189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 04/24/2017] [Indexed: 12/15/2022] Open
Abstract
Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.
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32
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Ma J, Du C, Zhou C, Sheng Y, Fan Z, Yue B, Zhang X. Complete mitochondrial genomes of two blattid cockroaches, Periplaneta australasiae and Neostylopyga rhombifolia, and phylogenetic relationships within the Blattaria. PLoS One 2017; 12:e0177162. [PMID: 28486518 PMCID: PMC5423650 DOI: 10.1371/journal.pone.0177162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA). Three different types of short tandem repeats in the N. rhombifolia control region (CR) were observed. The homologous alignments of these tandem repeats with other six cockroach mitogenome CRs revealed a low similarity. Three conserved sequence blocks (CSB) were detected in both cockroach mitochondrial CRs. CSB1 was specific for blattinine mitogenomes and was highly conserved with 95% similarity, speculating that this block was a possible molecular synapomorphy for this subfamily. CSB3 located nearby downstream of CSB1 and has more variations within blattinine mitogenomes compared with CSB1. The CSB3 was capable of forming stable stem-loop structure with a small T-stretch in the loop portion. We assessed the influence of four datasets and two inference methods on topology within Orthopteroidea. All genes excluding the third codon positions of PCGs could generate more stable topology, and higher posterior probabilities than bootstrap values were presented at some branch nodes. The phylogenetic analysis with different datasets and analytical methods supported the monophyly of Dictyoptera and supported strongly the proposal that Isoptera should be classified as a family (Termitidae) of the Blattaria. Specifically, Shelfordella lateralis was inserted in the clade Periplaneta. Considering the K2P genetic distance, morphological characters, and the phylogenetic trees, we suggested that S. lateralis should be placed in the genus Periplaneta.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chao Du
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuang Zhou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongmei Sheng
- Sichuan Key Laboratory of Medicinal American Cockroach, Chengdu, China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail:
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Che Y, Gui S, Lo N, Ritchie A, Wang Z. Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China. PLoS One 2017; 12:e0169006. [PMID: 28046038 PMCID: PMC5207705 DOI: 10.1371/journal.pone.0169006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/10/2016] [Indexed: 11/23/2022] Open
Abstract
We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37-65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125-110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.
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Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shunhua Gui
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Andrew Ritchie
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
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34
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Cruaud A, Rasplus JY. Testing cospeciation through large-scale cophylogenetic studies. CURRENT OPINION IN INSECT SCIENCE 2016; 18:53-59. [PMID: 27939711 DOI: 10.1016/j.cois.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Insects are involved in a multitude of interactions with other organisms, which make them ideal models for large-scale cophylogenetic studies. Once phylogenies of interacting lineages have been inferred, there are a number of questions we may wish to ask, such as what was the relationship between the partners in the past? Have they co-evolved for thousands or millions of years, or has one of the partners switched among different host species? To answer such questions, researchers may conduct cophylogenetic analysis, to explore the relationships between the phylogenies of interacting lineages and determine whether the match is significant or find explanations for observed differences. When combined with dating analyses, cophylogenetic analyses may support cospeciation of the partners or phylogenetic tracking. As they may reveal dynamics of host-pathogen coevolution, cophylogenetic studies may also help tackle global health issues (e.g. document the spread of disease causing pathogens). Cophylogenetic studies of parasitoids and their insect hosts may also help identify effective biocontrol agents. With the advent of next generation sequencing technologies and keeping in mind that systematic errors may occur, cophylogenetics will benefit from better-resolved trees, allowing more accurate reconciliation. However as trees become larger, current algorithms also become more computationally challenging. Nevertheless, both theoretical and methodological developments are leading to more accurate and powerful tests of cospeciation through cophylogenetic analysis.
