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Bustamante-Brito R, Vera-Ponce de León A, Rosenblueth M, Martínez-Romero E. Comparative genomics of the carmine cochineal symbiont Candidatus Dactylopiibacterium carminicum reveals possible protection to the host against viruses via CRISPR/Cas. Syst Appl Microbiol 2024; 47:126540. [PMID: 39068732 DOI: 10.1016/j.syapm.2024.126540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/25/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
We present new genomes from the bacterial symbiont Candidatus Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect Dactylopius (Hemiptera: Coccoidea: Dactylopiidae). As Dactylopiibacterium has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. Dactylopiibacterium is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had Dactylopiibacterium carminicum which has a highly conserved genome. All Dactylopiibacterium genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. Dactylopiibacterium genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all Dactylopiibacterium genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.
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Affiliation(s)
- Rafael Bustamante-Brito
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Arturo Vera-Ponce de León
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico; Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico
| | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
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2
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Arai H, Legeai F, Kageyama D, Sugio A, Simon JC. Genomic insights into Spiroplasma endosymbionts that induce male-killing and protective phenotypes in the pea aphid. FEMS Microbiol Lett 2024; 371:fnae027. [PMID: 38632047 DOI: 10.1093/femsle/fnae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
The endosymbiotic bacteria Spiroplasma (Mollicutes) infect diverse plants and arthropods, and some of which induce male killing, where male hosts are killed during development. Male-killing Spiroplasma strains belong to either the phylogenetically distant Citri-Poulsonii or Ixodetis groups. In Drosophila flies, Spiroplasma poulsonii induces male killing via the Spaid toxin. While Spiroplasma ixodetis infects a wide range of insects and arachnids, little is known about the genetic basis of S. ixodetis-induced male killing. Here, we analyzed the genome of S. ixodetis strains in the pea aphid Acyrthosiphon pisum (Aphididae, Hemiptera). Genome sequencing constructed a complete genome of a male-killing strain, sAp269, consisting of a 1.5 Mb circular chromosome and an 80 Kb plasmid. sAp269 encoded putative virulence factors containing either ankyrin repeat, ovarian tumor-like deubiquitinase, or ribosome inactivating protein domains, but lacked the Spaid toxin. Further comparative genomics of Spiroplasma strains in A. pisum biotypes adapted to different host plants revealed their phylogenetic associations and the diversity of putative virulence factors. Although the mechanisms of S. ixodetis-induced male killing in pea aphids remain elusive, this study underlines the dynamic genome evolution of S. ixodetis and proposes independent acquisition events of male-killing mechanisms in insects.
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Affiliation(s)
- Hiroshi Arai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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3
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Barak N, Fadeev E, Brekhman V, Aharonovich D, Lotan T, Sher D. Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica. Microorganisms 2023; 11:microorganisms11040955. [PMID: 37110378 PMCID: PMC10144005 DOI: 10.3390/microorganisms11040955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.
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Affiliation(s)
- Noga Barak
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
| | - Vera Brekhman
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Dikla Aharonovich
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Tamar Lotan
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
| | - Daniel Sher
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel
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Arai H, Inoue MN, Kageyama D. Male-killing mechanisms vary between Spiroplasma species. Front Microbiol 2022; 13:1075199. [PMID: 36519169 PMCID: PMC9742256 DOI: 10.3389/fmicb.2022.1075199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 03/11/2024] Open
Abstract
Male-killing, a male-specific death of arthropod hosts during development, is induced by Spiroplasma (Mollicutes) endosymbionts of the Citri-Poulsonii and the Ixodetis groups, which are phylogenetically distant groups. Spiroplasma poulsonii induces male-killing in Drosophila melanogaster (Diptera) using the Spaid toxin that harbors ankyrin repeats, whereas little is known about the origin and mechanisms of male-killing induced by Spiroplasma ixodetis. Here, we analyzed the genome and the biological characteristics of a male-killing S. ixodetis strain sHm in the moth Homona magnanima (Tortricidae, Lepidoptera). Strain sHm harbored a 2.1 Mb chromosome and two potential plasmids encoding Type IV effectors, putatively involved in virulence and host-symbiont interactions. Moreover, sHm did not harbor the spaid gene but harbored 10 ankyrin genes that were homologous to those in other S. ixodetis strains. In contrast to the predominant existence of S. poulsonii in hemolymph, our quantitative PCR assays revealed a systemic distribution of strain sHm in H. magnanima, with particularly high titers in Malpighian tubules but low titers in hemolymph. Furthermore, transinfection assays confirmed that strain sHm can infect cultured cells derived from distantly related insects, namely Aedes albopictus (Diptera) and Bombyx mori (Lepidoptera). These results suggest different origins and characteristics of S. ixodetis- and S. poulsonii-induced male-killing.
