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Sample records for chemoautotrophic symbiont genome

  1. The Calyptogena magnifica chemoautotrophic symbiont genome

    Energy Technology Data Exchange (ETDEWEB)

    Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C.; Fontanez, K.M.; Lau, E.; Stewart, F.J.; Richardson,P.M.; Barry, K.W.; Saunders, E.; Detter, J.C.; Wu, D.; Eisen, J.A.; Cavanaugh, C.M.

    2007-03-01

    Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

  2. Assimilation of Inorganic Nitrogen by Marine Invertebrates and Their Chemoautotrophic and Methanotrophic Symbionts

    OpenAIRE

    Lee, Raymond W; Childress, James J.

    1994-01-01

    Symbioses between marine invertebrates and their chemoautotrophic and methanotrophic symbionts are now known to exist in a variety of habitats where reduced chemical species are present. The utilization of chemical energy and reliance on C1 compounds by these symbioses are well documented. Much less is known about their metabolism of nitrogen. Earlier work has shown that the tissues of organisms in these associations are depleted of 15N compared with those of other marine organisms, indicatin...

  3. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca chemosynthetic symbionts

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    Girguis Peter R

    2008-12-01

    Full Text Available Abstract Background The Vesicomyidae (Bivalvia: Mollusca are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible. Results To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents. Conclusion The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.

  4. Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae.

    Science.gov (United States)

    Liao, Li; Wankel, Scott D; Wu, Min; Cavanaugh, Colleen M; Girguis, Peter R

    2014-03-01

    Chemoautotrophic symbionts of deep sea hydrothermal vent tubeworms are known to provide their hosts with all their primary nutrition. While studies have examined how chemoautotrophic symbionts provide the association with nitrogen, fewer have examined if symbiont nitrogen metabolism varies as a function of environmental conditions. Ridgeia piscesae tubeworms flourish at Northeastern Pacific vents, occupy a range of microhabitats, and exhibit a high degree of morphological plasticity [e.g. long-skinny (LS) and short-fat (SF) phenotypes] that may relate to environmental conditions. This plasticity affords an opportunity to examine whether symbiont nitrogen metabolism varies among host phenotypes. LS and SF R. piscesae were recovered from the Axial and Main Endeavour Field hydrothermal vents. Nitrate and ammonium were quantified in Ridgeia blood, and the expression of key nitrogen metabolism genes, as well as stable nitrogen isotope ratios, was quantified in host branchial plume and symbiont-containing tissues. Nitrate and ammonium were abundant in the blood of both phenotypes though environmental ammonium concentrations were, paradoxically, lowest among individuals with the highest blood ammonium. Assimilatory nitrate reductase transcripts were always below detection, though in both LS and SF R. piscesae symbionts, we observed elevated expression of dissimilatory nitrate reductase genes, as well as symbiont and host ammonium assimilation genes. Site-specific differences in expression, along with tissue stable isotope analyses, suggest that LS and SF Ridgeia symbionts are engaged in both dissimilatory nitrate reduction and ammonia assimilation to varying degrees. As such, it appears that environmental conditions -not host phenotype-primarily dictates symbiont nitrogen metabolism. PMID:24237389

  5. Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting?

    Science.gov (United States)

    Brune, A

    2016-07-01

    Mutualistic associations of bacteria and invertebrates are widespread and encompass an enormous diversity on the side of both partners. The advantages gained from the symbiosis favour reciprocal adaptations that increase the stability of the association and can lead to codiversification of symbiont and host. While numerous examples of a strictly vertical transfer of the symbionts from parent to offspring among intracellular associations abound, little is known about the fidelity of the partners in extracellular associations, where symbionts colonize the surface or body cavity of their host. In this issue of Molecular Ecology, Zimmermann et al. () investigated the evolutionary history of the symbiotic association between a monophyletic clade of sulphur-oxidizing Gammaproteobacteria and two distantly related lineages of marine worms (nematodes and annelids). The study supports the surprising conclusion that partner fidelity does not necessarily increase with the intimacy of the association. Ectosymbionts on the cuticle of the nematodes seem to be cospeciating with their hosts, whereas endosymbionts housed in the body cavity of the annelids must have originated multiple times, probably by host switching, from ectosymbionts of sympatric nematodes. This excellent case study on the evolutionary history of invertebrate-microbe interactions supports the emerging concept that the co-evolutionary processes shaping such mutualistic symbioses include both codiversification and ecological fitting. PMID:27373707

  6. Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis

    DEFF Research Database (Denmark)

    Travis, Anthony J.; Kelly, Denise; Flint, Harry J; Aminov, Rustam

    2015-01-01

    We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host...

  7. Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish.

    Science.gov (United States)

    Hendry, Tory A; de Wet, Jeffrey R; Dougan, Katherine E; Dunlap, Paul V

    2016-01-01

    The luminous bacterial symbionts of anomalopid flashlight fish are thought to be obligately dependent on their hosts for growth and share several aspects of genome evolution with unrelated obligate symbionts, including genome reduction. However, in contrast to most obligate bacteria, anomalopid symbionts have an active environmental phase that may be important for symbiont transmission. Here we investigated patterns of evolution between anomalopid symbionts compared with patterns in free-living relatives and unrelated obligate symbionts to determine if trends common to obligate symbionts are also found in anomalopid symbionts. Two symbionts, "Candidatus Photodesmus katoptron" and "Candidatus Photodesmus blepharus," have genomes that are highly similar in gene content and order, suggesting genome stasis similar to ancient obligate symbionts present in insect lineages. This genome stasis exists in spite of the symbiont's inferred ability to recombine, which is frequently lacking in obligate symbionts with stable genomes. Additionally, we used genome comparisons and tests of selection to infer which genes may be particularly important for the symbiont's ecology compared with relatives. In keeping with obligate dependence, substitution patterns suggest that most symbiont genes are experiencing relaxed purifying selection compared with relatives. However, genes involved in motility and carbon storage, which are likely to be used outside the host, appear to be under increased purifying selection. Two chemoreceptor chemotaxis genes are retained by both species and show high conservation with amino acid sensing genes, suggesting that the bacteria may actively seek out hosts using chemotaxis toward amino acids, which the symbionts are not able to synthesize. PMID:27389687

  8. Functional and Evolutionary Analysis of the Genome of an Obligate Fungal Symbiont

    OpenAIRE

    Vogel, Kevin J.; Moran, Nancy A.

    2013-01-01

    Nutritional symbionts of insects include some of the most bizarre genomes studied to date, with extremely reduced size, biased base composition, and limited metabolic abilities. A monophyletic group of aphids within the subfamily Cerataphidinae have lost the bacterial symbiont common to all other Aphididae (Buchnera aphidicola), which have been replaced by a eukaryotic one, the yeast-like symbiont (YLS). As symbionts are expected to experience reduced effective population size (N e) and large...

  9. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

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    Amelia R. I. Lindsey

    2016-07-01

    Full Text Available Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.

  10. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.

    Science.gov (United States)

    Lindsey, Amelia R I; Werren, John H; Richards, Stephen; Stouthamer, Richard

    2016-01-01

    Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. PMID:27194801

  11. Lineage-Specific Patterns of Genome Deterioration in Obligate Symbionts of Sharpshooter Leafhoppers.

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    Bennett, Gordon M; McCutcheon, John P; McDonald, Bradon R; Moran, Nancy A

    2016-01-01

    Plant sap-feeding insects (Hemiptera) rely on obligate bacterial symbionts that provision nutrients. Some of these symbionts are ancient and have evolved tiny genomes, whereas others are younger and retain larger, dynamic genomes. Baumannia cicadellinicola, an obligate symbiont of sharpshooter leafhoppers, is derived from a relatively recent symbiont replacement. To better understand evolutionary decay of genomes, we compared Baumannia from three host species. A newly sequenced genome for Baumannia from the green sharpshooter (B-GSS) was compared with genomes of Baumannia from the blue-green sharpshooter (B-BGSS, 759 kilobases [kb]) and from the glassy-winged sharpshooter (B-GWSS, 680 kb). B-GSS has the smallest Baumannia genome sequenced to date (633 kb), with only three unique genes, all involved in membrane function. It has lost nearly all pathways involved in vitamin and cofactor synthesis, as well as amino acid biosynthetic pathways that are redundant with pathways of the host or the symbiotic partner, Sulcia muelleri. The entire biosynthetic pathway for methionine is eliminated, suggesting that methionine has become a dietary requirement for hosts. B-GSS and B-BGSS share 33 genes involved in bacterial functions (e.g., cell division, membrane synthesis, metabolite transport, etc.) that are lost from the more distantly related B-GWSS and most other tiny genome symbionts. Finally, pairwise divergence estimates indicate that B-GSS has experienced a lineage-specific increase in substitution rates. This increase correlates with accelerated protein-level changes and widespread gene loss. Thus, the mode and tempo of genome reduction vary widely among symbiont lineages and result in wide variation in metabolic capabilities across hosts. PMID:26260652

  12. Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608.

    Science.gov (United States)

    Heavens, Darren; Tailford, Louise E; Crossman, Lisa; Jeffers, Faye; Mackenzie, Donald A; Caccamo, Mario; Juge, Nathalie

    2011-08-01

    Lactobacillus reuteri, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of L. reuteri ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization. PMID:21622738

  13. Genome Sequence of the Vertebrate Gut Symbiont Lactobacillus reuteri ATCC 53608 ▿

    OpenAIRE

    Heavens, Darren; Tailford, Louise E.; Crossman, Lisa; Jeffers, Faye; MacKenzie, Donald A.; Caccamo, Mario; Juge, Nathalie

    2011-01-01

    Lactobacillus reuteri, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of L. reuteri ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization.

  14. Genomics of "Candidatus Synechococcus spongiarium", a Cyanobacterial Sponge Symbiont

    Energy Technology Data Exchange (ETDEWEB)

    Slaby, Beate M. [Univ. of Wuerzburg (Germany); Copeland, Alex [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Woyke, Tanja [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hentschel, Ute [Univ. of Wuerzburg (Germany)

    2014-03-21

    Marine sponges (Porifera): ancient metazoans of ecological importance, that produce bioactive secondary metabolites and interact with various microorganisms including cyanobacteria1: Marine Synechococcus spp.: cyanobacteria, important contributors to the global carbon cycle and major primary producers in the oceans2 Ca. S. spongiarum: an ecotype of this genus, widespread and abundant symbiont of various marine sponges around the world3, e.g. Aplysina aerophoba

  15. Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A

    OpenAIRE

    Davis, Jeanette; Hill, Russell T.

    2014-01-01

    Bacteria belonging to the genus Vibrio are prevalent in the marine environment and are known for forming symbiotic relationships with hosts. Vibrio sp. strain ER1A is a dominant symbiont of the Hawaiian sea slug, Elysia rufescens. Here we report the draft genome sequence of Vibrio sp. ER1A.

  16. Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus pongiarum"

    KAUST Repository

    Gao, Zhao-Ming

    2014-04-01

    "Candidatus Synechococcus spongiarum" is a cyanobacterial symbiont widely distributed in sponges, but its functions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90% estimated genome recovery) of "Ca. Synechococcus spongiarum" strain SH4 inhabiting the Red Sea sponge Carteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and polyamines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in resistance to environmental toxins and in biosynthesis of capsular and extracellular polysaccharides. These genetic modifications imply that "Ca. Synechococcus spongiarum" SH4 represents a low-light-adapted cyanobacterial symbiont and has undergone genome streamlining to adapt to the sponge\\'s mild intercellular environment. 2014 Gao et al.

  17. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

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    Nobukazu Uchiike

    2011-10-01

    Full Text Available The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp. Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

  18. The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities

    OpenAIRE

    J. J. Childress; Peter R. Girguis

    2011-01-01

    While chemoautotrophic endosymbioses of hydrothermal vents and other reducing environments have been well studied, little attention has been paid to the magnitude of the metabolic demands placed upon the host by symbiont metabolism and the adaptations necessary to meet such demands. Here we make the first attempt at such an evaluation, and show that moderate to high rates of chemoautotrophic or methanotrophic metabolism impose oxygen uptake and proton equivalent elimination demands upon the h...

  19. The distribution of intra-genomically variable dinoflagellate symbionts at Lord Howe Island, Australia

    Science.gov (United States)

    Wilkinson, Shaun P.; Pontasch, Stefanie; Fisher, Paul L.; Davy, Simon K.

    2016-06-01

    The symbiotic dinoflagellates of corals and other marine invertebrates ( Symbiodinium) are essential to the development of shallow-water coral reefs. This genus contains considerable genetic diversity and a corresponding range of physiological and ecological traits. Most genetic variation arises through the accumulation of somatic mutations that arise during asexual reproduction. Yet growing evidence suggests that occasional sexual reproductive events also occur within, and perhaps between, Symbiodinium lineages, further contributing to the pool of genetic variation available for evolutionary adaptation. Intra-genomic variation can therefore arise from both sexual and asexual reproductive processes, making it difficult to discern its underlying causes and consequences. We used quantitative PCR targeting the ITS2 locus to estimate proportions of genetically homogeneous symbionts and intra-genomically variable Symbiodinium (IGV Symbiodinium) in the reef-building coral Pocillopora damicornis at Lord Howe Island, Australia. We then sampled colonies through time and at a variety of spatial scales to find out whether the distribution of these symbionts followed patterns consistent with niche partitioning. Estimated ratios of homogeneous to IGV Symbiodinium varied between colonies within sites (metres to tens of metres) and between sites separated by hundreds to thousands of metres, but remained stable within colonies through time. Symbiont ratios followed a temperature gradient, with the local thermal maximum emerging as a negative predictor for the estimated proportional abundance of IGV Symbiodinium. While this pattern may result from fine-scale spatial population structure, it is consistent with an increased susceptibility to thermal stress, suggesting that the evolutionary processes that generate IGV (such as inter-lineage recombination and the accumulation of somatic mutations at the ITS2 locus) may have important implications for the fitness of the symbiont and

  20. Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446T, a Nitrogen-Fixing Symbiont of the Legume Pasture Stylosanthes guianensis.

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Gomes, Douglas Fabiano; Souza, Renata Carolini; Chueire, Ligia Maria Oliveira; Hungria, Mariangela

    2016-01-01

    Bradyrhizobium stylosanthis BR 446(T) is a nitrogen-fixing symbiont of the tropical legume pasture Stylosanthes guianensis Its draft genome contains 8,801,717 bp and 8,239 coding sequences (CDSs). Several putative genes that might confer high competitiveness and saprophytic capacity under the stressful conditions of tropical soils were identified in the genome. PMID:27365354

  1. Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446T, a Nitrogen-Fixing Symbiont of the Legume Pasture Stylosanthes guianensis

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Gomes, Douglas Fabiano; Souza, Renata Carolini; Chueire, Ligia Maria Oliveira

    2016-01-01

    Bradyrhizobium stylosanthis BR 446T is a nitrogen-fixing symbiont of the tropical legume pasture Stylosanthes guianensis. Its draft genome contains 8,801,717 bp and 8,239 coding sequences (CDSs). Several putative genes that might confer high competitiveness and saprophytic capacity under the stressful conditions of tropical soils were identified in the genome. PMID:27365354

  2. Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

    Science.gov (United States)

    Mornico, Damien; Miché, Lucie; Béna, Gilles; Nouwen, Nico; Verméglio, André; Vallenet, David; Smith, Alexander A.T.; Giraud, Eric; Médigue, Claudine; Moulin, Lionel

    2011-01-01

    Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses. PMID:24704842

  3. Expression of genes derived from the genomic DNA fragments of the brown-winged green bug (Plautia stali) symbiont in Escherichia coli.

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    Fujii-Muramatsu, Rika; Kobayashi, Hideaki; Noda, Hiroaki; Takeishi, Keiichi

    2013-08-01

    Many insect species harbour symbiotic microorganisms (symbionts) that are generally unculturable in media. To utilize symbionts as genome resources, we examined whether insect symbiont genes can be expressed in Escherichia coli. 144 plasmid clones were isolated from gene libraries, which were constructed from the genomic DNA of the intestinal bacterial symbiont in the brown-winged green bug, Plautia stali, using an E. coli system. Proteins prepared from a culture of each clone were analysed using SDS-PAGE. A discrete symbiont-specific band was detected in six clones. From the structural analyses of the insert in each clone, the candidate gene encoding the symbiont-specific protein was predicted and the amino acid sequence of the protein was deduced. The amino acid sequence in the N-terminal region of each protein was identical to that deduced from the genomic DNA sequence of the symbiont, but not of the host. The promoter sequences of the symbiont genes, very similar to those of the corresponding E. coli genes, were found in the insert DNA. These findings clearly indicate that genes derived from genomic DNA fragments of the P. stali symbiont can be expressed in E. coli. PMID:23613025

  4. Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris

    OpenAIRE

    Althabegoiti, M. Julia; Lozano, Luis; Torres-Tejerizo, Gonzalo; Ormeño-Orrillo, Ernesto; Rogel, Marco A.; González, Víctor; Martínez-Romero, Esperanza

    2012-01-01

    Here we present the genome sequence of Rhizobium grahamii CCGE502. R. grahamii groups with other newly described broad-host-range species, which are not very efficient Phaseolus vulgaris symbionts, with a wide geographic distribution and which constitutes a novel Rhizobium clade.

  5. PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification.

    Science.gov (United States)

    Siegl, Alexander; Hentschel, Ute

    2010-08-01

    Whole genome amplification (WGA) approaches provide genomic information on single microbial cells and hold great promise for the field of environmental microbiology. Here, the microbial consortia of the marine sponge Aplysina aerophoba were sorted by fluorescence-activated cell sorting (FACS) and then subjected to WGA. A cosmid library was constructed from the WGA product of a sample containing two bacterial cells, one a member of the candidate phylum Poribacteria and one of a sponge-specific clade of Chloroflexi. Library screening led to the genomic characterization of three cosmid clones, encoding a polyketide synthase (PKS), a non-ribosomal peptide synthetase (NRPS) and the Chloroflexi 16S rRNA gene. PCR screening of WGA products from additional, FACS-sorted single bacterial symbiont cells supports the assignment of the Sup-PKS gene to the Poribacteria and the novel NRPS gene to the Chloroflexi. This promising single-cell genomics approach has permitted cloning of entire gene clusters from single microbial cells of known phylogenetic origin and thus provides a sought-after link between phylogeny and function. PMID:23766222

  6. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations.

    Science.gov (United States)

    Zheng, Jinshui; Zhao, Xin; Lin, Xiaoxi B; Gänzle, Michael

    2015-01-01

    Lactobacillus reuteri is a dominant member of intestinal microbiota of vertebrates, and occurs in food fermentations. The stable presence of L. reuteri in sourdough provides the opportunity to study the adaptation of vertebrate symbionts to an extra-intestinal habitat. This study evaluated this adaptation by comparative genomics of 16 strains of L. reuteri. A core genome phylogenetic tree grouped L. reuteri into 5 clusters corresponding to the host-adapted lineages. The topology of a gene content tree, which includes accessory genes, differed from the core genome phylogenetic tree, suggesting that the differentiation of L. reuteri is shaped by gene loss or acquisition. About 10% of the core genome (124 core genes) were under positive selection. In lineage III sourdough isolates, 177 genes were under positive selection, mainly related to energy conversion and carbohydrate metabolism. The analysis of the competitiveness of L. reuteri in sourdough revealed that the competitivess of sourdough isolates was equal or higher when compared to rodent isolates. This study provides new insights into the adaptation of L. reuteri to food and intestinal habitats, suggesting that these two habitats exert different selective pressure related to growth rate and energy (carbohydrate) metabolism. PMID:26658825

  7. Supergroup C Wolbachia, mutualist symbionts of filarial nematodes, have a distinct genome structure.

    Science.gov (United States)

    Comandatore, Francesco; Cordaux, Richard; Bandi, Claudio; Blaxter, Mark; Darby, Alistair; Makepeace, Benjamin L; Montagna, Matteo; Sassera, Davide

    2015-12-01

    Wolbachia pipientis is possibly the most widespread endosymbiont of arthropods and nematodes. While all Wolbachia strains have historically been defined as a single species, 16 monophyletic clusters of diversity (called supergroups) have been described. Different supergroups have distinct host ranges and symbiotic relationships, ranging from mutualism to reproductive manipulation. In filarial nematodes, which include parasites responsible for major diseases of humans (such as Onchocerca volvulus, agent of river blindness) and companion animals (Dirofilaria immitis, the dog heartworm), Wolbachia has an obligate mutualist role and is the target of new treatment regimens. Here, we compare the genomes of eight Wolbachia strains, spanning the diversity of the major supergroups (A-F), analysing synteny, transposable element content, GC skew and gene loss or gain. We detected genomic features that differ between Wolbachia supergroups, most notably in the C and D clades from filarial nematodes. In particular, strains from supergroup C (symbionts of O. volvulus and D. immitis) present a pattern of GC skew, conserved synteny and lack of transposable elements, unique in the Wolbachia genus. These features could be the consequence of a distinct symbiotic relationship between C Wolbachia strains and their hosts, highlighting underappreciated differences between the mutualistic supergroups found within filarial nematodes. PMID:26631376

  8. Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74

    OpenAIRE

    Crook, Matthew B.; Mitra, Shubhajit; Ané, Jean-Michel; Sadowsky, Michael J.; Gyaneshwar, Prasad

    2013-01-01

    Rhizobium sp. strain IRBG74 is the first known nitrogen-fixing symbiont in the Agrobacterium/Rhizobium clade that nodulates the aquatic legume Sesbania sp. and is also a growth-promoting endophyte of wetland rice. Here, we present the sequence of the IRBG74 genome, which is composed of a circular chromosome, a linear chromosome, and a symbiotic plasmid, pIRBG74a.

  9. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

    Directory of Open Access Journals (Sweden)

    Fatou Diouf

    Full Text Available Acacia senegal (L Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60% clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4. We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T, one in MSP1 (STM8789, MSP2 (ORS3359 and MSP3 (ORS3324. The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  10. Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach

    Science.gov (United States)

    Gupta, Vipin; Haider, Shazia; Sood, Utkarsh; Gilbert, Jack A.; Ramjee, Meenakshi; Forbes, Ken; Singh, Yogendra; Lopes, Bruno S.; Lal, Rup

    2016-01-01

    The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections. PMID:27378055

  11. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

    Directory of Open Access Journals (Sweden)

    Sujai eKumar

    2013-11-01

    Full Text Available Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratisation of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory reared model organisms. They are often small, and cannot be isolated free of their environment - whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programmes. Here we present an approach to extracting from mixed DNA sequence data subsets that correspond to single species' genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage and biological (best-matching sequence in annotated databases indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimised assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots. We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from http://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.

  12. Complete Genome Sequences of the Obligate Symbionts “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae)

    Science.gov (United States)

    Abbà, Simona; Kube, Michael; Marzachì, Cristina

    2016-01-01

    Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus (Hemiptera: Cicadellidae), were fully sequenced. “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” represent two of the smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome sequences are nearly identical to strains reported from the closely related host species, M. quadrilineatus. PMID:26798106

  13. Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

    Energy Technology Data Exchange (ETDEWEB)

    Goltsman, Daniela [University of California, Berkeley; Denef, Vincent [University of California, Berkeley; Singer, Steven [Lawrence Livermore National Laboratory (LLNL); Verberkmoes, Nathan C [ORNL; Lefsrud, Mark G [ORNL; Mueller, Ryan [University of California, Berkeley; Dick, Gregory J. [University of California, Berkeley; Sun, Christine [University of California, Berkeley; Wheeler, Korin [Lawrence Livermore National Laboratory (LLNL); Zelma, Adam [Lawrence Livermore National Laboratory (LLNL); Baker, Brett J. [University of California, Berkeley; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Shah, Manesh B [ORNL; Thelen, Michael P. [University of California, Berkeley; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

    2009-01-01

    We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.

  14. Community genomic and proteomic analysis of chemoautotrophic, iron-oxidizing "Leptospirillum rubarum" (Group II) and Leptospirillum ferrodiazotrophum (Group III) in acid mine drainage biofilms

    Energy Technology Data Exchange (ETDEWEB)

    Goltsman, Daniela [University of California, Berkeley; Denef, Vincent [University of California, Berkeley; Singer, Steven [Lawrence Livermore National Laboratory (LLNL); Verberkmoes, Nathan C [ORNL; Lefsrud, Mark G [McGill University, Montreal, Quebec; Mueller, Ryan [University of California, Berkeley; Dick, Gregory J. [University of California, Berkeley; Sun, Christine [University of California, Berkeley; Wheeler, Korin [Lawrence Livermore National Laboratory (LLNL); Zelma, Adam [Lawrence Livermore National Laboratory (LLNL); Baker, Brett J. [University of California, Berkeley; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Shah, Manesh B [ORNL; Thelen, Michael P. [University of California, Berkeley; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

    2009-01-01

    We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum Groups II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, CA acid mine drainage (AMD) biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum Groups II and III, respectively and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and > 60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid encodes conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacteria have genes for community-essential functions, including carbon fixation, biosynthesis of vitamins, fatty acids and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum Group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum Group II uses a methyl-dependent and Leptospirillum Group III a methyl-independent response pathway. Although only Leptospirillum Group III can fix nitrogen, these proteins were not identified by proteomics. Abundances of core proteins are similar in all communities, but abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum Groups II and III.

  15. The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis.

    Directory of Open Access Journals (Sweden)

    Yoji Nakamura

    Full Text Available Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb, which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35% are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.

  16. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.

    KAUST Repository

    Bayer, Till

    2012-04-18

    Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

  17. Presence of extensive Wolbachia symbiont insertions discovered in the genome of its host Glossina morsitans morsitans.

    Directory of Open Access Journals (Sweden)

    Corey Brelsfoard

    2014-04-01

    Full Text Available Tsetse flies (Glossina spp. are the cyclical vectors of Trypanosoma spp., which are unicellular parasites responsible for multiple diseases, including nagana in livestock and sleeping sickness in humans in Africa. Glossina species, including Glossina morsitans morsitans (Gmm, for which the Whole Genome Sequence (WGS is now available, have established symbiotic associations with three endosymbionts: Wigglesworthia glossinidia, Sodalis glossinidius and Wolbachia pipientis (Wolbachia. The presence of Wolbachia in both natural and laboratory populations of Glossina species, including the presence of horizontal gene transfer (HGT events in a laboratory colony of Gmm, has already been shown. We herein report on the draft genome sequence of the cytoplasmic Wolbachia endosymbiont (cytWol associated with Gmm. By in silico and molecular and cytogenetic analysis, we discovered and validated the presence of multiple insertions of Wolbachia (chrWol in the host Gmm genome. We identified at least two large insertions of chrWol, 527,507 and 484,123 bp in size, from Gmm WGS data. Southern hybridizations confirmed the presence of Wolbachia insertions in Gmm genome, and FISH revealed multiple insertions located on the two sex chromosomes (X and Y, as well as on the supernumerary B-chromosomes. We compare the chrWol insertions to the cytWol draft genome in an attempt to clarify the evolutionary history of the HGT events. We discuss our findings in light of the evolution of Wolbachia infections in the tsetse fly and their potential impacts on the control of tsetse populations and trypanosomiasis.

  18. Draft Genome Sequence of Capniomyces stellatus, the Obligate Gut Fungal Symbiont of Stonefly.

    Science.gov (United States)

    Wang, Yan; White, Merlin M; Moncalvo, Jean-Marc

    2016-01-01

    Capniomyces stellatus is a host-specific endosymbiotic fungus, living in the hindgut of stoneflies (especially in Allocapnia). Here, we present the first draft genome sequence of the fungus, as well as the ab initio gene prediction and function analyses, which will facilitate the study and comparative analyses of insect-associated fungi. PMID:27491991

  19. Immunochemical localization of ribulose-1,5-bisphosphate carboxylase in the symbiont-containing gills of Solemya velum (Bivalvia : Mollusca)

    NARCIS (Netherlands)

    Cavanaugh, Colleen M.; Abbott, Marilyn S.; Veenhuis, Marten

    1988-01-01

    The distribution of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase (RbuP2Case; EC 4.1.1.39) was examined by using two immunological methods in tissues of Solemya velum, an Atlantic coast bivalve containing putative chemoautotrophic symbionts. Antibodies elicited by the purified large

  20. A bacterial genome in transition - an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus

    Directory of Open Access Journals (Sweden)

    Penz Thomas

    2011-09-01

    Full Text Available Abstract Background Insertion sequence (IS elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilus asiaticus contains an unusually large number of transposase genes (n = 354; 23% of all genes. Results The transposase genes in the A. asiaticus genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the A. asiaticus genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143, as well as the absence of direct repeats in most IS elements suggest that the IS elements of A. asiaticus are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the A. asiaticus genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction. Conclusions Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity.

  1. Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

    Energy Technology Data Exchange (ETDEWEB)

    Moulin, Lionel [UMR, France; Klonowska, Agnieszka [UMR, France; Caroline, Bournaud [UMR, France; Booth, Kristina [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts; Melkonian, Remy [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom; Bena, Gilles [UMR, France; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lizotte-Waniewski, Michelle [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole

    2014-01-01

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

  2. Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata

    Science.gov (United States)

    Keller-Costa, Tina; Silva, Rúben; Lago-Lestón, Asunción

    2016-01-01

    To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome sequence of Aquimarina sp. strain EL33, a bacterium isolated from the gorgonian coral Eunicella labiata. This first-described (to our knowledge) animal-associated Aquimarina genome possesses a sophisticated repertoire of genes involved in drug/antibiotic resistance and biosynthesis. PMID:27540075

  3. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    Science.gov (United States)

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  4. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    Directory of Open Access Journals (Sweden)

    Rogier Braakman

    Full Text Available Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.

  5. Diverse strategies for vertical symbiont transmission among subsocial stinkbugs.

    Directory of Open Access Journals (Sweden)

    Takahiro Hosokawa

    Full Text Available Sociality may affect symbiosis and vice versa. Many plant-sucking stinkbugs harbor mutualistic bacterial symbionts in the midgut. In the superfamily Pentatomoidea, adult females excrete symbiont-containing materials from the anus, which their offspring ingest orally and establish vertical symbiont transmission. In many stinkbug families whose members are mostly non-social, females excrete symbiont-containing materials onto/beside eggs upon oviposition. However, exceptional cases have been reported from two subsocial species representing the closely related families Cydnidae and Parastrachiidae, wherein females remain nearby eggs for maternal care after oviposition, and provide their offspring with symbiont-containing secretions at later stages, either just before or after hatching. These observations suggested that sociality of the host stinkbugs may be correlated with their symbiont transmission strategies. However, we found that cydnid stinkbugs of the genus Adomerus, which are associated with gammaproteobacterial gut symbionts and exhibit elaborate maternal care over their offspring, smear symbiont-containing secretions onto eggs upon oviposition as many non-social stinkbugs do. Surface sterilization of the eggs resulted in aposymbiotic insects of slower growth, smaller size and abnormal body coloration, indicating vertical symbiont transmission via egg surface contamination and presumable beneficial nature of the symbiosis. The Adomerus symbionts exhibited AT-biased nucleotide compositions, accelerated molecular evolutionary rates and reduced genome size, while these degenerative genomic traits were less severe than those in the symbiont of a subsocial parastrachiid. These results suggest that not only sociality but also other ecological and evolutionary aspects of the host stinkbugs, including the host-symbiont co-evolutionary history, may have substantially affected their symbiont transmission strategies.

  6. Genome Structure of the Symbiont Bifidobacterium pseudocatenulatum CECT 7765 and Gene Expression Profiling in Response to Lactulose-Derived Oligosaccharides.

    Science.gov (United States)

    Benítez-Páez, Alfonso; Moreno, F Javier; Sanz, María L; Sanz, Yolanda

    2016-01-01

    Bifidobacterium pseudocatenulatum CECT 7765 was isolated from stools of a breast-fed infant. Although, this strain is generally considered an adult-type bifidobacterial species, it has also been shown to have pre-clinical efficacy in obesity models. In order to understand the molecular basis of its adaptation to complex carbohydrates and improve its potential functionality, we have analyzed its genome and transcriptome, as well as its metabolic output when growing in galacto-oligosaccharides derived from lactulose (GOS-Lu) as carbon source. B. pseudocatenulatum CECT 7765 shows strain-specific genome regions, including a great diversity of sugar metabolic-related genes. A preliminary and exploratory transcriptome analysis suggests candidate over-expression of several genes coding for sugar transporters and permeases; furthermore, five out of seven beta-galactosidases identified in the genome could be activated in response to GOS-Lu exposure. Here, we also propose that a specific gene cluster is involved in controlling the import and hydrolysis of certain di- and tri-saccharides, which seemed to be those primarily taken-up by the bifidobacterial strain. This was discerned from mass spectrometry-based quantification of different saccharide fractions of culture supernatants. Our results confirm that the expression of genes involved in sugar transport and metabolism and in the synthesis of leucine, an amino acid with a key role in glucose and energy homeostasis, was up-regulated by GOS-Lu. This was done using qPCR in addition to the exploratory information derived from the single-replicated RNAseq approach, together with the functional annotation of genes predicted to be encoded in the B. pseudocatenulatum CETC 7765 genome. PMID:27199952

  7. Genome Structure of the Symbiont Bifidobacterium pseudocatenulatum CECT 7765 and Gene Expression Profiling in Response to Lactulose-Derived Oligosaccharides

    Science.gov (United States)

    Benítez-Páez, Alfonso; Moreno, F. Javier; Sanz, María L.; Sanz, Yolanda

    2016-01-01

    Bifidobacterium pseudocatenulatum CECT 7765 was isolated from stools of a breast-fed infant. Although, this strain is generally considered an adult-type bifidobacterial species, it has also been shown to have pre-clinical efficacy in obesity models. In order to understand the molecular basis of its adaptation to complex carbohydrates and improve its potential functionality, we have analyzed its genome and transcriptome, as well as its metabolic output when growing in galacto-oligosaccharides derived from lactulose (GOS-Lu) as carbon source. B. pseudocatenulatum CECT 7765 shows strain-specific genome regions, including a great diversity of sugar metabolic-related genes. A preliminary and exploratory transcriptome analysis suggests candidate over-expression of several genes coding for sugar transporters and permeases; furthermore, five out of seven beta-galactosidases identified in the genome could be activated in response to GOS-Lu exposure. Here, we also propose that a specific gene cluster is involved in controlling the import and hydrolysis of certain di- and tri-saccharides, which seemed to be those primarily taken-up by the bifidobacterial strain. This was discerned from mass spectrometry-based quantification of different saccharide fractions of culture supernatants. Our results confirm that the expression of genes involved in sugar transport and metabolism and in the synthesis of leucine, an amino acid with a key role in glucose and energy homeostasis, was up-regulated by GOS-Lu. This was done using qPCR in addition to the exploratory information derived from the single-replicated RNAseq approach, together with the functional annotation of genes predicted to be encoded in the B. pseudocatenulatum CETC 7765 genome. PMID:27199952

  8. Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

    OpenAIRE

    McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A

    2009-01-01

    Author Summary The genetic code, which relates DNA sequence to protein sequence, is nearly universal across all life. Examples of recodings do exist, but new instances are rare. Genomes that exhibit recodings typically have other extreme properties, including reduced size, reduced gene sets, and low guanine plus cytosine (GC) content. The most common recoding event, the reassignment of UGA to Tryptophan instead of Stop (Stop→Trp), was previously known from several mitochondrial and one bacter...

  9. Symbiont-mediated protection

    OpenAIRE

    Haine, Eleanor R.

    2007-01-01

    Despite the fact that all vertically transmitted symbionts sequester resources from their hosts and are therefore costly to maintain, there is an extraordinary diversity of them in invertebrates. Some spread through host populations by providing their hosts with fitness benefits or by manipulating host sex ratio, but some do not: their maintenance in host lineages remains an enigma. In this review, I explore the evolutionary ecology of vertically transmitted symbionts and their impact on host...

  10. Chemoautotrophic Bacterial Production in the Redoxycline of an Ice-Covered Antarctic Lake (Invited)

    Science.gov (United States)

    Mikucki, J.; Kong, W.; Priscu, J. C.; Morgan-Kiss, R.

    2010-12-01

    Chemolithoautotrophic organisms obtain energy for growth from inorganic substrates and use simple inorganic carbon molecules to construct biomass. As such, chemosynthetic processes are tightly linked to biogeochemical cycles. In polar regions, winter darkness shuts down photosynthetic inputs and the contribution of chemosynthesis to total ecosystem energetics and carbon fixation may be significant. Few reports exist on chemosynthesis in polar environments and the rates of these processes remain largely unexplored. Here we present data on chemoautotrophic activity in the redoxycline (~15m depth) of the permanently ice-covered Lake Bonney in the McMurdo Dry Valleys, Antarctica (MCM). Rates of radio-labeled bicarbonate incorporation were measured under light and dark conditions using whole community and bacterial sized-fraction (< 3 μm) samples. Rates of uptake in the bacterial sized-fraction (0.18 μg C L-1 d-1) were comparable to that of heterotrophic bacterial activity (0.16 μg C L-1 d-1) as measured by radio-labeled thymidine incorporation. Molecular analyses of the (cbbM) Rubisco gene, a key enzyme in the Calvin cycle, revealed relatives to the Thiobacillus genera confirming the genomic potential for in situ bacterial carbon fixation. Further, quantification of cbbM gene copy number by real time PCR from samples collected throughout the trophogenic zones of the west and east lobes of Lake Bonney confirmed that chemotrophic bacteria harboring form II RubisCO are restricted to depths at or below the redoxycline of the west lobe. These data provide insight into the structure-function relationship between the microbial consortia and carbon budget and imply that chemoautotrophic production in the MCM may provide a significant source of previously un-quantified fixed carbon to the lake system. Studies on other icy systems, including dark, isolated subglacial environments report evidence for chemolithoautotrophy suggesting that chemoautotrophic production can sustain

  11. Physical proximity may promote lateral acquisition of bacterial symbionts in vesicomyid clams.

    Directory of Open Access Journals (Sweden)

    Carole Decker

    Full Text Available Vesicomyid clams harbor intracellular sulfur-oxidizing bacteria that are predominantly maternally inherited and co-speciate with their hosts. Genome recombination and the occurrence of non-parental strains were recently demonstrated in symbionts. However, mechanisms favoring such events remain to be identified. In this study, we investigated symbionts in two phylogenetically distant vesicomyid species, Christineconcha regab and Laubiericoncha chuni, which sometimes co-occur at a cold-seep site in the Gulf of Guinea. We showed that each of the two species harbored a single dominant bacterial symbiont strain. However, for both vesicomyid species, the symbiont from the other species was occasionally detected in the gills using fluorescence in situ hybridization and gene sequences analyses based on six symbiont marker genes. Symbiont strains co-occurred within a single host only at sites where both host species were found; whereas one single symbiont strain was detected in C. regab specimens from a site where no L. chuni individuals had been observed. These results suggest that physical proximity favored the acquisition of non-parental symbiont strains in Vesicomyidae. Over evolutionary time, this could potentially lead to genetic exchanges among symbiont species and eventually symbiont displacement. Symbiont densities estimated using 3D fluorescence in situ hybridization varied among host species and sites, suggesting flexibility in the association despite the fact that a similar type of metabolism is expected in all symbionts.