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Affiliation(s)
- Astrid Cruaud
- INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
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35
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Cheng XF, Zhang LP, Yu DN, Storey KB, Zhang JY. The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches. Gene 2016; 586:115-22. [DOI: 10.1016/j.gene.2016.03.057] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/17/2022]
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36
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Screening of spider mites (Acari: Tetranychidae) for reproductive endosymbionts reveals links between co-infection and evolutionary history. Sci Rep 2016; 6:27900. [PMID: 27291078 PMCID: PMC4904281 DOI: 10.1038/srep27900] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/27/2016] [Indexed: 01/01/2023] Open
Abstract
Reproductive endosymbionts have been shown to have wide-ranging effects on many aspects of their hosts’ biology. A first step to understanding how these endosymbionts interact with their hosts is to determine their incidences. Here, we screened for four reproductive endosymbionts (Wolbachia, Cardinium, Spiroplasma and Rickettsia) in 28 populations of spider mites (Acari: Tetranychidae) representing 12 species. Each of the four endosymbionts were identified in at least some of the tested specimens, and their infection patterns showed variations at the species-level and population-level, suggesting their distributions can be correlated with both the phylogeny and ecology of the hosts. Co-infections of unrelated bacteria, especially double infections of Wolbachia and Cardinium within the same individuals were common. Spiroplasma and Rickettsia infections were specific to particular host species, respectively. Further, the evolutionary histories of these endosymbionts were inferred by comparing the phylogenies of them and their hosts. These findings can help to clarify the interactions between endosymbionts and arthropods.
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37
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A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches. Mol Phylogenet Evol 2016; 98:201-9. [DOI: 10.1016/j.ympev.2016.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 01/27/2016] [Accepted: 02/07/2016] [Indexed: 11/21/2022]
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38
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Berlanga M, Llorens C, Comas J, Guerrero R. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana. PLoS One 2016; 11:e0152400. [PMID: 27054320 PMCID: PMC4824515 DOI: 10.1371/journal.pone.0152400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.
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Affiliation(s)
- Mercedes Berlanga
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Carlos Llorens
- Unity of Genomics. Scientific and Technological Centers, University of Barcelona (CCiTUB), Barcelona, Spain.,Biotechvana, Valencia, Spain
| | - Jaume Comas
- Unity of Genomics. Scientific and Technological Centers, University of Barcelona (CCiTUB), Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona-IDIBELL, Barcelona, Spain.,Barcelona Knowledge Hub, Academia Europaea, Barcelona, Spain
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Tegtmeier D, Thompson CL, Schauer C, Brune A. Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model. Appl Environ Microbiol 2016; 82:1080-1089. [PMID: 26637604 PMCID: PMC4751835 DOI: 10.1128/aem.03130-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/24/2015] [Indexed: 12/21/2022] Open
Abstract
The gut microbiota of termites and cockroaches represents complex metabolic networks of many diverse microbial populations. The distinct microenvironmental conditions within the gut and possible interactions among the microorganisms make it essential to investigate how far the metabolic properties of pure cultures reflect their activities in their natural environment. We established the cockroach Shelfordella lateralis as a gnotobiotic model and inoculated germfree nymphs with two bacterial strains isolated from the guts of conventional cockroaches. Fluorescence microscopy revealed that both strains specifically colonized the germfree hindgut. In diassociated cockroaches, the facultatively anaerobic strain EbSL (a new species of Enterobacteriaceae) always outnumbered the obligately anaerobic strain FuSL (a close relative of Fusobacterium varium), irrespective of the sequence of inoculation, which showed that precolonization by facultatively anaerobic bacteria does not necessarily favor colonization by obligate anaerobes. Comparison of the fermentation products of the cultures formed in vitro with those accumulated in situ indicated that the gut environment strongly affected the metabolic activities of both strains. The pure cultures formed the typical products of mixed-acid or butyrate fermentation, whereas the guts of gnotobiotic cockroaches accumulated mostly lactate and acetate. Similar shifts toward more-oxidized products were observed when the pure cultures were exposed to oxygen, which corroborated the strong effects of oxygen on the metabolic fluxes previously observed in termite guts. Oxygen microsensor profiles of the guts of germfree, gnotobiotic, and conventional cockroaches indicated that both gut tissue and microbiota contribute to oxygen consumption and suggest that the oxygen status influences the colonization success.
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Affiliation(s)
- Dorothee Tegtmeier
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Claire L Thompson
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Christine Schauer
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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The Role of Symbionts in the Evolution of Termites and Their Rise to Ecological Dominance in the Tropics. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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42
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Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches. Appl Environ Microbiol 2015; 82:1256-63. [PMID: 26655763 DOI: 10.1128/aem.03700-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/03/2015] [Indexed: 01/09/2023] Open
Abstract
The gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroach Shelfordella lateralis as a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such as Dysgonomonas and Parabacteroides spp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.