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Affiliation(s)
- Hiroshi Arai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Maki N. Inoue
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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5
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A
Mollicutes
Metagenome-Assembled Genome from the Gut of the Pteropod
Limacina rangii. Microbiol Resour Announc 2022; 11:e0075222. [DOI: 10.1128/mra.00752-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A nearly complete genome of an uncultured
Mollicutes
sp. was obtained from the metagenome of the gut of
Limacina rangii
(open-ocean snail), an important grazer and prey for higher trophic animals along the rapidly warming region of the western Antarctic Peninsula.
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Aubé J, Cambon-Bonavita MA, Velo-Suárez L, Cueff-Gauchard V, Lesongeur F, Guéganton M, Durand L, Reveillaud J. A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata. MICROBIOME 2022; 10:189. [PMID: 36333777 PMCID: PMC9636832 DOI: 10.1186/s40168-022-01380-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential. RESULTS We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this. CONCLUSION Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.
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Affiliation(s)
- Johanne Aubé
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lourdes Velo-Suárez
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France and Centre Brestois d’Analyse du Microbiote (CBAM), Brest University Hospital, Brest, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marion Guéganton
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lucile Durand
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Julie Reveillaud
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- MIVEGEC, Univ. Montpellier, INRAe, CNRS, IRD, Montpellier, France
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7
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Kakizawa S, Hosokawa T, Oguchi K, Miyakoshi K, Fukatsu T. Spiroplasma as facultative bacterial symbionts of stinkbugs. Front Microbiol 2022; 13:1044771. [PMID: 36353457 PMCID: PMC9638005 DOI: 10.3389/fmicb.2022.1044771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 12/05/2022] Open
Abstract
Many insects are associated with facultative symbiotic bacteria, and their infection prevalence provides an important clue to understand the biological impact of such microbial associates. Here we surveyed diverse stinkbugs representing 13 families, 69 genera, 97 species and 468 individuals for Spiroplasma infection. Diagnostic PCR detection revealed that 4 families (30.8%), 7 genera (10.1%), 11 species (11.3%) and 21 individuals (4.5%) were Spiroplasma positive. All the 21 stinkbug samples with Spiroplasma infection were subjected to PCR amplification and sequencing of Spiroplasma’s 16S rRNA gene. Molecular phylogenetic analysis uncovered that the stinkbug-associated Spiroplasma symbionts were placed in three distinct clades in the Spiroplasmataceae, highlighting multiple evolutionary origins of the stinkbug-Spiroplasma associations. The Spiroplasma phylogeny did not reflect the host stinkbug phylogeny, indicating the absence of host-symbiont co-speciation. On the other hand, the Spiroplasma symbionts associated with the same stinkbug family tended to be related to each other, suggesting the possibility of certain levels of host-symbiont specificity and/or ecological symbiont sharing. Amplicon sequencing analysis targeting bacterial 16S rRNA gene, FISH visualization of the symbiotic bacteria, and rearing experiments of the host stinkbugs uncovered that the Spiroplasma symbionts are generally much less abundant in comparison with the primary gut symbiotic bacteria, localized to various tissues and organs at relatively low densities, and vertically transmitted to the offspring. On the basis of these results, we conclude that the Spiroplasma symbionts are, in general, facultative bacterial associates of low infection prevalence that are not essential but rather commensalistic for the host stinkbugs, like the Spiroplasma symbionts of fruit flies and aphids, although their impact on the host phenotypes should be evaluated in future studies.