  12. Addicted? Reduced host resistance in populations with defensive symbionts.

    Science.gov (United States)

    Martinez, Julien; Cogni, Rodrigo; Cao, Chuan; Smith, Sophie; Illingworth, Christopher J R; Jiggins, Francis M

    2016-06-29

    Heritable symbionts that protect their hosts from pathogens have been described in a wide range of insect species. By reducing the incidence or severity of infection, these symbionts have the potential to reduce the strength of selection on genes in the insect genome that increase resistance. Therefore, the presence of such symbionts may slow down the evolution of resistance. Here we investigated this idea by exposing Drosophila melanogaster populations to infection with the pathogenic Drosophila C virus (DCV) in the presence or absence of Wolbachia, a heritable symbiont of arthropods that confers protection against viruses. After nine generations of selection, we found that resistance to DCV had increased in all populations. However, in the presence of Wolbachia the resistant allele of pastrel-a gene that has a major effect on resistance to DCV-was at a lower frequency than in the symbiont-free populations. This finding suggests that defensive symbionts have the potential to hamper the evolution of insect resistance genes, potentially leading to a state of evolutionary addiction where the genetically susceptible insect host mostly relies on its symbiont to fight pathogens. PMID:27335421

  13. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: A blueprint for thriving in and out of symbiosis

    Energy Technology Data Exchange (ETDEWEB)

    Dmytrenko, Oleg; Russell, Shelbi L.; Loo, Wesley T.; Fontanez, Kristina M.; Liao, Li; Roeselers, Guus; Sharma, Raghav; Stewart, Frank J.; Newton, Irene L. G.; Woyke, Tanja; Wu, Dongying; Lang, Jenna Morgan; Eisen, Jonathan A.; Cavanaugh, Colleen M.

    2014-09-25

    Background: Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. Results: Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.86 Mb), GC-rich (50.4percent), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. Conclusions: The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle

  14. Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO gene

    OpenAIRE

    Elsaied, Hosam Easa; Kaneko, Ryo; Naganuma, Takeshi

    2006-01-01

    In our previous investigation on the genes of 1,5-bisphosphate carboxylase/oxygenase (RuBisCO; EC 4.1.1.39) in deep-sea chemoautotrophic and methanotrophic endosymbioses, the gene encoding the large subunit of RuBisCO form I (cbbL) had been detected in the gill of a mussel belonging to the genus Bathymodiolus from a western Pacific back-arc hydrothermal vent. This study further revealed the symbiont source of the RuBisCO cbbL gene along with the genes of 16S ribosomal RNA (16S rDNA), particul...

  15. Evidence of horizontal gene transfer between obligate leaf nodule symbionts.

    Science.gov (United States)

    Pinto-Carbó, Marta; Sieber, Simon; Dessein, Steven; Wicker, Thomas; Verstraete, Brecht; Gademann, Karl; Eberl, Leo; Carlier, Aurelien

    2016-09-01

    Bacteria of the genus Burkholderia establish an obligate symbiosis with plant species of the Rubiaceae and Primulaceae families. The bacteria, housed within the leaves, are transmitted hereditarily and have not yet been cultured. We have sequenced and compared the genomes of eight bacterial leaf nodule symbionts of the Rubiaceae plant family. All of the genomes exhibit features consistent with genome erosion. Genes potentially involved in the biosynthesis of kirkamide, an insecticidal C7N aminocyclitol, are conserved in most Rubiaceae symbionts. However, some have partially lost the kirkamide pathway due to genome erosion and are unable to synthesize the compound. Kirkamide synthesis is therefore not responsible for the obligate nature of the symbiosis. More importantly, we find evidence of intra-clade horizontal gene transfer (HGT) events affecting genes of the secondary metabolism. This indicates that substantial gene flow can occur at the early stages following host restriction in leaf nodule symbioses. We propose that host-switching events and plasmid conjugative transfers could have promoted these HGTs. This genomic analysis of leaf nodule symbionts gives, for the first time, new insights in the genome evolution of obligate symbionts in their early stages of the association with plants. PMID:26978165

  16. Molecular Characterization of Methanotrophic and Chemoautotrophic Communities at Cold Seeps

    OpenAIRE

    Lösekann, Tina

    2006-01-01

    Cold seeps are complex ecosystems based on chemosynthesis. Sulfide and methane are available in high concentrations and support a variety of highly adapted microorganisms and symbiont-bearing invertebrates. The anaerobic oxidation of methane (AOM) is a key biogeochemical process at cold seeps and is assumed to be mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria. In this thesis I used 16S rRNA-based molecular methods to identify and quantify met...

  17. High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes

    Energy Technology Data Exchange (ETDEWEB)

    Isanapong, Jantiya [University of Texas, Arlington; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Rodrigues, Jorge L.M. [University of Texas, Arlington

    2012-01-01

    Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.

  18. Complete Genome Sequence of “Candidatus Portiera aleyrodidarum” BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci

    OpenAIRE

    Santos-Garcia, Diego; Farnier, Pierre-Antoine; Beitia, Francisco; Zchori-Fein, Einat; Vavre, Fabrice; Mouton, Laurence; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

    2012-01-01

    The genome of “Candidatus Portiera aleyrodidarum,” the primary endosymbiont of the whitefly Bemisia tabaci (Mediterranean species), is reported. It presents a reduced genome (357 kb) encoding the capability to synthetize, or participate in the synthesis of, several amino acids and carotenoids, being the first insect endosymbiont capable of supplying carotenoids.

  19. Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings

    Science.gov (United States)

    Li, Zhefei; Ma, Zhanqiang; Hao, Xiuli

    2012-01-01

    Sinorhizobium meliloti CCNWSX0020 was isolated from Medicago lupulina plants growing in lead-zinc mine tailings, which can establish a symbiotic relationship with Medicago species. Also, the genome of this bacterium contains a number of protein-coding sequences related to metal tolerance. We anticipate that the genomic sequence provides valuable information to explore environmental bioremediation. PMID:22328762

  20. Insect symbionts in food webs.

    Science.gov (United States)

    McLean, Ailsa H C; Parker, Benjamin J; Hrček, Jan; Henry, Lee M; Godfray, H Charles J

    2016-09-01

    Recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. Here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. Using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. Many symbionts are now known to help their hosts escape or resist natural enemy attack, and others can allow their hosts to withstand abiotic stress or affect host plant use. In addition to the direct effect of symbionts on aphid phenotypes there may be indirect effects mediated through trophic and non-trophic community interactions. We believe that by using data from barcoding studies to identify bacterial symbionts, this extra, microbial dimension to insect food webs can be better elucidated.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481779

  1. Insect symbionts in food webs

    Science.gov (United States)

    Henry, Lee M.

    2016-01-01

    Recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. Here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. Using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. Many symbionts are now known to help their hosts escape or resist natural enemy attack, and others can allow their hosts to withstand abiotic stress or affect host plant use. In addition to the direct effect of symbionts on aphid phenotypes there may be indirect effects mediated through trophic and non-trophic community interactions. We believe that by using data from barcoding studies to identify bacterial symbionts, this extra, microbial dimension to insect food webs can be better elucidated. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481779

  2. Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis.

    Science.gov (United States)

    Parkinson, Jasmine F; Gobin, Bruno; Hughes, William O H

    2016-04-01

    Beneficial eukaryotic-bacterial partnerships are integral to animal and plant evolution. Understanding the density regulation mechanisms behind bacterial symbiosis is essential to elucidating the functional balance between hosts and symbionts. Citrus mealybugs, Planococcus citri (Risso), present an excellent model system for investigating the mechanisms of symbiont density regulation. They contain two obligate nutritional symbionts, Moranella endobia, which resides inside Tremblaya princeps, which has been maternally transmitted for 100-200 million years. We investigate whether host genotype may influence symbiont density by crossing mealybugs from two inbred laboratory-reared populations that differ substantially in their symbiont density to create hybrids. The density of the M. endobia symbiont in the hybrid hosts matched that of the maternal parent population, in keeping with density being determined either by the symbiont or the maternal genotype. However, the density of the T. princeps symbiont was influenced by the paternal host genotype. The greater dependency of T. princeps on its host may be due to its highly reduced genome. The decoupling of T. princeps and M. endobia densities, in spite of their intimate association, suggests that distinct regulatory mechanisms can be at work in symbiotic partnerships, even when they are obligate and mutualistic. PMID:27099709

  3. Genetic connectivity between north and south Mid-Atlantic Ridge chemosynthetic bivalves and their symbionts.

    Directory of Open Access Journals (Sweden)

    Karina van der Heijden

    Full Text Available Transform faults are geological structures that interrupt the continuity of mid-ocean ridges and can act as dispersal barriers for hydrothermal vent organisms. In the equatorial Atlantic Ocean, it has been hypothesized that long transform faults impede gene flow between the northern and the southern Mid-Atlantic Ridge (MAR and disconnect a northern from a southern biogeographic province. To test if there is a barrier effect in the equatorial Atlantic, we examined phylogenetic relationships of chemosynthetic bivalves and their bacterial symbionts from the recently discovered southern MAR hydrothermal vents at 5°S and 9°S. We examined Bathymodiolus spp. mussels and Abyssogena southwardae clams using the mitochondrial cytochrome c oxidase subunit I (COI gene as a phylogenetic marker for the hosts and the bacterial 16S rRNA gene as a marker for the symbionts. Bathymodiolus spp. from the two southern sites were genetically divergent from the northern MAR species B. azoricus and B. puteoserpentis but all four host lineages form a monophyletic group indicating that they radiated after divergence from their northern Atlantic sister group, the B. boomerang species complex. This suggests dispersal of Bathymodiolus species from north to south across the equatorial belt. 16S rRNA genealogies of chemoautotrophic and methanotrophic symbionts of Bathymodiolus spp. were inconsistent and did not match the host COI genealogy indicating disconnected biogeography patterns. The vesicomyid clam Abyssogena southwardae from 5°S shared an identical COI haplotype with A. southwardae from the Logatchev vent field on the northern MAR and their symbionts shared identical 16S phylotypes, suggesting gene flow across the Equator. Our results indicate genetic connectivity between the northern and southern MAR and suggest that a strict dispersal barrier does not exist.

  4. Obligate symbiont involved in pest status of host insect

    OpenAIRE

    Hosokawa, Takahiro; Kikuchi, Yoshitomo; Shimada, Masakazu; Fukatsu, Takema

    2007-01-01

    The origin of specific insect genotypes that enable efficient use of agricultural plants is an important subject not only in applied fields like pest control and management but also in basic disciplines like evolutionary biology. Conventionally, it has been presupposed that such pest-related ecological traits are attributed to genes encoded in the insect genomes. Here, however, we report that pest status of an insect is principally determined by symbiont genotype rather than by insect genotyp...

  5. Insect symbionts and molecular phylogenetics

    Czech Academy of Sciences Publication Activity Database

    Hypša, Václav; Nováková, Eva

    Vol. 3. Boca Raton, FL: CRC Press, 2008 - (Bourtzis, K.; Miller, T.), s. 1-32. (Contemporary Topics in Entomology. 4). ISBN 1-4200-6410-X R&D Projects: GA AV ČR IAA601410708; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60220518 Keywords : symbiosis * molecular phylogeny * insect symbionts * coevolution Subject RIV: EG - Zoology

  6. Evolution: Welcome to Symbiont Prison.

    Science.gov (United States)

    Kiers, E Toby; West, Stuart A

    2016-01-25

    Can egalitarian partnerships exist in nature? A new study demonstrates how protist hosts use and abuse their algal symbionts depending on their needs. While this relationship allows protists to survive in low nutrient conditions, it leaves little room for algal retaliation. PMID:26811890

  7. Independent phylogenetic origins of methanotrophic and chemoautotrophic bacterial endosymbioses in marine bivalves

    OpenAIRE

    Distel, D L; Cavanaugh, Colleen Marie

    1994-01-01

    The discovery of bacterium-bivalve symbioses capable of utilizing methane as a carbon and energy source indicates that the endosymbionts of hydrothermal vent and cold seep bivalves are not restricted to sulfur-oxidizing chemoautotrophic bacteria but also include methanotrophic bacteria. The phylogenetic origin of methanotrophic endosymbionts and their relationship to known symbiotic and free-living bacteria, however, have remained unexplored. In situ localization and phylogenetic analysis of ...

  8. Exploring symbiont management in lichens.

    Science.gov (United States)

    Grube, Martin; Spribille, Toby

    2012-07-01

    Lichens are unique among fungal symbioses in that their mycelial structures are compact and exposed to the light as thallus structures. The myriad intersections of unique fungal species with photosynthetic partner organisms (green algae in 90% of lichens) produce a wide variety of diverse shapes and colours of the fully synthesized lichen thallus when growing in nature. This characteristic complex morphology is, however, not achieved in the fungal axenic state. Even under ideal environmental conditions, the lichen life cycle faces considerable odds: first, meiotic spores are only produced on well-established thalli and often only after achieving considerable age in a stable environment, and second, even then in vivo resynthesis requires the presence of compatible algal strains where fungal spores germinate. Many lichen species have evolved a way around the resynthesis bottleneck by producing asexual propagules for joint propagation of symbionts. These different dispersal strategies ostensibly shape the population genetic structure of lichen symbioses, but the relative contributions of vertical (joint) and horizontal (independent) symbiont transmission have long eluded lichen evolutionary biologists. In this issue of Molecular Ecology, Dal Grande et al. (2012) close in on this question with the lung lichen, Lobaria pulmonaria, a flagship species in the conservation of old growth forests. By capitalizing on available microsatellite markers for both fungal and algal symbionts, they show that while vertical transmission is the predominant mode of reproduction, horizontal transmission is demonstrable and actively shapes population genetic structure. The resulting mixed propagation system is a highly successful balance of safe recruitment of symbiotic clones and endless possibilities for fungal recombination and symbiont shuffling. PMID:22916345

  9. Symbiont-mediated functions in insect hosts

    OpenAIRE

    Su, Qi; Zhou, Xiaomao; Zhang, Youjun

    2013-01-01

    The bacterial endosymbionts occur in a diverse array of insect species and are usually rely within the vertical transmission from mothers to offspring. In addition to primary symbionts, plant sap-sucking insects may also harbor several diverse secondary symbionts. Bacterial symbionts play a prominent role in insect nutritional ecology by aiding in digestion of food or supplementing nutrients that insect hosts can’t obtain sufficient amounts from a restricted diet of plant phloem. Currently, s...

  10. Complementary symbiont contributions to plant decomposition in a fungus-farming termite

    DEFF Research Database (Denmark)

    Thomas-Poulsen, Michael; Hu, Haofu; Li, Cai;

    2014-01-01

    Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis...... have remained enigmatic. We obtained high-quality annotated draft genomes of the termite Macrotermes natalensis, its Termitomyces symbiont, and gut metagenomes from workers, soldiers, and a queen. We show that members from 111 of the 128 known glycoside hydrolase families are represented...

  11. Comparative Genomics of Symbiotic Bacteria in Earthworm Nephridia

    DEFF Research Database (Denmark)

    Kjeldsen, Kasper Urup; Pinel, Nicolas; Lund, Marie Braad;

    The excretory and osmoregulatory organs (nephridia) of lumbricid earthworms are densely colonized by extracellular bacterial symbionts belonging to the newly established betaproteobacterial genus Verminephrobacter. The nephridial symbiont of the earthworm Eisenia fetida was subjected to full genome...... sequencing along with two of its closest relatives; the plant pathogenic Acidovorax avena subsp. citrulli and the free-living Acidovorax sp. JS42. In addition, the genome of the nephridial symbiont of the earthworm Aporrectodea tuberculata was partially sequenced. In order to resolve the functional...

  12. Environmental controls on chemoautotrophic primary producers at deep-sea vents

    Science.gov (United States)

    Le Bris, Nadine; Mullineaux, Lauren; Sievert, Stefan

    2014-05-01

    High biomasses and fast growth rates of dominant chemosynthetic species characterize hydrothermal ecosystems, raising the issue of their contribution to energy transfer and carbon cycling in the deep-sea. Addressing this issue, however, needs to account for the temporal instability of hydrothermal systems, both, in terms of biological colonization and habitat conditions. Volcanic eruptions on mid-ocean ridges offer the opportunity to investigate the environmental conditions favoring the successive modes of chemoautotrophic primary production (i.e. free living microbes and symbiotic invertebrates). In that perspective, habitat-scale approaches distinguish from vent field-scale approaches based on fluid composition and provide relevant information on environmental constraints exerted at different stages of colonization focusing on parameters linked with physiological limits and available energy. Investigation of habitat physicochemical properties along a typical successional sequence of recolonization at 9°50'N EPR diffuse-flow vents, between 2006 and 2014, was performed in order to examine potential changes in environmental features associated with chemoautotrophic primary producers, from early microbial colonizers to symbiotic invertebrates. Combined in situ measurements of temperature, pH and hydrogen sulfide were used and their variability documented over a series of assemblages characterizing recolonization stages. The distributions of mature assemblages of dominant invertebrate species associate with substantial differences in habitat conditions, pointing to a strong influence of habitat properties on potential productivity. Among the differences observed, however, the amplitude and rate of environmental fluctuation appear more important than average conditions in the succession, highlighting the role of spatial heterogeneity and temporal dynamics as a control on primary producers. Invertebrate species acting as engineer species are expected to play a primary

  13. Maintenance of essential amino acid synthesis pathways in the Blattabacterium cuenoti symbiont of a wood-feeding cockroach.

    Science.gov (United States)

    Tokuda, Gaku; Elbourne, Liam D H; Kinjo, Yukihiro; Saitoh, Seikoh; Sabree, Zakee; Hojo, Masaru; Yamada, Akinori; Hayashi, Yoshinobu; Shigenobu, Shuji; Bandi, Claudio; Paulsen, Ian T; Watanabe, Hirofumi; Lo, Nathan

    2013-06-23

    In addition to harbouring intestinal symbionts, some animal species also possess intracellular symbiotic microbes. The relative contributions of gut-resident and intracellular symbionts to host metabolism, and how they coevolve are not well understood. Cockroaches and the termite Mastotermes darwiniensis present a unique opportunity to examine the evolution of spatially separated symbionts, as they harbour gut symbionts and the intracellular symbiont Blattabacterium cuenoti. The genomes of B. cuenoti from M. darwiniensis and the social wood-feeding cockroach Cryptocercus punctulatus are each missing most of the pathways for the synthesis of essential amino acids found in the genomes of relatives from non-wood-feeding hosts. Hypotheses to explain this pathway degradation include: (i) feeding on microbes present in rotting wood by ancestral hosts; (ii) the evolution of high-fidelity transfer of gut microbes via social behaviour. To test these hypotheses, we sequenced the B. cuenoti genome of a third wood-feeding species, the phylogenetically distant and non-social Panesthia angustipennis. We show that host wood-feeding does not necessarily lead to degradation of essential amino acid synthesis pathways in B. cuenoti, and argue that ancestral high-fidelity transfer of gut microbes best explains their loss in strains from M. darwiniensis and C. punctulatus. PMID:23515978

  14. Long-term Cultivation of the Deep-Sea Clam Calyptogena okutanii: Changes in the Abundance of Chemoautotrophic Symbiont, Elemental Sulfur, and Mucus.

    Science.gov (United States)

    Ohishi, Kazue; Yamamoto, Masahiro; Tame, Akihiro; Kusaka, Chiho; Nagai, Yukiko; Sugimura, Makoto; Inoue, Koji; Uematsu, Katsuyuki; Yoshida, Takao; Ikuta, Tetsuro; Toyofuku, Takashi; Maruyama, Tadashi

    2016-06-01

    Survival of deep-sea Calyptogena clams depends on organic carbon produced by symbiotic, sulfur-oxidizing, autotrophic bacteria present in the epithelial cells of the gill. To understand the mechanism underlying this symbiosis, the development of a long-term cultivation system is essential. We cultivated specimens of Calyptogena okutanii in an artificial chemosynthetic aquarium with a hydrogen sulfide (H2S) supply system provided by the sulfate reduction of dog food buried in the sediment. We studied morphological and histochemical changes in the clams' gills by immunohistochemical and energy-dispersive X-ray analyses. The freshly collected clams contained a high amount of elemental sulfur in the gill epithelial cells, as well as densely packed symbiotic bacteria. Neither elemental sulfur nor symbiotic bacteria was detected in any other organs except the ovaries, where symbiotic bacteria, but not sulfur, was detected. The longest survival of an individual clam in this aquarium was 151 days. In the 3 clams dissected on Days 57 and 91 of the experiment, no elemental sulfur was detected in the gills. The symbiotic bacteria content had significantly decreased by Day 57, and was absent by Day 91. For comparison, we also studied the deep-sea mussel Bathymodiolus septemdierum, which harbors a phylogenetically close, sulfur-oxidizing, symbiotic bacterium with similar sulfur oxidation pathways. Sulfur particles were not detected, even in the gills of the freshly collected mussels. We discuss the importance of the proportion of available H2S and oxygen to the bivalves for elemental sulfur accumulation. Storage of nontoxic elemental sulfur, an energy source, seems to be an adaptive strategy of C. okutanii. PMID:27365420

  15. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts.

    Directory of Open Access Journals (Sweden)

    Helen E Dunbar

    2007-05-01

    Full Text Available Symbiosis is a ubiquitous phenomenon generating biological complexity, affecting adaptation, and expanding ecological capabilities. However, symbionts, which can be subject to genetic limitations such as clonality and genomic degradation, also impose constraints on hosts. A model of obligate symbiosis is that between aphids and the bacterium Buchnera aphidicola, which supplies essential nutrients. We report a mutation in Buchnera of the aphid Acyrthosiphon pisum that recurs in laboratory lines and occurs in field populations. This single nucleotide deletion affects a homopolymeric run within the heat-shock transcriptional promoter for ibpA, encoding a small heat-shock protein. This Buchnera mutation virtually eliminates the transcriptional response of ibpA to heat stress and lowers its expression even at cool or moderate temperatures. Furthermore, this symbiont mutation dramatically affects host fitness in a manner dependent on thermal environment. Following a short heat exposure as juveniles, aphids bearing short-allele symbionts produced few or no progeny and contained almost no Buchnera, in contrast to aphids bearing symbionts without the deletion. Conversely, under constant cool conditions, aphids containing symbionts with the short allele reproduced earlier and maintained higher reproductive rates. The short allele has appreciable frequencies in field populations (up to 20%, further supporting the view that lowering of ibpA expression improves host fitness under some conditions. This recurring Buchnera mutation governs thermal tolerance of aphid hosts. Other cases in which symbiont microevolution has a major effect on host ecological tolerance are likely to be widespread because of the high mutation rates of symbiotic bacteria and their crucial roles in host metabolism and development.

  16. Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

    Science.gov (United States)

    Hoeft, S.E.; Blum, J.S.; Stolz, J.F.; Tabita, F.R.; Witte, B.; King, G.M.; Santini, J.M.; Oremland, R.S.

    2007-01-01

    A facultative chemoautotrophic bacterium, strain MLHE-1T, was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1T were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1T could oxidize but not grow on CO, while CH4 neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1T assimilated inorganic carbon via the Calvin-Benson-Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1T grew over broad ranges of pH (7.3-10.0; optimum, 9.3), salinity (115-190 g l-1; optimum 30 g l-1) and temperature (113-40 ??C; optimum, 30 ??C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1T in the class Gammaproteobacteria (family Ectothiorhodospiraceae) and most closely related to Alkalispirillum mobile (98.5%) and Alkalilimnicola halodurans (98.6%), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1T was able to oxidize As(III). On the basis of physiological characteristics and DNA-DNA hybridization data, it is suggested that strain MLHE-1T represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1T (=DSM 17681T =ATCC BAA-1101T). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology. ?? 2007 IUMS.

  17. Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

    Science.gov (United States)

    Davis, R.; Tebo, B. M.

    2013-12-01

    Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn

  18. Characterization of the symbiosis between chemoautotrophic bacteria and the bivalve Lucinoma aequizonata: morphology, biochemistry, and phylogeny

    International Nuclear Information System (INIS)

    Low magnification electron microscopy and light microscopy were performed on plastic embedded and fresh samples of bacteriocyte tissues from L. annulata, L. aequizonata and L. floridana. Serial sectioning was used to determine the three dimensional relationship between host tissues, symbiont cells, and the external environment. Possible effects of structure on the exchange of metabolites and inorganic molecules are discussed. Density gradient centrifugation was used to purify symbiotic bacteria from homogenates of host bacteriocyte tissue. The results demonstrate that bacteria can be recovered intact, biologically active and nearly free of contaminants from host tissue. Incorporation of H14CO3- into acid soluble metabolic intermediates by either whole gills, isolated bacteria or bacteria isolated from gills previously exposed to label was examined in L. aequizonata. HPLC, paper chromatography and enzymatic techniques were used to identify and quantify labeled products. The initial fixation product in whole gills is malate. In the symbionts aspartate and 3-phosphoglycerate are the major labeled compounds. Possible pathways of carbon exchange between hosts and symbionts are discussed

  19. Spatial distribution of mud flows, chemoautotrophic communities, and biogeochemical habitats at Håkon Mosby Mud Volcano

    OpenAIRE

    Jerosch, Kerstin; Schlüter, Michael; Foucher, J. P.; Allais, A. G.; Klages, Michael; Edy, C.

    2007-01-01

    Marine mud volcanoes are significant source locations contributing to the marine methane cycle. Enhanced heat flow, unique chemoautotrophic communities, occurrence of massive gas hydrates and large gas plumes are direct evidences of elevated methane concentrations and the dynamic environment of mud volcanoes. Related to the high concentrations and large inventories of CH4 in surface sediments only a fraction of the methane is exported to the bottom water. This is mainly due to chemoautotrophi...

  20. A remarkable finding that suggests the existence of a new groundwater biome based on chemoautotrophic resources, named

    OpenAIRE

    Ştefan Negrea

    2009-01-01

    An important work of subterranean biology, signed by Francis Dov Por, Ophel: a groundwater biome based on chemoautotrophic resources. The global significance of the Ayyalon cave finds, Israel is presented and discussed in the present paper. The subject is a remarkable discovery suggesting the existence of a new aquatic subterranean biome autonomous energy based the author calls Ophel, the Hebrew word for “darkness” and “netherworld”). For F.D. Por, this biome links different marine chemosynth...

  1. Adaptation by Deletogenic Replication Slippage in a Nascent Symbiont.

    Science.gov (United States)

    Clayton, Adam L; Jackson, D Grant; Weiss, Robert B; Dale, Colin

    2016-08-01

    As a consequence of population level constraints in the obligate, host-associated lifestyle, intracellular symbiotic bacteria typically exhibit high rates of molecular sequence evolution and extensive genome degeneration over the course of their host association. While the rationale for genome degeneration is well understood, little is known about the molecular mechanisms driving this change. To understand these mechanisms we compared the genome of Sodalis praecaptivus, a nonhost associated bacterium that is closely related to members of the Sodalis-allied clade of insect endosymbionts, with the very recently derived insect symbiont Candidatus Sodalis pierantonius. The characterization of indel mutations in the genome of Ca Sodalis pierantonius shows that the replication system in this organism is highly prone to deletions resulting from polymerase slippage events in regions encoding G+C-rich repetitive sequences. This slippage-prone phenotype is mechanistically associated with the loss of certain components of the bacterial DNA recombination machinery at an early stage in symbiotic life and is expected to facilitate rapid adaptation to the novel host environment. This is analogous to the emergence of mutator strains in both natural and laboratory populations of bacteria, which tend to reach high frequencies in clonal populations due to linkage between the mutator allele and the resulting adaptive mutations. PMID:27189544

  2. Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy

    Directory of Open Access Journals (Sweden)

    Dattagupta Sharmishtha

    2010-06-01

    Full Text Available Abstract Background The sulfide-rich Frasassi caves in central Italy contain a rare example of a freshwater ecosystem supported entirely by chemoautotrophy. Niphargus ictus, the sole amphipod species previously reported from this locality, was recently shown to host the first known case of a freshwater chemoautotrophic symbiosis. Since the habitat of N. ictus is highly fragmented and is comprised of streams and lakes with various sulfide concentrations, we conducted a detailed study to examine the potential genetic diversity of this species within Frasassi. Results By sequencing one nuclear (ITS and two mitochondrial (COI and 12S regions, we show that four partially sympatric Niphargus clades are present in Frasassi. Morphological and behavioral data obtained for three of these clades are perfectly congruent with this molecular delineation and make it possible to distinguish them in the field. Phylogenetic analyses of 28S ribosomal DNA sequences reveal that, among the four clades, only two are closely related to each other. Moreover, these four clades occupy distinct niches that seem to be related to the chemical properties and flow regimes of the various water bodies within Frasassi. Conclusions Our results suggest that four distinct Niphargus species are present in Frasassi and that they originated from three or four independent invasions of the cave system. At least two among the four species harbor Thiothrix epibionts, which paves the way for further studies of the specificity and evolutionary history of this symbiosis.

  3. Social insect symbionts: evolution in homeostatic fortresses

    DEFF Research Database (Denmark)

    Hughes, David P; Pierce, Naomi E; Boomsma, Jacobus J

    2008-01-01

    The massive environmentally buffered nests of some social insects can contain millions of individuals and a wide variety of parasites, commensals and mutualists. We suggest that the ways in which these homeostatic fortress environments affect the evolution of social insect symbionts are relevant...

  4. Evolving aphids: one genome-one organism insects or holobionts?

    Directory of Open Access Journals (Sweden)

    M Mandrioli

    2013-01-01

    Full Text Available Aphids have obligate mutualistic relationships with microorganisms that provide them with essential substances lacking in their diet, together with symbionts conferring them conditional adaptive advantages related, for instance, to the thermal tolerance and to the resistance to parasitoid wasps. The presence/absence of a secondary symbiont may have a relevant phenotypic effect so that aphid microbial symbionts constitute a sort of second genome with its own genetic inheritance. On the whole, genes important for aphid survival and reproduction are not uniquely present in the aphid nuclear and mitochondrial genomes, but also in the chromosomes of each symbiont. As a consequence, aphids should be viewed as holobionts with an extended genome (the hologenome including the host and its symbiotic microbiome. In this connection, the true unit of selection in evolution must be considered the aphid holobiont, in place of the single host as individual separated from its symbionts.

  5. POSSIBLE NEW INTRANUCLEAR SYMBIONTS OF PARAMECIUM CAUDATUM

    OpenAIRE

    Vishnyakov, Andrew; Rautian, Maria; Lebedeva, Natalja

    2001-01-01

    Intranuclear bacteria inhabiting macronucleus of Paramecium caudatum isolated from three populations from North America and Eastern Europe were studied. Interference contrast and electron microscopy was used to describe symbiont morphology. Symbiotic bacteria from such distant populations are rather similar. They are rod-shaped with 1-2 μm length and 0.3-0.4 μm diameter; cell wall is typical for gram-negative bacteria; membrane vesicles on the surface of some bacteria indicate the secretion o...

  6. Potential applications of insect symbionts in biotechnology

    OpenAIRE

    Berasategui, A.; Shukla, S; Salem, H; Kaltenpoth, M.

    2015-01-01

    Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biote...

  7. Multiple symbiont acquisition strategies as an adaptive mechanism in the coral Stylophora pistillata.

    Directory of Open Access Journals (Sweden)

    Kristen A Byler

    Full Text Available In obligate symbioses, the host's survival relies on the successful acquisition and maintenance of symbionts. Symbionts can either be transferred from parent to offspring via direct inheritance (vertical transmission or acquired anew each generation from the environment (horizontal transmission. With vertical symbiont transmission, progeny benefit by not having to search for their obligate symbionts, and, with symbiont inheritance, a mechanism exists for perpetuating advantageous symbionts. But, if the progeny encounter an environment that differs from that of their parent, they may be disadvantaged if the inherited symbionts prove suboptimal. Conversely, while in horizontal symbiont acquisition host survival hinges on an unpredictable symbiont source, an individual host may acquire genetically diverse symbionts well suited to any given environment. In horizontal acquisition, however, a potentially advantageous symbiont will not be transmitted to subsequent generations. Adaptation in obligate symbioses may require mechanisms for both novel symbiont acquisition and symbiont inheritance. Using denaturing-gradient gel electrophoresis and real-time PCR, we identified the dinoflagellate symbionts (genus Symbiodinium hosted by the Red Sea coral Stylophora pistillata throughout its ontogenesis and over depth. We present evidence that S. pistillata juvenile colonies may utilize both vertical and horizontal symbiont acquisition strategies. By releasing progeny with maternally derived symbionts, that are also capable of subsequent horizontal symbiont acquisition, coral colonies may acquire physiologically advantageous novel symbionts that are then perpetuated via vertical transmission to subsequent generations. With symbiont inheritance, natural selection can act upon the symbiotic variability, providing a mechanism for coral adaptation.

  8. Housekeeping mutualisms: do more symbionts facilitate host performance?

    Directory of Open Access Journals (Sweden)

    Adrian C Stier

    Full Text Available Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod symbionts on removal of sediment from their coral host. Our field survey showed that all common symbionts typically occur as pairs and never at greater abundances. Two species, the crab Trapezia serenei and the shrimp Alpheus lottini, were most common and co-occurred more often than expected by chance. We conducted a mesocosm experiment to test for effects of decapod identity and density on sediment removal. Alone, corals removed 10% of sediment, but removal increased to 30% and 48% with the presence of two and four symbionts, respectively. Per-capita effects of symbionts were independent of density and identity. Our results suggest that symbiont density is restricted by intraspecific competition. Thus, increased sediment removal from a coral host can only be achieved by increasing the number of species of symbionts on that coral, even though these species are functionally equivalent. Symbiont diversity plays a key role, not through added functionality but by overcoming density limitation likely imposed by intraspecific mating systems.

  9. Earthworm ecology affects the population structure of their Verminephrobacter symbionts.

    Science.gov (United States)

    Viana, Flávia; Jensen, Christopher Erik; Macey, Michael; Schramm, Andreas; Lund, Marie Braad

    2016-05-01

    Earthworms carry species-specific Verminephrobacter symbionts in their nephridia (excretory organs). The symbionts are vertically transmitted via the cocoon, can only colonize the host during early embryonic development, and have co-speciated with their host for about 100 million years. Although several studies have addressed Verminephrobacter diversity between worm species, the intra-species diversity of the symbiont population has never been investigated. In this study, symbiont population structure was examined by using a multi-locus sequence typing (MLST) approach on Verminephrobacter isolated from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and Eisenia fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils. Three distinct populations were investigated for both types and, according to MLST analysis of 193 Verminephrobacter isolates, the symbiont community in each worm individual was very homogeneous. The more solitary A. tuberculata carried unique symbiont populations in 9 out of 10 host individuals, whereas the symbiont populations in the social compost worms were homogeneous across host individuals from the same population. These data suggested that host ecology shaped the population structure of Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms led to the hypothesis that Verminephrobacter could be transferred bi-parentally or via leaky horizontal transmission in high-density, frequently mating worm populations. PMID:27040820

  10. Modeling arsenite oxidation by chemoautotrophic Thiomonas arsenivorans strain b6 in a packed-bed bioreactor

    International Nuclear Information System (INIS)

    Arsenic is a major toxic pollutant of concern for the human health. Biological treatment of arsenic contaminated water is an alternative strategy to the prevalent conventional treatments. The biological treatment involves a pre-oxidation step transforming the most toxic form of arsenic, As (III), to the least toxic form, As (V), respectively. This intermediate process improves the overall efficiency of total arsenic removal from the contaminated water. As (III) oxidation by the chemoautotrophic bacterium Thiomonas arsenivorans strain b6 was investigated in a fixed-film reactor under variable influent As (III) concentrations (500–4000 mg/L) and hydraulic residence times (HRTs) (0.2–1 day) for a duration of 137 days. During the entire operation, seven steady-state conditions were obtained with As (III) oxidation efficiency ranging from 48.2% to 99.3%. The strong resilience of the culture was exhibited by the recovery of the bioreactor from an As (III) overloading of 5300 ± 400 mg As (III)/L day operated at a HRT of 0.2 day. An arsenic mass balance revealed that As (III) was mainly oxidized to As (V) with unaccounted arsenic (≤ 4%) well within the analytical error of measurement. A modified Monod flux expression was used to determine the biokinetic parameters by fitting the model against the observed steady-state flux data obtained from operating the bioreactor under a range of HRTs (0.2–1 day) and a constant influent As (III) concentration of 500 mg/L. Model parameters, k = 0.71 ± 0.1 mg As (III)/mg cells h, and Ks = 13.2 ± 2.8 mg As (III)/L were obtained using a non-linear estimation routine and employing the Marquardt–Levenberg algorithm. Sensitivity analysis revealed k to be more sensitive to model simulations of As (III) oxidation under steady-state conditions than parameter Ks. -- Highlights: ► As (III) oxidation. ► Biokinetic parameters. ► Model validation and sensitivity analysis.