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Mikaelyan A, Dietrich C, Köhler T, Poulsen M, Sillam-Dussès D, Brune A. Diet is the primary determinant of bacterial community structure in the guts of higher termites. Mol Ecol 2015; 24:5284-95. [PMID: 26348261 DOI: 10.1111/mec.13376] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
Abstract
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
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Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tim Köhler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen East, Denmark
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), University of Paris 13, Sorbonne Paris Cité, Villetaneuse, France.,Institute of Ecology and Environmental Sciences - Paris (iEES-Paris), Institute of Research for Development, Sorbonne Universités, Bondy, France
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
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44
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Legendre F, Nel A, Svenson GJ, Robillard T, Pellens R, Grandcolas P. Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence. PLoS One 2015; 10:e0130127. [PMID: 26200914 PMCID: PMC4511787 DOI: 10.1371/journal.pone.0130127] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/18/2015] [Indexed: 12/03/2022] Open
Abstract
Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera-and stem-mantises-would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies.
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Affiliation(s)
- Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - André Nel
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Gavin J. Svenson
- Department of Invertebrate Zoology, Cleveland Museum of Natural History, Cleveland, Ohio, United States of America
| | - Tony Robillard
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB—UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d’Histoire naturelle, Département Systématique et Evolution, Paris, France
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Kinjo Y, Saitoh S, Tokuda G. An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. Microbes Environ 2015; 30:208-20. [PMID: 26156552 PMCID: PMC4567559 DOI: 10.1264/jsme2.me14153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Whole-genome sequencing has emerged as one of the most effective means to elucidate the biological roles and molecular features of obligate intracellular symbionts (endosymbionts). However, the de novo assembly of an endosymbiont genome remains a challenge when host and/or mitochondrial DNA sequences are present in a dataset and hinder the assembly of the genome. By focusing on the traits of genome evolution in endosymbionts, we herein developed and investigated a genome-assembly strategy that consisted of two consecutive procedures: the selection of endosymbiont contigs from an output obtained from a de novo assembly performed using a TBLASTX search against a reference genome, named TBLASTX Contig Selection and Filtering (TCSF), and the iterative reassembling of the genome from reads mapped on the selected contigs, named Iterative Mapping and ReAssembling (IMRA), to merge the contigs. In order to validate this approach, we sequenced two strains of the cockroach endosymbiont Blattabacterium cuenoti and applied this strategy to the datasets. TCSF was determined to be highly accurate and sensitive in contig selection even when the genome of a distantly related free-living bacterium was used as a reference genome. Furthermore, the use of IMRA markedly improved sequence assemblies: the genomic sequence of an endosymbiont was almost completed from a dataset containing only 3% of the sequences of the endosymbiont’s genome. The efficiency of our strategy may facilitate further studies on endosymbionts.
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Affiliation(s)
- Yukihiro Kinjo
- Tropical Biosphere Research Center, University of the Ryukyus
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46
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Identifying possible sister groups of Cryptocercidae+Isoptera: A combined molecular and morphological phylogeny of Dictyoptera. Mol Phylogenet Evol 2015; 84:284-303. [DOI: 10.1016/j.ympev.2014.08.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/16/2014] [Accepted: 08/18/2014] [Indexed: 11/23/2022]
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47
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Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole. Proc Natl Acad Sci U S A 2015; 112:10169-76. [PMID: 25713367 DOI: 10.1073/pnas.1421388112] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Many eukaryotes have obligate associations with microorganisms that are transmitted directly between generations. A model for heritable symbiosis is the association of aphids, a clade of sap-feeding insects, and Buchnera aphidicola, a gammaproteobacterium that colonized an aphid ancestor 150 million years ago and persists in almost all 5,000 aphid species. Symbiont acquisition enables evolutionary and ecological expansion; aphids are one of many insect groups that would not exist without heritable symbiosis. Receiving less attention are potential negative ramifications of symbiotic alliances. In the short run, symbionts impose metabolic costs. Over evolutionary time, hosts evolve dependence beyond the original benefits of the symbiosis. Symbiotic partners enter into an evolutionary spiral that leads to irreversible codependence and associated risks. Host adaptations to symbiosis (e.g., immune-system modification) may impose vulnerabilities. Symbiont genomes also continuously accumulate deleterious mutations, limiting their beneficial contributions and environmental tolerance. Finally, the fitness interests of obligate heritable symbionts are distinct from those of their hosts, leading to selfish tendencies. Thus, genes underlying the host-symbiont interface are predicted to follow a coevolutionary arms race, as observed for genes governing host-pathogen interactions. On the macroevolutionary scale, the rapid evolution of interacting symbiont and host genes is predicted to accelerate host speciation rates by generating genetic incompatibilities. However, degeneration of symbiont genomes may ultimately limit the ecological range of host species, potentially increasing extinction risk. Recent results for the aphid-Buchnera symbiosis and related systems illustrate that, whereas heritable symbiosis can expand ecological range and spur diversification, it also presents potential perils.