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Affiliation(s)
- Shigeyuki Kakizawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- *Correspondence: Shigeyuki Kakizawa, ; Takema Fukatsu,
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Misaki Marine Biological Station (MMBS), School of Science, The University of Tokyo, Miura, Japan
| | - Kaori Miyakoshi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Shigeyuki Kakizawa, ; Takema Fukatsu,
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8
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Dolmatova LS, Smolina TP. Morphofunctional Features of Two Types of Phagocytes in the Holothurian Еupentacta fraudatrix (Djakonov et Baranova, 1958). J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022040020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Chu Y, Zhao Z, Cai L, Zhang G. Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. ENVIRONMENTAL RESEARCH 2022; 210:112901. [PMID: 35227678 DOI: 10.1016/j.envres.2022.112901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.
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Affiliation(s)
- Yunmeng Chu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd., Shanghai, 201800, China
| | - Lixi Cai
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China; Faculty of Basic Medicine, Putian University, Putian, 351100, Fujian, China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China.
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10
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Pollmann M, Moore LD, Krimmer E, D'Alvise P, Hasselmann M, Perlman SJ, Ballinger MJ, Steidle JL, Gottlieb Y. Highly transmissible cytoplasmic incompatibility by the extracellular insect symbiont Spiroplasma. iScience 2022; 25:104335. [PMID: 35602967 PMCID: PMC9118660 DOI: 10.1016/j.isci.2022.104335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic incompatibility (CI) is a form of reproductive manipulation caused by maternally inherited endosymbionts infecting arthropods, like Wolbachia, whereby matings between infected males and uninfected females produce few or no offspring. We report the discovery of a new CI symbiont, a strain of Spiroplasma causing CI in the parasitoid wasp Lariophagus distinguendus. Its extracellular occurrence enabled us to establish CI in uninfected adult insects by transferring Spiroplasma-infected hemolymph. We sequenced the CI-Spiroplasma genome and did not find any homologues of any of the cif genes discovered to cause CI in Wolbachia, suggesting independent evolution of CI. Instead, the genome contains other potential CI-causing candidate genes, such as homologues of high-mobility group (HMG) box proteins that are crucial in eukaryotic development but rare in bacterial genomes. Spiroplasma's extracellular nature and broad host range encompassing medically and agriculturally important arthropods make it a promising tool to study CI and its applications.
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Affiliation(s)
- Marie Pollmann
- Department of Chemical Ecology 190t, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Logan D. Moore
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Elena Krimmer
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Paul D'Alvise
- Institute of Medical Microbiology and Hygiene, University Hospital of Tuebingen, 72016 Tuebingen, Germany
| | - Martin Hasselmann
- Department of Livestock Population Genomics 460h, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany
| | - Steve J. Perlman
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Johannes L.M. Steidle
- Department of Chemical Ecology 190t, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
- KomBioTa - Center of Biodiversity and Integrative Taxonomy, University of Hohenheim, 70599 Stuttgart, Germany
| | - Yuval Gottlieb
- Koret School of Veterinary Medicine, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, POB 12, Rehovot 76100, Israel
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11
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Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
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Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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12
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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13
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Alghetaa H, Mohammed A, Zhou J, Singh N, Nagarkatti M, Nagarkatti P. Resveratrol-mediated attenuation of superantigen-driven acute respiratory distress syndrome is mediated by microbiota in the lungs and gut. Pharmacol Res 2021; 167:105548. [PMID: 33722710 PMCID: PMC10116750 DOI: 10.1016/j.phrs.2021.105548] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/23/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022]