  11. Magnetosome-containing bacteria living as symbionts of bivalves.

    Science.gov (United States)

    Dufour, Suzanne C; Laurich, Jason R; Batstone, Rebecca T; McCuaig, Bonita; Elliott, Alexander; Poduska, Kristin M

    2014-12-01

    Bacteria containing magnetosomes (protein-bound nanoparticles of magnetite or greigite) are common to many sedimentary habitats, but have never been found before to live within another organism. Here, we show that octahedral inclusions in the extracellular symbionts of the marine bivalve Thyasira cf. gouldi contain iron, can exhibit magnetic contrast and are most likely magnetosomes. Based on 16S rRNA sequence analysis, T. cf. gouldi symbionts group with symbiotic and free-living sulfur-oxidizing, chemolithoautotrophic gammaproteobacteria, including the symbionts of other thyasirids. T. cf. gouldi symbionts occur both among the microvilli of gill epithelial cells and in sediments surrounding the bivalves, and are therefore facultative. We propose that free-living T. cf. gouldi symbionts use magnetotaxis as a means of locating the oxic-anoxic interface, an optimal microhabitat for chemolithoautotrophy. T. cf. gouldi could acquire their symbionts from near-burrow sediments (where oxic-anoxic interfaces likely develop due to the host's bioirrigating behavior) using their superextensile feet, which could transfer symbionts to gill surfaces upon retraction into the mantle cavity. Once associated with their host, however, symbionts need not maintain structures for magnetotaxis as the host makes oxygen and reduced sulfur available via bioirrigation and sulfur-mining behaviors. Indeed, we show that within the host, symbionts lose the integrity of their magnetosome chain (and possibly their flagellum). Symbionts are eventually endocytosed and digested in host epithelial cells, and magnetosomes accumulate in host cytoplasm. Both host and symbiont behaviors appear important to symbiosis establishment in thyasirids. PMID:24914799

  12. Earthworm symbiont Verminephrobacter eiseniae mediates natural transformation within the host egg capsules using type IV pili

    Directory of Open Access Journals (Sweden)

    SEANA Kelyn DAVIDSON

    2014-10-01

    Full Text Available The dense microbial communities commonly associated with plants and animals should offer many opportunities for horizontal gene transfer (HGT through described mechanisms of DNA exchange including natural transformation. However, studies of the significance of natural transformation have focused primarily on pathogens. The study presented here demonstrates highly efficient DNA exchange by natural transformation in a common symbiont of earthworms. The obligate bacterial symbiont Verminephrobacter eiseniae is a member of a microbial consortium of the earthworm Eisenia fetida that is transmitted into the egg capsules to colonize the embryonic worms. In the study presented here, by testing for transformants under different conditions in culture, we demonstrate that V. eiseniae can incorporate free DNA from the environment, that competency is regulated by environmental factors, and that it is sequence specific. Mutations in the type IV pili of V. eiseniae resulted in loss of DNA uptake, implicating the type IV pilus (TFP apparatus in DNA uptake. Furthermore, injection of DNA carrying antibiotic-resistance genes into egg capsules resulted in transformants within the capsule, demonstrating the relevance of DNA uptake within the earthworm system. The ability to take up species-specific DNA from the environment may explain the maintenance of the relatively large, intact genome of this long-associated obligate symbiont, and provides a mechanism for acquisition of foreign genes within the earthworm system.

  13. Standard methods for research on Apis mellifera gut symbionts

    Science.gov (United States)

    Gut microbes can play an important role in digestion, disease resistance, and the general health of animals, but little is known about the biology of gut symbionts in Apis mellifera. This paper is part of a series on honey bee research methods, providing protocols for studying gut symbionts. We desc...

  14. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  15. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  16. Isotopic evidences and constraints in the chemoautotrophic system of the Movile cave, Romania

    International Nuclear Information System (INIS)

    The stable isotope (2H, 13C, 34S) content for samples from the chemoautotrophic ecosystem of the Movile cave have been used to provide information about the life in this closed system.. The groundwater is rich in H2S (8-12 mg/l) and the cave atmosphere is poor in oxygen (7-10%), rich in CO2 (2-3.5%) and contains a significant amount of CH4 (1-2%). The 13C content of cave organic matter exhibits low values of δ13C (between -47.5 and -37.5 0/00) and does not reflect the isotopic composition of the local organic materials from surface and subsurface. The concentration of 13C in the area near to cave is typical for aquatic and terrestrial ecosystems that use photoautotrophic carbon fixation (between -30 and -23 0/00). This discrepancy suggests other way of carbon fixation in the trophic web and it is possible that the organic matter is derived from lipid-rich organisms biosynthesized by chemosynthetic microorganisms which use H2S as energy source for carbon fixation. Gases collected from the groundwater (H2S) and the cave atmosphere (CH4 and CO2) have isotope ratios that point out the following: the groundwater from cave is not originated from Black Sea. The δ34S values range between +3.5 to +4.2 0/00 for cave being rich in 34S versus isotopic composition of deep water from Black Sea (-40 0/00); the sulphur isotope content from H2S (+5.9 to +8.3 0/00) and SO42-(+1.1 0/00) presents a contrast trend versus the general trend of the isotopic fractionation of the microbially mediated sulphur transformations. In the cave, H2S with δ34S values lower than that of the SO42- reactant were not recorded; the carbon isotope data for CO2-CH4 pairs (-23 0/00 for CO2 and -56.5 0/00 for CH4) of the cave gases cannot clearly delineate the biogenic methane origin as marine or non-marine provenance; the equilibrium carbon isotope fractionation between CH4 and CO2 is αc = 1. 35 indicating that the CO2 reduction pathway for methanogenesis is very improbable and the natural conditions of

  17. The symbiont side of symbiosis: do microbes really benefit?

    Directory of Open Access Journals (Sweden)

    Justine Rebecca Garcia

    2014-09-01

    Full Text Available Microbial associations are integral to all eukaryotes. Mutualism, the interaction of two species for the benefit of both, is an important aspect of microbial associations, with evidence that multicellular organisms in particular benefit from microbes. However, the microbe’s perspective has largely been ignored, and it is unknown whether most microbial symbionts benefit from their associations with hosts. It has been presumed that microbial symbionts receive host-derived nutrients or a competition-free environment with reduced predation, but there have been few empirical tests, or even critical assessments, of these assumptions. We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. Some symbionts do receive nutrients from their host, but this has not always been linked to a corresponding increase in symbiont fitness. We recommend experiments to test symbiont fitness using current experimental systems of symbiosis and detail considerations for other systems. Incorporating symbiont fitness into symbiosis research will provide insight into the evolution of mutualistic interactions and cooperation in general.

  18. An ancient but promiscuous host–symbiont association between Burkholderia gut symbionts and their heteropteran hosts

    OpenAIRE

    Kikuchi, Yoshitomo; Hosokawa, Takahiro; Fukatsu, Takema

    2010-01-01

    Here, we investigated 124 stinkbug species representing 20 families and 5 superfamilies for their Burkholderia gut symbionts, of which 39 species representing 6 families of the superfamilies Lygaeoidea and Coreoidea were Burkholderia-positive. Diagnostic PCR surveys revealed high frequencies of Burkholderia infection in natural populations of the stinkbugs, and substantial absence of vertical transmission of Burkholderia infection to their eggs. In situ hybridization confirmed localization of...

  19. The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

    Energy Technology Data Exchange (ETDEWEB)

    Frese, Steven A. [University of Nebraska, Lincoln; Benson, Andrew K. [University of Nebraska, Lincoln; Tannock, Gerald W. [University of Otago, Dunedin, New Zealand; Loach, Diane M. [University of Otago, Dunedin, New Zealand; Kim, Jaehyoung [University of Nebraska, Lincoln; Zhang, Min [University of Nebraska, Lincoln; Oh, Phaik Lyn [University of Nebraska, Lincoln; Heng, Nicholas C. K. [University of Otago, Dunedin, New Zealand; Patil, Prabhu [University of Nebraska, Lincoln; Juge, Nathalie [Institute of Food Research, Norwich Research Park, Norwich, United Kingdom; MacKenzie, Donald A. [Institute of Food Research, Norwich Research Park, Norwich, United Kingdom; Pearson, Bruce M. [Institute of Food Research, Norwich Research Park, Norwich, United Kingdom; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Goltsman, Eugene [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Walter, Jens [University of Nebraska, Lincoln

    2011-01-01

    Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.

  20. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri.

    Directory of Open Access Journals (Sweden)

    Steven A Frese

    2011-02-01

    Full Text Available Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.

  1. Microbial minimalism: genome reduction in bacterial pathogens.

    Science.gov (United States)

    Moran, Nancy A

    2002-03-01

    When bacterial lineages make the transition from free-living or facultatively parasitic life cycles to permanent associations with hosts, they undergo a major loss of genes and DNA. Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts. PMID:11893328

  2. Farming termites determine the genetic population structure of Termitomyces fungal symbionts

    DEFF Research Database (Denmark)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J;

    2011-01-01

    fungal symbionts. However, even in the few termite lineages that secondarily adopted vertical symbiont transmission, the fungal symbionts are not monophyletic. We addressed this paradox by studying differential transmission of fungal symbionts by alate male and female reproductives, and the genetic...... population structure of Termitomyces fungus gardens across 74 colonies of Macrotermes bellicosus in four west and central African countries. We confirm earlier, more limited, studies showing that the Termitomyces symbionts of M. bellicosus are normally transmitted vertically and clonally by dispersing males...

  3. Symbiont-mediated RNA interference in insects

    Science.gov (United States)

    Whitten, Miranda M. A.; Facey, Paul D.; Del Sol, Ricardo; Fernández-Martínez, Lorena T.; Evans, Meirwyn C.; Mitchell, Jacob J.; Bodger, Owen G.

    2016-01-01

    RNA interference (RNAi) methods for insects are often limited by problems with double-stranded (ds) RNA delivery, which restricts reverse genetics studies and the development of RNAi-based biocides. We therefore delegated to insect symbiotic bacteria the task of: (i) constitutive dsRNA synthesis and (ii) trauma-free delivery. RNaseIII-deficient, dsRNA-expressing bacterial strains were created from the symbionts of two very diverse pest species: a long-lived blood-sucking bug, Rhodnius prolixus, and a short-lived globally invasive polyphagous agricultural pest, western flower thrips (Frankliniella occidentalis). When ingested, the manipulated bacteria colonized the insects, successfully competed with the wild-type microflora, and sustainably mediated systemic knockdown phenotypes that were horizontally transmissible. This represents a significant advance in the ability to deliver RNAi, potentially to a large range of non-model insects. PMID:26911963

  4. A journey into the wild of the cnidarian model system Aiptasia and its symbionts

    KAUST Repository

    Voolstra, Christian R.

    2013-08-27

    The existence of coral reef ecosystems relies critically on the mutualistic relationship between calcifying cnidarians and photosynthetic, dinoflagellate endosymbionts in the genus Symbiodinium. Reef-corals have declined globally due to anthropogenic stressors, for example, rising sea-surface temperatures and pollution that often disrupt these symbiotic relationships (known as coral bleaching), exacerbating mass mortality and the spread of disease. This threatens one of the most biodiverse marine ecosystems providing habitats to millions of species and supporting an estimated 500 million people globally (Hoegh-Guldberg et al. 2007). Our understanding of cnidarian-dinoflagellate symbioses has improved notably with the recent application of genomic and transcriptomic tools (e.g. Voolstra et al. 2009; Bayer et al. 2012; Davy et al. 2012), but a model system that allows for easy manipulation in a laboratory environment is needed to decipher underlying cellular mechanisms important to the functioning of these symbioses. To this end, the sea anemone Aiptasia, otherwise known as a \\'pest\\' to aquarium hobbyists, is emerging as such a model system (Schoenberg & Trench 1980; Sunagawa et al. 2009; Lehnert et al. 2012). Aiptasia is easy to grow in culture and, in contrast to its stony relatives, can be maintained aposymbiotically (i.e. dinoflagellate free) with regular feeding. However, we lack basic information on the natural distribution and genetic diversity of these anemones and their endosymbiotic dinoflagellates. These data are essential for placing the significance of this model system into an ecological context. In this issue of Molecular Ecology, Thornhill et al. (2013) are the first to present genetic evidence on the global distribution, diversity and population structure of Aiptasia and its associated Symbiodinium spp. By integrating analyses of the host and symbiont, this research concludes that the current Aitpasia taxonomy probably needs revision and that two

  5. Complementary symbiont contributions to plant decomposition in a fungus-farming termite.

    Science.gov (United States)

    Poulsen, Michael; Hu, Haofu; Li, Cai; Chen, Zhensheng; Xu, Luohao; Otani, Saria; Nygaard, Sanne; Nobre, Tania; Klaubauf, Sylvia; Schindler, Philipp M; Hauser, Frank; Pan, Hailin; Yang, Zhikai; Sonnenberg, Anton S M; de Beer, Z Wilhelm; Zhang, Yong; Wingfield, Michael J; Grimmelikhuijzen, Cornelis J P; de Vries, Ronald P; Korb, Judith; Aanen, Duur K; Wang, Jun; Boomsma, Jacobus J; Zhang, Guojie

    2014-10-01

    Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis have remained enigmatic. We obtained high-quality annotated draft genomes of the termite Macrotermes natalensis, its Termitomyces symbiont, and gut metagenomes from workers, soldiers, and a queen. We show that members from 111 of the 128 known glycoside hydrolase families are represented in the symbiosis, that Termitomyces has the genomic capacity to handle complex carbohydrates, and that worker gut microbes primarily contribute enzymes for final digestion of oligosaccharides. This apparent division of labor is consistent with the Macrotermes gut microbes being most important during the second passage of comb material through the termite gut, after a first gut passage where the crude plant substrate is inoculated with Termitomyces asexual spores so that initial fungal growth and polysaccharide decomposition can proceed with high efficiency. Complex conversion of biomass in termite mounds thus appears to be mainly accomplished by complementary cooperation between a domesticated fungal monoculture and a specialized bacterial community. In sharp contrast, the gut microbiota of the queen had highly reduced plant decomposition potential, suggesting that mature reproductives digest fungal material provided by workers rather than plant substrate. PMID:25246537

  6. Defensive insect symbiont leads to cascading extinctions and community collapse.

    Science.gov (United States)

    Sanders, Dirk; Kehoe, Rachel; van Veen, Fj Frank; McLean, Ailsa; Godfray, H Charles J; Dicke, Marcel; Gols, Rieta; Frago, Enric

    2016-07-01

    Animals often engage in mutualistic associations with microorganisms that protect them from predation, parasitism or pathogen infection. Studies of these interactions in insects have mostly focussed on the direct effects of symbiont infection on natural enemies without studying community-wide effects. Here, we explore the effect of a defensive symbiont on population dynamics and species extinctions in an experimental community composed of three aphid species and their associated specialist parasitoids. We found that introducing a bacterial symbiont with a protective (but not a non-protective) phenotype into one aphid species led to it being able to escape from its natural enemy and increase in density. This changed the relative density of the three aphid species which resulted in the extinction of the two other parasitoid species. Our results show that defensive symbionts can cause extinction cascades in experimental communities and so may play a significant role in the stability of consumer-herbivore communities in the field. PMID:27282315

  7. Bacterial symbionts of a devastating coffee plant pest, the stinkbug Antestiopsis thunbergii (Hemiptera: Pentatomidae).

    Science.gov (United States)

    Matsuura, Yu; Hosokawa, Takahiro; Serracin, Mario; Tulgetske, Genet M; Miller, Thomas A; Fukatsu, Takema

    2014-06-01

    Stinkbugs of the genus Antestiopsis, so-called antestia bugs or variegated coffee bugs, are notorious pests of coffee plants in Africa. We investigated the symbiotic bacteria associated with Antestiopsis thunbergii, a major coffee plant pest in Rwanda. PCR, cloning, sequencing, and phylogenetic analysis of bacterial genes identified four distinct bacterial lineages associated with A. thunbergii: a gammaproteobacterial gut symbiont and symbionts representing the genera Sodalis, Spiroplasma, and Rickettsia. In situ hybridization showed that the gut symbiont densely occupied the lumen of midgut crypts, whereas the Sodalis symbiont, the Spiroplasma symbiont, and the Rickettsia symbiont sparsely and sporadically infected various cells and tissues. Diagnostic PCR survey of 154 A. thunbergii individuals collected at 8 localities in Rwanda revealed high infection frequencies (100% for the gut symbiont, 51.3% for the Sodalis symbiont, 52.6% for the Spiroplasma symbiont, and 24.0% for the Rickettsia symbiont). These results suggest that the gut symbiont is the primary symbiotic associate of obligate nature for A. thunbergii, whereas the Sodalis symbiont, the Spiroplasma symbiont, and the Rickettsia symbiont are the secondary symbiotic associates of facultative nature. We observed high coinfection frequencies, i.e., 7.8% of individuals with quadruple infection with all the symbionts, 32.5% with triple infections with the gut symbiont and two of the secondary symbionts, and 39.6% with double infections with the gut symbiont and any of the three secondary symbionts, which were statistically not different from the expected coinfection frequencies and probably reflected random associations. The knowledge of symbiotic microbiota in A. thunbergii will provide useful background information for controlling this devastating coffee plant pest. PMID:24727277

  8. Symbiont diversity may help coral reefs survive moderate climate change

    OpenAIRE

    Baskett, ML; Gaines, SD; Nisbet, RM

    2009-01-01

    Given climate change, thermal stress-related mass coral-bleaching events present one of the greatest anthropogenic threats to coral reefs. While corals and their symbiotic algae may respond to future temperatures through genetic adaptation and shifts in community compositions, the climate may change too rapidly for coral response. To test this potential for response, here we develop a model of coral and symbiont ecological dynamics and symbiont evolutionary dynamics. Model results without var...

  9. Magnetosome-containing bacteria living as symbionts of bivalves

    OpenAIRE

    Dufour, Suzanne C.; Laurich, Jason R; Batstone, Rebecca T; McCuaig, Bonita; Elliott, Alexander, 1983-; Poduska, Kristin M

    2014-01-01

    Bacteria containing magnetosomes (protein-bound nanoparticles of magnetite or greigite) are common to many sedimentary habitats, but have never been found before to live within another organism. Here, we show that octahedral inclusions in the extracellular symbionts of the marine bivalve Thyasira cf. gouldi contain iron, can exhibit magnetic contrast and are most likely magnetosomes. Based on 16S rRNA sequence analysis, T. cf. gouldi symbionts group with symbiotic and free-living sulfur-oxidi...

  10. Parasitic wasp responses to symbiont-based defense in aphids

    Directory of Open Access Journals (Sweden)

    Oliver Kerry M

    2012-02-01

    Full Text Available Abstract Background Recent findings indicate that several insect lineages receive protection against particular natural enemies through infection with heritable symbionts, but little is yet known about whether enemies are able to discriminate and respond to symbiont-based defense. The pea aphid, Acyrthosiphon pisum, receives protection against the parasitic wasp, Aphidius ervi, when infected with the bacterial symbiont Hamiltonella defensa and its associated bacteriophage APSE (Acyrthosiphon pisum secondary endosymbiont. Internally developing parasitoid wasps, such as A. ervi, use maternal and embryonic factors to create an environment suitable for developing wasps. If more than one parasitoid egg is deposited into a single aphid host (superparasitism, then additional complements of these factors may contribute to the successful development of the single parasitoid that emerges. Results We performed experiments to determine if superparasitism is a tactic allowing wasps to overcome symbiont-mediated defense. We found that the deposition of two eggs into symbiont-protected aphids significantly increased rates of successful parasitism relative to singly parasitized aphids. We then conducted behavioral assays to determine whether A. ervi selectively superparasitizes H. defensa-infected aphids. In choice tests, we found that A. ervi tends to deposit a single egg in uninfected aphids, but two or more eggs in H. defensa-infected aphids, indicating that oviposition choices may be largely determined by infection status. Finally, we identified differences in the quantity of the trans-β-farnesene, the major component of aphid alarm pheromone, between H. defensa-infected and uninfected aphids, which may form the basis for discrimination. Conclusions Here we show that the parasitic wasp A. ervi discriminates among symbiont-infected and uninfected aphids, and changes its oviposition behavior in a way that increases the likelihood of overcoming symbiont

  11. Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

    OpenAIRE

    Freeman, Christopher J.; Thacker, Robert W.; Baker, David M.; Fogel, Marilyn L.

    2013-01-01

    By forming symbiotic interactions with microbes, many animals and plants gain access to the products of novel metabolic pathways. We investigated the transfer of symbiont-derived carbon and nitrogen to the sponges Aplysina cauliformis, Aplysina fulva, Chondrilla caribensis, Neopetrosia subtriangularis and Xestospongia bocatorensis, all of which host abundant microbial populations, and Niphates erecta, which hosts a sparse symbiont community. We incubated sponges in light and dark bottles cont...

  12. Contact and voter processes on the infinite percolation cluster as models of host-symbiont interactions

    CERN Document Server

    Bertacchi, Daniela; Zucca, Fabio

    2009-01-01

    We introduce spatially explicit stochastic processes to model multispecies hostsymbiont interactions. The host environment is static, modeled by the infinite percolation cluster of site percolation. Symbionts evolve on the infinite cluster through contact or voter type interactions, where each host may be infected by a colony of symbionts. In the presence of a single symbiont species, the condition for invasion as a function of the density of the habitat of hosts and the maximal size of the colonies is investigated in details. In the presence of multiple symbiont species, it is proved that the community of symbionts clusters in two dimensions whereas symbiont species may coexist in higher dimensions.

  13. The uncultured luminous symbiont of Anomalops katoptron (Beryciformes: Anomalopidae) represents a new bacterial genus.

    Science.gov (United States)

    Hendry, Tory A; Dunlap, Paul V

    2011-12-01

    Flashlight fishes (Beryciformes: Anomalopidae) harbor luminous symbiotic bacteria in subocular light organs and use the bacterial light for predator avoidance, feeding, and communication. Despite many attempts anomalopid symbionts have not been brought into laboratory culture, which has restricted progress in understanding their phylogenetic relationships with other luminous bacteria, identification of the genes of their luminescence system, as well as the nature of their symbiotic interactions with their fish hosts. To begin addressing these issues, we used culture-independent analysis of the bacteria symbiotic with the anomalopid fish, Anomalops katoptron, to characterize the phylogeny of the bacteria and to identify the genes of their luminescence system including those involved in the regulation of luminescence. Analysis of the 16S rRNA, atpA, gapA, gyrB, pyrH, recA, rpoA, and topA genes resolved the A. katoptron symbionts as a clade nested within and deeply divergent from other members of Vibrionaceae. The bacterial luminescence (lux) genes were identified as a contiguous set (luxCDABEG), as found for the lux operons of other luminous bacteria. Phylogenetic analysis based on the lux genes confirmed the housekeeping gene phylogenetic placement. Furthermore, genes flanking the lux operon in the A. katoptron symbionts differed from those flanking lux operons of other genera of luminous bacteria. We therefore propose the candidate name Candidatus Photodesmus (Greek: photo = light, desmus = servant) katoptron for the species of bacteria symbiotic with A. katoptron. Results of a preliminary genomic analysis for genes regulating luminescence in other bacteria identified only a Vibrio harveyi-type luxR gene. These results suggest that expression of the luminescence system might be continuous in P. katoptron. PMID:21864694

  14. A remarkable finding that suggests the existence of a new groundwater biome based on chemoautotrophic resources, named

    Directory of Open Access Journals (Sweden)

    Ştefan Negrea

    2009-01-01

    Full Text Available An important work of subterranean biology, signed by Francis Dov Por, Ophel: a groundwater biome based on chemoautotrophic resources. The global significance of the Ayyalon cave finds, Israel is presented and discussed in the present paper. The subject is a remarkable discovery suggesting the existence of a new aquatic subterranean biome autonomous energy based the author calls Ophel, the Hebrew word for “darkness” and “netherworld”. For F.D. Por, this biome links different marine chemosynthetic ecosystems in a global biospheric entity. Finally, F.D. POR hypothesizes on the existence of three overlapped biospheres: the bacteriosphere in the depths of the planet’s crust, which does not require light or oxygen; the aphotic, subterranean deuterobiosphere, formed of bacterial chemosynthesis based eukaryotes and limited-supplied dissolved oxygen from above-ground; the above-ground eubiosphere, based on aerobic photosynthesis. I would like to emphasize that, at my suggestion, Prof. Dr. F.D. Por participated at the 18th International Symposium of Biospeleology from Cluj-Napoca (Romania at 10th to 15th July 2006 where he mentioned for the first time orally some data on the Ayyalon Cave and the Ophel biome.

  15. Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

    Science.gov (United States)

    Freeman, Christopher J; Thacker, Robert W; Baker, David M; Fogel, Marilyn L

    2013-06-01

    By forming symbiotic interactions with microbes, many animals and plants gain access to the products of novel metabolic pathways. We investigated the transfer of symbiont-derived carbon and nitrogen to the sponges Aplysina cauliformis, Aplysina fulva, Chondrilla caribensis, Neopetrosia subtriangularis and Xestospongia bocatorensis, all of which host abundant microbial populations, and Niphates erecta, which hosts a sparse symbiont community. We incubated sponges in light and dark bottles containing seawater spiked with (13)C- and (15)N-enriched inorganic compounds and then measured (13)C and (15)N enrichment in the microbial (nutrient assimilation) and sponge (nutrient transfer) fractions. Surprisingly, although most sponges hosting abundant microbial communities were more enriched in (13)C than N. erecta, only N. subtriangularis was more enriched in (15)N than N. erecta. Although photosymbiont abundance varied substantially across species, (13)C and (15)N enrichment was not significantly correlated with photosymbiont abundance. Enrichment was significantly correlated with the ratio of gross productivity to respiration (P:R), which varied across host species and symbiont phylotype. Because irradiance impacts P:R ratios, we also incubated A. cauliformis in (13)C-enriched seawater under different irradiances to determine whether symbiont carbon fixation and transfer are dependent on irradiance. Carbon fixation and transfer to the sponge host occurred in all treatments, but was greatest at higher irradiances and was significantly correlated with P:R ratios. Taken together, these results demonstrate that nutrient transfer from microbial symbionts to host sponges is influenced more by host-symbiont identities and P:R ratios than by symbiont abundance. PMID:23407307

  16. Acetic acid bacteria genomes reveal functional traits for adaptation to life in insect guts

    OpenAIRE

    B. Chouaia; Gaiarsa, S.; Crotti, E.; Comandatore, F.; Degli Esposti, M.; I. RICCI; Alma, A.; Favia, G.; Bandi, C.; D. Daffonchio

    2014-01-01

    Acetic acid bacteria (AAB) live in sugar rich environments, including food matrices, plant tissues, and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia platycodi and Saccharibacter sp., symbionts of Anopheles stephensi and Apis mellifera, respectively, with those of 14 other AAB, we provide a genomic view of the evolutionary pattern of this bacterial group and clues on traits that explain the success of AAB as insect symbionts. A specific pre-adaptive trait...

  17. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance.

    Science.gov (United States)

    Coleman-Derr, Devin; Tringe, Susannah G

    2014-01-01

    The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions. PMID:24936202

  18. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, Susannah; Coleman-Derr, Devin

    2014-05-22

    The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions

  19. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

    Directory of Open Access Journals (Sweden)

    DevinColeman-Derr

    2014-06-01

    Full Text Available The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions.

  20. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Coleman-Derr, Devin [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, Susannah G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2014-06-06

    The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here in this paper, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions

  1. The biogeography and phylogeny of unicellular cyanobacterial symbionts in sponges from Australia and the Mediterranean.

    Science.gov (United States)

    Usher, K M; Fromont, J; Sutton, D C; Toze, S

    2004-08-01

    The distribution, host associations, and phylogenetic relationships of the unicellular cyanobacterial symbionts of selected marine sponges were investigated with direct 16s rDNA sequencing. The results indicate that the symbionts of the marine sponges Aplysina aerophoba, Ircinia variabilis, and Petrosia ficiformis from the Mediterranean, four Chondrilla species from Australia and the Mediterranean, and Haliclona sp. from Australia support a diversity of symbionts comprising at least four closely related species of Synechococcus. These include the symbionts presently described as Aphanocapsa feldmannii from P. ficiformis and Chondrilla nucula. A fifth symbiont from Cymbastela marshae in Australia is an undescribed symbiont of sponges, related to Oscillatoria rosea. One symbiont, Candidatus Synechococcus spongiarum, was found in diverse sponge genera in the Mediterranean Sea and the Indian, Pacific, and Southern oceans, whereas others were apparently more restricted in host association and distribution. These results are discussed in terms of the biodiversity and biogeographic distributions of cyanobacterial symbionts. PMID:15546037

  2. Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boeffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-05-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

  3. Genetic diversity in cyanobacterial symbionts of thalloid bryophytes.

    Science.gov (United States)

    Rikkinen, Jouko; Virtanen, Viivi

    2008-01-01

    Two species of thalloid liverworts, Blasia pusilla and Cavicularia densa, form stable symbioses with nitrogen-fixing cyanobacteria. Both bryophytes promote the persistence of their cyanobacterial associations by producing specialized gemmae, which facilitate the simultaneous dispersal of the host and its nitrogen-fixing symbionts. Here the genetic diversity of cyanobacterial symbionts of Blasia and Cavicularia is examined. The results indicate that the primary symbionts of both bryophytes are closely related and belong to a specific group of symbiotic Nostoc strains. Related strains have previously been reported from hornworts and cycads, and from many terricolous cyanolichens. The evolutionary origins of all these symbioses may trace back to pre-Permian times. While the laboratory strain Nostoc punctiforme PCC 73102 has been widely used in experimental studies of bryophyte-Nostoc associations, sequence-identical cyanobionts have not yet been identified from thalloid liverworts in the field. PMID:18325923

  4. Evolutionary Relationships of “Candidatus Endobugula” Bacterial Symbionts and Their Bugula Bryozoan Hosts▿

    OpenAIRE

    Lim-Fong, Grace E.; Regali, Lindsay A.; Haygood, Margo G.

    2008-01-01

    Ribosomal gene sequences were obtained from bryozoans in the genus Bugula and their bacterial symbionts; analyses of host and symbiont phylogenetic trees did not support a history of strict cospeciation. Symbiont-derived compounds known to defend host larvae from predation were only detected in two out of four symbiotic Bugula species.

  5. Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.

    KAUST Repository

    Baumgarten, Sebastian

    2013-10-12

    Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.

  6. Ultrastructure, molecular phylogenetics, and chlorophyll a content of novel cyanobacterial symbionts in temperate sponges.

    Science.gov (United States)

    Erwin, Patrick M; López-Legentil, Susanna; Turon, Xavier

    2012-10-01

    Marine sponges often harbor photosynthetic symbionts that may enhance host metabolism and ecological success, yet little is known about the factors that structure the diversity, specificity, and nature of these relationships. Here, we characterized the cyanobacterial symbionts in two congeneric and sympatric host sponges that exhibit distinct habitat preferences correlated with irradiance: Ircinia fasciculata (higher irradiance) and Ircinia variabilis (lower irradiance). Symbiont composition was similar among hosts and dominated by the sponge-specific cyanobacterium Synechococcus spongiarum. Phylogenetic analyses of 16S-23S rRNA internal transcribed spacer (ITS) gene sequences revealed that Mediterranean Ircinia spp. host a specific, novel symbiont clade ("M") within the S. spongiarum species complex. A second, rare cyanobacterium related to the ascidian symbiont Synechocystis trididemni was observed in low abundance in I. fasciculata and likewise corresponded to a new symbiont clade. Symbiont communities in I. fasciculata exhibited nearly twice the chlorophyll a concentrations of I. variabilis. Further, S. spongiarum clade M symbionts in I. fasciculata exhibited dense intracellular aggregations of glycogen granules, a storage product of photosynthetic carbon assimilation rarely observed in I. variabilis symbionts. In both host sponges, S. spongiarum cells were observed interacting with host archeocytes, although the lower photosynthetic activity of Cyanobacteria in I. variabilis suggests less symbiont-derived nutritional benefit. The observed differences in clade M symbionts among sponge hosts suggest that ambient irradiance conditions dictate symbiont photosynthetic activity and consequently may mediate the nature of host-symbiont relationships. In addition, the plasticity exhibited by clade M symbionts may be an adaptive attribute that allows for flexibility in host-symbiont interactions across the seasonal fluctuations in light and temperature characteristic of

  7. Defensive insect symbiont leads to cascading extinctions and community collapse

    NARCIS (Netherlands)

    Sanders, Dirk; Kehoe, Rachel; Veen, van F.J.F.; McLean, Ailsa; Godfray, H.C.J.; Dicke, Marcel; Gols, Rieta; Frago, Enric

    2016-01-01

    Animals often engage in mutualistic associations with microorganisms that protect them from predation, parasitism or pathogen infection. Studies of these interactions in insects have mostly focussed on the direct effects of symbiont infection on natural enemies without studying community-wide eff

  8. Chemotypic diversity of epichloae, fungal symbionts of grasses

    Science.gov (United States)

    The epichloid fungi - comprising sexual Epichlo€e species and asexual Neotyphodium species - are symbionts of cool-season grasses (subfamily Po€oideae), mostly vertically transmissible (seedborne), and well known for production of anti-herbivore alkaloids. Four classes of alkaloids are known to be p...

  9. Evidence for specificity in symbiont-conferred protection against parasitoids.

    Science.gov (United States)

    McLean, Ailsa H C; Godfray, H Charles J

    2015-07-22

    Many insects harbour facultative symbiotic bacteria, some of which have been shown to provide resistance against natural enemies. One of the best-known protective symbionts is Hamiltonella defensa, which in pea aphid (Acyrthosiphon pisum) confers resistance against attack by parasitoid wasps in the genus Aphidius (Braconidae).We asked (i) whether this symbiont also confers protection against a phylogenetically distant group of parasitoids (Aphelinidae) and (ii) whether there are consistent differences in the effects of bacteria found in pea aphid biotypes adapted to different host plants. We found that some H. defensa strains do provide protection against an aphelinid parasitoid Aphelinus abdominalis. Hamiltonella defensa from the Lotus biotype provided high resistance to A. abdominalis and moderate to low resistance to Aphidius ervi, while the reverse was seen from Medicago biotype isolates. Aphids from Ononis showed no evidence of symbiont-mediated protection against either wasp species and were relatively vulnerable to both. Our results may reflect the different selection pressures exerted by the parasitoid community on aphids feeding on different host plants, and could help explain the maintenance of genetic diversity in bacterial symbionts. PMID:26136451

  10. Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly Bemisia tabaci

    OpenAIRE

    Rao, Qiong; Wang, Shuang; Zhu, Dan-Tong; Wang, Xiao-Wei; Liu, Shu-Sheng

    2012-01-01

    We report the draft genome sequence of the Rickettsia sp. strain MEAM1, which is a facultative symbiont from an invasive species of the whitefly Bemisia tabaci. The total length of the assembled genome is approximately 1.24 Mb, with 335 scaffolds and 1,247 coding sequences predicted within the genome.

  11. Cryptic diversity and symbiont interactions in rock-posy lichens.

    Science.gov (United States)

    Leavitt, Steven D; Kraichak, Ekaphan; Vondrak, Jan; Nelsen, Matthew P; Sohrabi, Mohammad; Perez-Ortega, Sergio; St Clair, Larry L; Lumbsch, H Thorsten

    2016-06-01

    Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont=Rhizoplaca s. lat. species; photobiont=Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a

  12. Environmental symbiont acquisition may not be the solution to warming seas for reef-building corals.

    Directory of Open Access Journals (Sweden)

    Mary Alice Coffroth

    Full Text Available BACKGROUND: Coral reefs worldwide are in decline. Much of the mortality can be attributed to coral bleaching (loss of the coral's intracellular photosynthetic algal symbiont associated with global warming. How corals will respond to increasing oceanic temperatures has been an area of extensive study and debate. Recovery after a bleaching event is dependent on regaining symbionts, but the source of repopulating symbionts is poorly understood. Possibilities include recovery from the proliferation of endogenous symbionts or recovery by uptake of exogenous stress-tolerant symbionts. METHODOLOGY/PRINCIPAL FINDINGS: To test one of these possibilities, the ability of corals to acquire exogenous symbionts, bleached colonies of Porites divaricata were exposed to symbiont types not normally found within this coral and symbiont acquisition was monitored. After three weeks exposure to exogenous symbionts, these novel symbionts were detected in some of the recovering corals, providing the first experimental evidence that scleractinian corals are capable of temporarily acquiring symbionts from the water column after bleaching. However, the acquisition was transient, indicating that the new symbioses were unstable. Only those symbiont types present before bleaching were stable upon recovery, demonstrating that recovery was from the resident in situ symbiont populations. CONCLUSIONS/SIGNIFICANCE: These findings suggest that some corals do not have the ability to adjust to climate warming by acquiring and maintaining exogenous, more stress-tolerant symbionts. This has serious ramifications for the success of coral reefs and surrounding ecosystems and suggests that unless actions are taken to reverse it, climate change will lead to decreases in biodiversity and a loss of coral reefs.

  13. Influence of seep emission on the non-symbiont-bearing fauna and vagrant species at an active giant pockmark in the Gulf of Guinea (Congo-Angola margin)

    Science.gov (United States)

    Olu, K.; Caprais, J. C.; Galéron, J.; Causse, R.; von Cosel, R.; Budzinski, H.; Ménach, K. Le; Roux, C. Le; Levaché, D.; Khripounoff, A.; Sibuet, M.

    2009-12-01

    Detailed surveying with an ROV found that a dense and diverse cold-seep community colonises a giant pockmark located at 3200 m depth, 8 km north from the deep Congo channel. Several types of assemblages, either dominated by Mytilidae and Vesicomyidae bivalves or Siboglinidae polychaetes, are distributed on the 800-m diameter active area. The site is characterised by a most active central zone in a depression with abundant carbonate concretions and high methane fluxes where high-density clusters of mussels and siboglinids dominate. In contrast, the peripheral zones display large fields of dead and live vesicomyids on soft sediment, with a lower mean density and lower methane concentration in seawater. The associated megafauna includes Alvinocarididae shrimps, echinoids, holothurians of the family Synaptidae, several species of gastropods, two species of galatheids, and Zoarcidae and Ophidiidae fishes. Multivariate analyses of video transect data show that the distribution of these major megafauna species at the pockmark scale is influenced by the habitat heterogeneity due to fluid or gas emission, occurrence of hydrates, substratum variability and by the presence of large symbiont-bearing species. Several assemblages dominated either by mytilids, vesicomyids, or siboglinids have been sampled for megafauna densities and biomass estimations and stable isotope measurements ( δ13C and δ15N) of dominant species and food sources. The highest estimates of megafauna densities have been obtained in mytilid beds. According to their stable isotopes values, non-symbiont-bearing species mainly rely on chemosynthesis-originated carbon, either as primary consumers of chemoautotrophic microorganisms, or at higher trophic level recycling organic matter, or relying on bivalve and tubeworm production. Most of them likely feed on different sources like shrimps, but differences according to habitat have been evidenced. Carbon and nitrogen isotope ratios of galatheids and benthic or

  14. Differential temporal changes of primary and secondary bacterial symbionts and whitefly host fitness following antibiotic treatments.

    Science.gov (United States)

    Zhang, Chang-Rong; Shan, Hong-Wei; Xiao, Na; Zhang, Fan-Di; Wang, Xiao-Wei; Liu, Yin-Quan; Liu, Shu-Sheng

    2015-01-01

    Where multiple symbionts coexist in the same host, the selective elimination of a specific symbiont may enable the roles of a given symbiont to be investigated. We treated the Mediterranean species of the whitefly Bemisia tabaci complex by oral delivery of the antibiotic rifampicin, and then examined the temporal changes of its primary symbiont "Candidatus Portiera aleyrodidarum" and secondary symbiont "Ca. Hamiltonella defensa" as well as host fitness for three generations. In adults treated with rifampicin (F0), the secondary symbiont was rapidly reduced, approaching complete disappearance as adults aged. In contrast, the primary symbiont was little affected until later in the adult life. In the offspring of these adults (F1), both symbionts were significantly reduced and barely detectable when the hosts reached the adult stage. The F1 adults laid few eggs (F2), all of which failed to hatch. Mating experiments illustrated that the negative effects of rifampicin on host fitness were exerted via female hosts but not males. This study provides the first evidence of differential temporal reductions of primary and secondary symbionts in whiteflies following an antibiotic treatment. Studies that disrupt functions of bacterial symbionts must consider their temporal changes. PMID:26510682

  15. Understanding regulation of the host-mediated gut symbiont population and the symbiont-mediated host immunity in the Riptortus-Burkholderia symbiosis system.