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48
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Mullins DE. Physiology of environmental adaptations and resource acquisition in cockroaches. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:473-492. [PMID: 25564743 DOI: 10.1146/annurev-ento-011613-162036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cockroaches are a group of insects that evolved early in geological time. Because of their antiquity, they for the most part display generalized behavior and physiology and accordingly have frequently been used as model insects to examine physiological and biochemical mechanisms involved with water balance, nutrition, reproduction, genetics, and insecticide resistance. As a result, a considerable amount of information on these topics is available. However, there is much more to be learned by employing new protocols, microchemical analytical techniques, and molecular biology tools to explore many unanswered questions.
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Affiliation(s)
- Donald E Mullins
- Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061;
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49
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Kim JK, Lee BL. Symbiotic factors in Burkholderia essential for establishing an association with the bean bug, Riptortus pedestris. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2015; 88:4-17. [PMID: 25521625 DOI: 10.1002/arch.21218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Symbiotic bacteria are common in insects and intimately affect the various aspects of insect host biology. In a number of insect symbiosis models, it has been possible to elucidate the effects of the symbiont on host biology, whereas there is a limited understanding of the impact of the association on the bacterial symbiont, mainly due to the difficulty of cultivating insect symbionts in vitro. Furthermore, the molecular features that determine the establishment and persistence of the symbionts in their host (i.e., symbiotic factors) have remained elusive. However, the recently established model, the bean bug Riptortus pedestris, provides a good opportunity to study bacterial symbiotic factors at a molecular level through their cultivable symbionts. Bean bugs acquire genus Burkholderia cells from the environment and harbor them as gut symbionts in the specialized posterior midgut. The genome of the Burkholderia symbiont was sequenced, and the genomic information was used to generate genetically manipulated Burkholderia symbiont strains. Using mutant symbionts, we identified several novel symbiotic factors necessary for establishing a successful association with the host gut. In this review, these symbiotic factors are classified into three categories based on the colonization dynamics of the mutant symbiont strains: initiation, accommodation, and persistence factors. In addition, the molecular characteristics of the symbiotic factors are described. These newly identified symbiotic factors and on-going studies of the Riptortus-Burkholderia symbiosis are expected to contribute to the understanding of the molecular cross-talk between insects and bacterial symbionts that are of ecological and evolutionary importance.
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Affiliation(s)
- Jiyeun Kate Kim
- Global Research Laboratory for Insect Symbiosis, College of Pharmacy, Pusan National University, Busan 609-735, South Korea
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50
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Bauer E, Lampert N, Mikaelyan A, Köhler T, Maekawa K, Brune A. Physicochemical conditions, metabolites and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae). FEMS Microbiol Ecol 2014; 91:1-14. [PMID: 25764554 DOI: 10.1093/femsec/fiu028] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While the gut microbiota of termites and its role in symbiotic digestion have been studied for decades, little is known about the bacteria colonizing the intestinal tract of the distantly related wood-feeding cockroaches (Blaberidae: Panesthiinae). Here, we show that physicochemical gut conditions and microbial fermentation products in the gut of Panesthia angustipennis resemble that of other cockroaches. Microsensor measurements confirmed that all gut compartments were anoxic at the center and had a slightly acidic to neutral pH and a negative redox potential. While acetate dominated in all compartments, lactate and hydrogen accumulated only in the crop. The high, hydrogen-limited rates of methane emission from living cockroaches were in agreement with the restriction of F420-fluorescent methanogens to the hindgut. The gut microbiota of both P. angustipennis and Salganea esakii differed strongly between compartments, with the highest density and diversity in the hindgut, but similarities between homologous compartments of both cockroaches indicated a specificity of the microbiota for their respective habitats. While some lineages were most closely related to the gut microbiota of omnivorous cockroaches and wood- or litter-feeding termites, others have been encountered also in vertebrates, reinforcing the hypothesis that strong environmental selection drives community structure in the cockroach gut.
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Affiliation(s)
- Eugen Bauer
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Niclas Lampert
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tim Köhler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Kiyoto Maekawa
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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