Abstract
Acute Respiratory Distress Syndrome (ARDS) is triggered by a variety of agents, including Staphylococcal Enterotoxin B (SEB). Interestingly, a significant proportion of patients with COVID-19, also develop ARDS. In the absence of effective treatments, ARDS results in almost 40% mortality. Previous studies from our laboratory demonstrated that resveratrol (RES), a stilbenoid, with potent anti-inflammatory properties can attenuate SEB-induced ARDS. In the current study, we investigated the role of RES-induced alterations in the gut and lung microbiota in the regulation of ARDS. Our studies revealed that SEB administration induced inflammatory cytokines, ARDS, and 100% mortality in C3H/HeJ mice. Additionally, SEB caused a significant increase in pathogenic Proteobacteria phylum and Propionibacterium acnes species in the lungs. In contrast, RES treatment attenuated SEB-mediated ARDS and mortality in mice, and significantly increased probiotic Actinobacteria phylum, Tenericutes phylum, and Lactobacillus reuteri species in both the colon and lungs. Colonic Microbiota Transplantation (CMT) from SEB-injected mice that were treated with RES as well as the transfer of L. reuteri into recipient mice inhibited the production of SEB-mediated induction of pro-inflammatory cytokines such as IFN-γ and IL-17 but increased that of anti-inflammatory IL-10. Additionally, such CMT and L. reuteri recipient mice exposed to SEB, showed a decrease in lung-infiltrating mononuclear cells, cytotoxic CD8+ T cells, NKT cells, Th1 cells, and Th17 cells, but an increase in the population of regulatory T cells (Tregs) and Th3 cells, and increase in the survival of mice from SEB-mediated ARDS. Together, the current study demonstrates that ARDS induced by SEB triggers dysbiosis in the lungs and gut and that attenuation of ARDS by RES may be mediated, at least in part, by alterations in microbiota in the lungs and the gut, especially through the induction of beneficial bacteria such as L. reuteri.
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Affiliation(s)
- Hasan Alghetaa
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Amira Mohammed
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Juhua Zhou
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Narendra Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
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14
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Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, Siozios S, Lemaitre B, Mateos M, Hurst GDD. Rapid molecular evolution of Spiroplasma symbionts of Drosophila. Microb Genom 2021; 7:000503. [PMID: 33591248 PMCID: PMC8208695 DOI: 10.1099/mgen.0.000503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.
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Affiliation(s)
- Michael Gerth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Humberto Martinez-Montoya
- Laboratorio de Genética y Genómica Comparativa, Unidad Académica Multidisciplinaria Reynosa Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Mexico
| | - Paulino Ramirez
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Florent Masson
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Joanne S. Griffin
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Mariana Mateos
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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15
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Zhu FC, Lian CA, He LS. Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine. Microorganisms 2020; 8:microorganisms8121874. [PMID: 33260795 PMCID: PMC7761423 DOI: 10.3390/microorganisms8121874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction–modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named “Candidatus Bathyoplasma sp. NZ”. This was the first time describing host-associated Izemoplasmatales.
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Affiliation(s)
- Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- Correspondence: ; Tel.: +86-898-88380060
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16
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Sea Cucumber Intestinal Regeneration Reveals Deterministic Assembly of the Gut Microbiome. Appl Environ Microbiol 2020; 86:AEM.00489-20. [PMID: 32358014 DOI: 10.1128/aem.00489-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber Sclerodactyla briareus, and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens.IMPORTANCE The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) Sclerodactyla briareus was explored as an experimental system to study microbial colonization in the gut, as S. briareus individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.