    Science.gov (United States)

    Kim, Jiyeun Kate; Lee, Jun Beom; Jang, Ho Am; Han, Yeon Soo; Fukatsu, Takema; Lee, Bok Luel

    2016-11-01

    Valuable insect models have tremendously contributed to our understanding of innate immunity and symbiosis. Bean bug, Riptortus pedestris, is a useful insect symbiosis model due to harboring cultivable monospecific gut symbiont, genus Burkholderia. Bean bug is a hemimetabolous insect whose immunity is not well-understood. However, we recently identified three major antimicrobial peptides of Riptortus and examined the relationship between gut symbiosis and host immunity. We found that the presence of Burkholderia gut symbiont positively affects Riptortus immunity. From studying host regulation mechanisms of symbiont population, we revealed that the symbiotic Burkholderia cells are much more susceptible to Riptortus immune responses than the cultured cells. We further elucidated that the immune-susceptibility of the Burkholderia gut symbionts is due to the drastic change of bacterial cell envelope. Finally, we show that the immune-susceptible Burkholderia symbionts are able to prosper in host owing to the suppression of immune responses of the symbiotic midgut. PMID:26774501

  16. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  17. Phylogeny of ambrosia beetle symbionts in the genus Raffaelea.

    Science.gov (United States)

    Dreaden, Tyler J; Davis, John M; de Beer, Z Wilhelm; Ploetz, Randy C; Soltis, Pamela S; Wingfield, Michael J; Smith, Jason A

    2014-12-01

    The genus Raffaelea was established in 1965 when the type species, Raffaelea ambrosia, a symbiont of Platypus ambrosia beetles was described. Since then, many additional ambrosia beetle symbionts have been added to the genus, including the important tree pathogens Raffaelea quercivora, Raffaelea quercus-mongolicae, and Raffaelea lauricola, causal agents of Japanese and Korean oak wilt and laurel wilt, respectively. The discovery of new and the dispersal of described species of Raffaelea to new areas, where they can become invasive, presents challenges for diagnosticians as well as plant protection and quarantine efforts. In this paper, we present the first comprehensive multigene phylogenetic analysis of Raffaelea. As it is currently defined, the genus was found to not be monophyletic. On the basis of this work, Raffaelea sensu stricto is defined and the affinities of undescribed isolates are considered. PMID:25457944

  18. Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts

    OpenAIRE

    Bontemps, C.; Rogel, M. A.; Wiechmann, A.; Mussabekova, A.; Moody, S.; Simon, M F; Moulin, Lionel; Elliott, G. N.; Lacercat-Didier, L.; Dasilva, C.; Grether, R; Camargo-Ricalde, S. L.; Chen, W.M.; SPRENT, J. I.; Martinez-Romero, E.

    2016-01-01

    The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species. We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for ...

  19. Life at the Limits: Capacities of Isolated and Cultured Lichen Symbionts to Resist Extreme Environmental Stresses

    Science.gov (United States)

    de Vera, J.-P.; Rettberg, P.; Ott, S.

    2008-10-01

    Lichens are described as a symbiosis formed by a myco- and photobiont, capable of colonizing habitats where their separate symbionts would not be able to survive. Space simulation studies on the separated symbionts of the lichen Xanthoria elegans have been performed to test their capacity to resist the most extreme conditions. The isolated cultured symbiont cells were exposed to different doses of the UV spectrum, and to vacuum. Cultures of both symbionts were analysed by specific vitality tests (LIVE/DEAD-staining detected by Confocal Laser Scanning Microscopy). Growth capacity of symbiont cultures on different media was analysed after exposure to extreme environmental stresses. The data obtained support the hypothesis that the symbiotic state considerably enhances the ability of the respective symbionts to survive exposure to extreme conditions, including the conditions of space simulation. Species such as X. elegans may, therefore, be suitable for use as model organisms in exobiological studies.

  20. Harold Kirby's symbionts of termites: karyomastigont reproduction and calonymphid taxonomy

    Science.gov (United States)

    Kirby, H.; Margulis, L.

    1994-01-01

    Harold Kirby's brilliant principle of mastigont multiplicity is published here posthumously more than 40 years after it was written. He applies this principle to large multinucleate protist symbionts of termites in establishing the taxonomy of Calonymphids (Family Calonymphidae in Phylum Zoomastigina, Kingdom Protoctista). The nuclei and kinetosomes in these heterotrophic cells are organized into trichomonad-style mastigont units which reproduce independently of cytokinesis to generate nine new Calonympha and nineteen new Stephanonympha species. The total of six genera (Calonympha, Coronympha, Diplonympha, Metacoronympha, Snyderella and Stephanonympha, all symbionts of dry-wood-eating termites, Kalotermitidae) are recognized. With the aid of Michael Yamin, the distribution of all twenty-eight of Kirby's Calonympha and Stephanonympha species are tabulated. In italic type I have annotated this paper to be comprehensible to a wide readership of cell biologists, protistologists and those interested in insect symbionts. Although this extremely original and careful work was not finished when Kirby died suddenly in 1952, I deemed it important and complete enough to finally publish it so that it would not be lost to scientific posterity.

  1. Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles.

    Science.gov (United States)

    Dohet, Loïc; Grégoire, Jean-Claude; Berasategui, Aileen; Kaltenpoth, Martin; Biedermann, Peter H W

    2016-09-01

    Bark beetles (Curculionidae: Scolytinae) are one of the most species-rich herbivorous insect groups with many shifts in ecology and host-plant use, which may be mediated by their bacterial and fungal symbionts. While symbionts are well studied in economically important, tree-killing species, little is known about parasitic species whose broods develop in living trees. Here, using culture-dependent and independent methods, we provide a comprehensive overview of the associated bacteria, yeasts and filamentous fungi of the parasitic Dendroctonus micans, D. punctatus and D. valens, and compare them to those of other tree-inhabiting insects. Despite inhabiting different geographical regions and/or host trees, the three species showed similar microbial communities. Enterobacteria were the most prevalent bacteria, in particular Rahnella, Pantoea and Ewingella, in addition to Streptomyces Likewise, the yeasts Candida/Cyberlindnera were the most prominent fungi. All these microorganisms are widespread among tree-inhabiting insects with various ecologies, but their high prevalence overall might indicate a beneficial role such as detoxification of tree defenses, diet supplementation or protection against pathogens. As such, our results enable comparisons of symbiont communities of parasitic bark beetles with those of other beetles, and will contribute to our understanding of how microbial symbioses facilitate dietary shifts in insects. PMID:27387908

  2. A novel bacterial symbiont in the nematode Spirocerca lupi

    Directory of Open Access Journals (Sweden)

    Gottlieb Yuval

    2012-07-01

    Full Text Available Abstract Background The parasitic nematode Spirocerca lupi (Spirurida: Thelaziidae, the canine esophageal worm, is the causative agent of spirocercosis, a disease causing morbidity and mortality in dogs. Spirocerca lupi has a complex life cycle, involving an obligatory coleopteran intermediate host (vector, an optional paratenic host, and a definitive canid host. The diagnosis of spirocercosis is challenging, especially in the early disease stages, when adult worms and clinical signs are absent. Thus, alternative approaches are needed to promote early diagnosis. The interaction between nematodes and their bacterial symbionts has recently become a focus of novel treatment regimens for other helminthic diseases. Results Using 16S rDNA-based molecular methods, here we found a novel bacterial symbiont in S. lupi that is closely related to Comamonas species (Brukholderiales: Comamonadaceae of the beta-proteobacteria. Its DNA was detected in eggs, larvae and adult stages of S. lupi. Using fluorescent in situ hybridization technique, we localized Comamonas sp. to the gut epithelial cells of the nematode larvae. Specific PCR enabled the detection of this symbiont's DNA in blood obtained from dogs diagnosed with spirocercosis. Conclusions The discovery of a new Comamonas sp. in S. lupi increase the complexity of the interactions among the organisms involved in this system, and may open innovative approaches for diagnosis and control of spirocercosis in dogs.

  3. Evolutionary Relationships of Three New Species of Enterobacteriaceae Living as Symbionts of Aphids and Other Insects

    OpenAIRE

    Moran, Nancy A.; Russell, Jacob A; Koga, Ryuichi; Fukatsu, Takema

    2005-01-01

    Ecological studies on three bacterial lineages symbiotic in aphids have shown that they impose a variety of effects on their hosts, including resistance to parasitoids and tolerance to heat stress. Phylogenetic analyses of partial sequences of gyrB and recA are consistent with previous analyses limited to 16S rRNA gene sequences and yield improved confidence of the evolutionary relationships of these symbionts. All three symbionts are in the Enterobacteriaceae. One of the symbionts, here give...

  4. Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei

    OpenAIRE

    Piel, Jörn; Hui, Dequan; Wen, Gaiping; Butzke, Daniel; Platzer, Matthias; Fusetani, Nobuhiro; Matsunaga, Shigeki

    2004-01-01

    Bacterial symbionts have long been suspected to be the true producers of many drug candidates isolated from marine invertebrates. Sponges, the most important marine source of biologically active natural products, have been frequently hypothesized to contain compounds of bacterial origin. This symbiont hypothesis, however, remained unproven because of a general inability to cultivate the suspected producers. However, we have recently identified an uncultured Pseudomonas sp. symbiont as the mos...

  5. Oxygen Metabolic Responses of Three Species of Large Benthic Foraminifers with Algal Symbionts to Temperature Stress

    OpenAIRE

    Fujita, Kazuhiko; Okai, Takaaki; Hosono, Takashi

    2014-01-01

    Water temperature affects the physiology of large benthic foraminifers (LBFs) with algal symbionts dwelling in coral reef environments. However, the detailed physiological responses of LBF holobionts to temperature ranges occurring in their habitats are not known. We report net oxygen (O2) production and respiration rates of three LBF holobionts (Baculogypsina sphaerulata and Calcarina gaudichaudii hosting diatom symbionts, and Amphisorus kudakajimensis hosting dinoflagellate symbionts) measu...

  6. Phagosome-lysosome fusion inhibited by algal symbionts of Hydra viridis

    OpenAIRE

    1982-01-01

    Certain species of Chlorella live within the digestive cells of the fresh water cnidarian Hydra viridis. When introduced into the hydra gut, these symbiotic algae are phagocytized by digestive cells but avoid host digestion and persist at relatively constant numbers within host cells. In contrast, heat-killed symbionts are rapidly degraded after phagocytosis. Live symbionts appear to persist because host lysosomes fail to fuse with phagosomes containing live symbionts. Neither acid phosphatas...

  7. Characterization of a Newly Discovered Symbiont of the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

    OpenAIRE

    Bing, Xiao-Li; Yang, Jiao; Zchori-Fein, Einat; Wang, Xiao-Wei; Liu, Shu-Sheng

    2013-01-01

    Bemisia tabaci (Hemiptera: Aleyrodidae) is a species complex containing >28 cryptic species, some of which are important crop pests worldwide. Like many other sap-sucking insects, whiteflies harbor an obligatory symbiont, “Candidatus Portiera aleyrodidarum,” and a number of secondary symbionts. So far, six genera of secondary symbionts have been identified in B. tabaci. In this study, we report and describe the finding of an additional bacterium in the indigenous B. tabaci cryptic species Chi...

  8. Phylogenetic analysis of symbionts in feather-feeding lice of the genus Columbicola: evidence for repeated symbiont replacements

    OpenAIRE

    Smith, Wendy A; Oakeson, Kelly F.; Johnson, Kevin P.; Reed, David L; Carter, Tamar; Smith, Kari L; Koga, Ryuichi; Fukatsu, Takema; Clayton, Dale H.; Dale, Colin

    2013-01-01

    Background Many groups of insects have obligate bacterial symbionts that are vertically transmitted. Such associations are typically characterized by the presence of a monophyletic group of bacteria living in a well-defined host clade. In addition the phylogeny of the symbiotic bacteria is typically congruent with that of the host, signifying co-speciation. Here we show that bacteria living in a single genus of feather lice, Columbicola (Insecta: Phthiraptera), present an exception to this ty...

  9. Farming termites determine the genetic population structure of Termitomyces fungal symbionts.

    Science.gov (United States)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J; Korb, Judith; Aanen, Duur K

    2011-05-01

    Symbiotic interactions between macrotermitine termites and their fungal symbionts have a moderate degree of specificity. Consistent with horizontal symbiont transmission, host switching has been frequent over evolutionary time so that single termite species can often be associated with several fungal symbionts. However, even in the few termite lineages that secondarily adopted vertical symbiont transmission, the fungal symbionts are not monophyletic. We addressed this paradox by studying differential transmission of fungal symbionts by alate male and female reproductives, and the genetic population structure of Termitomyces fungus gardens across 74 colonies of Macrotermes bellicosus in four west and central African countries. We confirm earlier, more limited, studies showing that the Termitomyces symbionts of M. bellicosus are normally transmitted vertically and clonally by dispersing males. We also document that the symbionts associated with this termite species belong to three main lineages that do not constitute a monophyletic group. The most common lineage occurs over the entire geographical region that we studied, including west, central and southern Africa, where it is also associated with the alternative termite hosts Macrotermes subhyalinus and Macrotermes natalensis. While Termitomyces associated with these alternative hosts are horizontally transmitted and recombine freely, the genetic population structure of the same Termitomyces associated with M. bellicosus is consistent with predominantly clonal reproduction and only occasional recombination. This implies that the genetic population structure of Termitomyces is controlled by the termite host and not by the Termitomyces symbiont. PMID:21410808

  10. Caste-specific symbiont policing by workers of Acromyrmex fungus-growing ants

    DEFF Research Database (Denmark)

    Ivens, Aniek B.F.; Nash, David R.; Poulsen, Michael;

    2009-01-01

    and transmission of symbionts. Symbiont transmission is vertical by default, and both the ants and resident fungus actively protect the fungal monoculture growing in their nest against secondary introductions of genetically dissimilar symbionts from other colonies. An earlier study showed that...... mixtures of major and minor Acromyrmex workers eliminate alien fungus fragments even in subcolonies where their resident symbiont is not present. We hypothesize that the different tasks and behaviors performed by majors and minors are likely to select for differential responses to alien fungi. Major...

  11. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.

    Science.gov (United States)

    Lin, Senjie; Cheng, Shifeng; Song, Bo; Zhong, Xiao; Lin, Xin; Li, Wujiao; Li, Ling; Zhang, Yaqun; Zhang, Huan; Ji, Zhiliang; Cai, Meichun; Zhuang, Yunyun; Shi, Xinguo; Lin, Lingxiao; Wang, Lu; Wang, Zhaobao; Liu, Xin; Yu, Sheng; Zeng, Peng; Hao, Han; Zou, Quan; Chen, Chengxuan; Li, Yanjun; Wang, Ying; Xu, Chunyan; Meng, Shanshan; Xu, Xun; Wang, Jun; Yang, Huanming; Campbell, David A; Sturm, Nancy R; Dagenais-Bellefeuille, Steve; Morse, David

    2015-11-01

    Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro)transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst formation, novel promoter elements, and a microRNA system potentially regulating gene expression in both symbiont and coral. We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora, indicative of host-symbiont coevolution, providing a resource for studying the molecular basis and evolution of coral symbiosis. PMID:26542574

  12. A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei.

    Science.gov (United States)

    Britstein, Maya; Devescovi, Giulia; Handley, Kim M; Malik, Assaf; Haber, Markus; Saurav, Kumar; Teta, Roberta; Costantino, Valeria; Burgsdorf, Ilia; Gilbert, Jack A; Sher, Noa; Venturi, Vittorio; Steindler, Laura

    2016-02-01

    Sponges harbor a remarkable diversity of microbial symbionts in which signal molecules can accumulate and enable cell-cell communication, such as quorum sensing (QS). Bacteria capable of QS were isolated from marine sponges; however, an extremely small fraction of the sponge microbiome is amenable to cultivation. We took advantage of community genome assembly and binning to investigate the uncultured majority of sponge symbionts. We identified a complete N-acyl-homoserine lactone (AHL)-QS system (designated TswIR) and seven partial luxI homologues in the microbiome of Theonella swinhoei. The TswIR system was novel and shown to be associated with an alphaproteobacterium of the order Rhodobacterales, here termed Rhodobacterales bacterium TS309. The tswI gene, when expressed in Escherichia coli, produced three AHLs, two of which were also identified in a T. swinhoei sponge extract. The taxonomic affiliation of the 16S rRNA of Rhodobacterales bacterium TS309 to a sponge-coral specific clade, its enrichment in sponge versus seawater and marine sediment samples, and the presence of sponge-specific features, such as ankyrin-like domains and tetratricopeptide repeats, indicate a likely symbiotic nature of this bacterium. PMID:26655754

  13. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts.

    Science.gov (United States)

    Della Sala, Gerardo; Hochmuth, Thomas; Costantino, Valeria; Teta, Roberta; Gerwick, William; Gerwick, Lena; Piel, Jörn; Mangoni, Alfonso

    2013-12-01

    Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two different examples of the swf cluster were present in the metagenome of P. simplex. A third example of the cluster is present in the previously sequenced genome of a poribacterium from the sponge Aplysina aerophoba but was formerly considered orthologous to the wcb/rkp cluster. The swf cluster was also found in six additional species of sponges. Therefore, the swf cluster represents the second group of mono-modular PKS, after the supA family, to be widespread in marine sponges. The putative swf operon consists of swfA (type I PKS/FAS), swfB (reductase and sulphotransferase domains) and swfC (radical S-adenosylmethionine, or radical SAM). Activation of the acyl carrier protein (ACP) domain of the SwfA protein to its holo-form by co-expression with Svp is the first functional proof of swf type genes in marine sponges. However, the precise biosynthetic role of the swf clusters remains unknown. PMID:24249289

  14. A ribosome-inactivating protein in a Drosophila defensive symbiont.

    Science.gov (United States)

    Hamilton, Phineas T; Peng, Fangni; Boulanger, Martin J; Perlman, Steve J

    2016-01-12

    Vertically transmitted symbionts that protect their hosts against parasites and pathogens are well known from insects, yet the underlying mechanisms of symbiont-mediated defense are largely unclear. A striking example of an ecologically important defensive symbiosis involves the woodland fly Drosophila neotestacea, which is protected by the bacterial endosymbiont Spiroplasma when parasitized by the nematode Howardula aoronymphium. The benefit of this defense strategy has led to the rapid spread of Spiroplasma throughout the range of D. neotestacea, although the molecular basis for this protection has been unresolved. Here, we show that Spiroplasma encodes a ribosome-inactivating protein (RIP) related to Shiga-like toxins from enterohemorrhagic Escherichia coli and that Howardula ribosomal RNA (rRNA) is depurinated during Spiroplasma-mediated protection of D. neotestacea. First, we show that recombinant Spiroplasma RIP catalyzes depurination of 28S rRNAs in a cell-free assay, as well as Howardula rRNA in vitro at the canonical RIP target site within the α-sarcin/ricin loop (SRL) of 28S rRNA. We then show that Howardula parasites in Spiroplasma-infected flies show a strong signal of rRNA depurination consistent with RIP-dependent modification and large decreases in the proportion of 28S rRNA intact at the α-sarcin/ricin loop. Notably, host 28S rRNA is largely unaffected, suggesting targeted specificity. Collectively, our study identifies a novel RIP in an insect defensive symbiont and suggests an underlying RIP-dependent mechanism in Spiroplasma-mediated defense. PMID:26712000

  15. Excess algal symbionts increase the susceptibility of reef corals to bleaching

    Science.gov (United States)

    Cunning, Ross; Baker, Andrew C.

    2013-03-01

    Rising ocean temperatures associated with global climate change are causing mass coral bleaching and mortality worldwide. Understanding the genetic and environmental factors that mitigate coral bleaching susceptibility may aid local management efforts to help coral reefs survive climate change. Although bleaching susceptibility depends partly on the genetic identity of a coral's algal symbionts, the effect of symbiont density, and the factors controlling it, remain poorly understood. By applying a new metric of symbiont density to study the coral Pocillopora damicornis during seasonal warming and acute bleaching, we show that symbiont cell ratio density is a function of both symbiont type and environmental conditions, and that corals with high densities are more susceptible to bleaching. Higher vulnerability of corals with more symbionts establishes a quantitative mechanistic link between symbiont density and the molecular basis for coral bleaching, and indicates that high densities do not buffer corals from thermal stress, as has been previously suggested. These results indicate that environmental conditions that increase symbiont densities, such as nutrient pollution, will exacerbate climate-change-induced coral bleaching, providing a mechanistic explanation for why local management to reduce these stressors will help coral reefs survive future warming.

  16. Symbiont Succession during Embryonic Development of the European Medicinal Leech, Hirudo verbana▿

    OpenAIRE

    Rita V M Rio; Maltz, Michele; McCormick, Benjamin; Reiss, Alexander; Graf, Joerg

    2009-01-01

    The European medicinal leech, Hirudo verbana, harbors simple microbial communities in the digestive tract and bladder. The colonization history, infection frequency, and growth dynamics of symbionts through host embryogenesis are described using diagnostic PCR and quantitative PCR. Symbiont species displayed diversity in temporal establishment and proliferation through leech development.

  17. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  18. The role of symbiont genetic distance and potential adaptability in host preference towards Pseudonocardia symbionts in Acromyrmex leaf-cutting ants

    DEFF Research Database (Denmark)

    Poulsen, Michael; Maynard, Janielle; Roland, Damien;

    2011-01-01

    two non-native strains, elucidating the role of genetic distance on preference between strains and Pseudonocardia origin. Our findings suggest that ants tend to prefer bacteria more closely related to their native bacterium and that genetic similarity is probably more important than whether symbionts...... to the role of adaptive recognition, potential ecological flexibility in symbiont preference, and more broadly, in relation to self versus non-self recognition....

  19. Direct evidence for maternal inheritance of bacterial symbionts in small deep-sea clams (Bivalvia: Vesicomyidae)

    Science.gov (United States)

    Szafranski, Kamil M.; Gaudron, Sylvie M.; Duperron, Sébastien

    2014-05-01

    Bacterial symbiont transmission is a key step in the renewal of the symbiotic interaction at each host generation, and different modes of transmission can be distinguished. Vesicomyidae are chemosynthetic bivalves from reducing habitats that rely on symbiosis with sulfur-oxidizing bacteria, in which two studies suggesting vertical transmission of symbionts have been published, both limited by the imaging techniques used. Using fluorescence in situ hybridization and transmission electron microscopy, we demonstrate that bacterial symbionts of Isorropodon bigoti, a gonochoristic Vesicomyidae from the Guiness cold seep site, occur intracellularly within female gametes at all stages of gametogenesis from germ cells to mature oocytes and in early postlarval stage. Symbionts are completely absent from the male gonad and gametes. This study confirms the transovarial transmission of symbionts in Vesicomyidae and extends it to the smaller species for which no data were previously available.

  20. Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts.

    Science.gov (United States)

    Bontemps, Cyril; Rogel, Marco Antonio; Wiechmann, Anja; Mussabekova, Assel; Moody, Sarah; Simon, Marcelo F; Moulin, Lionel; Elliott, Geoffrey N; Lacercat-Didier, Laurence; Dasilva, Cindy; Grether, Rosaura; Camargo-Ricalde, Sara L; Chen, Weimin; Sprent, Janet I; Martínez-Romero, Esperanza; Young, J Peter W; James, Euan K

    2016-01-01

    The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species. We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for betaproteobacteria using in situ immunolocalization. Rhizobia isolated from the nodules were genetically characterized and tested for their ability to nodulate Mimosa spp. Immunological analysis of 25 host taxa suggested that most (including all the highland endemics) were not nodulated by betaproteobacteria. Phylogenetic analyses of 16S rRNA, recA, nodA, nodC and nifH genes from 87 strains isolated from 20 taxa confirmed that the endemic Mexican Mimosa species favoured alphaproteobacteria in the genera Rhizobium and Ensifer: this was confirmed by nodulation tests. Host phylogeny, geographic isolation and coevolution with symbionts derived from very different soils have potentially contributed to the striking difference in the choice of symbiotic partners by Mexican and Brazilian Mimosa species. PMID:26214613

  1. Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts.

    Science.gov (United States)

    Parker, Matthew A; Jankowiak, Jennifer G; Landrigan, Grace K

    2015-07-01

    Desmodium and Hylodesmum (Papilionoideae Subtribe Desmodiinae) are among the most common herbaceous perennial legumes native to eastern North America. To analyze the population structure of their Bradyrhizobium sp. root-nodule bacteria, 159 isolates were sampled from ten host species across a 1000 km region. Phylogenetic analysis of four housekeeping loci (2164 bp) and two loci in the symbiosis island (SI) chromosomal region (1374 bp) indicated extensive overlap in symbiont utilization, with each common bacterial clade found on 2-7 species of these legume genera. However, host species differed considerably in the relative proportion of symbionts belonging to different Bradyrhizobium clades. High phylogenetic incongruence between trees for housekeeping loci and SI loci suggested that diversification of these Bradyrhizobium lineages involved substantial horizontal gene transfer. Plant inoculation with strains from six Bradyrhizobium clades revealed marked disparity in relative bacterial reproductive success across four Desmodium species. Estimated yield of Bradyrhizobium progeny cells per plant ranged from zero to >10(9), and strains with high fitness on one host sometimes reproduced poorly on other host species. Diversifying selection on bacteria, arising from differential success in habitats with different Desmodium and Hylodesmum taxa, is therefore likely to affect Bradyrhizobium diversity patterns at the landscape level. PMID:26130822

  2. The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals

    KAUST Repository

    Baumgarten, Sebastian

    2013-07-01

    Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

  3. Gammaproteobacteria as essential primary symbionts in the striped shield bug, Graphosoma Lineatum (Hemiptera: Pentatomidae).

    Science.gov (United States)

    Karamipour, Naeime; Mehrabadi, Mohammad; Fathipour, Yaghoub

    2016-01-01

    Many members of suborder Heteroptra harbor heritable symbiotic bacteria. Here we characterize the gut symbiotic bacterium in Graphosoma lineatum (Hemiptera: Pentatomidae) by using molecular phylogeny, real-time PCR analysis as well as light and electron microscopy observations. The microscopy observations revealed the presence of a large number of rod-shaped bacterial cells in the crypts. A very high prevalence (98 to 100%) of the symbiont infection was found in the insect populations that strongly supports an intimate association between these two organisms. Real-time PCR analysis also showed that the Gammaproteobacteria dominated the crypts. The sequences of 16sr RNA and groEL genes of symbiont showed high levels of similarity (93 to 95%) to Pantoea agglomeranse and Erwinia herbicola Gammaproteobacteria. Phylogenetic analyses placed G. lineatum symbiont in a well-defined branch, divergent from other stink bug bacterial symbionts. Co-evolutionary analysis showed lack of host-symbiont phylogenetic congruence. Surface sterilization of eggs resulted in increased pre-adult stage in the offspring (aposymbionts) in comparison to the normal. Also, fecundity, longevity, and adult stage were significantly decreased in the aposymbionts. Therefore, it seems that the symbiont might play a vital function in the host biology, in which host optimal development depends on the symbiont. PMID:27609055

  4. Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice

    OpenAIRE

    Boyd, Bret M.; Allen, Julie M; de Crécy-Lagard, Valérie; Reed, David L

    2014-01-01

    The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time: faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed ph...

  5. Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

    Directory of Open Access Journals (Sweden)

    de Beer Z Wilhelm

    2007-07-01

    Full Text Available Abstract Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species divided over three genera. Knowledge of interaction specificity is important to test the hypothesis that inhabitants (symbionts are taxonomically less diverse than 'exhabitants' (hosts and to test the hypothesis that transmission mode is an important determinant for interaction specificity. Results Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual specificity was found for the single Macrotermes species studied, as M. natalensis was associated with a single unique fungal haplotype. The three species of the genus Odontotermes showed low symbiont specificity: they were all associated with a genetically diverse set of fungal symbionts, but their fungal symbionts showed some host specificity, as none of the fungal haplotypes were shared between the studied Odontotermes species. Finally, bilaterally low specificity was found for the four tentatively recognized species of the genus Microtermes, which shared and apparently freely exchanged a common pool of divergent fungal symbionts. Conclusion Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general pattern of an endosymbiont, as we found either similar diversity at both sides or higher diversity in the symbiont. Our results further challenge the

  6. Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp.

    Directory of Open Access Journals (Sweden)

    Steven R Parratt

    2016-06-01

    Full Text Available Heritable microbial symbionts have profound impacts upon the biology of their arthropod hosts. Whilst our current understanding of the dynamics of these symbionts is typically cast within a framework of vertical transmission only, horizontal transmission has been observed in a number of cases. For instance, several symbionts can transmit horizontally when their parasitoid hosts share oviposition patches with uninfected conspecifics, a phenomenon called superparasitism. Despite this, horizontal transmission, and the host contact structures that facilitates it, have not been considered in heritable symbiont epidemiology. Here, we tested for the importance of host contact, and resulting horizontal transmission, for the epidemiology of a male-killing heritable symbiont (Arsenophonus nasoniae in parasitoid wasp hosts. We observed that host contact through superparasitism is necessary for this symbiont's spread in populations of its primary host Nasonia vitripennis, such that when superparasitism rates are high, A. nasoniae almost reaches fixation, causes highly female biased population sex ratios and consequently causes local host extinction. We further tested if natural interspecific variation in superparasitism behaviours predicted symbiont dynamics among parasitoid species. We found that A. nasoniae was maintained in laboratory populations of a closely related set of Nasonia species, but declined in other, more distantly related pteromalid hosts. The natural proclivity of a species to superparasitise was the primary factor determining symbiont persistence. Our results thus indicate that host contact behaviour is a key factor for heritable microbe dynamics when horizontal transmission is possible, and that 'reproductive parasite' phenotypes, such as male-killing, may be of secondary importance in the dynamics of such symbiont infections.

  7. Interspecific competition between entomopathogenic nematodes (Steinernema is modified by their bacterial symbionts (Xenorhabdus

    Directory of Open Access Journals (Sweden)

    Pages Sylvie

    2006-09-01

    Full Text Available Abstract Background Symbioses between invertebrates and prokaryotes are biological systems of particular interest in order to study the evolution of mutualism. The symbioses between the entomopathogenic nematodes Steinernema and their bacterial symbiont Xenorhabdus are very tractable model systems. Previous studies demonstrated (i a highly specialized relationship between each strain of nematodes and its naturally associated bacterial strain and (ii that mutualism plays a role in several important life history traits of each partner such as access to insect host resources, dispersal and protection against various biotic and abiotic factors. The goal of the present study was to address the question of the impact of Xenorhabdus symbionts on the progression and outcome of interspecific competition between individuals belonging to different Steinernema species. For this, we monitored experimental interspecific competition between (i two nematode species: S. carpocapsae and S. scapterisci and (ii their respective symbionts: X. nematophila and X. innexi within an experimental insect-host (Galleria mellonella. Three conditions of competition between nematodes were tested: (i infection of insects with aposymbiotic IJs (i.e. without symbiont of both species (ii infection of insects with aposymbiotic IJs of both species in presence of variable proportion of their two Xenorhabdus symbionts and (iii infection of insects with symbiotic IJs (i.e. naturally associated with their symbionts of both species. Results We found that both the progression and the outcome of interspecific competition between entomopathogenic nematodes were influenced by their bacterial symbionts. Thus, the results obtained with aposymbiotic nematodes were totally opposite to those obtained with symbiotic nematodes. Moreover, the experimental introduction of different ratios of Xenorhabdus symbionts in the insect-host during competition between Steinernema modified the proportion of

  8. Spectral Reflectance of Palauan Reef-Building Coral with Different Symbionts in Response to Elevated Temperature

    Directory of Open Access Journals (Sweden)

    Brandon J. Russell

    2016-02-01

    Full Text Available Spectral reflectance patterns of corals are driven largely by the pigments of photosynthetic symbionts within the host cnidarian. The warm inshore bays and cooler offshore reefs of Palau share a variety of coral species with differing endosymbiotic dinoflagellates (genus: Symbiodinium, with the thermally tolerant Symbiodinium trenchii (S. trenchii (= type D1a or D1-4 predominating under the elevated temperature regimes inshore, and primarily Clade C types in the cooler reefs offshore. Spectral reflectance of two species of stony coral, Cyphastrea serailia (C. serailia and Pachyseris rugosa (P. rugosa, from both inshore and offshore locations shared multiple features both between sites and to similar global data from other studies. No clear reflectance features were evident which might serve as markers of thermally tolerant S. trenchii symbionts compared to the same species of coral with different symbionts. Reflectance from C. serailia colonies from inshore had a fluorescence peak at approximately 500 nm which was absent from offshore animals. Integrated reflectance across visible wavelengths had an inverse correlation to symbiont cell density and could be used as a relative indicator of the symbiont abundance for each type of coral. As hypothesized, coral colonies from offshore with Clade C symbionts showed a greater response to experimental heating, manifested as decreased symbiont density and increased reflectance or “bleaching” than their inshore counterparts with S. trenchii. Although no unique spectral features were found to distinguish species of symbiont, spectral differences related to the abundance of symbionts could prove useful in field and remote sensing studies.

  9. High Symbiont Relatedness Stabilizes Mutualistic Cooperation in Fungus-Growing Termites

    DEFF Research Database (Denmark)

    Aanen, Duur K; de Fine Licht, Henrik H; Debets, Alfons J M;

    2009-01-01

    studied. We show that African fungus-growing termites propagate single variants of their Termitomyces symbiont, despite initiating cultures from genetically variable spores from the habitat. High inoculation density in the substrate followed by fusion among clonally related mycelia enhances the efficiency...... of spore production in proportion to strain frequency. This positive reinforcement results in an exclusive lifetime association of each host colony with a single fungal symbiont and hinders the evolution of cheating. Our findings explain why vertical symbiont transmission in fungus-growing termites...

  10. Construction of a Metagenomic DNA Library of Sponge Symbionts and Screening of Antibacterial Metabolites

    Institute of Scientific and Technical Information of China (English)

    CHEN Juan; ZHU Tianjiao; LI Dehai; CUI Chengbin; FANG Yuchun; LIU Hongbing; LIU Peipei; GU Qianqun; ZHU Weiming

    2006-01-01

    To study the bioactive metabolites produced by sponge-derived uncultured symbionts, a metagenomic DNA library of the symbionts of sponge Gelliodes gracilis was constructed. The average size of DNA inserts in the library was 20 kb. This library was screened for antibiotic activity using paper disc assaying. Two clones displayed the antibacterial activity against Micrococcus tetragenus. The metabolites of these two clones were analyzed through HPLC. The result showed that their metabolites were quite different from those of the host E. coli DH5α and the host containing vector pHZ132. This study may present a new approach to exploring bioactive metabolites of sponge symbionts.

  11. Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Boomsma, Jacobus Jan; Aanen, Duur Kornelis

    2006-01-01

    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would...... transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic...

  12. Co-Speciation of Earthworms and their nephridial symbionts, Acidovorax Spp

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Fritz, Michael; Holmstrup, Martin;

    2006-01-01

    Earthworms (Annelida; Lumbricidae) harbour species-specific symbiotic bacteria in their nephridia (excretory organs) where the symbionts densely colonize a specific part of the nephridia called the ampulla [1]. The symbiosis is universal among earthworms, the symbionts form a monophyletic cluster...... of these non-Acidovorax symbionts are still to be investigated. [1] Knop, J. 1926. Z Morph Ökol Tiere, 6(3):588-624. [2] Schramm, A. et al. 2003. Environ Microbiol 5(9):804-809. [3] Davidson, S.K. & Stahl, D.A. 2006. Appl Environ Microbiol 72(1):769-775....

  13. Biomineralization of magnet nanoparticles with bacterial symbionts of man

    Directory of Open Access Journals (Sweden)

    Horobets S.V.

    2014-06-01

    Full Text Available Bioinformational analysis of human’s bacterial symbionts (BS to study the process of biomineralization of biogenic magnetic nanoparticles (BMN was conducted. For this purpose in this paper a comparative analysis of amino acid sequences of proteins of magnetosome island of magnetotactic bacteria (MI MTB with human BS proteins using the program "BLAST-online" was made. A number of human BS may be potential producers of magnetic nanoparticles as evidenced by the experimental work of other authors. Considering obtained results it was shown that the interaction between tumor cells and some strains of human’s BS may occur due to the forces of magnetic dipole interaction, occuring between the endogenous magnetic nanoparticles of tumor cells and endogenous magnetosensitive particles of bacteria.

  14. Strong strand specific composition bias-a genomic character of some obligate parasites or symbionts%强烈的复制链组成偏差——某些专性寄生(共生)菌特有的基因组学特征

    Institute of Scientific and Technical Information of China (English)

    郭锋彪

    2011-01-01

    DNA复制是一个不对称的过程.不对称的一个体现是复制链分为前导链和滞后链,前者连续复制而后者的复制却不连续.这种不对称最终导致两条链上核酸组成的不对称.链特异的核酸组成偏差最先发现于棘皮类动物和脊椎动物的线粒体DNA上.随着全基因组的大量测序,越来越多的细菌被发现具有类似的链特异的核酸组成偏差,甚至很多真核生物的染色体基因组也被发现具有类似偏差.在某些细菌中,链特异的组成偏差强烈到足以使前导链和滞后链的基因间具有分离的密码子使用,至今,共有11种细菌被发现具有和复制相关的分离的密码子使用.这11种细菌无一例外都属于专性寄生(共生)菌.对于链组成偏差产生的内在机制以及特定细菌具有强烈链组成偏差的成因,目前学术界尚没有统一的理论解释.文章对这一遗传学及基因组学的重要问题进行了综述和展望.%DNA replication includes a set of asymmetric mechanisms, which is a division into lagging and leading strands. The former is synthesized continuously whereas the synthesis for the latter is discontinuous. Such a asymmetric mechanism leads to distinct nucleotide composition of these two strands. Strands specific nucleotide composition bias was originally found in genomes of echinoderm and vertebrate mitochondria and then in several bacterial genomes. With the rapid growth in the number of sequenced genomes, many bacteria and even eukaryotes are found to have the consistent strand composition bias. In some bacteria, the extent of strand specific composition bias was so strong that genes on the two replicating strands could be separated according to their codon usages. Till now, 11 obligate intracellular bacteria have been found to have separate codon usages according to whether genes located on the leading or lagging strands. However, there is still not a well-accepted theory that could interpret the

  15. Towards a molecular understanding of symbiont function: Identification of a fungal gene for the degradation of xylan in the fungus gardens of leaf-cutting ants

    Directory of Open Access Journals (Sweden)

    Lange Lene

    2008-02-01

    Full Text Available Abstract Background Leaf-cutting ants live in symbiosis with a fungus that they rear for food by providing it with live plant material. Until recently the fungus' main inferred function was to make otherwise inaccessible cell wall degradation products available to the ants, but new studies have shed doubt on this idea. To provide evidence for the cell wall degrading capacity of the attine ant symbiont, we designed PCR primers from conserved regions of known xylanase genes, to be used in PCR with genomic DNA from the symbiont as template. We also measured xylanase, cellulase and proteinase activities in the fungus gardens in order to investigate the dynamics of degradation activities. Results We cloned a xylanase gene from the mutualistic fungus of Acromyrmex echinatior, determined its protein sequence, and inserted it in a yeast expression vector to confirm its substrate specificity. Our results show that the fungus has a functional xylanase gene. We also show by lab experiments in vivo that the activity of fungal xylanase and cellulase is not evenly distributed, but concentrated in the lower layer of fungus gardens, with only modest activity in the middle layer where gongylidia are produced and intermediate activity in the newly established top layer. This vertical distribution appears to be negatively correlated with the concentration of glucose, which indicates a directly regulating role of glucose, as has been found in other fungi and has been previously suggested for the ant fungal symbiont. Conclusion The mutualistic fungus of Acromyrmex echinatior has a functional xylanase gene and is thus presumably able to at least partially degrade the cell walls of leaves. This finding supports a saprotrophic origin of the fungal symbiont. The observed distribution of enzyme activity leads us to propose that leaf-substrate degradation in fungus gardens is a multi-step process comparable to normal biodegradation of organic matter in soil ecosystems

  16. Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

    DEFF Research Database (Denmark)

    Aanen, Duur K; Ros, Vera I D; de Fine Licht, Henrik H;

    2007-01-01

    BACKGROUND: Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species......: Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual...... divergent fungal symbionts. CONCLUSION: Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general...

  17. Baseline shifts in coral skeletal oxygen isotopic composition: a signature of symbiont shuffling?

    Science.gov (United States)

    Carilli, J. E.; Charles, C. D.; Garren, M.; McField, M.; Norris, R. D.

    2013-06-01

    Decades-long records of the stable isotopic composition of coral skeletal cores were analyzed from four sites on the Mesoamerican Reef. Two of the sites exhibited baseline shifts in oxygen isotopic composition after known coral bleaching events. Changes in pH at the calcification site caused by a change in the associated symbiont community are invoked to explain the observed shift in the isotopic composition. To test the hypothesis that changes in symbiont clade could affect skeletal chemistry, additional coral samples were collected from Belize for paired Symbiodinium identification and skeletal stable isotopic analysis. We found some evidence that skeletal stable isotopic composition may be affected by symbiont clade and suggest this is an important topic for future investigation. If different Symbiodinium clades leave consistent signatures in skeletal geochemical composition, the signature will provide a method to quantify past symbiont shuffling events, important for understanding how corals are likely to respond to climate change.

  18. Plasticity of symbiont acquisition throughout the life cycle of the shallow-water tropical lucinid Codakia orbiculata (Mollusca: Bivalvia).

    Science.gov (United States)

    Gros, Olivier; Elisabeth, Nathalie H; Gustave, Sylvie D D; Caro, Audrey; Dubilier, Nicole

    2012-06-01

    In marine invertebrates that acquire their symbionts from the environment, these are generally only taken up during early developmental stages. In the symbiosis between lucinid clams and their intracellular sulfur-oxidizing bacteria, it has been shown that the juveniles acquire their symbionts from an environmental stock of free-living symbiont forms, but it is not known if adult clams are still competent to take up symbiotic bacteria from the environment. In this study, we investigated symbiont acquisition in adult specimens of the lucinid clam Codakia orbiculata, using transmission electron microscopy, fluorescence in situ hybridization, immunohistochemistry and PCR. We show here that adults that had no detectable symbionts after starvation in aquaria for 6 months, rapidly reacquired symbionts within days after being returned to their natural environments in the field. Control specimens that were starved and then exposed to seawater aquaria with sulfide did not reacquire symbionts. This indicates that the reacquisition of symbionts in the starved clams returned to the field was not caused by high division rates of a small pool of remaining symbionts that we were not able to detect with the methods used here. Immunohistochemistry with an antibody against actin, a protein involved in the phagocytosis of intracellular bacteria, showed that actin was expressed at the apical ends of the gill cells that took up symbionts, providing further evidence that the symbionts were acquired from the environment. Interestingly, actin expression was also observed in symbiont-containing cells of untreated lucinids freshly collected from the environment, indicating that symbiont acquisition from the environment occurs continuously in these clams throughout their lifetime. PMID:22672589

  19. Temporal changes of symbiont density and host fitness after rifampicin treatment in a whitefly of the Bemisia tabaci species complex.

    Science.gov (United States)

    Shan, Hong-Wei; Zhang, Chang-Rong; Yan, Ting-Ting; Tang, Hai-Qin; Wang, Xiao-Wei; Liu, Shu-Sheng; Liu, Yin-Quan

    2016-04-01

    Microbial symbionts are essential or important partners to phloem-feeding insects. Antibiotics have been used to selectively eliminate symbionts from their host insects and establish host lines with or without certain symbionts for investigating functions of the symbionts. In this study, using the antibiotic rifampicin we attempted to selectively eliminate certain symbionts from a population of the Middle East-Asia Minor 1 whitefly of the Bemisia tabaci species complex, which harbors the primary symbiont "Candidatus Portiera aleyrodidarum" and two secondary symbionts "Candidatus Hamiltonella defensa" and Rickettsia. Neither the primary nor the secondary symbionts were completely depleted in the adults (F0) that fed for 48 h on a diet treated with rifampicin at concentrations of 1-100 μg/mL. However, both the primary and secondary symbionts were nearly completely depleted in the offspring (F1) of the rifampicin-treated adults. Although the F1 adults produced some eggs (F2), most of the eggs failed to hatch and none of them reached the second instar, and consequently the rifampicin-treated whitefly colony vanished at the F2 generation. Interestingly, quantitative polymerase chain reaction assays showed that in the rifampicin-treated whiteflies, the density of the primary symbiont was reduced at an obviously slower pace than the secondary symbionts. Mating experiments between rifampicin-treated and untreated adults demonstrated that the negative effects of rifampicin on host fitness were expressed when the females were treated by the antibiotic, and whether males were treated or not by the antibiotic had little contribution to the negative effects. These observations indicate that with this whitefly population it is not feasible to selectively eliminate the secondary symbionts using rifampicin without affecting the primary symbiont and establish host lines for experimental studies. However, the extinction of the whitefly colony at the second generation after

  20. Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp

    Science.gov (United States)

    Parratt, Steven R.; Frost, Crystal L.; Schenkel, Martijn A.; Rice, Annabel

    2016-01-01

    Heritable microbial symbionts have profound impacts upon the biology of their arthropod hosts. Whilst our current understanding of the dynamics of these symbionts is typically cast within a framework of vertical transmission only, horizontal transmission has been observed in a number of cases. For instance, several symbionts can transmit horizontally when their parasitoid hosts share oviposition patches with uninfected conspecifics, a phenomenon called superparasitism. Despite this, horizontal transmission, and the host contact structures that facilitates it, have not been considered in heritable symbiont epidemiology. Here, we tested for the importance of host contact, and resulting horizontal transmission, for the epidemiology of a male-killing heritable symbiont (Arsenophonus nasoniae) in parasitoid wasp hosts. We observed that host contact through superparasitism is necessary for this symbiont’s spread in populations of its primary host Nasonia vitripennis, such that when superparasitism rates are high, A. nasoniae almost reaches fixation, causes highly female biased population sex ratios and consequently causes local host extinction. We further tested if natural interspecific variation in superparasitism behaviours predicted symbiont dynamics among parasitoid species. We found that A. nasoniae was maintained in laboratory populations of a closely related set of Nasonia species, but declined in other, more distantly related pteromalid hosts. The natural proclivity of a species to superparasitise was the primary factor determining symbiont persistence. Our results thus indicate that host contact behaviour is a key factor for heritable microbe dynamics when horizontal transmission is possible, and that ‘reproductive parasite’ phenotypes, such as male-killing, may be of secondary importance in the dynamics of such symbiont infections. PMID:27322651

  1. Radiative energy budget reveals high photosynthetic efficiency in symbiont-bearing corals

    OpenAIRE

    Brodersen, Kasper Elgetti; Lichtenberg, Mads; Ralph, Peter J.; Kühl, Michael; Wangpraseurt, Daniel

    2014-01-01

    The light field on coral reefs varies in intensity and spectral composition, and is the key regulating factor for phototrophic reef organisms, for example scleractinian corals harbouring microalgal symbionts. However, the actual efficiency of light utilization in corals and the mechanisms affecting the radiative energy budget of corals are underexplored. We present the first balanced light energy budget for a symbiont-bearing coral based on a fine-scale study of the microenvironmental photobi...

  2. Bacterial Symbionts of a Devastating Coffee Plant Pest, the Stinkbug Antestiopsis thunbergii (Hemiptera: Pentatomidae)

    OpenAIRE

    Matsuura, Yu; Hosokawa, Takahiro; Serracin, Mario; Tulgetske, Genet M.; Miller, Thomas A.; Fukatsu, Takema

    2014-01-01

    Stinkbugs of the genus Antestiopsis, so-called antestia bugs or variegated coffee bugs, are notorious pests of coffee plants in Africa. We investigated the symbiotic bacteria associated with Antestiopsis thunbergii, a major coffee plant pest in Rwanda. PCR, cloning, sequencing, and phylogenetic analysis of bacterial genes identified four distinct bacterial lineages associated with A. thunbergii: a gammaproteobacterial gut symbiont and symbionts representing the genera Sodalis, Spiroplasma, an...

  3. The symbiotic role of O-antigen of Burkholderia symbiont in association with host Riptortus pedestris.

    Science.gov (United States)

    Kim, Jiyeun Kate; Park, Ha Young; Lee, Bok Luel

    2016-07-01

    Riptortus pedestris harboring Burkholderia symbiont is a useful symbiosis model to study the molecular interactions between insects and bacteria. We recently reported that the lipopolysaccharide O-antigen is absent in the Burkholderia symbionts isolated from Riptortus guts. Here, we investigated the symbiotic role of O-antigen comprehensively in the Riptortus-Burkholderia model. Firstly, Burkholderia mutant strains deficient of O-antigen biosynthesis genes were generated and confirmed for their different patterns of the lipopolysaccharide by electrophoretic analysis. The O-antigen-deficient mutant strains initially exhibited a reduction of infectivity, having significantly lower level of symbiont population at the second-instar stage. However, both the wild-type and O-antigen mutant symbionts exhibited a similar level of symbiont population from the third-instar stage, indicating that the O-antigen deficiency did not affect the bacterial persistence in the host midgut. Taken together, we showed that the lipopolysaccharide O-antigen of gut symbiont plays an exclusive role in the initial symbiotic association. PMID:26875632

  4. Ephemeral windows of opportunity for horizontal transmission of fungal symbionts in leaf-cutting ants

    DEFF Research Database (Denmark)

    Poulsen, Michael; Fernández-Marín, Hermógenes; Currie, Cameron R.;

    2009-01-01

    Evolutionary theory predicts that hosts are selected to prevent mixing of genetically different symbionts when competition among lineages reduces the productivity of a mutualism. The symbionts themselves may also defend their interests: recent studies of Acromyrmex leaf-cutting ants showed that s...... droplets remain compatible with alternative strains during the early stage of colony founding. We discuss how brief stages of low commitment between partners may increase the evolutionary stability of ancient coevolved mutualisms.......Evolutionary theory predicts that hosts are selected to prevent mixing of genetically different symbionts when competition among lineages reduces the productivity of a mutualism. The symbionts themselves may also defend their interests: recent studies of Acromyrmex leaf-cutting ants showed that...... original symbiont, and by the ant species the novel symbiont came from. The colony founding stage may thus provide an efficient but transient window for horizontal transmission, in which the fungus is unable to actively defend its partnership position before the host feeds on it, so that host fecal...

  5. Bacterial symbionts of the leafhopper Evacanthus interruptus (Linnaeus, 1758) (Insecta, Hemiptera, Cicadellidae: Evacanthinae).

    Science.gov (United States)

    Szklarzewicz, Teresa; Grzywacz, Beata; Szwedo, Jacek; Michalik, Anna

    2016-03-01

    Plant sap-feeding hemipterans harbor obligate symbiotic microorganisms which are responsible for the synthesis of amino acids missing in their diet. In this study, we characterized the obligate symbionts hosted in the body of the xylem-feeding leafhopper Evacanthus interruptus (Cicadellidae: Evacanthinae: Evacanthini) by means of histological, ultrastructural and molecular methods. We observed that E. interruptus is associated with two types of symbiotic microorganisms: bacterium 'Candidatus Sulcia muelleri' (Bacteroidetes) and betaproteobacterium that is closely related to symbionts which reside in two other Cicadellidae representatives: Pagaronia tredecimpunctata (Evacanthinae: Pagaronini) and Hylaius oregonensis (Bathysmatophorinae: Bathysmatophorini). Both symbionts are harbored in their own bacteriocytes which are localized between the body wall and ovaries. In E. interruptus, both Sulcia and betaproteobacterial symbionts are transovarially transmitted from one generation to the next. In the mature female, symbionts leave the bacteriocytes and gather around the posterior pole of the terminal oocytes. Then, they gradually pass through the cytoplasm of follicular cells surrounding the posterior pole of the oocyte and enter the space between them and the oocyte. The bacteria accumulate in the deep depression of the oolemma and form a characteristic 'symbiont ball'. In the light of the results obtained, the phylogenetic relationships within modern Cicadomorpha and some Cicadellidae subfamilies are discussed. PMID:25900723

  6. Report on the Workshop on DNA Isolation and Detection of Tsetse Pathogens and Symbionts using PCR

    International Nuclear Information System (INIS)

    The workshop on DNA isolation and detection of tsetse pathogens and symbionts using PCR was hosted by the Centre International de Recherche-Developpement Sur l'Elevage en Zone Subhumide (CIRDES) and was attended by eight participants and three lecturers from eleven countries. Several oral presentations were given that provided an overview on general principles of the PCR, on the factors that might affect the obtained results, on the different applications of the PCR for the Salivary Gland Hyperplasia Virus (SGHV) work, and on the current progress of the work on Wolbachia and Sodalis. Two sessions of tsetse dissections were organised, which focussed on the detection of hypertrophied salivary gland symptoms, on the separation of ovaries and testes, and on the collection of the haemolymph under aseptic conditions to initiate Sodalis cultures. Using the monitor connected to the microscope, all participants could view the dissection demonstrations, and were given later the opportunity to practice the dissections themselves. In addition, demonstrations were given on how to prepare slides to observe Sodalis bacteria under the compound microscope. In addition, several practical sessions were organised on DNA extraction for virus detection and demonstrations were given on extractions of the genomic DNA from the tsetse abdomen using the cetyltrimethylammo-niumbromide (CTAB) for Wolbachia diagnosis and using the DNeasy kit (Qiagen) method for Sodalis diagnosis. Finally, there were three sessions on the use of PCR and how to detect the virus in the samples extracted by the manual method using two sets of primers. Methods were likewise demonstrated on detecting Wolbachia and Sodalis in the DNA samples extracted by the CTAB and DNeasy methods, and a comparison was made of the three different methods to detect the SGHV, Wolbachia and Sodalis

  7. Co-infection and localization of secondary symbionts in two whitefly species

    Directory of Open Access Journals (Sweden)

    Kontsedalov Svetlana

    2010-05-01

    Full Text Available Abstract Background Whiteflies are cosmopolitan phloem-feeding pests that cause serious damage to many crops worldwide due to direct feeding and vectoring of many plant viruses. The sweetpotato whitefly Bemisia tabaci (Gennadius and the greenhouse whitefly Trialeurodes vaporariorum (Westwood are two of the most widespread and damaging whitefly species. To complete their unbalanced diet, whiteflies harbor the obligatory bacterium Portiera aleyrodidarum. B. tabaci further harbors a diverse array of secondary symbionts, including Hamiltonella, Arsenophonus, Cardinium, Wolbachia, Rickettsia and Fritschea. T. vaporariorum is only known to harbor P. aleyrodidarum and Arsenophonus. We conducted a study to survey the distribution of whitefly species in Croatia, their infection status by secondary symbionts, and the spatial distribution of these symbionts in the developmental stages of the two whitefly species. Results T. vaporariorum was found to be the predominant whitefly species across Croatia, while only the Q biotype of B. tabaci was found across the coastal part of the country. Arsenophonus and Hamiltonella were detected in collected T. vaporariorum populations, however, not all populations harbored both symbionts, and both symbionts showed 100% infection rate in some of the populations. Only the Q biotype of B. tabaci was found in the populations tested and they harbored Hamiltonella, Rickettsia, Wolbachia and Cardinium, while Arsenophonus and Fritschea were not detected in any B. tabaci populations. None of the detected symbionts appeared in all populations tested, and multiple infections were detected in some of the populations. All endosymbionts tested were localized inside the bacteriocyte in both species, but only Rickettsia and Cardinium in B. tabaci showed additional localization outside the bacteriocyte. Conclusions Our study revealed unique co-infection patterns by secondary symbionts in B. tabaci and T. vaporariorum. Co-sharing of the

  8. Transcriptomic immune response of the cotton stainer Dysdercus fasciatus to experimental elimination of vitamin-supplementing intestinal symbionts

    OpenAIRE

    Bauer, E.; Salem, H.; Marz, M.; Vogel, H.; Kaltenpoth, M.

    2014-01-01

    The acquisition and vertical transmission of bacterial symbionts plays an important role in insect evolution and ecology. However, the molecular mechanisms underlying the stable maintenance and control of mutualistic bacteria remain poorly understood. The cotton stainer Dysdercus fasciatus harbours the actinobacterial symbionts Coriobacterium glomerans and Gordonibacter sp. in its midgut. The symbionts supplement limiting B vitamins and thereby significantly contribute to the host’s fitness. ...

  9. Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change

    OpenAIRE

    Cunning, R.; Silverstein, R. N.; Baker, A. C.

    2015-01-01

    Dynamic symbioses may critically mediate impacts of climate change on diverse organisms, with repercussions for ecosystem persistence in some cases. On coral reefs, increases in heat-tolerant symbionts after thermal bleaching can reduce coral susceptibility to future stress. However, the relevance of this adaptive response is equivocal owing to conflicting reports of symbiont stability and change. We help reconcile this conflict by showing that change in symbiont community composition (symbio...

  10. Frequency of Secondary Symbiont Infection in an Invasive Psyllid Relates to Parasitism Pressure on a Geographic Scale in California▿

    OpenAIRE

    Hansen, A.K.; Jeong, G.; Paine, T. D.; Stouthamer, R

    2007-01-01

    Two endosymbionts, an obligate primary symbiont and a facultative secondary symbiont, are harbored within the invasive red gum (eucalyptus) lerp psyllid, Glycaspis brimblecombei, in California. An extensive survey of diversity and frequency of G. brimblecombei's secondary symbiont in multiple populations throughout the state of California was conducted using PCR detection, restriction enzymes, cloning, and sequencing. A total of 380 G. brimblecombei individuals in 19 populations were screened...

  11. Aspects of the life cycles of chemosynthetic bacterial symbionts associated with bivalves from deep-sea chemosynthesis-based ecosystems

    OpenAIRE

    Szafranski, Kamil,

    2014-01-01

    Metazoans colonizing deep-sea reducing habitats often employ chemosymbiotic bacterial associations. Hosts become dependent upon their sulfur-oxidizing and/or methanotrophic symbionts, which provide organic carbon compounds. Various larval dispersal strategies have evolved in the hosts, ensuring the colonization of new sites. The continuity of the symbiotic association is maintained by symbiont transmission. Symbionts may pass directly to the host’s progeny via gametes (vertical transmission) ...

  12. Environmental genomics reveals a single species ecosystem deep within the Earth

    Energy Technology Data Exchange (ETDEWEB)

    Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd Z.; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, Gordon; Wanger, Greg; Pratt, Lisa M.; Andersen, Gary L.; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, Tullis C.

    2008-09-17

    DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

  13. Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

    Science.gov (United States)

    Schreiber, Lars; Kjeldsen, Kasper U.; Funch, Peter; Jensen, Jeppe; Obst, Matthias; López-Legentil, Susanna; Schramm, Andreas

    2016-01-01

    Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25–100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas. PMID:27462299

  14. Combined thermal and herbicide stress in functionally diverse coral symbionts

    International Nuclear Information System (INIS)

    Most reef building corals rely on symbiotic microalgae (genus Symbiodinium) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. - Highlights: • Water quality influences thermal stress thresholds in different Symbiodinium types. • Photosystem of clade D tested more sensitive than C1 to a common herbicide. • Increased thermal tolerance quickly countered in presence of herbicide. • Mixture toxicity approach demonstrated response additivity for combined stressors. • Symbiotic partnership may be compromised in areas subjected to terrestrial runoff. - Thermal-tolerant Symbiodinium type D tested especially vulnerable to a common herbicide, emphasizing the significance of cumulative stressors in ecological risk management

  15. The Arthromitus stage of Bacillus cereus: intestinal symbionts of animals

    Science.gov (United States)

    Margulis, L.; Jorgensen, J. Z.; Dolan, S.; Kolchinsky, R.; Rainey, F. A.; Lo, S. C.

    1998-01-01

    In the guts of more than 25 species of arthropods we observed filaments containing refractile inclusions previously discovered and named "Arthromitus" in 1849 by Joseph Leidy [Leidy, J. (1849) Proc. Acad. Nat. Sci. Philadelphia 4, 225-233]. We cultivated these microbes from boiled intestines of 10 different species of surface-cleaned soil insects and isopod crustaceans. Literature review and these observations lead us to conclude that Arthromitus are spore-forming, variably motile, cultivable bacilli. As long rod-shaped bacteria, they lose their flagella, attach by fibers or fuzz to the intestinal epithelium, grow filamentously, and sporulate from their distal ends. When these organisms are incubated in culture, their life history stages are accelerated by light and inhibited by anoxia. Characterization of new Arthromitus isolates from digestive tracts of common sow bugs (Porcellio scaber), roaches (Gromphodorhina portentosa, Blaberus giganteus) and termites (Cryptotermes brevis, Kalotermes flavicollis) identifies these flagellated, spore-forming symbionts as a Bacillus sp. Complete sequencing of the 16S rRNA gene from four isolates (two sow bug, one hissing roach, one death's head roach) confirms these as the low-G+C Gram-positive eubacterium Bacillus cereus. We suggest that B. cereus and its close relatives, easily isolated from soil and grown on nutrient agar, enjoy filamentous growth in moist nutrient-rich intestines of healthy arthropods and similar habitats.

  16. Ontogenetic shifts in a freshwater cleaning symbiosis: consequences for hosts and their symbionts.

    Science.gov (United States)

    Thomas, Michael J; Creed, Robert P; Skelton, James; Brown, Bryan L

    2016-06-01

    Animal fitness is influenced by diverse assemblages of internal and external symbionts. These assemblages often change throughout host ontogeny, but the mechanisms that underlie these changes and their consequences for host fitness are seldom revealed. Here we examine a cleaning symbiosis between crayfish and an assemblage of ectosymbiotic branchiobdellidan worms to uncover what mechanisms drive changes in symbiont composition during host ontogeny and the consequences of these changes for both the host and symbionts. In surveys of a North Carolina river, the dominant worm species shifted from Cambarincola philadelphicus to Cambarincola ingens as crayfish (Cambarus bartonii) increased in size. We demonstrate that this shift is a function of host regulation by small crayfish and exclusion by a dominant symbiont on large crayfish. In a controlled lab experiment, small crayfish often removed their symbionts but C. ingens was removed at a higher rate than C. philadelphicus. In contrast, C. ingens had higher survivorship and reproduction than C. philadelphicus on large crayfish. We also measured the effect of each worm species on crayfish growth through ontogeny; neither worm species had an effect on small crayfish but both species had similar positive effects on the growth of large crayfish relative to controls. Evidence from another experiment suggested that intraguild predation by C. ingens caused a decline in C. philadelphicus on large crayfish. We have shown that shifts in partner fitness are a function of host size and that these shifts can involve the succession of symbionts. Further, our results suggest that changes in the outcome of symbioses can remain robust throughout host ontogeny despite interactive mechanisms that lead to shifts in symbiont community structure. PMID:27459781

  17. Niche acclimatization in Red Sea corals is dependent on flexibility of host-symbiont association

    KAUST Repository

    Ziegler, Maren

    2015-08-06

    Knowledge of host-symbiont specificity and acclimatization capacity of corals is crucial for understanding implications of environmental change. Whilst some corals have been shown to associate with a number of symbionts that may comprise different physiologies, most corals associate with only one dominant Symbiodinium species at a time. Coral communities in the Red Sea thrive under large fluctuations of environmental conditions, but the degree and mechanisms of coral acclimatization are largely unexplored. Here we investigated the potential for niche acclimatization in 2 dominant corals from the central Red Sea, Pocillopora verrucosa and Porites lutea, in relation to the fidelity of the underlying coral-symbiont association. Repeated sampling over 2 seasons along a cross-shelf and depth gradient revealed a stable symbiont association in P. verrucosa and flexible association in P. lutea. A statistical biological-environmental matching routine revealed that the high plasticity of photophysiology and photopigments in the stable Symbiodinium microadriaticum (type A1) community in P. verrucosa were correlated with environmental influences along spatio-temporal dimensions. In contrast, photophysiology and pigments were less variable within each symbiont type from P. lutea indicating that niche acclimatization was rather regulated by a flexible association with a variable Symbiodinium community. Based on these data, we advocate an extended concept of phenotypic plasticity of the coral holobiont, in which the scleractinian host either associates with a specific Symbiodinium type with a broad physiological tolerance, or the host-symbiont pairing is more flexible to accommodate for different symbiont associations, each adapted to specific environmental settings.

  18. Progress in the insect symbiont Rickettsia%昆虫共生细菌 Rickettsia 的研究进展

    Institute of Scientific and Technical Information of China (English)

    潘慧鹏; 张友军

    2012-01-01

    species. It can transmit vertically through eggs, and horizontally through parasitic wasps and host plants. It can influence the host reproduction by male-killing and parthenogenesis- It has beneficial or detrimental effects on its hosts and can increase the tolerance of its hosts to high temperature and parasitic wasps, and is correlated with its hosts ' susceptibility to insecticides, The insect symbiont Rickettsia has a reduced genome and might undergo considerable further reduction.

  19. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  20. Accelerated evolutionary rate in sulfur-oxidizing endosymbiotic bacteria associated with the mode of symbiont transmission.

    Science.gov (United States)

    Peek, A S; Vrijenhoek, R C; Gaut, B S

    1998-11-01

    The nearly neutral theory of molecular evolution predicts that the rate of nucleotide substitution should accelerate in small populations at sites under low selective constraint. We examined these predictions with respect to the relative population sizes for three bacterial life histories within chemolithoautotrophic sulfur-oxidizing bacteria: (1) free-living bacteria, (2) environmentally captured symbionts, and (3) maternally transmitted symbionts. Both relative rates of nucleotide substitution and relative ratios of loop, stem, and domain substitutions from 1,165 nt of the small-subunit 16S rDNA were consistent with expectations of the nearly neutral theory. Relative to free-living sulfur-oxidizing autotrophic bacteria, the maternally transmitted symbionts have faster substitution rates overall and also in low-constraint domains of 16S rDNA. Nucleotide substitition rates also differ between loop and stem positions. All of these findings are consistent with the predictions that these symbionts have relatively small effective population sizes. In contrast, the rates of nucleotide substitution in environmentally captured symbionts are slower, particularly in high-constraint domains, than in free-living bacteria. PMID:12572615

  1. Cyanobacterial diversity and a new acaryochloris-like symbiont from Bahamian sea-squirts.

    Directory of Open Access Journals (Sweden)

    Susanna López-Legentil

    Full Text Available Symbiotic interactions between ascidians (sea-squirts and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS and by examining symbiont morphology with transmission electron (TEM and confocal microscopy (CM. As described previously for other species, Trididemnum spp. mostly contained symbionts associated with the Prochloron-Synechocystis group. However, sequence analysis of the symbionts in Lissoclinum revealed two unique clades. The first contained a novel cyanobacterial clade, while the second clade was closely associated with Acaryochloris marina. CM revealed the presence of chlorophyll d (chl d and phycobiliproteins (PBPs within these symbiont cells, as is characteristic of Acaryochloris species. The presence of symbionts was also observed by TEM inside the tunic of both the adult and larvae of L. fragile, indicating vertical transmission to progeny. Based on molecular phylogenetic and microscopic analyses, Candidatus Acaryochloris bahamiensis nov. sp. is proposed for this symbiotic cyanobacterium. Our results support the hypothesis that photosymbiont communities in ascidians are structured by host phylogeny, but in some cases, also by sampling location.

  2. Differential responses of the coral host and their algal symbiont to thermal stress.

    Directory of Open Access Journals (Sweden)

    William Leggat

    Full Text Available The success of any symbiosis under stress conditions is dependent upon the responses of both partners to that stress. The coral symbiosis is particularly susceptible to small increases of temperature above the long term summer maxima, which leads to the phenomenon known as coral bleaching, where the intracellular dinoflagellate symbionts are expelled. Here we for the first time used quantitative PCR to simultaneously examine the gene expression response of orthologs of the coral Acropora aspera and their dinoflagellate symbiont Symbiodinium. During an experimental bleaching event significant up-regulation of genes involved in stress response (HSP90 and HSP70 and carbon metabolism (glyceraldehyde-3-phosphate dehydrogenase, α-ketoglutarate dehydrogenase, glycogen synthase and glycogen phosphorylase from the coral host were observed. In contrast in the symbiont, HSP90 expression decreased, while HSP70 levels were increased on only one day, and only the α-ketoglutarate dehydrogenase expression levels were found to increase. In addition the changes seen in expression patterns of the coral host were much larger, up to 10.5 fold, compared to the symbiont response, which in all cases was less than 2-fold. This targeted study of the expression of key metabolic and stress genes demonstrates that the response of the coral and their symbiont vary significantly, also a response in the host transcriptome was observed prior to what has previously been thought to be the temperatures at which thermal stress events occur.

  3. Recognition- and defense-related gene expression at 3 resynthesis stages in lichen symbionts.

    Science.gov (United States)

    Athukorala, Sarangi N P; Piercey-Normore, Michele D

    2015-01-01

    Recognition and defense responses are early events in plant-pathogen interactions and between lichen symbionts. The effect of elicitors on responses between lichen symbionts is not well understood. The objective of this study was to compare the difference in recognition- and defense-related gene expression as a result of culture extracts (containing secreted water-soluble elicitors) from compatible and incompatible interactions at each of 3 resynthesis stages in the symbionts of Cladonia rangiferina. This study investigated gene expression by quantitative PCR in cultures of C. rangiferina and its algal partner, Asterochloris glomerata/irregularis, after incubation with liquid extracts from cultures of compatible and incompatible interactions at 3 early resynthesis stages. Recognition-related genes were significantly upregulated only after physical contact, demonstrating symbiont recognition in later resynthesis stages than expected. One of 3 defense-related genes, chit, showed significant downregulation in early resynthesis stages and upregulation in the third resynthesis stage, demonstrating a need for the absence of chitinase early in thallus formation and a need for its presence in later stages as an algal defense reaction. This study revealed that recognition- and defense-related genes are triggered by components in culture extracts at 3 stages of resynthesis, and some defense-related genes may be induced throughout thallus growth. The parasitic nature of the interaction shows parallels between lichen symbionts and plant pathogenic systems. PMID:25485526

  4. Genome sequence of the pea aphid Acyrthosiphon pisum

    DEFF Research Database (Denmark)

    Richards, S.; Gibbs, R. A.; Gerardo, N. M.;

    2010-01-01

    Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first...... published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we...

  5. Enterobacter cloacae is an endophytic symbiont of corn.

    Science.gov (United States)

    Hinton, D M; Bacon, C W

    1995-01-01

    The bacterium Enterobacter cloacae is presently used for biocontrol of postharvest diseases of fruits and vegetables and as a preplant seed treatment for suppression of damping-off. This bacterium has apparent affinities for several grass species, but it is not considered to be an endophyte. While screening corn for fungi and bacteria with potential for biocontrol of various corn diseases, the surface-sterilized kernels of one unknown Italian corn cultivar produced fungus-free corn seedlings with roots endophytically infected by E. cloacae. This paper describes the microscopic nature of E. cloacae RRC 101 with corn, and the in vitro control of Fusarium moniliforme and other fungi with this bacterium. Light and electron microscopy determined that this isolate of E. cloacae was biologically associated with corn seedling roots, where it was distributed intercellularly within the cortex and stele. This is a first report of a strain of this bacterium as an endophytic symbiont of roots. Following a topical application of E. cloacae to kernels, and upon germination this bacterium readily infected roots of two other corn cultivars. The bacterium was observed within the endosperm of germinating corn seedling, but germination was not affected. Further, the bacterium was isolated from leaves and stems of 3- to 6-week-old seedlings indicating that the above ground portions of corn were also colonized. There was no evidence of damage to cells of the root during a three to four week observation period. This bacterium was antagonistic to several isolates of the corn pathogen Fusarium moniliforme, and to two other species of fungi, all of which produce mycotoxins on corn. PMID:7659140

  6. Formation of Zn- and Fe-sulfides near hydrothermal vents at the Eastern Lau Spreading Center: implications for sulfide bioavailability to chemoautotrophs

    Directory of Open Access Journals (Sweden)

    Yucel Mustafa

    2008-05-01

    Full Text Available Abstract Background The speciation of dissolved sulfide in the water immediately surrounding deep-ocean hydrothermal vents is critical to chemoautotrophic organisms that are the primary producers of these ecosystems. The objective of this research was to identify the role of Zn and Fe for controlling the speciation of sulfide in the hydrothermal vent fields at the Eastern Lau Spreading Center (ELSC in the southern Pacific Ocean. Compared to other well-studied hydrothermal systems in the Pacific, the ELSC is notable for unique ridge characteristics and gradients over short distances along the north-south ridge axis. Results In June 2005, diffuse-flow ( 250°C vent fluids were collected from four field sites along the ELSC ridge axis. Total and filtered Zn and Fe concentrations were quantified in the vent fluid samples using voltammetric and spectrometric analyses. The results indicated north-to-south variability in vent fluid composition. In the high temperature vent fluids, the ratio of total Fe to total Zn varied from 39 at Kilo Moana, the most northern site, to less than 7 at the other three sites. The concentrations of total Zn, Fe, and acid-volatile sulfide indicated that oversaturation and precipitation of sphalerite (ZnS(s and pyrite (FeS2(s were possible during cooling of the vent fluids as they mixed with the surrounding seawater. In contrast, most samples were undersaturated with respect to mackinawite (FeS(s. The reactivity of Zn(II in the filtered samples was tested by adding Cu(II to the samples to induce metal-exchange reactions. In a portion of the samples, the concentration of labile Zn2+ increased after the addition of Cu(II, indicating the presence of strongly-bound Zn(II species such as ZnS clusters and nanoparticles. Conclusion Results of this study suggest that Zn is important to sulfide speciation at ELSC vent habitats, particularly at the southern sites where Zn concentrations increase relative to Fe. As the hydrothermal

  7. Fickle or Faithful: The Roles of Host and Environmental Context in Determining Symbiont Composition in Two Bathymodioline Mussels.

    Directory of Open Access Journals (Sweden)

    Sven R Laming

    Full Text Available The Mediterranean Sea and adjoining East Atlantic Ocean host a diverse array of small-sized mussels that predominantly live on sunken, decomposing organic remains. At least two of these, Idas modiolaeformis and Idas simpsoni, are known to engage in gill-associated symbioses; however, the composition, diversity and variability of these symbioses with changing habitat and location is poorly defined. The current study presents bacterial symbiont assemblage data, derived from 454 pyrosequencing carried out on replicate specimens of these two host species, collected across seven sample sites found in three oceanographic regions in the Mediterranean and East Atlantic. The presence of several bacterial OTUs in both the Mediterranean Sea and eastern Atlantic suggests that similar symbiont candidates occur on both sides of the Strait of Gibraltar. The results reveal markedly different symbiotic modes in the two species. Idas modiolaeformis displays high symbiont diversity and flexibility, with strong variation in symbiont composition from the East Mediterranean to the East Atlantic. Idas simpsoni displays low symbiont diversity but high symbiont fidelity, with a single dominant OTU occurring in all specimens analysed. These differences are argued to be a function of the host species, where subtle differences in host evolution, life-history and behaviour could partially explain the observed patterns. The variability in symbiont compositions, particularly in Idas modiolaeformis, is thought to be a function of the nature, context and location of the habitat from which symbiont candidates are sourced.

  8. Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change.

    Science.gov (United States)

    Cunning, R; Silverstein, R N; Baker, A C

    2015-06-22

    Dynamic symbioses may critically mediate impacts of climate change on diverse organisms, with repercussions for ecosystem persistence in some cases. On coral reefs, increases in heat-tolerant symbionts after thermal bleaching can reduce coral susceptibility to future stress. However, the relevance of this adaptive response is equivocal owing to conflicting reports of symbiont stability and change. We help reconcile this conflict by showing that change in symbiont community composition (symbiont shuffling) in Orbicella faveolata depends on the disturbance severity and recovery environment. The proportion of heat-tolerant symbionts dramatically increased following severe experimental bleaching, especially in a warmer recovery environment, but tended to decrease if bleaching was less severe. These patterns can be explained by variation in symbiont performance in the changing microenvironments created by differentially bleached host tissues. Furthermore, higher proportions of heat-tolerant symbionts linearly increased bleaching resistance but reduced photochemical efficiency, suggesting that any change in community structure oppositely impacts performance and stress tolerance. Therefore, even minor symbiont shuffling can adaptively benefit corals, although fitness effects of resulting trade-offs are difficult to predict. This work helps elucidate causes and consequences of dynamism in symbiosis, which is critical to predicting responses of multi-partner symbioses such as O. faveolata to environmental change. PMID:26041354

  9. Plant-mediated interspecific horizontal transmission of an intracellular symbiont in insects

    KAUST Repository

    Gonella, Elena

    2015-11-13

    Intracellular reproductive manipulators, such as Candidatus Cardinium and Wolbachia are vertically transmitted to progeny but rarely show co-speciation with the host. In sap-feeding insects, plant tissues have been proposed as alternative horizontal routes of interspecific transmission, but experimental evidence is limited. Here we report results from experiments that show that Cardinium is horizontally transmitted between different phloem sap-feeding insect species through plants. Quantitative PCR and in situ hybridization experiments indicated that the leafhopper Scaphoideus titanus releases Cardinium from its salivary glands during feeding on both artificial media and grapevine leaves. Successional time-course feeding experiments with S. titanus initially fed sugar solutions or small areas of grapevine leaves followed by feeding by the phytoplasma vector Macrosteles quadripunctulatus or the grapevine feeder Empoasca vitis revealed that the symbionts were transmitted to both species. Explaining interspecific horizontal transmission through plants improves our understanding of how symbionts spread, their lifestyle and the symbiont-host intermixed evolutionary pattern.