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17
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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18
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Lian CA, Yan GY, Huang JM, Danchin A, Wang Y, He LS. Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish. Front Microbiol 2020; 10:2978. [PMID: 31998265 PMCID: PMC6965317 DOI: 10.3389/fmicb.2019.02978] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/10/2019] [Indexed: 01/30/2023] Open
Abstract
Hadal trenches are characterized by not only high hydrostatic pressure but also scarcity of nutrients and high diversity of viruses. Snailfishes, as the dominant vertebrates, play an important role in hadal ecology. Although studies have suggested possible reasons for the tolerance of hadal snailfish to high hydrostatic pressure, little is known about the strategies employed by hadal snailfish to cope with low-nutrient and virus-rich conditions. In this study, the gut microbiota of hadal snailfish was investigated. A novel bacterium named "Candidatus Mycoplasma liparidae" was dominant in the guts of three snailfish individuals from both the Mariana and Yap trenches. A draft genome of "Ca. Mycoplasma liparidae" was successfully assembled with 97.8% completeness by hybrid sequencing. A set of genes encoding riboflavin biosynthesis proteins and a clustered regularly interspaced short palindromic repeats (CRISPR) system was present in the genome of "Ca. Mycoplasma liparidae," which was unusual for Mycoplasma. The functional repertoire of the "Ca. Mycoplasma liparidae" genome is likely set to help the host in riboflavin supplementation and to provide protection against viruses via a super CRISPR system. Remarkably, genes encoding common virulence factors usually exist in Tenericutes pathogens but were lacking in the genome of "Ca. Mycoplasma liparidae." All of these characteristics supported an essential role of "Ca. Mycoplasma liparidae" in snailfish living in the hadal zone. Our findings provide further insights into symbiotic associations in the hadal biosphere.
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Affiliation(s)
- Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Yong Yan
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Antoine Danchin
- Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016 – CNRS UMR 8104 – Université Paris Descartes, Paris, France
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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19
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Multiplex real-time PCR for the detection of Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and pathogenic Xanthomonas species on tomato plants. PLoS One 2020; 15:e0227559. [PMID: 31910230 PMCID: PMC6946519 DOI: 10.1371/journal.pone.0227559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 01/08/2023] Open
Abstract
A multiplex real-time PCR method based on fluorescent TaqMan® probes was developed for the simultaneous detection of the tomato pathogenic bacteria Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato and bacterial spot-causing xanthomonads. The specificity of the multiplex assay was validated on 44 bacterial strains, including 32 target pathogen strains as well as closely related species and nontarget tomato pathogenic bacteria. The designed multiplex real-time PCR showed high sensitivity when positive amplification was observed for one pg of bacterial DNA in the cases of Clavibacter michiganensis subsp. michiganensis and Pseudomonas syringae pv. tomato bacteria and 100 pg for bacterial spot-causing xanthomonads. The reliability of the developed multiplex real-time PCR assay for in planta detection was verified by recognition of the target pathogens in 18 tomato plants artificially inoculated by each of the target bacteria and tomato samples from production greenhouses.
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20
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Wang Y, Zhu FC, He LS, Danchin A. Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma. Nucleic Acids Res 2019; 46:2197-2203. [PMID: 29390076 PMCID: PMC5861454 DOI: 10.1093/nar/gky045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes. In the tRNA fragments detected in the gut transcriptome, mismatches expected to be caused by some tRNA modifications were not shown in their alignments with the corresponding genes. However, the probable paucity of modified anticodons did not fundamentally change the codon usage pattern of the Spiroplasma. The tRNA gene profile that probably resulted from the paucity of tRNA(34) modifications was not observed in other symbionts and deep-sea bacteria, indicating that this phenomenon was an evolutionary dead-end. This study provides insights on co-evolution of translation machine and tRNA genes and steric constraints of codon-anticodon interactions in deep-sea extreme environment.
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Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 boulevard de l'Hôpital, 75013 Paris, France.,School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong Kong, 21 Sassoon Road, SAR Hong Kong, China
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21
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Complete Genome Sequence of Spiroplasma phoeniceum Strain P40 T, a Plant Pathogen Isolated from Diseased Plants of Madagascar Periwinkle [ Catharanthus roseus (L.) G. Don]. Microbiol Resour Announc 2019; 8:8/12/e01612-18. [PMID: 30938707 PMCID: PMC6430324 DOI: 10.1128/mra.01612-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phytopathogen Spiroplasma phoeniceum was isolated from diseased plants of Madagascar periwinkle [Catharanthus roseus (L.) G. Don]. Here, we report the nucleotide sequence of the 1,791,576-bp circular chromosome and three plasmids of strain P40T This information serves as a resource for comparative analyses of spiroplasmal adaptations to diverse ecological niches.