  10. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    DEFF Research Database (Denmark)

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR...... aerophoba. Absolute quantification of archaeal amoA-genes provided evidence of highly abundant ammonia-oxidizing archaea (AOA) in both HMA and LMA sponge species. Interestingly, detected amoA-transcripts indicated the activity of AOA only in the HMA representative. The variable abundance of AOA in chimneys......Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...

  11. Fueling the Future with Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

  12. Nitrogen transfer in the interface between the symbionts in pea root nodules

    DEFF Research Database (Denmark)

    Rosendahl, L.; Mouritzen, P.; Rudbeck, A.

    2001-01-01

    Transport mechanisms for transfer of nitrogen from the bacteroid side across the symbiosome membrane of pea (Pisum sativum L.) root nodules were identified by the use of energised bacteroid side-out symbiosome membrane vesicles. Such membrane vesicles were used to study a mechanism with high...... observed. The ammonium transporter has been identified as a voltage-driven channel whereas the symbiosome membrane aspartate transporter appears to be a H+/aspartate symport. The results suggest that nitrogen transfer between the symbionts in pea root nodules involves transfer of amino acids as well as...... constitute a component of the transfer of nitrogen between the symbionts....

  13. Spatial distribution of symbiont-bearing dinoflagellates in the Indian Ocean in relation to oceanographic regimes

    DEFF Research Database (Denmark)

    Tarangkoon, Woraporn; Hansen, Gert; Hansen, Per Juel

    2010-01-01

    as ectosymbionts, while the genera Amphisolenia and Triposolenia contained both intact cyanobacterial and eukaryotic endosymbionts. The symbiont-bearing dinoflagellates were mainly found in the upper 100 m of the water column. Their distribution was restricted to water temperatures exceeding 16.5°C......, and the highest species diversity and cell concentrations were found at temperatures around 20 to 30°C. The symbiont-bearing dinoflagellates were always associated with water masses with low nutrient (N-limited) and chl a concentrations. Special attention was given to the ectosymbiont...

  14. Global diversity of marine isopods (except Asellota and crustacean symbionts.

    Directory of Open Access Journals (Sweden)

    Gary C B Poore

    Full Text Available The crustacean order Isopoda (excluding Asellota, crustacean symbionts and freshwater taxa comprise 3154 described marine species in 379 genera in 37 families according to the WoRMS catalogue. The history of taxonomic discovery over the last two centuries is reviewed. Although a well defined order with the Peracarida, their relationship to other orders is not yet resolved but systematics of the major subordinal taxa is relatively well understood. Isopods range in size from less than 1 mm to Bathynomus giganteus at 365 mm long. They inhabit all marine habitats down to 7280 m depth but with few doubtful exceptions species have restricted biogeographic and bathymetric ranges. Four feeding categories are recognised as much on the basis of anecdotal evidence as hard data: detritus feeders and browsers, carnivores, parasites, and filter feeders. Notable among these are the Cymothooidea that range from predators and scavengers to external blood-sucking micropredators and parasites. Isopods brood 10-1600 eggs depending on individual species. Strong sexual dimorphism is characteristic of several families, notably in Gnathiidae where sessile males live with a harem of females while juvenile praniza stages are ectoparasites of fish. Protandry is known in Cymothoidae and protogyny in Anthuroidea. Some Paranthuridae are neotenous. About half of all coastal, shelf and upper bathyal species have been recorded in the MEOW temperate realms, 40% in tropical regions and the remainder in polar seas. The greatest concentration of temperate species is in Australasia; more have been recorded from temperate North Pacific than the North Atlantic. Of tropical regions, the Central Indo-Pacific is home to more species any other region. Isopods are decidedly asymmetrical latitudinally with 1.35 times as many species in temperate Southern Hemisphere than the temperate North Atlantic and northern Pacific, and almost four times as many Antarctic as Arctic species. More species

  15. Global diversity of marine isopods (except Asellota and crustacean symbionts).

    Science.gov (United States)

    Poore, Gary C B; Bruce, Niel L

    2012-01-01

    The crustacean order Isopoda (excluding Asellota, crustacean symbionts and freshwater taxa) comprise 3154 described marine species in 379 genera in 37 families according to the WoRMS catalogue. The history of taxonomic discovery over the last two centuries is reviewed. Although a well defined order with the Peracarida, their relationship to other orders is not yet resolved but systematics of the major subordinal taxa is relatively well understood. Isopods range in size from less than 1 mm to Bathynomus giganteus at 365 mm long. They inhabit all marine habitats down to 7280 m depth but with few doubtful exceptions species have restricted biogeographic and bathymetric ranges. Four feeding categories are recognised as much on the basis of anecdotal evidence as hard data: detritus feeders and browsers, carnivores, parasites, and filter feeders. Notable among these are the Cymothooidea that range from predators and scavengers to external blood-sucking micropredators and parasites. Isopods brood 10-1600 eggs depending on individual species. Strong sexual dimorphism is characteristic of several families, notably in Gnathiidae where sessile males live with a harem of females while juvenile praniza stages are ectoparasites of fish. Protandry is known in Cymothoidae and protogyny in Anthuroidea. Some Paranthuridae are neotenous. About half of all coastal, shelf and upper bathyal species have been recorded in the MEOW temperate realms, 40% in tropical regions and the remainder in polar seas. The greatest concentration of temperate species is in Australasia; more have been recorded from temperate North Pacific than the North Atlantic. Of tropical regions, the Central Indo-Pacific is home to more species any other region. Isopods are decidedly asymmetrical latitudinally with 1.35 times as many species in temperate Southern Hemisphere than the temperate North Atlantic and northern Pacific, and almost four times as many Antarctic as Arctic species. More species are known from the

  16. Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events

    Science.gov (United States)

    Augustinos, Antonios A.; Drosopoulou, Elena; Gariou-Papalexiou, Aggeliki; Asimakis, Elias D.; Cáceres, Carlos; Tsiamis, George; Bourtzis, Kostas; Penelope Mavragani-Tsipidou; Zacharopoulou, Antigone

    2015-01-01

    Abstract The Bactrocera dorsalis species complex, currently comprising about 90 entities has received much attention. During the last decades, considerable effort has been devoted to delimiting the species of the complex. This information is of great importance for agriculture and world trade, since the complex harbours several pest species of major economic importance and other species that could evolve into global threats. Speciation in Diptera is usually accompanied by chromosomal rearrangements, particularly inversions that are assumed to reduce/eliminate gene flow. Other candidates currently receiving much attention regarding their possible involvement in speciation are reproductive symbionts, such as Wolbachia, Spiroplasma, Arsenophonus, Rickettsia and Cardinium. Such symbionts tend to spread quickly through natural populations and can cause a variety of phenotypes that promote pre-mating and/or post-mating isolation and, in addition, can affect the biology, physiology, ecology and evolution of their insect hosts in various ways. Considering all these aspects, we present: (a) a summary of the recently gained knowledge on the cytogenetics of five members of the Bactrocera dorsalis complex, namely Bactrocera dorsalis s.s., Bactrocera invadens, Bactrocera philippinensis, Bactrocera papayae and Bactrocera carambolae, supplemented by additional data from a Bactrocera dorsalis s.s. colony from China, as well as by a cytogenetic comparison between the dorsalis complex and the genetically close species, Bactrocera tryoni, and, (b) a reproductive symbiont screening of 18 different colonized populations of these five taxa. Our analysis did not reveal any chromosomal rearrangements that could differentiate among them. Moreover, screening for reproductive symbionts was negative for all colonies derived from different geographic origins and/or hosts. There are many different factors that can lead to speciation, and our data do not support chromosomal and/or symbiotic

  17. Bacterial symbionts, Buchnera, and starvation on wing dimorphism in English grain aphid, Sitobion avenae (F. (Homoptera: Aphididae

    Directory of Open Access Journals (Sweden)

    Fangmei eZhang

    2015-05-01

    Full Text Available Wing dimorphism in aphids can be affected by multiple cues, including both biotic (nutrition, crowding, interspecific interactions, the presence of natural enemies, maternal and transgenerational effects, and alarm pheromone and abiotic factors (temperature, humidity, and photoperiod. The majority of the phloem-feeding aphids carry Buchnera, an obligate symbiotic proteobacteria. Buchnera has a highly reduced genome size, but encode key enzymes in the tryptophan biosynthetic pathway and is crucial for nutritional balance, development and reproduction in aphids. In this study, we investigated the impact of two nutritional-based biotic factors, symbionts and starvation, on the wing dimorphism in the English grain aphid, Sitobion avenae, a devastating insect pest of cereal crops (e.g., wheat worldwide. Elimination of Buchnera using the antibiotic rifampicin significantly reduced the formation of winged morphs, body mass and fecundity in S. avenae. Furthermore, the absence of this primary endosymbiont may disrupt the nutrient acquisition in aphids and alter transgenerational phenotypic expression. Similarly, both survival rate and the formation of winged morphs were substantially reduced after neonatal (< 24h old offspring were starved for a period of time. The combined results shed light on the impact of two nutritional-based biotic factors on the phenotypic plasticity in aphids. A better understanding of the wing dimorphism in aphids will provide the theoretical basis for the prediction and integrated management of these phloem-feeding insect pests.

  18. Asymmetric interaction specificity between two sympatric termites and their fungal symbionts.

    NARCIS (Netherlands)

    Fine Licht, De H.H.; Boomsma, J.J.

    2007-01-01

    1. Fungus-growing termites live in an obligate mutualistic symbiosis with Termitomyces fungi. The functions of the fungal symbiont have been hypothesised to differ between species and to range from highly specific roles of providing plant-degrading enzymes complementary to termite gut enzymes, to no

  19. Growth tradeoffs associated with thermotolerant symbionts in the coral Pocillopora damicornis are lost in warmer oceans

    Science.gov (United States)

    Cunning, R.; Gillette, P.; Capo, T.; Galvez, K.; Baker, A. C.

    2015-03-01

    The growth and survival of reef corals are influenced by their symbiotic algal partners ( Symbiodinium spp.), which may be flexible in space and time. Tradeoffs among partnerships exist such that corals with thermotolerant symbionts (e.g., clade D) resist bleaching but grow more slowly, making the long-term ecosystem-level impacts of different host-symbiont associations uncertain. However, much of this uncertainty is due to limited data regarding these tradeoffs and particularly how they are mediated by the environment. To address this knowledge gap, we measured growth and survival of Pocillopora damicornis with thermally sensitive (clade C) or tolerant (clade D) symbionts at three temperatures over 18-55 weeks. Warming reduced coral growth overall, but altered the tradeoffs associated with symbiont type. While clade D corals grew 35-40 % slower than clade C corals at cooler temperatures (26 °C), warming of 1.5-3 °C reduced and eliminated this growth disadvantage. These results suggest that although warmer oceans will negatively impact corals, clade D may enhance survival at no cost to growth relative to clade C. Understanding these genotype-environment interactions can help improve modeling efforts and conservation strategies for reefs under global climate change.

  20. Symbiont type influences trophic plasticity of a model cnidarian-dinoflagellate symbiosis.

    Science.gov (United States)

    Leal, Miguel C; Hoadley, Kenneth; Pettay, D Tye; Grajales, Alejandro; Calado, Ricardo; Warner, Mark E

    2015-03-01

    The association between cnidarians and photosynthetic dinoflagellates within the genus Symbiodinium is a prevalent relationship in tropical and subtropical marine environments. Although the diversity of Symbiodinium provides a possible axis for niche diversification, increased functional range and resilience to physical stressors such as elevated temperature, how such diversity relates to the physiological balance between autotrophy and heterotrophy of the host animal remains unknown. Here, we experimentally show interspecific and intraspecific variability of photosynthetic carbon fixation and subsequent translocation by Symbiodinium to the model cnidarian host Aiptasia pallida. By using a clonal anemone line harboring different species of Symbiodinium, we determined that symbiont identity influences trophic plasticity through its density, capacity to fix carbon, quantity of translocated carbon and ultimately the host's capacity to ingest and digest prey. Symbiont carbon translocation and host prey ingestion were positively correlated across symbiont combinations that consisted of different isoclonal lines of Symbiodinium minutum, while a combination with type D4-5 Symbiodinium displayed lower carbon translocation, and prey capture and digestion more similar to Aiptasia lacking symbionts. The absence of a shift toward greater heterotrophy when carbon translocation is low suggests that the metabolic demand of feeding and digestion may overwhelm nutritional stores when photosynthesis is reduced, and amends the possible role of animal feeding in resistance to or recovery from the effects of climate change in more obligate symbioses such as reef-building corals. PMID:25617454

  1. igh Symbiont Relatedness Stabilizes Mutualistic Cooperation in Fungus-Growing Termites

    NARCIS (Netherlands)

    Aanen, D.K.; Fine Licht, De H.H.; Debets, A.J.M.; Kerstes, N.A.G.; Hoekstra, R.F.; Boomsma, J.J.

    2009-01-01

    It is unclear how mutualistic relationships can be stable when partners disperse freely and have the possibility of forming associations with many alternative genotypes. Theory predicts that high symbiont relatedness should resolve this problem, but the mechanisms to enforce this have rarely been st

  2. Marine Maladies? Worms, Germs, and Other Symbionts from the Northern Gulf of Mexico.

    Science.gov (United States)

    Overstreet, Robin M.

    Parasites and related symbionts of marine and estuarine hosts of the northern Gulf of Mexico are described in this guidebook. It is meant primarily to serve as a teaching aid for the novice student, but it also contains more technical aspects for the experienced parasitologist. Forms and examples of symbiosis are explained in an introductory…

  3. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians

    Science.gov (United States)

    Wolfowicz, Iliona; Baumgarten, Sebastian; Voss, Philipp A.; Hambleton, Elizabeth A.; Voolstra, Christian R.; Hatta, Masayuki; Guse, Annika

    2016-01-01

    Symbiosis, defined as the persistent association between two distinct species, is an evolutionary and ecologically critical phenomenon facilitating survival of both partners in diverse habitats. The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus Symbiodinium, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two Acropora coral species and the model anemone Aiptasia are similar under controlled conditions. We find that Aiptasia larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of Aiptasia larvae as a powerful model for cnidarian endosymbiosis establishment. PMID:27582179

  4. Gastrointestinal symbionts of chimpanzees in Cantanhez National Park, Guinea-Bissau with respect to habitat fragmentation

    Czech Academy of Sciences Publication Activity Database

    Sá, R. M.; Petrášová, J.; Pomajbíková, K.; Profousová, I.; Petrželková, Klára Judita; Sousa, C.; Cable, J.; Bruford, M. W.; Modrý, David

    2013-01-01

    Roč. 75, č. 10 (2013), s. 1032-1041. ISSN 0275-2565 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : Cantanhez National Park * fragmentation * Pan troglodytes verus * parasites * symbionts * Trichuris sp Subject RIV: EG - Zoology Impact factor: 2.136, year: 2013

  5. Environmental Transmission of the Gut Symbiont Burkholderia to Phloem-Feeding Blissus insularis.

    Science.gov (United States)

    Xu, Yao; Buss, Eileen A; Boucias, Drion G

    2016-01-01

    The plant-phloem-feeding Blissus insularis possesses specialized midgut crypts, which harbor a dense population of the exocellular bacterial symbiont Burkholderia. Most individual B. insularis harbor a single Burkholderia ribotype in their midgut crypts; however, a diverse Burkholderia community exists within a host population. To understand the mechanism underlying the consistent occurrence of various Burkholderia in B. insularis and their specific association, we investigated potential gut symbiont transmission routes. PCR amplification detected a low titer of Burkholderia in adult reproductive tracts; however, fluorescence in situ hybridization assays failed to produce detectable signals in these tracts. Furthermore, no Burkholderia-specific PCR signals were detected in eggs and neonates, suggesting that it is unlikely that B. insularis prenatally transmits gut symbionts via ovarioles. In rearing experiments, most nymphs reared on St. Augustinegrass treated with cultured Burkholderia harbored the cultured Burkholderia strains. Burkholderia was detected in the untreated host grass of B. insularis, and most nymphs reared on untreated grass harbored a Burkholderia ribotype that was closely related to a plant-associated Burkholderia strain. These findings revealed that B. insularis neonates acquired Burkholderia primarily from the environment (i.e., plants and soils), even though the possibility of acquisition via egg surface cannot be excluded. In addition, our study explains how the diverse Burkholderia symbiont community in B. insularis populations can be maintained. PMID:27548682

  6. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians.

    Science.gov (United States)

    Wolfowicz, Iliona; Baumgarten, Sebastian; Voss, Philipp A; Hambleton, Elizabeth A; Voolstra, Christian R; Hatta, Masayuki; Guse, Annika

    2016-01-01

    Symbiosis, defined as the persistent association between two distinct species, is an evolutionary and ecologically critical phenomenon facilitating survival of both partners in diverse habitats. The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus Symbiodinium, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two Acropora coral species and the model anemone Aiptasia are similar under controlled conditions. We find that Aiptasia larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of Aiptasia larvae as a powerful model for cnidarian endosymbiosis establishment. PMID:27582179

  7. The roles and interactions of symbiont, host and environment in defining coral fitness

    NARCIS (Netherlands)

    Mieog, J.C.; Olsen, J.L.; Berkelmans, R; Bleuler-Martinez, S.A.; Willis, B.; van Oppen, M.J H

    2009-01-01

    Background: Reef-building corals live in symbiosis with a diverse range of dinoflagellate algae ( genus Symbiodinium) that differentially influence the fitness of the coral holobiont. The comparative role of symbiont type in holobiont fitness in relation to host genotype or the environment, however,

  8. Conditional fitness benefits of the Rickettsia bacterial symbiont in an insect pest.

    Science.gov (United States)

    Cass, Bodil N; Himler, Anna G; Bondy, Elizabeth C; Bergen, Jacquelyn E; Fung, Sierra K; Kelly, Suzanne E; Hunter, Martha S

    2016-01-01

    Inherited bacterial symbionts are common in arthropods and can have strong effects on the biology of their hosts. These effects are often mediated by host ecology. The Rickettsia symbiont can provide strong fitness benefits to its insect host, Bemisia tabaci, under laboratory and field conditions. However, the frequency of the symbiont is heterogeneous among field collection sites across the USA, suggesting that the benefits of the symbiont are contingent on additional factors. In two whitefly genetic lines collected from the same location, we tested the effect of Rickettsia on whitefly survival after heat shock, on whitefly competitiveness at different temperatures, and on whitefly competitiveness at different starting frequencies of Rickettsia. Rickettsia did not provide protection against heat shock nor affect the competitiveness of whiteflies at different temperatures or starting frequencies. However, there was a strong interaction between Rickettsia infection and whitefly genetic line. Performance measures indicated that Rickettsia was associated with significant female bias in both whitefly genetic lines, but in the second whitefly genetic line it conferred no significant fitness benefits nor conferred any competitive advantage to its host over uninfected whiteflies in population cages. These results help to explain other reports of variation in the phenotype of the symbiosis. Furthermore, they demonstrate the complex nature of these close symbiotic associations and the need to consider these interactions in the context of host population structure. PMID:26376661

  9. One Bacterial Cell, One Complete Genome

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

    2010-04-26

    While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  10. One bacterial cell, one complete genome.

    Directory of Open Access Journals (Sweden)

    Tanja Woyke

    Full Text Available While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA. Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs, indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  11. Oxygen Metabolic Responses of Three Species of Large Benthic Foraminifers with Algal Symbionts to Temperature Stress

    Science.gov (United States)

    Fujita, Kazuhiko; Okai, Takaaki; Hosono, Takashi

    2014-01-01

    Water temperature affects the physiology of large benthic foraminifers (LBFs) with algal symbionts dwelling in coral reef environments. However, the detailed physiological responses of LBF holobionts to temperature ranges occurring in their habitats are not known. We report net oxygen (O2) production and respiration rates of three LBF holobionts (Baculogypsina sphaerulata and Calcarina gaudichaudii hosting diatom symbionts, and Amphisorus kudakajimensis hosting dinoflagellate symbionts) measured in the laboratory at water temperatures ranging from 5°C to 45°C in 2.5°C or 5°C intervals and with light saturation levels of ∼500 µmol m−2 s−1. In addition, the recovery of net O2 production and respiration rates after exposure to temperature stress was assessed. The net O2 production and respiration rates of the three LBF holobionts peaked at ∼30°C, indicating their optimal temperature for a short exposure period. At extreme high temperatures (≥40°C), the net O2 production rates of all three LBF holobionts declined to less than zero and the respiration rates slightly decreased, indicating that photosynthesis of algal symbionts was inactivated. At extreme low temperatures (≤10°C for two calcarinid species and ≤5°C for A. kudakajimensis), the net O2 production and respiration rates were near zero, indicating a weakening of holobiont activity. After exposure to extreme high or low temperature, the net O2 production rates did not recover until the following day, whereas the respiration rates recovered rapidly, suggesting that a longer time (days) is required for recovery from damage to the photosystem by temperature stress compared to the respiration system. These results indicate that the oxygen metabolism of LBF holobionts can generally cope well with conditions that fluctuate diurnally and seasonally in their habitats. However, temporal heat and cold stresses with high light levels may induce severe damage to algal symbionts and also damage to host

  12. Long-term ungulate exclusion reduces fungal symbiont prevalence in native grasslands.

    Science.gov (United States)

    Rudgers, Jennifer A; Fletcher, Rebecca A; Olivas, Eric; Young, Carolyn A; Charlton, Nikki D; Pearson, Dean E; Maron, John L

    2016-08-01

    When symbionts are inherited by offspring, they can have substantial ecological and evolutionary consequences because they occur in all host life stages. Although natural frequencies of inherited symbionts are commonly fungal endophytes can improve resistance to herbivory, growth under drought, and competitive ability. We evaluated whether native ungulate herbivory increased the prevalence of a fungal endophyte in the common, native bunchgrass, Festuca campestris (rough fescue, Poaceae). We used large-scale (1 ha) and long-term (7-10 year) fencing treatments to exclude native ungulates and recorded shifts in endophyte prevalence at the scale of plant populations and for individual plants. We characterized the fungal endophyte in F. campestris, Epichloë species FcaTG-1 (F. campestris taxonomic group 1) for the first time. Under ungulate exclusion, endophyte prevalence was 19 % lower in plant populations, 25 % lower within plant individuals, and 39 % lower in offspring (seeds) than in ungulate-exposed controls. Population-level endophyte frequencies were also negatively correlated with soil moisture across geographic sites. Observations of high within-plant variability in symbiont prevalence are novel for the Epichloë species, and contribute to a small, but growing, literature that documents phenotypic plasticity in plant-endophyte symbiota. Altogether, we show that native ungulates can be an important driver of symbiont prevalence in native plant populations, even in the absence of evidence for direct mechanisms of mammal deterrence. Understanding the ecological controls on symbiont prevalence could help to predict future shifts in grasslands that are dominated by Epichloë host plants. PMID:27113054

  13. The roles and interactions of symbiont, host and environment in defining coral fitness.

    Directory of Open Access Journals (Sweden)

    Jos C Mieog

    Full Text Available BACKGROUND: Reef-building corals live in symbiosis with a diverse range of dinoflagellate algae (genus Symbiodinium that differentially influence the fitness of the coral holobiont. The comparative role of symbiont type in holobiont fitness in relation to host genotype or the environment, however, is largely unknown. We addressed this knowledge gap by manipulating host-symbiont combinations and comparing growth, survival and thermal tolerance among the resultant holobionts in different environments. METHODOLOGY/PRINCIPAL FINDINGS: Offspring of the coral, Acropora millepora, from two thermally contrasting locations, were experimentally infected with one of six Symbiodinium types, which spanned three phylogenetic clades (A, C and D, and then outplanted to the two parental field locations (central and southern inshore Great Barrier Reef, Australia. Growth and survival of juvenile corals were monitored for 31-35 weeks, after which their thermo-tolerance was experimentally assessed. Our results showed that: (1 Symbiodinium type was the most important predictor of holobiont fitness, as measured by growth, survival, and thermo-tolerance; (2 growth and survival, but not heat-tolerance, were also affected by local environmental conditions; and (3 host population had little to no effect on holobiont fitness. Furthermore, coral-algal associations were established with symbiont types belonging to clades A, C and D, but three out of four symbiont types belonging to clade C failed to establish a symbiosis. Associations with clade A had the lowest fitness and were unstable in the field. Lastly, Symbiodinium types C1 and D were found to be relatively thermo-tolerant, with type D conferring the highest tolerance in A. millepora. CONCLUSIONS/SIGNIFICANCE: These results highlight the complex interactions that occur between the coral host, the algal symbiont, and the environment to shape the fitness of the coral holobiont. An improved understanding of the factors

  14. Contrasting physiological plasticity in response to environmental stress within different cnidarians and their respective symbionts

    Science.gov (United States)

    Hoadley, Kenneth D.; Pettay, Daniel. T.; Dodge, Danielle; Warner, Mark E.

    2016-06-01

    Given concerns surrounding coral bleaching and ocean acidification, there is renewed interest in characterizing the physiological differences across the multiple host-algal symbiont combinations commonly found on coral reefs. Elevated temperature and CO2 were used to compare physiological responses within the scleractinian corals Montipora hirsuta ( Symbiodinium C15) and Pocillopora damicornis ( Symbiodinium D1), as well as the corallimorph (a non-calcifying anthozoan closely related to scleractinians) Discosoma nummiforme ( Symbiodinium C3). Several physiological proxies were affected more by temperature than CO2, including photochemistry, algal number and cellular chlorophyll a. Marked differences in symbiont number, chlorophyll and volume contributed to distinctive patterns of chlorophyll absorption among these animals. In contrast, carbon fixation either did not change or increased under elevated temperature. Also, the rate of photosynthetically fixed carbon translocated to each host did not change, and the percent of carbon translocated to the host increased in the corallimorph. Comparing all data revealed a significant negative correlation between photosynthetic rate and symbiont density that corroborates previous hypotheses about carbon limitation in these symbioses. The ratio of symbiont-normalized photosynthetic rate relative to the rate of symbiont-normalized carbon translocation (P:T) was compared in these organisms as well as the anemone, Exaiptasia pallida hosting Symbiodinium minutum, and revealed a P:T close to unity ( D. nummiforme) to a range of 2.0-4.5, with the lowest carbon translocation in the sea anemone. Major differences in the thermal responses across these organisms provide further evidence of a range of acclimation potential and physiological plasticity that highlights the need for continued study of these symbioses across a larger group of host taxa.

  15. Does coral disease affect symbiodinium? Investigating the impacts of growth anomaly on symbiont photophysiology.

    Directory of Open Access Journals (Sweden)

    John Henrik Robert Burns

    Full Text Available Growth anomaly (GA is a commonly observed coral disease that impairs biological functions of the affected tissue. GA is prevalent at Wai 'ōpae tide pools, southeast Hawai 'i Island. Here two distinct forms of this disease, Type A and Type B, affect the coral, Montiporacapitata. While the effects of GA on biology and ecology of the coral host are beginning to be understood, the impact of this disease on the photophysiology of the dinoflagellate symbiont, Symbiodinium spp., has not been investigated. The GA clearly alters coral tissue structure and skeletal morphology and density. These tissue and skeletal changes are likely to modify not only the light micro-environment of the coral tissue, which has a direct impact on the photosynthetic potential of Symbiodinium spp., but also the physiological interactions within the symbiosis. This study utilized Pulse amplitude modulation fluorometry (PAM to characterize the photophysiology of healthy and GA-affected M. capitata tissue. Overall, endosymbionts within GA-affected tissue exhibit reduced photochemical efficiency. Values of both Fv/Fm and ΔF/ Fm' were significantly lower (p<0.01 in GA tissue compared to healthy and unaffected tissues. Tracking the photophysiology of symbionts over a diurnal time period enabled a comparison of symbiont responses to photosynthetically available radiation (PAR among tissue conditions. Symbionts within GA tissue exhibited the lowest values of ΔF/Fm' as well as the highest pressure over photosystem II (p<0.01. This study provides evidence that the symbionts within GA-affected tissue are photochemically compromised compared to those residing in healthy tissue.

  16. What stories can the Frankia genomes start to tell us?

    Science.gov (United States)

    Tisa, Louis S; Beauchemin, Nicholas; Gtari, Maher; Sen, Arnab; Wall, Luis G

    2013-11-01

    Among the Actinobacteria, the genus Frankia is well known for its facultative lifestyle as a plant symbiont of dicotyledonous plants and as a free-living soil dweller. Frankia sp. strains are generally classified into one of four major phylogenetic groups that have distinctive plant host ranges. Our understanding of these bacteria has been greatly facilitated by the availability of the first three complete genome sequences, which suggested a correlation between genome size and plant host range. Since that first report, eight more Frankia genomes have been sequenced. Representatives from all four lineages have been sequenced to provide vital baseline information for genomic approaches toward understanding these novel bacteria. An overview of the Frankia genomes will be presented to stimulate discussion on the potential of these organisms and a greater understanding of their physiology and evolution. PMID:24287651

  17. What stories can the Frankia genomes start to tell us?

    Indian Academy of Sciences (India)

    Louis Tisa; Nicholas Beauchemin; Maher Gtari; Arnab Sen; Luis G Wall

    2013-11-01

    Among the Actinobacteria, the genus Frankia is well known for its facultative lifestyle as a plant symbiont of dicotyledonous plants and as a free-living soil dweller. Frankia sp. strains are generally classified into one of four major phylogenetic groups that have distinctive plant host ranges. Our understanding of these bacteria has been greatly facilitated by the availability of the first three complete genome sequences, which suggested a correlation between genome size and plant host range. Since that first report, eight more Frankia genomes have been sequenced. Representatives from all four lineages have been sequenced to provide vital baseline information for genomic approaches toward understanding these novel bacteria. An overview of the Frankia genomes will be presented to stimulate discussion on the potential of these organisms and a greater understanding of their physiology and evolution.

  18. Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

    DEFF Research Database (Denmark)

    Liberti, Joanito; Sapountzis, Panagiotis; Hansen, Lars H.; Sørensen, Søren Johannes; Adams, Rachelle Martha Marie; Boomsma, Jacobus Jan

    2015-01-01

    symbionts, primarily consisting of Entomoplasmatales, Bartonellaceae, Acinetobacter, Wolbachia and Pseudonocardia and that Entomoplasmatales and Bartonellaceae can co-infect specifically associated combinations of hosts and social parasites with identical 16S rRNA genotypes. We reconstructed in more detail...

  19. From Prediction to Function Using Evolutionary Genomics: Human-Specific Ecotypes of Lactobacillus reuteri Have Diverse Probiotic Functions

    OpenAIRE

    Spinler, Jennifer K.; Sontakke, Amrita; Emily B. Hollister; Venable, Susan F.; Oh, Phaik Lyn; Balderas, Miriam A.; Saulnier, Delphine M.A.; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; Highlander, Sarah K.

    2014-01-01

    The vertebrate gut symbiont Lactobacillus reuteri has diversified into separate clades reflecting host origin. Strains show evidence of host adaptation, but how host–microbe coevolution influences microbial-derived effects on hosts is poorly understood. Emphasizing human-derived strains of L. reuteri, we combined comparative genomic analyses with functional assays to examine variations in host interaction among genetically distinct ecotypes. Within clade II or VI, the genomes of human-derived...

  20. Effects of ocean acidification on calcification of symbiont-bearing reef foraminifers

    Directory of Open Access Journals (Sweden)

    K. Fujita

    2011-08-01

    Full Text Available Ocean acidification (decreases in carbonate ion concentration and pH in response to rising atmospheric pCO2 is generally expected to reduce rates of calcification by reef calcifying organisms, with potentially severe implications for coral reef ecosystems. Large, algal symbiont-bearing benthic foraminifers, which are important primary and carbonate producers in coral reefs, produce high-Mg calcite shells, whose solubility can exceed that of aragonite produced by corals, making them the "first responder" in coral reefs to the decreasing carbonate saturation state of seawater. Here we report results of culture experiments performed to assess the effects of ongoing ocean acidification on the calcification of symbiont-bearing reef foraminifers using a high-precision pCO2 control system. Living clone individuals of three foraminiferal species (Baculogypsina sphaerulata, Calcarina gaudichaudii, and Amphisorus hemprichii were subjected to seawater at five pCO2 levels from 260 to 970 μatm. Cultured individuals were maintained for about 12 weeks in an indoor flow-through system under constant water temperature, light intensity, and photoperiod. After the experiments, the shell diameter and weight of each cultured specimen were measured. Net calcification of B. sphaerulata and C. gaudichaudii, which secrete a hyaline shell and host diatom symbionts, increased under intermediate levels of pCO2 (580 and/or 770 μatm and decreased at a higher pCO2 level (970 μatm. Net calcification of A. hemprichii, which secretes a porcelaneous shell and hosts dinoflagellate symbionts, tended to decrease at elevated pCO2. Observed different responses between hyaline and porcelaneous species are possibly caused by the relative importance of elevated pCO2, which induces CO2 fertilization effects by

  1. Apoptosis and autophagy as mechanisms of dinoflagellate symbiont release during cnidarian bleaching: every which way you lose

    OpenAIRE

    Dunn, Simon R.; Schnitzler, Christine E; Weis, Virginia M.

    2007-01-01

    Cnidarian bleaching results from the breakdown in the symbiosis between the host cnidarian and its dinoflagellate symbiont. Coral bleaching in recent years has increasingly caused degradation and mortality of coral reefs on a global scale. Although much is understood about the environmental causes of bleaching, the underlying cellular mechanisms of symbiont release that drive the process are just beginning to be described. In this study, we investigated the roles of two cellular pathways, hos...

  2. Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens.

    Directory of Open Access Journals (Sweden)

    Karin Aistleitner

    Full Text Available The Chlamydiae constitute an evolutionary well separated group of intracellular bacteria comprising important pathogens of humans as well as symbionts of protozoa. The amoeba symbiont Protochlamydia amoebophila lacks a homologue of the most abundant outer membrane protein of the Chlamydiaceae, the major outer membrane protein MOMP, highlighting a major difference between environmental chlamydiae and their pathogenic counterparts. We recently identified a novel family of putative porins encoded in the genome of P. amoebophila by in silico analysis. Two of these Protochlamydiaouter membrane proteins, PomS (pc1489 and PomT (pc1077, are highly abundant in outer membrane preparations of this organism. Here we show that all four members of this putative porin family are toxic when expressed in the heterologous host Escherichia coli. Immunofluorescence analysis using antibodies against heterologously expressed PomT and PomS purified directly from elementary bodies, respectively, demonstrated the location of both proteins in the outer membrane of P. amoebophila. The location of the most abundant protein PomS was further confirmed by immuno-transmission electron microscopy. We could show that pomS is transcribed, and the corresponding protein is present in the outer membrane throughout the complete developmental cycle, suggesting an essential role for P. amoebophila. Lipid bilayer measurements demonstrated that PomS functions as a porin with anion-selectivity and a pore size similar to the Chlamydiaceae MOMP. Taken together, our results suggest that PomS, possibly in concert with PomT and other members of this porin family, is the functional equivalent of MOMP in P. amoebophila. This work contributes to our understanding of the adaptations of symbiotic and pathogenic chlamydiae to their different eukaryotic hosts.

  3. Anthropogenic perturbation of coral reef environments near Natal, Brazil: Clues from symbiont-bearing benthic foraminifera

    Science.gov (United States)

    Eichler, P.; Vital, H.; Sen Gupta, B. K.

    2014-12-01

    Besides global stressors such as temperature rise and acidification, local anthropogenic disturbances, especially those connected with tourism, affect many Atlantic patch reefs off the Brazilian shore. Using reef-inhabiting foraminifera with algal symbionts as environmental indicators, we confirmed this problem in coastal reefs near Natal, Rio Grande do Norte. The foraminiferal community is particularly depauperate in the small reefs of Pirangi, about 25 km south of Natal (~6o S, water depth tourism. However, living Amphistegina is still rare, and the only living Amphisorus is found in seagrass habitats. In contrast, many symbiont-bearing taxa, including peneroplids (virtually absent in Pirangi and Maracajaú) exist in sizeable populations northwest of Maracajaú, in the small patch reefs of the drowned Açu river valley (~4o 50' S).

  4. Symbiont recognition of mutualistic bacteria by Acromyrmex leaf-cutting ants

    DEFF Research Database (Denmark)

    Zhang, Mingzi; Poulsen, Michael; Currie, Cameron R

    2007-01-01

    actinomycete bacterial mutualist (genus Pseudonocardia). Despite the potential of being infected by phylogenetically diverse strains of parasites, each ant colony maintains only a single Pseudonocardia symbiont strain, which is primarily vertically transmitted between colonies by the founding queens. In this......Symbiont choice has been proposed to play an important role in shaping many symbiotic relationships, including the fungus-growing ant-microbe mutualism. Over millions of years, fungus-growing ants have defended their fungus gardens from specialized parasites with antibiotics produced by an...... study, we show that Acromyrmex leaf-cutter ants are able to differentiate between their native actinomycete strain and a variety of foreign strains isolated from sympatric and allopatric Acromyrmex species, in addition to strains originating from other fungus-growing ant genera. The recognition...

  5. Alder-Frankia symbionts enhance the remediation and revegetation of oil sands tailings

    Energy Technology Data Exchange (ETDEWEB)

    Greer, C.W.; Lefrancois, E.; Quoreshi, A.; Khasa, D.; Fung, M.; Whyte, L.G.; Roy, S. [National Research Council of Canada, Edmonton, AB (Canada)

    2007-07-01

    This presentation discussed the bioremediation and revegetation of oil sand tailings at Mildred Lake in Fort McMurray, Alberta. A study was conducted to develop efficient greenhouse production procedures for alder-Frankia symbionts and to develop a protocol for studying rhizosphere microflora inside and outside of the root system. Alders and symbionts were screened in greenhouse trails for use on tailings sands and composite tailings. The impact of rhizosphere microflora on the degradation of hydrocarbon contaminants was investigated. Field trials on tailings sands were initiated in 2005 using Frankia-inoculated and Hebeloma-inoculated green alders. The former showed comparable results to greenhouse trails after more than 2.5 years in the field. After only 1 year of field trials, soil quality characteristics improved for pH, electric conductivity, bulk density and nutrients and salt content, thus indicating the promise of this technology. Analysis of field plants after 2.5 years is currently in progress. tabs., figs.

  6. Riding the Trojan horse: combating pest insects with their own symbionts

    OpenAIRE

    Jurkevitch, Edouard

    2011-01-01

    Summary Insects form an extremely large group of animals and bear a consequently large variety of associated microbes. This microbiota includes very specific and obligate symbionts that provide essential functions to the host, and facultative partners that are not necessarily required for survival. The Tephritidae is a large family that includes many fruit pests such as the Mediterranean fruit fly (the medfly, Ceratitis capitata) and the Olive fly (Bactrocera oleae). Community and functional ...

  7. Cyanobacterial Diversity and a New Acaryochloris-Like Symbiont from Bahamian Sea-Squirts

    OpenAIRE

    Susanna López-Legentil; Bongkeun Song; Manel Bosch; Joseph R Pawlik; Xavier Turon

    2011-01-01

    Symbiotic interactions between ascidians (sea-squirts) and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS) and by examining symbiont morphology with transmission electron (TEM) and confocal microscopy (CM). As described previously for other s...

  8. Shared Ancestry of Symbionts? Sagrinae and Donaciinae (Coleoptera, Chrysomelidae) Harbor Similar Bacteria

    OpenAIRE

    Dimitra Synefiaridou; Gregor Kölsch

    2012-01-01

    When symbioses between insects and bacteria are discussed, the origin of a given association is regularly of interest. We examined the evolution of the symbiosis between reed beetles (Coleoptera, Chrysomelidae, Donaciinae) and intracellular symbionts belonging to the Enterobacteriaceae. We analyzed the partial sequence of the 16S rRNA to assess the phylogenetic relationships with bacteria we found in other beetle groups (Cerambycidae, Anobiidae, other Chrysomelidae). We discuss the ecology of...

  9. Co-occurrence of three fungal root symbionts in Gaultheria poeppiggi DC in central Argentina.

    Science.gov (United States)

    Urcelay, Carlos

    2002-04-01

    The roots of Gaultheria poeppiggi (Ericaceae) were examined for fungal symbiont colonization. Typical structures of ericoid mycorrhizas (hyphae and intracellular coil hyphae complexes), dark septate fungal endophytes (hyphae and sclerotia), and arbuscular mycorrhizas (hyphae, coils, vesicles and arbuscules) were found in the roots of all the individuals examined. The evolutionarily derived position of Gaultheria within the Ericales may suggest that G. poeppiggi recently acquired the ability to form arbuscular mycorrhizas rather than having retained it from ancestral lines. PMID:12035732

  10. Endobiotic Rugosan Symbionts in Stromatoporoids from the Sheinwoodian (Silurian) of Baltica

    OpenAIRE

    Vinn, Olev; Mõtus, Mari-Ann

    2014-01-01

    A paleoecological study of stromatoporoid endobionts was carried out to discern the relationships between symbiotic rugosans and their stromatoporoid hosts. The earliest endobiotic rugosan symbiont Palaeophyllum sp. in Baltica has only been found in the stromatoporoid Ecclimadictyon astrolaxum from Saaremaa, Estonia. The rugosans are vertically oriented inside the stromatoporoid skeleton. Numerous rugosans have their corallites open at the upper, external surface of stromatoporoids, but many ...

  11. Advances in Marine Microbial Symbionts in the China Sea and Related Pharmaceutical Metabolites

    OpenAIRE

    Zhiyong Li

    2009-01-01

    Marine animals and plants such as sponges, sea squirts, corals, worms and algae host diverse and abundant symbiotic microorganisms. Marine microbial symbionts are possible the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts. Investigation of the pharmaceutical metabolites may reveal the biosynthesis mechanisms of related natural products and solve the current problem of supply limitation in marine drug developme...

  12. Antimicrobial susceptibility of ileal symbiont intracellularis isolated from pigs with proliferative enteropathy.

    OpenAIRE

    McOrist, S.; Mackie, R A; Lawson, G H

    1995-01-01

    Proliferative enteropathy is caused by the microaerophilic obligate intracellular bacterium ileal symbiont (IS) intracellularis. Treatment of this disease is problematic because of the lack of in vivo or in vitro data on the activities of antimicrobial agents. A new procedure for determining the susceptibility of IS intracellularis was developed by using a tissue culture system which promotes the in vitro multiplication of this organism. Nineteen antimicrobial agents were evaluated in triplic...

  13. Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific.

    OpenAIRE

    R Iglesias-Prieto; Beltrán, V. H.; LaJeunesse, T. C.; Reyes-Bonilla, H.; Thomé, P. E.

    2004-01-01

    Symbiotic reef corals occupy the entire photic zone; however, most species have distinct zonation patterns within the light intensity gradient. It is hypothesized that the presence of specific symbionts adapted to different light regimes may determine the vertical distribution of particular hosts. We have tested this hypothesis by genetic and in situ physiological analyses of the algal populations occupying two dominant eastern Pacific corals, over their vertical distribution in the Gulf of C...

  14. Host immunostimulation and substrate utilization of the gut symbiont Akkermansia muciniphila

    OpenAIRE

    Ottman, N.A.

    2015-01-01

    Host immunostimulation and substrate utilization of the gut symbiont Akkermansia muciniphila Noora A. Ottman The human gastrointestinal tract is colonized by a complex community of micro-organisms, the gut microbiota. The majority of these are bacteria, which perform various functions involved in host energy metabolism and immune system stimulation. The field of gut microbiology is continuously expanding as novel species are isolated and high-throughput techniques are developed. The research ...

  15. Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type

    OpenAIRE

    Sampayo, E.M.; Ridgway, T.; Bongaerts, P.; Hoegh-Guldberg, O

    2008-01-01

    Coral bleaching has been identified as one of the major contributors to coral reef decline, and the occurrence of different symbionts determined by broad genetic groupings (clades A–H) is commonly used to explain thermal responses of reef-building corals. By using Stylophora pistillata as a model, we monitored individual tagged colonies in situ over a two-year period and show that fine level genetic variability within clade C is correlated to differences in bleaching susceptibility. Based on ...

  16. Symbiont-Mediated Modification of Mosquitocide Toxicity in the Dengue Vector, Aedes aegypti

    OpenAIRE

    Scates, Sara Stuart

    2015-01-01

    The incidence of mosquito-borne human diseases is increasing worldwide, with effective chemical control limited due to widespread insecticide resistance in the insect. Recent evidence also suggests that bacterial symbionts of mosquitoes, known to be essential in nutritional homeostasis and pathogen defense, may play a significant role in facilitating mosquitocide resistance. Here, I examined the metabolic detoxification and toxicity of two mosquitocides, propoxur and naled, and the capacity o...

  17. Symbiont-derived beta-1,3-glucanases in a social insect: mutualism beyond nutrition

    OpenAIRE

    Rosengaus, Rebeca B.; Schultheis, Kelley F.; Alla eYalonetskaya; Bulmer, Mark S.; William S DuComb; Benson, Ryan W.; John Paul eThottam; Veronica eGodoy-Carter

    2014-01-01

    Termites have had a long co-evolutionary history with prokaryotic and eukaryotic gut microbes. Historically, the role of these anaerobic obligate symbionts has been attributed to the nutritional welfare of the host. We provide evidence that protozoa (and/or their associated bacteria) colonizing the hindgut of the dampwood termite Zootermopsis angusticollis, synthesize multiple functional beta-1,3-glucanases, enzymes known for breaking down beta-1,3-glucans, the main component of fungal cell w...

  18. Promiscuous and specific bacterial symbiont acquisition in the amoeboid genus Nuclearia (Opisthokonta).

    Science.gov (United States)

    Dirren, Sebastian; Posch, Thomas

    2016-08-01

    We isolated 17 strains of the amoeboid genus Nuclearia (Opisthokonta) from five Swiss lakes. Eight of these nucleariid isolates were associated with bacterial endosymbionts and/or ectosymbionts. Amoebae were characterized morphologically and by their 18S rRNA genes. Phylogeny based on molecular data resulted in four established monophyletic branches and two new clusters. A heterogeneous picture emerged by highlighting nucleariids with associated bacteria. Apart from one cluster which consisted of only isolates with and three groups of amoebae without symbionts, we also found mixed clusters. The picture got even more 'blurred' by regarding the phylogeny of symbiotic bacteria. Although seven different bacterial strains could be identified, it seems that we still are only scratching the surface of symbionts' diversity. Furthermore, types of symbioses might be different depending on host species. Strains of Nuclearia thermophila harboured the same endosymbiont even when isolated from different lakes. This pointed to a specific and obligate interaction. However, two isolates of N. delicatula were associated with different endosymbiotic bacteria. Here the symbiont acquisition seemed to be rather promiscuous. This behaviour regarding symbiotic associations is especially remarkable considering the phylogenetic position of these basal opisthokonts. PMID:27199347

  19. Depth specialization in mesophotic corals (Leptoseris spp.) and associated algal symbionts in Hawai'i

    Science.gov (United States)

    Pochon, X.; Forsman, Z. H.; Spalding, H. L.; Padilla-Gamiño, J. L.; Smith, C. M.; Gates, R. D.

    2015-01-01

    Corals at the lower limits of mesophotic habitats are likely to have unique photosynthetic adaptations that allow them to persist and dominate in these extreme low light ecosystems. We examined the host–symbiont relationships from the dominant coral genus Leptoseris in mesophotic environments from Hawai'i collected by submersibles across a depth gradient of 65–125 m. Coral and Symbiodinium genotypes were compared with three distinct molecular markers including coral (COX1–1-rRNA intron) and Symbiodinium (COI) mitochondrial markers and nuclear ITS2. The phylogenetic reconstruction clearly resolved five Leptoseris species, including one species (Leptoseris hawaiiensis) exclusively found in deeper habitats (115–125 m). The Symbiodinium mitochondrial marker resolved three unambiguous haplotypes in clade C, which were found at significantly different frequencies between host species and depths, with one haplotype exclusively found at the lower mesophotic extremes (95–125 m). These patterns of host–symbiont depth specialization indicate that there are limits to connectivity between upper and lower mesophotic zones, suggesting that niche specialization plays a critical role in host–symbiont evolution at mesophotic extremes. PMID:26064599

  20. Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses.

    Science.gov (United States)

    Baker, David M; Freeman, Christopher J; Knowlton, Nancy; Thacker, Robert W; Kim, Kiho; Fogel, Marilyn L

    2015-12-01

    Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean. While current research has focused on the phylo- and population genetics of gorgonian symbiont types and their photo-physiology, relatively less work has focused on biogeochemical benefits conferred to the host and how these benefits vary across host species. Here we examine this symbiosis among 11 gorgonian species collected in Bocas del Toro, Panama. By coupling light and dark bottle incubations (P/R) with (13)C-bicarbonate tracers, we quantified the link between holobiont oxygen metabolism with carbon assimilation and translocation from symbiont to host. Our data show that P/R varied among species, and was correlated with colony morphology and polyp size. Sea fans and sea plumes were net autotrophs (P/R>1.5), while nine species of sea rods were net heterotrophs with most below compensation (P/Rcoral bleaching, whereas generalist and facultative associations are common among sea rods that have higher bleaching sensitivities. Overall, productivity and polyp size had strong phylogenetic signals with carbon fixation and polyp size showing evidence of trait covariance. PMID:25989369

  1. Gene expression in gut symbiotic organ of stinkbug affected by extracellular bacterial symbiont.

    Directory of Open Access Journals (Sweden)

    Ryo Futahashi

    Full Text Available The bean bug Riptortus pedestris possesses a specialized symbiotic organ in a posterior region of the midgut, where numerous crypts harbor extracellular betaproteobacterial symbionts of the genus Burkholderia. Second instar nymphs orally acquire the symbiont from the environment, and the symbiont infection benefits the host by facilitating growth and by occasionally conferring insecticide resistance. Here we performed comparative transcriptomic analyses of insect genes expressed in symbiotic and non-symbiotic regions of the midgut dissected from Burkholderia-infected and uninfected R. pedestris. Expression sequence tag analysis of cDNA libraries and quantitative reverse transcription PCR identified a number of insect genes expressed in symbiosis- or aposymbiosis-associated patterns. For example, genes up-regulated in symbiotic relative to aposymbiotic individuals, including many cysteine-rich secreted protein genes and many cathepsin protease genes, are likely to play a role in regulating the symbiosis. Conversely, genes up-regulated in aposymbiotic relative to symbiotic individuals, including a chicken-type lysozyme gene and a defensin-like protein gene, are possibly involved in regulation of non-symbiotic bacterial infections. Our study presents the first transcriptomic data on gut symbiotic organ of a stinkbug, which provides initial clues to understanding of molecular mechanisms underlying the insect-bacterium gut symbiosis and sheds light on several intriguing commonalities between endocellular and extracellular symbiotic associations.

  2. Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt

    OpenAIRE

    Hurst, Sheldon G.; Oshone, Rediet; Ghodhbane-Gtari, Faten; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Mansour, Samira; Gtari, Maher; Tisa, Louis S.

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt.

  3. Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt.

    Science.gov (United States)

    Hurst, Sheldon G; Oshone, Rediet; Ghodhbane-Gtari, Faten; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Mansour, Samira; Gtari, Maher; Tisa, Louis S

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt. PMID:24855310

  4. Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi.

    Science.gov (United States)

    Nerva, L; Ciuffo, M; Vallino, M; Margaria, P; Varese, G C; Gnavi, G; Turina, M

    2016-07-01

    The number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment. The GenBank/eMBL/DDBJ accession numbers of the sequences reported in this paper are: KT601099-KT601110; KT601114-KT601120; KT592305; KT950836-KT950841. PMID:26546154

  5. A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury.

    Science.gov (United States)

    Mathew, Dony Chacko; Ho, Ying-Ning; Gicana, Ronnie Gicaraya; Mathew, Gincy Marina; Chien, Mei-Chieh; Huang, Chieh-Chen

    2015-01-01

    Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1) mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1), 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury. PMID:25816328

  6. A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury.

    Directory of Open Access Journals (Sweden)

    Dony Chacko Mathew

    Full Text Available Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1 mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis. While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1, 24 h and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury.

  7. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts

    OpenAIRE

    Della Sala, Gerardo; Hochmuth, Thomas; Costantino, Valeria; Teta, Roberta; Gerwick, William; Gerwick, Lena; Piel, Jörn; Mangoni, Alfonso

    2013-01-01

    Summary Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two differ...

  8. Relative amount of symbionts in Bemisia tabaci (Gennadius) Q changes with host plant and establishing the method of analyzing free amino acid in B. tabaci

    OpenAIRE

    Pan, Huipeng; Su, Qi; Jiao, Xiaoguo; Zhou, Long; Liu, Baiming; Xie, Wen; Wang, Shaoli; Wu, Qingjun; Xu, Baoyun; Zhang, Youjun

    2013-01-01

    The impact of symbionts on their insect hosts depends on their infection density. In the current study, we investigated the effects of host plants (cucumber, cabbage, and cotton) on the relative amount of symbionts Portiera and Hamiltonella in the whitefly Bemisia tabaci (Gennadius) Q. The relative amounts of symbionts in 3 host plant B. tabaci Q populations with the same genetic background were evaluated by quantitative PCR. The whiteflies of cabbage population harbored more Portiera than th...

  9. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

    DEFF Research Database (Denmark)

    Lin, Senjie; Cheng, Shifeng; Song, Bo;

    2015-01-01

    Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro) transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst...... molecular basis and evolution of coral symbiosis.......Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified...

  10. Taxonomy of lice and their endosymbiotic bacteria in the post-genomic era.

    Science.gov (United States)

    Boyd, B M; Reed, D L

    2012-04-01

    Recent studies of molecular and genomic data from the parasitic lice of birds and mammals, as well as their mutualistic endosymbiotic bacteria, are changing the phylogenetic relationships and taxonomy of these organisms. Phylogenetic studies of lice suggest that vertebrate parasitism arose multiple times from free-living book and bark lice. Molecular clocks show that the major families of lice arose in the late Mesozoic and radiated in the early Cenozoic, following the radiation of mammals and birds. The recent release of the human louse genome has provided new opportunities for research. The genome is being used to find new genetic markers for phylogenetics and population genetics, to understand the complex evolutionary relationships of mitochondrial genes, and to study genome evolution. Genomes are informing us not only about lice, but also about their obligate endosymbiotic bacteria. In contrast to lice and their hosts, lice and their endosymbionts do not share common evolutionary histories, suggesting that endosymbionts are either replaced over time or that there are multiple independent origins of symbiosis in lice. Molecular phylogenetics and whole genome sequencing have recently provided the first insights into the phylogenetic placement and metabolic characteristics of these distantly related bacteria. Comparative genomics between distantly related louse symbionts can provide insights into conserved metabolic functions and can help to explain how distantly related species are fulfilling their role as mutualistic symbionts. In lice and their endosymbionts, molecular data and genome sequencing are driving our understanding of evolutionary relationships and classification, and will for the foreseeable future. PMID:22429457

  11. Comparative Profiling of coral symbiont communities from the Caribbean, Indo-Pacific, and Arabian Seas

    KAUST Repository

    Arif, Chatchanit

    2014-12-01

    Coral reef ecosystems are in rapid decline due to global and local anthropogenic factors. Being among the most diverse ecosystems on Earth, a loss will decrease species diversity, and remove food source for people along the coast. The coral together with its symbionts (i.e. Symbiodinium, bacteria, and other microorganisms) is called the ‘coral holobiont’. The coral host offers its associated symbionts suitable habitats and nutrients, while Symbiodinium and coral-associated bacteria provide the host with photosynthates and vital nutrients. Association of corals with certain types of Symbiodinium and bacteria confer coral stress tolerance, and lack or loss of these symbionts coincides with diseased or bleached corals. However, a detailed understanding of the coral holobiont diversity and structure in regard to diseases and health states or across global scales is missing. This dissertation addressed coral-associated symbiont diversity, specifically of Symbiodinium and bacteria, in various coral species from different geographic locations and different health states. The main aims were (1) to expand the scope of existing technologies, (2) to establish a standardized framework to facilitate comparison of symbiont assemblages over coral species and sites, (3) to assess Symbiodinium diversity in the Arabian Seas, and (4) to elucidate whether coral health states have conserved bacterial footprints. In summary, a next generation sequencing pipeline for Symbiodinium diversity typing of the ITS2 marker is developed and applied to describe Symbiodinium diversity in corals around the Arabian Peninsula. The data show that corals in the Arabian Seas are dominated by a single Symbiodinium type, but harbor a rich variety of types in low abundant. Further, association with different Symbiodinium types is structured according to geographic locations. In addition, the application of 16S rRNA gene microarrays to investigate how differences in microbiome structure relate to

  12. Effects of ocean acidification on calcification of symbiont-bearing reef foraminifers

    Directory of Open Access Journals (Sweden)

    K. Fujita

    2011-02-01

    Full Text Available Ocean acidification (decreases in carbonate ion concentration and pH in response to rising atmospheric pCO2 is generally expected to reduce rates of calcification by reef calcifying organisms, with potentially severe implications for coral reef ecosystems. Large, algal symbiont-bearing benthic foraminifers, which are important primary and carbonate producers in coral reefs, produce high-Mg calcite shells, whose solubility can exceed that of aragonite produced by corals, making them the "first responder" in coral reefs to the decreasing carbonate saturation state of seawater. Here we report results of culture experiments performed to assess the effects of ongoing ocean acidification on the calcification of symbiont-bearing reef foraminifers using a high-precision pCO2 control system. Living clone individuals of three foraminiferal species (Baculogypsina sphaerulata, Calcarina gaudichaudii, and Amphisorus hemprichii were subjected to seawater at five pCO2 levels from 260 to 970 μatm. Cultured individuals were maintained for about 12 weeks in an indoor flow-through system under constant water temperature, light intensity, and photoperiod. After the experiments, the shell diameter and weight of each cultured specimen were measured. Net calcification of Baculogypsina and Calcarina, which secrete a hyaline shell and host diatom symbionts, increased under intermediate levels of pCO2 (580 and/or 770 μatm and decreased at a higher pCO2 level (970 μatm. Net calcification of Amphisorus, which secretes a porcelaneous shell and hosts dinoflagellate symbionts, tended to decrease at elevated pCO2. These different responses among the three species are possibly due to differences in calcification mechanisms (in particular, the specific carbonate species used for calcification between hyaline and porcelaneous

  13. Infectious speciation revisited: impact of symbiont-depletion on female fitness and mating behavior of Drosophila paulistorum.

    Directory of Open Access Journals (Sweden)

    Wolfgang J Miller

    Full Text Available The neotropical Drosophila paulistorum superspecies, consisting of at least six geographically overlapping but reproductively isolated semispecies, has been the object of extensive research since at least 1955, when it was initially trapped mid-evolution in flagrant statu nascendi. In this classic system females express strong premating isolation patterns against mates belonging to any other semispecies, and yet uncharacterized microbial reproductive tract symbionts were described triggering hybrid inviability and male sterility. Based on theoretical models and limited experimental data, prime candidates fostering symbiont-driven speciation in arthropods are intracellular bacteria belonging to the genus Wolbachia. They are maternally inherited symbionts of many arthropods capable of manipulating host reproductive biology for their own benefits. However, it is an ongoing debate as to whether or not reproductive symbionts are capable of driving host speciation in nature and if so, to what extent. Here we have reevaluated this classic case of infectious speciation by means of present day molecular approaches and artificial symbiont depletion experiments. We have isolated the α-proteobacteria Wolbachia as the maternally transmitted core endosymbionts of all D. paulistorum semispecies that have coevolved towards obligate mutualism with their respective native hosts. In hybrids, however, these mutualists transform into pathogens by overreplication causing embryonic inviability and male sterility. We show that experimental reduction in native Wolbachia titer causes alterations in sex ratio, fecundity, and mate discrimination. Our results indicate that formerly designated Mycoplasma-like organisms are most likely Wolbachia that have evolved by becoming essential mutualistic symbionts in their respective natural hosts; they have the potential to trigger pre- and postmating isolation. Furthermore, in light of our new findings, we revisit the concept of

  14. The dominant detritus-feeding invertebrate in Arctic peat soils derives its essential amino acids from gut symbionts.

    Science.gov (United States)

    Larsen, Thomas; Ventura, Marc; Maraldo, Kristine; Triadó-Margarit, Xavier; Casamayor, Emilio O; Wang, Yiming V; Andersen, Nils; O'Brien, Diane M

    2016-09-01

    Supplementation of nutrients by symbionts enables consumers to thrive on resources that might otherwise be insufficient to meet nutritional demands. Such nutritional subsidies by intracellular symbionts have been well studied; however, supplementation of de novo synthesized nutrients to hosts by extracellular gut symbionts is poorly documented, especially for generalists with relatively undifferentiated intestinal tracts. Although gut symbionts facilitate degradation of resources that would otherwise remain inaccessible to the host, such digestive actions alone cannot make up for dietary insufficiencies of macronutrients such as essential amino acids (EAA). Documenting whether gut symbionts also function as partners for symbiotic EAA supplementation is important because the question of how some detritivores are able to subsist on nutritionally insufficient diets has remained unresolved. To answer this poorly understood nutritional aspect of symbiont-host interactions, we studied the enchytraeid worm, a bulk soil feeder that thrives in Arctic peatlands. In a combined field and laboratory study, we employed stable isotope fingerprinting of amino acids to identify the biosynthetic origins of amino acids to bacteria, fungi and plants in enchytraeids. Enchytraeids collected from Arctic peatlands derived more than 80% of their EAA from bacteria. In a controlled feeding study with the enchytraeid Enchytraeus crypticus, EAA derived almost exclusively from gut bacteria when the worms fed on higher fibre diets, whereas most of the enchytraeids' EAA derived from dietary sources when fed on lower fibre diets. Our gene sequencing results of gut microbiota showed that the worms harbour several taxa in their gut lumen absent from their diets and substrates. Almost all gut taxa are candidates for EAA supplementation because almost all belong to clades capable of biosynthesizing EAA. Our study provides the first evidence of extensive symbiotic supplementation of EAA by microbial

  15. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

    Science.gov (United States)

    Benoit, Joshua B; Adelman, Zach N; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C; Szuter, Elise M; Hagan, Richard W; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M; Nelson, David R; Rosendale, Andrew J; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R; Ioannidis, Panagiotis; Waterhouse, Robert M; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J Spencer; Gondhalekar, Ameya D; Scharf, Michael E; Peterson, Brittany F; Raje, Kapil R; Hottel, Benjamin A; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S T; Duncan, Elizabeth J; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C; Muzny, Donna M; Wheeler, David; Panfilio, Kristen A; Vargas Jentzsch, Iris M; Vargo, Edward L; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T; Anderson, Michelle A E; Jones, Jeffery W; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D; Attardo, Geoffrey M; Robertson, Hugh M; Zdobnov, Evgeny M; Ribeiro, Jose M C; Gibbs, Richard A; Werren, John H; Palli, Subba R; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  16. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes.

    Science.gov (United States)

    Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Ormeño-Orrillo, Ernesto; Parma, Marcia Maria; Melo, Itamar Soares; Martínez-Romero, Esperanza; Hungria, Mariangela

    2015-12-01

    Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T

  17. Should Symbionts Be Nice or Selfish? Antiviral Effects of Wolbachia Are Costly but Reproductive Parasitism Is Not.

    Directory of Open Access Journals (Sweden)

    Julien Martinez

    2015-07-01

    Full Text Available Symbionts can have mutualistic effects that increase their host's fitness and/or parasitic effects that reduce it. Which of these strategies evolves depends in part on the balance of their costs and benefits to the symbiont. We have examined these questions in Wolbachia, a vertically transmitted endosymbiont of insects that can provide protection against viral infection and/or parasitically manipulate its hosts' reproduction. Across multiple symbiont strains we find that the parasitic phenotype of cytoplasmic incompatibility and antiviral protection are uncorrelated. Strong antiviral protection is associated with substantial reductions in other fitness-related traits, whereas no such trade-off was detected for cytoplasmic incompatibility. The reason for this difference is likely that antiviral protection requires high symbiont densities but cytoplasmic incompatibility does not. These results are important for the use of Wolbachia to block dengue virus transmission by mosquitoes, as natural selection to reduce these costs may lead to reduced symbiont density and the loss of antiviral protection.

  18. Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae).

    Science.gov (United States)

    Duperron, Sébastien; Halary, Sébastien; Lorion, Julien; Sibuet, Myriam; Gaill, Françoise

    2008-02-01

    Bathymodioline mussels occur in chemosynthesis-based ecosystems such as cold seeps, hydrothermal vents and organic debris worldwide. Their key adaptation to these environments is their association with bacterial endosymbionts which ensure a chemosynthetic primary production based on the oxidation of reduced compounds such as methane and sulfide. We herein report a multiple symbiosis involving six distinct bacterial 16S rRNA phylotypes, including two belonging to groups not yet reported as symbionts in mytilids, in a small Idas mussel found on carbonate crusts in a cold seep area located north to the Nile deep-sea fan (Eastern Mediterranean). Symbionts co-occur within hosts bacteriocytes based on fluorescence in situ hybridizations, and sequencing of functional genes suggests they have the potential to perform autotrophy, and sulfide and methane oxidation. Previous studies indicated the presence of only one or two symbiont 16S rRNA phylotypes in bathymodioline mussels. Together with the recent discovery of four bacterial symbionts in the large seep species Bathymodiolus heckerae, this study shows that symbiont diversity has probably been underestimated, and questions whether the common ancestor of bathymodioline mussels was associated with multiple bacteria. PMID:18093159

  19. Complete Genome Sequence of “Candidatus Tremblaya princeps” Strain PCVAL, an Intriguing Translational Machine below the Living-Cell Status

    OpenAIRE

    López-Madrigal, Sergio; Latorre, Amparo; Porcar, Manuel; Moya, Andrés; Gil Benso, Rosario

    2011-01-01

    The sequence of the genome of “Candidatus Tremblaya princeps” strain PCVAL, the primary endosymbiont of the citrus mealybug Planococcus citri, has been determined. “Ca. Tremblaya princeps” presents an unusual nested endosymbiosis and harbors a gammaproteobacterial symbiont within its cytoplasm in all analyzed mealybugs. The genome sequence reveals that “Ca. Tremblaya princeps” cannot be considered an independent organism but that the consortium with its gammaproteobacterial symbiotic associat...

  20. Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants is accepted for publication in MPMI

    Energy Technology Data Exchange (ETDEWEB)

    Karpinets, Tatiana V [ORNL; Park, Byung H [ORNL; Syed, Mustafa H [ORNL; Klotz, Martin G [University of North Carolina, Charlotte; Uberbacher, Edward C [ORNL

    2014-01-01

    Most bacterial symbionts of plants are phenotypically characterized by their parasitic or matualistic relationship with the host; however, the genomic characteristics that likely discriminate mutualistic symbionts from pathogens of plants are poorly understood. This study comparatively analyzed the genomes of 54 plant-symbiontic bacteria, 27 mutualists and 27 pathogens, to discover genomic determinants of their parasitic and mutualistic nature in terms of protein family domains, KEGG orthologous groups, metabolic pathways and families of carbohydrate-active enzymes (CAZymes). We further used all bacteria with sequenced genomesl, published microarrays and transcriptomics experimental datasets, and literature to validate and to explore results of the comparison. The analysis revealed that genomes of mutualists are larger in size and higher in GC content and encode greater molecular, functional and metabolic diversity than the investigated genomes of pathogens. This enriched molecular and functional enzyme diversity included constructive biosynthetic signatures of CAZymes and metabolic pathways in genomes of mutualists compared with catabolic signatures dominant in the genomes of pathogens. Another discriminative characteristic of mutualists is the co-occurence of gene clusters required for the expression and function of nitrogenase and RuBisCO. Analysis of previously published experimental data indicate that nitrogen-fixing mutualists may employ Rubisco to fix CO2 not in the canonical Calvin-Benson-Basham cycle but in a novel metabolic pathway, here called Rubisco-based glycolysis , to increase efficiency of sugar utilization during the symbiosis with plants. An important discriminative characteristic of plant pathogenic bacteria is two groups of genes likely encoding effector proteins involved in host invasion and a genomic locus encoding a putative secretion system that includes a DUF1525 domain protein conserved in pathogens of plants and of other organisms. The

  1. The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis.

    Science.gov (United States)

    Carlier, Aurelien; Fehr, Linda; Pinto-Carbó, Marta; Schäberle, Till; Reher, Raphael; Dessein, Steven; König, Gabriele; Eberl, Leo

    2016-09-01

    A majority of Ardisia species harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted hereditarily and have not yet been cultured outside of their host. Because the plants cannot develop beyond the seedling stage without their symbionts, the symbiosis is considered obligatory. We sequenced for the first time the genome of Candidatus Burkholderia crenata (Ca. B. crenata), the leaf nodule symbiont of Ardisia crenata. The genome of Ca. B. crenata is the smallest Burkholderia genome to date. It contains a large amount of insertion sequences and pseudogenes and displays features consistent with reductive genome evolution. The genome does not encode functions commonly associated with plant symbioses such as nitrogen fixation and plant hormone metabolism. However, we identified unique genes with a predicted role in secondary metabolism in the genome of Ca. B. crenata. Specifically, we provide evidence that the bacterial symbionts are responsible for the synthesis of compound FR900359, a cyclic depsipeptide with biomedical properties previously isolated from leaves of A. crenata. PMID:26663534

  2. Molecular evidence for Lessepsian invasion of soritids (larger symbiont bearing benthic foraminifera.

    Directory of Open Access Journals (Sweden)

    Gily Merkado

    Full Text Available The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea and from a known hotspot in Shikmona (northern Israel that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.

  3. Comparative lipid profiling of the cnidarian Aiptasia pallida and its dinoflagellate symbiont.

    Directory of Open Access Journals (Sweden)

    Teresa A Garrett

    Full Text Available Corals and other cnidarians house photosynthetic dinoflagellate symbionts within membrane-bound compartments inside gastrodermal cells. Nutritional interchanges between the partners produce carbohydrates and lipids for metabolism, growth, energy stores, and cellular structures. Although lipids play a central role in the both the energetics and the structural/morphological features of the symbiosis, previous research has primarily focused on the fatty acid and neutral lipid composition of the host and symbiont. In this study we conducted a mass spectrometry-based survey of the lipidomic changes associated with symbiosis in the sea anemone Aiptasia pallida, an important model system for coral symbiosis. Lipid extracts from A. pallida in and out of symbiosis with its symbiont Symbiodinium were prepared and analyzed using negative-ion electrospray ionization quadrupole time-of-flight mass spectrometry. Through this analysis we have identified, by exact mass and collision-induced dissociation mass spectrometry (MS/MS, several classes of glycerophospholipids in A. pallida. Several molecular species of di-acyl phosphatidylinositol and phosphatidylserine as well as 1-alkyl, 2-acyl phosphatidylethanolamine (PE and phosphatidycholine were identified. The 1-alkyl, 2-acyl PEs are acid sensitive suggestive that they are plasmalogen PEs possessing a double bond at the 1-position of the alkyl linked chain. In addition, we identified several molecular species of phosphonosphingolipids called ceramide aminoethylphosphonates in anemone lipid extracts by the release of a characteristic negative product ion at m/z 124.014 during MS/MS analysis. Sulfoquinovosyldiacylglycerol (SQDG, an anionic lipid often found in photosynthetic organisms, was identified as a prominent component of Symbiodinium lipid extracts. A comparison of anemone lipid profiles revealed a subset of lipids that show dramatic differences in abundance when anemones are in the symbiotic state as

  4. The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae

    Directory of Open Access Journals (Sweden)

    Szurek Boris

    2009-12-01

    Full Text Available Abstract Background The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess hrp genes which encode a Type III secretion system found in most plant pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group based on phylogenetic analyses with rRNA sequences. Results The complete genome of X. albilineans was sequenced and annotated. X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. Phylogenetic analysis using X. albilineans genomic sequences showed that X. fastidiosa belongs to the Xanthomonas group. Order of divergence of the Xanthomonadaceae revealed that X. albilineans and X. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the Xanthomonas genus. Reductive genome evolutions of the two xylem-limited Xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. Conclusion The two xylem-limited Xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of X. albilineans differ from those of X. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by X. albilineans, is discussed.

  5. Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

    Directory of Open Access Journals (Sweden)

    Ying eZhang

    2014-03-01

    Full Text Available The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to 1 genomes of species belonging to the same genus, but inhabiting different environments, and 2 genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.

  6. In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, and algal symbiont

    NARCIS (Netherlands)

    P.R. Frade; P. Bongaerts; A.J.S. Winkelhagen; L. Tonk; R.P.M. Bak

    2008-01-01

    We applied a multivariate analysis to investigate the roles of host and symbiont on the in situ physiological response of genus Madracis holobionts towards light. Across a large depth gradient (5-40 m) and for four Madracis species and three symbiont genotypes, we assessed several variables by measu

  7. Real-time PCR reveals a high incidence of Symbiodinium clade D at low levels in four scleractinian corals across the Great Barrier Reef : implications for symbiont shuffling

    NARCIS (Netherlands)

    Mieog, J. C.; van Oppen, M. J. H.; Cantin, N. E.; Stam, W. T.; Olsen, J. L.

    2007-01-01

    Reef corals form associations with an array of genetically and physiologically distinct endosymbionts from the genus Symbiodinium. Some corals harbor different clades of symbionts simultaneously, and over time the relative abundances of these clades may change through a process called symbiont shuff

  8. Endobiotic rugosan symbionts in stromatoporoids from the Sheinwoodian (Silurian of Baltica.

    Directory of Open Access Journals (Sweden)

    Olev Vinn

    Full Text Available A paleoecological study of stromatoporoid endobionts was carried out to discern the relationships between symbiotic rugosans and their stromatoporoid hosts. The earliest endobiotic rugosan symbiont Palaeophyllum sp. in Baltica has only been found in the stromatoporoid Ecclimadictyon astrolaxum from Saaremaa, Estonia. The rugosans are vertically oriented inside the stromatoporoid skeleton. Numerous rugosans have their corallites open at the upper, external surface of stromatoporoids, but many are completely embedded within the stromatoporoids. Stromatoporoid hosts were presumably beneficial for rugosans as elevated substrates on a sea floor that offered a higher tier for feeding. Relative substrate stability in the hydrodynamically active shallow waters may have also been beneficial for the rugosans.

  9. Acetobacter tropicalis is a major symbiont of the olive fruit fly (Bactrocera oleae)

    DEFF Research Database (Denmark)

    Kounatidis, Ilias; Crotti, Elena; Sapountzis, Panagiotis;

    2009-01-01

    taxa associated with this insect, among which Acetobacter tropicalis was predominant. The recent increased detection of acetic acid bacteria as symbionts of other insect model organisms, such as Anopheles stephensi (G. Favia et al., Proc. Natl. Acad. Sci. USA 104:9047-9051, 2007) or Drosophila......-collected from different locations in Greece. This acetic acid bacterium was successfully established in cell-free medium, and typing analyses, carried out on a collection of isolates, revealed that different A. tropicalis strains are present in fly populations. The capability to colonize and lodge in the...

  10. Earthworms and their Nephridial Symbionts: Co-diversification and Maintenance of the Symbiosis

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Holmstrup, Martin; Davidson, Seana K.;

    Earthworms harbor in their nephridia (excretory organs) symbiotic bacteria which densely colonize a specific part of the nephridia, called the ampulla [1]. The symbiosis is species-specific and the symbionts form their own monophyletic genus Verminephrobacter (β-proteobacteria) [2] and are vertic......] Knop,J. 1926. Z Morph Ökol Tiere, 6(3):588-624. [2] Schramm,A. et al. 2003. Environ Microbiol 5(9):804-809. [3] Davidson,S.K. & Stahl,D.A. 2006. Appl Environ Microbiol 72(1):769-775. [4] Pandazis,G. 1931. Zentralbl Bakteriol 120:440-453....

  11. The pink shrimp Farfantepenaeus duorarum, its symbionts and helminths as bioindicators of chemical pollution in Campeche Sound, Mexico.