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22
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Bolaños LM, Rosenblueth M, Manrique de Lara A, Migueles-Lozano A, Gil-Aguillón C, Mateo-Estrada V, González-Serrano F, Santibáñez-López CE, García-Santibáñez T, Martínez-Romero E. Cophylogenetic analysis suggests cospeciation between the Scorpion Mycoplasma Clade symbionts and their hosts. PLoS One 2019; 14:e0209588. [PMID: 30625167 PMCID: PMC6326461 DOI: 10.1371/journal.pone.0209588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/08/2018] [Indexed: 11/19/2022] Open
Abstract
Scorpions are predator arachnids of ancient origin and worldwide distribution. Two scorpion species, Vaejovis smithi and Centruroides limpidus, were found to harbor two different Mollicutes phylotypes: a Scorpion Mycoplasma Clade (SMC) and Scorpion Group 1 (SG1). Here we investigated, using a targeted gene sequencing strategy, whether these Mollicutes were present in 23 scorpion morphospecies belonging to the Vaejovidae, Carboctonidae, Euscorpiidae, Diplocentridae, and Buthidae families. Our results revealed that SMC is found in a species-specific association with Vaejovidae and Buthidae, whereas SG1 is uniquely found in Vaejovidae. SMC and SG1 co-occur only in Vaejovis smithi where 43% of the individuals host both phylotypes. A phylogenetic analysis of Mollicutes 16S rRNA showed that SMC and SG1 constitute well-delineated phylotypes. Additionally, we found that SMC and scorpion phylogenies are significantly congruent, supporting the observation that a cospeciation process may have occurred. This study highlights the phylogenetic diversity of the scorpion associated Mollicutes through different species revealing a possible cospeciation pattern.
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Affiliation(s)
- Luis M. Bolaños
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Mónica Rosenblueth
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Amaranta Manrique de Lara
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Analí Migueles-Lozano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Citlali Gil-Aguillón
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Valeria Mateo-Estrada
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Francisco González-Serrano
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Carlos E. Santibáñez-López
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Tonalli García-Santibáñez
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Esperanza Martínez-Romero
- Laboratorio de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
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23
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Danchin A. Bacteria in the ageing gut: did the taming of fire promote a long human lifespan? Environ Microbiol 2018; 20:1966-1987. [PMID: 29727052 DOI: 10.1111/1462-2920.14255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Unique among animals as they evolved towards Homo sapiens, hominins progressively cooked their food on a routine basis. Cooked products are characterized by singular chemical compounds, derived from the pervasive Maillard reaction. This same reaction is omnipresent in normal metabolism involving carbonyls and amines, and its products accumulate with age. The gut microbiota acts as a first line of defence against the toxicity of cooked Maillard compounds, that also selectively shape the microbial flora, letting specific metabolites to reach the blood stream. Positive selection of metabolic functions allowed the body of hominins who tamed fire to use and dispose of these age-related compounds. I propose here that, as a hopeful accidental consequence, this resulted in extending human lifespan far beyond that of our great ape cousins. The limited data exploring the role of taming fire on the human genetic setup and on its microbiota is discussed in relation with ageing.
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Affiliation(s)
- Antoine Danchin
- Integromics, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, Paris, 75013, France.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong
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24
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Subhan F, Shahzad R, Tauseef I, Haleem KS, Rehman AU, Mahmood S, Lee IJ. Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytes in vitro. PeerJ 2018; 6:e4245. [PMID: 29441229 PMCID: PMC5807979 DOI: 10.7717/peerj.4245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 01/22/2023] Open
Abstract
Background Beaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand. Method This study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified as Pseudomonas stutzeri using 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession number MF599548. The isolated P. stutzeri bacterium was cultured in Luria-Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect of P. stutzeri on human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay. Result The crude P. stutzeri extract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract of P. stutzeri FSRS had a strong pathological effect on human skin cells. Discussion Beach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacterium P. stutzeri may, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.
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Affiliation(s)
- Fazli Subhan
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Raheem Shahzad
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Isfahan Tauseef
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | | | - Atta-Ur Rehman
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Sajid Mahmood
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.,Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
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