    Science.gov (United States)

    Vidal-Martínez, V M; Aguirre-Macedo, M L; Del Rio-Rodríguez, R; Gold-Bouchot, G; Rendón-von Osten, J; Miranda-Rosas, G A

    2006-06-01

    The pink shrimp Farfantepenaeus duorarum may acquire pollutants, helminths and symbionts from their environment. Statistical associations were studied between the symbionts and helminths of F. duorarum and pollutants in sediments, water and shrimps in Campeche Sound, Mexico. The study area spatially overlapped between offshore oil platforms and natural shrimp mating grounds. Spatial autocorrelation of data was controlled with spatial analysis using distance indices (SADIE) which identifies parasite or pollutant patches (high levels) and gaps (low levels), expressing them as clustering indices compared at each point to produce a measure of spatial association. Symbionts included the peritrich ciliates Epistylis sp. and Zoothamnium penaei and all symbionts were pooled. Helminths included Hysterothylacium sp., Opecoeloides fimbriatus, Prochristianella penaei and an unidentified cestode. Thirty-five pollutants were identified, including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), pesticides and heavy metals. The PAHs (2-3 ring) in water, unresolved complex mixture (UCM), Ni and V in sediments, and Zn, Cr and heptachlor in shrimps were significantly clustered. The remaining pollutants were randomly distributed in the study area. Juvenile shrimps acquired pesticides, PAHs (2-3 rings) and Zn, while adults acquired PAHs (4-5 rings), Cu and V. Results suggest natural PAH spillovers, and continental runoff of dichlorodiphenyltrichloroethane (DDT), PCBs and PAHs (2-3 ring). There were no significant associations between pollutants and helminths. However, there were significant negative associations of pesticides, UCM and PCBs with symbiont numbers after controlling shrimp size and spatial autocorrelation. Shrimps and their symbionts appear to be promising bioindicators of organic chemical pollution in Campeche Sound. PMID:16768859

  12. Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I.

    Science.gov (United States)

    Zhu, Dan-Tong; Xia, Wen-Qiang; Rao, Qiong; Liu, Shu-Sheng; Ghanim, Murad; Wang, Xiao-Wei

    2016-08-01

    The whitefly, Bemisia tabaci, harbors the primary symbiont 'Candidatus Portiera aleyrodidarum' and a variety of secondary symbionts. Among these secondary symbionts, Rickettsia is the only one that can be detected both inside and outside the bacteriomes. Infection with Rickettsia has been reported to influence several aspects of the whitefly biology, such as fitness, sex ratio, virus transmission and resistance to pesticides. However, mechanisms underlying these differences remain unclear, largely due to the lack of genomic information of Rickettsia. In this study, we sequenced the genome of two Rickettsia strains isolated from the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex in China and Israel. Both Rickettsia genomes were of high coding density and AT-rich, containing more than 1000 coding sequences, much larger than that of the coexisted primary symbiont, Portiera. Moreover, the two Rickettsia strains isolated from China and Israel shared most of the genes with 100% identity and only nine genes showed sequence differences. The phylogenetic analysis using orthologs shared in the genus, inferred the proximity of Rickettsia in MEAM1 and Rickettsia bellii. Functional analysis revealed that Rickettsia was unable to synthesize amino acids required for complementing the whitefly nutrition. Besides, a type IV secretion system and a number of virulence-related genes were detected in the Rickettsia genome. The presence of virulence-related genes might benefit the symbiotic life of the bacteria, and hint on potential effects of Rickettsia on whiteflies. The genome sequences of Rickettsia provided a basis for further understanding the function of Rickettsia in whiteflies. PMID:27273750

  13. Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia.

    Science.gov (United States)

    Ghodhbane-Gtari, Faten; Hurst, Sheldon G; Oshone, Rediet; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Gtari, Maher; Tisa, Louis S

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia. PMID:24874687

  14. Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia

    OpenAIRE

    Ghodhbane-Gtari, Faten; Hurst, Sheldon G.; Oshone, Rediet; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Gtari, Maher; Tisa, Louis S.

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia.

  15. Change in algal symbiont communities after bleaching, not prior heat exposure, increases heat tolerance of reef corals.

    Science.gov (United States)

    Silverstein, Rachel N; Cunning, Ross; Baker, Andrew C

    2015-01-01

    Mutualistic organisms can be particularly susceptible to climate change stress, as their survivorship is often limited by the most vulnerable partner. However, symbiotic plasticity can also help organisms in changing environments by expanding their realized niche space. Coral-algal (Symbiodinium spp.) symbiosis exemplifies this dichotomy: the partnership is highly susceptible to 'bleaching' (stress-induced symbiosis breakdown), but stress-tolerant symbionts can also sometimes mitigate bleaching. Here, we investigate the role of diverse and mutable symbiotic partnerships in increasing corals' ability to thrive in high temperature conditions. We conducted repeat bleaching and recovery experiments on the coral Montastraea cavernosa, and used quantitative PCR and chlorophyll fluorometry to assess the structure and function of Symbiodinium communities within coral hosts. During an initial heat exposure (32 °C for 10 days), corals hosting only stress-sensitive symbionts (Symbiodinium C3) bleached, but recovered (at either 24 °C or 29 °C) with predominantly (>90%) stress-tolerant symbionts (Symbiodinium D1a), which were not detected before bleaching (either due to absence or extreme low abundance). When a second heat stress (also 32 °C for 10 days) was applied 3 months later, corals that previously bleached and were now dominated by D1a Symbiodinium experienced less photodamage and symbiont loss compared to control corals that had not been previously bleached, and were therefore still dominated by Symbiodinium C3. Additional corals that were initially bleached without heat by a herbicide (DCMU, at 24 °C) also recovered predominantly with D1a symbionts, and similarly lost fewer symbionts during subsequent thermal stress. Increased thermotolerance was also not observed in C3-dominated corals that were acclimated for 3 months to warmer temperatures (29 °C) before heat stress. These findings indicate that increased thermotolerance post-bleaching resulted from

  16. THE ROLE OF BACTERIAL SYMBIONTS IN AMINO ACID COMPOSITION OF BLACK BEAN APHIDS

    Institute of Scientific and Technical Information of China (English)

    MingGan; De-ChengDing; Xue-xiaMiao

    2003-01-01

    To evaluate the role of bacterial symbionts ( Buchnera spp. ) in the black bean aphids ( Aphis craccivora Koch), the aphids were treated with the antibiotic, rifampicin, to eliminate their intracellular symbiotic bacteria. Analysis of protein and amino acid concentration in 7-day-old of aposymbiotic aphids showed that the total protein content per mg fresh weight was significantly reduced by 29 %, but free amino acid titers were increased by 17% . The ratio of the essential amino acids was in general only around 20% essential amino acids in phloem sap of broad bean, whereas it was 44% and 37% in symbiotic and aposymbiotic aphids, respectively,suggesting that the composition of the free amino acids was unbalanced. For example, the essential amino acid,threonine represented 21. 6% of essential amino acids in symbiotic aphids, but it was only 16.7% in aposymbiotic aphids. Likewise, two nonessential amino acids, tyrosine and serine, represented 8.9% and 5.6% of total amino acids in symbiontic aphids, respectively, but they enhanced to 21.1% and 13.6% in aposymbiotic aphids. It seems likely that the elevated free amino acid concentration in aposymbiotic aphids was caused by the limited protein anabolism as the result of the unbalanced amino acid composition.

  17. Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

    Science.gov (United States)

    Wexler, Aaron G; Bao, Yiqiao; Whitney, John C; Bobay, Louis-Marie; Xavier, Joao B; Schofield, Whitman B; Barry, Natasha A; Russell, Alistair B; Tran, Bao Q; Goo, Young Ah; Goodlett, David R; Ochman, Howard; Mougous, Joseph D; Goodman, Andrew L

    2016-03-29

    The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes-one of two major phyla in the gut-also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation. PMID:26957597

  18. Conditional Reduction of Predation Risk Associated with a Facultative Symbiont in an Insect.

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    Sarah Polin

    Full Text Available Symbionts are widespread among eukaryotes and their impacts on the ecology and evolution of their hosts are meaningful. Most insects harbour obligate and facultative symbiotic bacteria that can influence their phenotype. In the pea aphid Acyrthosiphon pisum, an astounding symbiotic-mediated phenotype has been recently observed: when infected with the symbiotic bacteria Rickettsiella viridis, young red aphid larvae become greener at adulthood and even darker green when co-infected with Rickettsiella viridis and Hamiltonella defensa. As body colour affects the susceptibility towards natural enemies in aphids, the influence of the colour change due to these facultative symbionts on the host survival in presence of predators was tested. Our results suggested that the Rickettsiella viridis infection may impact positively host survival by reducing predation risk. Due to results from uninfected aphids (i.e., more green ones attacked, the main assumption is that this symbiotic infection would deter the predatory ladybird feeding by reducing the profitability of their hosts rather than decreasing host detection through body colour change. Aphids co-infected with Rickettsiella viridis and Hamiltonella defensa were, however, more exposed to predation suggesting an ecological cost associated with multiple infections. The underlying mechanisms and ecological consequences of these symbiotic effects are discussed.

  19. Antagonistic interactions between honey bee bacterial symbionts and implications for disease

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    Armstrong Tamieka-Nicole

    2006-03-01

    Full Text Available Abstract Background Honey bees, Apis mellifera, face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. One route by which honey bees and other insects might combat disease is through the shielding effects of their microbial symbionts. Bees carry a diverse assemblage of bacteria, very few of which appear to be pathogenic. Here we explore the inhibitory effects of these resident bacteria against the primary bacterial pathogen of honey bees, Paenibacillus larvae. Results Here we isolate, culture, and describe by 16S rRNA and protein-coding gene sequences 61 bacterial isolates from honey bee larvae, reflecting a total of 43 distinct bacterial taxa. We culture these bacteria alongside the primary larval pathogen of honey bees, Paenibacillus larvae, and show that many of these isolates severely inhibit the growth of this pathogen. Accordingly, symbiotic bacteria including those described here are plausible natural antagonists toward this widespread pathogen. Conclusion The results suggest a tradeoff in social insect colonies between the maintenance of potentially beneficial bacterial symbionts and deterrence at the individual and colony level of pathogenic species. They also provide a novel mechanism for recently described social components behind disease resistance in insect colonies, and point toward a potential control strategy for an important bee disease.

  20. Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

    Energy Technology Data Exchange (ETDEWEB)

    Aylward, Frank O.; Khadempour, Lily; Tremmel, Daniel; McDonald, Bradon R.; Nicora, Carrie D.; Wu, Si; Moore, Ronald J.; Orton, Daniel J.; Monroe, Matthew E.; Piehowski, Paul D.; Purvine, Samuel O.; Smith, Richard D.; Lipton, Mary S.; Burnum-Johnson, Kristin E.; Currie, Cameron R.

    2015-08-28

    Leaf-cutter ants are prolific and conspicuous Neotropical herbivores that derive energy from specialized fungus gardens they cultivate using foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary food source of ant colonies. Gongylidia also contain lignocellulases that become concentrated in ant digestive tracts and are deposited within fecal droplets onto fresh foliar material as it is foraged by the ants. Although the enzymes concentrated by L. gongylophorus within gongylidia are thought to be critical to the initial degradation of plant biomass, only a few enzymes present in these hyphal swellings have been identified. Here we use proteomic methods to identify proteins present in the gongylidia of three Atta cephalotes colonies. Our results demonstrate that a diverse but consistent set of enzymes is present in gongylidia, including numerous lignocellulases likely involved in the degradation of polysaccharides, plant toxins, and proteins. Overall, gongylidia contained over three-quarters of all lignocellulases identified in the L. gongylophorus genome, demonstrating that the majority of the enzymes produced by this fungus for biomass breakdown are ingested by the ants. We also identify a set of 23 lignocellulases enriched in gongylidia compared to whole fungus garden samples, suggesting that certain enzymes may be particularly important in the initial degradation of foliar material. Our work sheds light on the complex interplay between leaf-cutter ants and their fungal symbiont that allows for the host insects to occupy an herbivorous niche by indirectly deriving energy from plant biomass.

  1. Rhizobial and bradyrhizobial symbionts of mesquite from the Sonoran Desert: Salt tolerance, facultative halophily, and nitrate respiration

    Science.gov (United States)

    Rhizobial symbionts from surface and phreatic absorbing root environments of a mature mesquite woodland in the Sonoran Desert of Southern California were tested for their ability to tolerate high salinity, and respire nitrate as mechanisms of free-living survival. Isolates were grown in yeast-extra...

  2. Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri.

    Directory of Open Access Journals (Sweden)

    Tyler R Schleicher

    Full Text Available The beneficial symbiosis between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium, Vibrio fischeri, provides a unique opportunity to study host/microbe interactions within a natural microenvironment. Colonization of the squid light organ by V. fischeri begins a lifelong association with a regulated daily rhythm. Each morning the host expels an exudate from the light organ consisting of 95% of the symbiont population in addition to host hemocytes and shed epithelial cells. We analyzed the host and symbiont proteomes of adult squid exudate and surrounding light organ epithelial tissue using 1D- and 2D-polyacrylamide gel electrophoresis and multidimensional protein identification technology (MudPIT in an effort to understand the contribution of both partners to the maintenance of this association. These proteomic analyses putatively identified 1581 unique proteins, 870 proteins originating from the symbiont and 711 from the host. Identified host proteins indicate a role of the innate immune system and reactive oxygen species (ROS in regulating the symbiosis. Symbiont proteins detected enhance our understanding of the role of quorum sensing, two-component signaling, motility, and detoxification of ROS and reactive nitrogen species (RNS inside the light organ. This study offers the first proteomic analysis of the symbiotic microenvironment of the adult light organ and provides the identification of proteins important to the regulation of this beneficial association.

  3. Special structures of hoopoe eggshells enhance the adhesion of symbionts-carrying uropygial secretion to prevent embryo infection

    OpenAIRE

    Mart??n-Vivaldi, Manuel; Soler Cruz, Juan Jos??; Peralta-S??nchez, Juan Manuel; Arco, Laura; Mart??n-Platero, Antonio Manuel; Mart??nez Bueno, Manuel; Ruiz-Rodr??guez, Magdalena; Valdivia Mart??nez, Eva

    2014-01-01

    This is the pre-peer-reviewed version of the following article: Mart??n-Vivaldi, M.; et al. Special structures of hoopoe eggshells enhance the adhesion of symbionts-carrying uropygial secretion to prevent embryo infection. Journal of Animal Ecology, (2014). which has been published in final form at: http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12243/abstract

  4. Application of RT-PCR to study in vitro development of Cryptosporidium parvum and its viral symbiont CPV

    Science.gov (United States)

    Cryptosporidium parvum and C. hominis contain a double-stranded RNA viral symbiont termed CPV. Our research seeks to find a role for CPV in the pathogenicity and development of C. parvum. Cell cultures were infected with C. parvum sporozoites, and extracted at various times post-infection for DNA ...

  5. Fusarium symbionts of an ambrosia beetle (Euwallacea sp.) in southern Florida are pathogens of avocado, Persea americana

    Science.gov (United States)

    Fusarium dieback, a destructive disease of avocado (Persea americana), was reported in California and Israel in 2012. It is associated with an ambrosia beetle, Euwallacea sp., and damage caused by an unnamed symbiont of the beetle in Clade 3 of the Fusarium solani species complex (FSSC) designated p...

  6. Influence of chemosynthetic substrates availability on symbiont densities, carbon assimilation and transfer in the dual symbiotic vent mussel Bathymodiolus azoricus

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    R. S. Santos

    2008-05-01

    Full Text Available High densities of mussels of the genus Bathymodiolus are present at hydrothermal vents of the Mid-Atlantic Ridge. It was already proposed that the chemistry at vent sites would affect their sulphide- and methane-oxidizing endosymbionts' abundance. In this study, we confirmed the latter assumption using fluorescence in situ hybridization on Bathymodiolus azoricus specimens maintained in a controlled laboratory environment at atmospheric pressure with one, both or none of the chemical substrates. A high level of symbiosis plasticity was observed, methane-oxidizers occupying between 4 and 39% of total bacterial area and both symbionts developing accordingly to the presence or absence of their substrates. Using H13CO3− in the presence of sulphide, 13CH4 or 13CH3OH, we monitored carbon assimilation by the endosymbionts and its translocation to symbiont-free mussel tissues. Although no significant carbon assimilation could be evidenced with methanol, carbon was incorporated from methane and sulphide-oxidized inorganic carbon at rates 3 to 10 times slower in the host muscle tissue than in the symbiont-containing gill tissue. Both symbionts thus contribute actively to B. azoricus nutrition and adapt to the availability of their substrates. Further experiments with varying substrate concentrations using the same set-up should provide useful tools to study and even model the effects of changes in hydrothermal fluids on B. azoricus' chemosynthetic nutrition.

  7. Expression patterns of mRNAs for methanotrophy and thiotrophy in symbionts of the hydrothermal vent mussel Bathymodiolus puteoserpentis.

    Science.gov (United States)

    Wendeberg, Annelie; Zielinski, Frank U; Borowski, Christian; Dubilier, Nicole

    2012-01-01

    The hydrothermal vent mussel Bathymodiolus puteoserpentis (Mytilidae) from the Mid-Atlantic Ridge hosts symbiotic sulfur- and methane-oxidizing bacteria in its gills. In this study, we investigated the activity and distribution of these two symbionts in juvenile mussels from the Logatchev hydrothermal vent field (14°45'N Mid-Atlantic Ridge). Expression patterns of two key genes for chemosynthesis were examined: pmoA (encoding subunit A of the particulate methane monooxygenase) as an indicator for methanotrophy, and aprA (encoding the subunit A of the dissimilatory adenosine-5'-phosphosulfate reductase) as an indicator for thiotrophy. Using simultaneous fluorescence in situ hybridization (FISH) of rRNA and mRNA we observed highest mRNA FISH signals toward the ciliated epithelium where seawater enters the gills. The levels of mRNA expression differed between individual specimens collected in a single grab from the same sampling site, whereas no obvious differences in symbiont abundance or distribution were observed. We propose that the symbionts respond to the steep temporal and spatial gradients in methane, reduced sulfur compounds and oxygen by modifying gene transcription, whereas changes in symbiont abundance and distribution take much longer than regulation of mRNA expression and may only occur in response to long-term changes in vent fluid geochemistry. PMID:21734728

  8. Comparative genome analysis of Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

    2013-08-07

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

  9. Wolbachia symbiont infections induce strong cytoplasmic incompatibility in the tsetse fly Glossina morsitans.

    Directory of Open Access Journals (Sweden)

    Uzma Alam

    2011-12-01

    Full Text Available Tsetse flies are vectors of the protozoan parasite African trypanosomes, which cause sleeping sickness disease in humans and nagana in livestock. Although there are no effective vaccines and efficacious drugs against this parasite, vector reduction methods have been successful in curbing the disease, especially for nagana. Potential vector control methods that do not involve use of chemicals is a genetic modification approach where flies engineered to be parasite resistant are allowed to replace their susceptible natural counterparts, and Sterile Insect technique (SIT where males sterilized by chemical means are released to suppress female fecundity. The success of genetic modification approaches requires identification of strong drive systems to spread the desirable traits and the efficacy of SIT can be enhanced by identification of natural mating incompatibility. One such drive mechanism results from the cytoplasmic incompatibility (CI phenomenon induced by the symbiont Wolbachia. CI can also be used to induce natural mating incompatibility between release males and natural populations. Although Wolbachia infections have been reported in tsetse, it has been a challenge to understand their functional biology as attempts to cure tsetse of Wolbachia infections by antibiotic treatment damages the obligate mutualistic symbiont (Wigglesworthia, without which the flies are sterile. Here, we developed aposymbiotic (symbiont-free and fertile tsetse lines by dietary provisioning of tetracycline supplemented blood meals with yeast extract, which rescues Wigglesworthia-induced sterility. Our results reveal that Wolbachia infections confer strong CI during embryogenesis in Wolbachia-free (Gmm(Apo females when mated with Wolbachia-infected (Gmm(Wt males. These results are the first demonstration of the biological significance of Wolbachia infections in tsetse. Furthermore, when incorporated into a mathematical model, our results confirm that Wolbachia can

  10. Wolbachia symbiont infections induce strong cytoplasmic incompatibility in the tsetse fly Glossina morsitans.

    Science.gov (United States)

    Alam, Uzma; Medlock, Jan; Brelsfoard, Corey; Pais, Roshan; Lohs, Claudia; Balmand, Séverine; Carnogursky, Jozef; Heddi, Abdelaziz; Takac, Peter; Galvani, Alison; Aksoy, Serap

    2011-12-01

    Tsetse flies are vectors of the protozoan parasite African trypanosomes, which cause sleeping sickness disease in humans and nagana in livestock. Although there are no effective vaccines and efficacious drugs against this parasite, vector reduction methods have been successful in curbing the disease, especially for nagana. Potential vector control methods that do not involve use of chemicals is a genetic modification approach where flies engineered to be parasite resistant are allowed to replace their susceptible natural counterparts, and Sterile Insect technique (SIT) where males sterilized by chemical means are released to suppress female fecundity. The success of genetic modification approaches requires identification of strong drive systems to spread the desirable traits and the efficacy of SIT can be enhanced by identification of natural mating incompatibility. One such drive mechanism results from the cytoplasmic incompatibility (CI) phenomenon induced by the symbiont Wolbachia. CI can also be used to induce natural mating incompatibility between release males and natural populations. Although Wolbachia infections have been reported in tsetse, it has been a challenge to understand their functional biology as attempts to cure tsetse of Wolbachia infections by antibiotic treatment damages the obligate mutualistic symbiont (Wigglesworthia), without which the flies are sterile. Here, we developed aposymbiotic (symbiont-free) and fertile tsetse lines by dietary provisioning of tetracycline supplemented blood meals with yeast extract, which rescues Wigglesworthia-induced sterility. Our results reveal that Wolbachia infections confer strong CI during embryogenesis in Wolbachia-free (Gmm(Apo)) females when mated with Wolbachia-infected (Gmm(Wt)) males. These results are the first demonstration of the biological significance of Wolbachia infections in tsetse. Furthermore, when incorporated into a mathematical model, our results confirm that Wolbachia can be used

  11. The importance of gut symbionts in the development of the brown marmorated stink bug, Halyomorpha halys (Stal.

    Directory of Open Access Journals (Sweden)

    Christopher M Taylor

    Full Text Available The invasive brown marmorated stink bug, Halyomorpha halys (Stål, has become a severe agricultural pest and nuisance problem since its introduction in the U.S. Research is being conducted to understand its biology and to find management solutions. Its symbiotic relationship with gut symbionts is one aspect of its biology that is not understood. In the family Pentatomidae, the reliance on gut symbionts for successful development seems to vary depending on the species of stink bug. This research assessed the role of gut symbionts in the development, survivorship, and fecundity of H. halys. We compared various fitness parameters of nymphs and adults reared from surface sterilized and untreated egg masses during two consecutive generations under laboratory conditions. Results provided direct evidence that H. halys is negatively impacted by the prevention of vertical transmission of its gut symbionts and that this impact is significant in the first generation and manifests dramatically in the subsequent generation. Developmental time and survivorship of treated cohorts in the first generation were significantly affected during third instar development through to the adult stage. Adults from the sterilized treatment group exhibited longer pre-oviposition periods, produced fewer egg masses, had significantly smaller clutch sizes, and the hatch rate and survivorship of those eggs were significantly reduced. Observations following hatch of surface sterilized eggs also revealed significant effects on wandering behavior of the first instars. The second generation progeny from adults of the sterilized cohorts showed significantly lower survival to adulthood, averaging only 0.3% compared to 20.8% for the control cohorts. Taken together, results demonstrate that H. halys is heavily impacted by deprival of its gut symbionts. Given the economic status of this invasive pest, further investigations may lead to management tactics that disrupt this close symbiotic

  12. The importance of gut symbionts in the development of the brown marmorated stink bug, Halyomorpha halys (Stål).

    Science.gov (United States)

    Taylor, Christopher M; Coffey, Peter L; DeLay, Bridget D; Dively, Galen P

    2014-01-01

    The invasive brown marmorated stink bug, Halyomorpha halys (Stål), has become a severe agricultural pest and nuisance problem since its introduction in the U.S. Research is being conducted to understand its biology and to find management solutions. Its symbiotic relationship with gut symbionts is one aspect of its biology that is not understood. In the family Pentatomidae, the reliance on gut symbionts for successful development seems to vary depending on the species of stink bug. This research assessed the role of gut symbionts in the development, survivorship, and fecundity of H. halys. We compared various fitness parameters of nymphs and adults reared from surface sterilized and untreated egg masses during two consecutive generations under laboratory conditions. Results provided direct evidence that H. halys is negatively impacted by the prevention of vertical transmission of its gut symbionts and that this impact is significant in the first generation and manifests dramatically in the subsequent generation. Developmental time and survivorship of treated cohorts in the first generation were significantly affected during third instar development through to the adult stage. Adults from the sterilized treatment group exhibited longer pre-oviposition periods, produced fewer egg masses, had significantly smaller clutch sizes, and the hatch rate and survivorship of those eggs were significantly reduced. Observations following hatch of surface sterilized eggs also revealed significant effects on wandering behavior of the first instars. The second generation progeny from adults of the sterilized cohorts showed significantly lower survival to adulthood, averaging only 0.3% compared to 20.8% for the control cohorts. Taken together, results demonstrate that H. halys is heavily impacted by deprival of its gut symbionts. Given the economic status of this invasive pest, further investigations may lead to management tactics that disrupt this close symbiotic relationship in

  13. The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont coronympha.

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    James T Harper

    Full Text Available BACKGROUND: For the majority of microbial eukaryotes (protists, algae, there is no clearly superior species concept that is consistently applied. In the absence of a practical biological species concept, most species and genus level delineations have historically been based on morphology, which may lead to an underestimate of the diversity of microbial eukaryotes. Indeed, a growing body of molecular evidence, such as barcoding surveys, is beginning to support the conclusion that significant cryptic species diversity exists. This underestimate of diversity appears to be due to a combination of using morphology as the sole basis for assessing diversity and our inability to culture the vast majority of microbial life. Here we have used molecular markers to assess the species delineations in two related but morphologically distinct genera of uncultivated symbionts found in the hindgut of termites. METHODOLOGY/PRINCIPAL FINDINGS: Using single-cell isolation and environmental PCR, we have used a barcoding approach to characterize the diversity of Coronympha and Metacoronympha symbionts in four species of Incisitermes termites, which were also examined using scanning electron microscopy and light microcopy. Despite the fact that these genera are significantly different in morphological complexity and structural organisation, we find they are two life history stages of the same species. At the same time, we show that the symbionts from different termite hosts show an equal or greater level of sequence diversity than do the hosts, despite the fact that the symbionts are all classified as one species. CONCLUSIONS/SIGNIFICANCE: The morphological information used to describe the diversity of these microbial symbionts is misleading at both the genus and species levels, and led to an underestimate of species level diversity as well as an overestimate of genus level diversity. The genus 'Metacoronympha' is invalid and appears to be a life history stage of

  14. Antagonistic bacterial interactions help shape host-symbiont dynamics within the fungus-growing ant-microbe mutualism.

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    Michael Poulsen

    Full Text Available Conflict within mutually beneficial associations is predicted to destabilize relationships, and theoretical and empirical work exploring this has provided significant insight into the dynamics of cooperative interactions. Within mutualistic associations, the expression and regulation of conflict is likely more complex than in intraspecific cooperative relationship, because of the potential presence of: i multiple genotypes of microbial species associated with individual hosts, ii multiple species of symbiotic lineages forming cooperative partner pairings, and iii additional symbiont lineages. Here we explore complexity of conflict expression within the ancient and coevolved mutualistic association between attine ants, their fungal cultivar, and actinomycetous bacteria (Pseudonocardia. Specifically, we examine conflict between the ants and their Pseudonocardia symbionts maintained to derive antibiotics against parasitic microfungi (Escovopsis infecting the ants' fungus garden. Symbiont assays pairing isolates of Pseudonocardia spp. associated with fungus-growing ants spanning the phylogenetic diversity of the mutualism revealed that antagonism between strains is common. In contrast, antagonism was substantially less common between more closely related bacteria associated with Acromyrmex leaf-cutting ants. In both experiments, the observed variation in antagonism across pairings was primarily due to the inhibitory capabilities and susceptibility of individual strains, but also the phylogenetic relationships between the ant host of the symbionts, as well as the pair-wise genetic distances between strains. The presence of antagonism throughout the phylogenetic diversity of Pseudonocardia symbionts indicates that these reactions likely have shaped the symbiosis from its origin. Antagonism is expected to prevent novel strains from invading colonies, enforcing single-strain rearing within individual ant colonies. While this may align ant

  15. Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species.

    Science.gov (United States)

    Bisch, Gaëlle; Ogier, Jean-Claude; Médigue, Claudine; Rouy, Zoé; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2016-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Within Xenorhabdus bovienii species, the X. bovienii CS03 strain (Xb CS03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its Steinernema symbiont. The genome of Xb CS03 was sequenced and compared with the genome of a virulent strain, X. bovienii SS-2004 (Xb SS-2004). The genome size and content widely differed between the two strains. Indeed, Xb CS03 had a large genome containing several specific loci involved in the inhibition of competitors, including a few NRPS-PKS loci (nonribosomal peptide synthetases and polyketide synthases) producing antimicrobial molecules. Consistently, Xb CS03 had a greater antimicrobial activity than Xb SS-2004. The Xb CS03 strain contained more pseudogenes than Xb SS-2004. Decay of genes involved in the host invasion and exploitation (toxins, invasins, or extracellular enzymes) was particularly important in Xb CS03. This may provide an explanation for the nonvirulence of the strain when injected into an insect host. We suggest that Xb CS03 and Xb SS-2004 followed divergent evolutionary scenarios to cope with their peculiar life cycle. The fitness strategy of Xb CS03 would involve competitor inhibition, whereas Xb SS-2004 would quickly and efficiently kill the insect host. Hence, Xenorhabdus strains would have widely divergent host exploitation strategies, which impact their genome structure. PMID:26769959

  16. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  17. Symbiont-derived beta-1,3-glucanases in a social insect: mutualism beyond nutrition

    Directory of Open Access Journals (Sweden)

    Rebeca B Rosengaus

    2014-11-01

    Full Text Available Termites have had a long co-evolutionary history with prokaryotic and eukaryotic gut microbes. Historically, the role of these anaerobic obligate symbionts has been attributed to the nutritional welfare of the host. We provide evidence that protozoa (and/or their associated bacteria colonizing the hindgut of the dampwood termite Zootermopsis angusticollis, synthesize multiple functional beta-1,3-glucanases, enzymes known for breaking down beta-1,3-glucans, the main component of fungal cell walls. These enzymes, we propose, may help in both digestion of ingested fungal hyphae and protection against invasion by fungal pathogens. This research points to an additional novel role for the mutualistic hindgut microbial consortia of termites, an association that may extend beyond ligno-cellulolytic activity and nitrogen fixation to include a reduction in the risks of mycosis at both the individual- and colony-levels while nesting in and feeding on microbial-rich decayed wood.

  18. A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses

    CERN Document Server

    Schardl, Chris L; Lindstrom, Adam; Speakman, Skyler; Stromberg, Arnold; Yoshida, Ruriko

    2007-01-01

    Significant phylogenetic codivergence between plant or animal hosts ($H$) and their symbionts or parasites ($P$) indicate the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). These widespread symbioses often help protect host plants from herbivory and stresses, and affect species diversity and food web structures. Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichlo\\"e codivergence. MRCALink applied to ultrametric $H$ and $P$ trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random $H$ and $P$ tree pairs estimated by a Monte Carlo method.

  19. Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific.

    Science.gov (United States)

    Iglesias-Prieto, R.; Beltrán, V. H.; LaJeunesse, T. C.; Reyes-Bonilla, H.; Thomé, P. E.

    2004-01-01

    Symbiotic reef corals occupy the entire photic zone; however, most species have distinct zonation patterns within the light intensity gradient. It is hypothesized that the presence of specific symbionts adapted to different light regimes may determine the vertical distribution of particular hosts. We have tested this hypothesis by genetic and in situ physiological analyses of the algal populations occupying two dominant eastern Pacific corals, over their vertical distribution in the Gulf of California. Our findings indicate that each coral species hosts a distinct algal taxon adapted to a particular light regime. The differential use of light by specific symbiotic dinoflagellates constitutes an important axis for niche diversification and is sufficient to explain the vertical distribution patterns of these two coral species. PMID:15306298

  20. Exploring the potential for actinobacteria as defensive symbionts in fungus-growing termites

    DEFF Research Database (Denmark)

    Visser, Anna A.; Nobre, Tânia; Currie, Cameron R.;

    2012-01-01

    for morphological (288 isolates, grouped in 44 morphotypes) and for 16S rRNA (35 isolates, spanning the majority of morphotypes) characterisation. Actinobacteria were found throughout all sampled nests and colony parts and, phylogenetically, they are interspersed with Actinobacteria from origins other than fungus...... a role as defensive symbionts against Pseudoxylaria in fungus-growing termites. We sampled for Actinobacteria from 30 fungus-growing termite colonies, spanning the three main termite genera and two geographically distant sites. Our isolations yielded 360 Actinobacteria, from which we selected subsets......-growing termites, indicating lack of specificity. Antibiotic-activity screening of 288 isolates against the fungal cultivar and competitor revealed that most of the Actinobacteria-produced molecules with antifungal activity. A more detailed bioassay on 53 isolates, to test the specificity of antibiotics, showed...

  1. The presence of a mycangium in European Sinodendron cylindricum (Coleoptera: Lucanidae) and the associated yeast symbionts

    Science.gov (United States)

    Tanahashi, Masahiko; Hawes, Colin J.

    2016-01-01

    Part of the exoskeleton of some wood-inhabiting insects is modified to form a mycangium, which is a specialized organ used to convey fungal spores or yeasts to their offspring. Although most stag beetles (Coleoptera: Lucanidae) are known to have female-specific mycangia and associated yeast symbionts, the evolutionary origin of the mycangium in this group remains unresolved. Here, we report the presence of a mycangium and associated yeast symbionts in the European horned stag beetle Sinodendron cylindricum (L.), which belongs to an ancestral clade of the Lucanidae. The mycangium of S. cylindricum is shown to be female-specific and have the same developmental origin as that of other stag beetles. A total of five yeast strains were isolated from adult mycangia and larval gut of S. cylindricum. Of these, we suggest that SICYAM1 is an undescribed yeast with taxonomic novelty, and have identified SICYLG3 as the xylose-fermenting yeast Scheffersomyces insectosa using nuclear ribosomal RNA and ITS sequences. The remaining three yeast strains, SICYAM2, SICYLG1, and SICYLG2, were assigned to the genus Sugiyamaella. Yeast density in the adult mycangium was lower than that of the more evolutionarily advanced stag beetles, the European Lucanus cervus (L.) and Dorcus parallelipipedus (L.), which were also examined in this study. No living yeasts were isolated from the adult guts. However, a third instar larva of S. cylindricum harbored 104–106 living yeasts in each gut region, which suggests that gut yeasts play an important role in these wood-feeding larvae. PMID:27432353

  2. Reductive genome evolution, host–symbiont co-speciation and uterine transmission of endosymbiotic bacteria in bat flies

    OpenAIRE

    Hosokawa, Takahiro; Nikoh, Naruo; Koga, Ryuichi; Satô, Masahiko; Tanahashi, Masahiko; Meng, Xian-Ying; Fukatsu, Takema

    2011-01-01

    Bat flies of the family Nycteribiidae are known for their extreme morphological and physiological traits specialized for ectoparasitic blood-feeding lifestyle on bats, including lack of wings, reduced head and eyes, adenotrophic viviparity with a highly developed uterus and milk glands, as well as association with endosymbiotic bacteria. We investigated Japanese nycteribiid bat flies representing 4 genera, 8 species and 27 populations for their bacterial endosymbionts. From all the nycteribii...

  3. Recovery from bleaching is mediated by threshold densities of background thermo-tolerant symbiont types in a reef-building coral

    Science.gov (United States)

    Bay, Line K.; Doyle, Jason; Logan, Murray; Berkelmans, Ray

    2016-01-01

    Sensitive molecular analyses show that most corals host a complement of Symbiodinium genotypes that includes thermo-tolerant types in low abundance. While tolerant symbiont types are hypothesized to facilitate tolerance to temperature and recovery from bleaching, empirical data on their distribution and relative abundance in corals under ambient and stress conditions are still rare. We quantified visual bleaching and mortality of coral hosts, along with relative abundance of C- and D-type Symbiodinium cells in 82 Acropora millepora colonies from three locations on the Great Barrier Reef transplanted to a central inshore site over a 13 month period. Our analyses reveal dynamic change in symbiont associations within colonies and among populations over time. Coral bleaching and declines in C- but not D-type symbionts were observed in transplanted corals. Survival and recovery of 25% of corals from one population was associated with either initial D-dominance or an increase in D-type symbionts that could be predicted by a minimum pre-stress D : C ratio of 0.003. One-third of corals from this population became D dominated at the bleached stage despite no initial detection of this symbiont type, but failed to recover and died in mid to late summer. These results provide a predictive threshold minimum density of background D-type symbionts in A. millepora, above which survival following extreme thermal stress is increased. PMID:27429786

  4. Recovery from bleaching is mediated by threshold densities of background thermo-tolerant symbiont types in a reef-building coral.

    Science.gov (United States)

    Bay, Line K; Doyle, Jason; Logan, Murray; Berkelmans, Ray

    2016-06-01

    Sensitive molecular analyses show that most corals host a complement of Symbiodinium genotypes that includes thermo-tolerant types in low abundance. While tolerant symbiont types are hypothesized to facilitate tolerance to temperature and recovery from bleaching, empirical data on their distribution and relative abundance in corals under ambient and stress conditions are still rare. We quantified visual bleaching and mortality of coral hosts, along with relative abundance of C- and D-type Symbiodinium cells in 82 Acropora millepora colonies from three locations on the Great Barrier Reef transplanted to a central inshore site over a 13 month period. Our analyses reveal dynamic change in symbiont associations within colonies and among populations over time. Coral bleaching and declines in C- but not D-type symbionts were observed in transplanted corals. Survival and recovery of 25% of corals from one population was associated with either initial D-dominance or an increase in D-type symbionts that could be predicted by a minimum pre-stress D : C ratio of 0.003. One-third of corals from this population became D dominated at the bleached stage despite no initial detection of this symbiont type, but failed to recover and died in mid to late summer. These results provide a predictive threshold minimum density of background D-type symbionts in A. millepora, above which survival following extreme thermal stress is increased. PMID:27429786

  5. Integrative study of a new cold-seep mussel (Mollusca: Bivalvia) associated with chemosynthetic symbionts in the Marmara Sea

    Science.gov (United States)

    Ritt, Bénédicte; Duperron, Sébastien; Lorion, Julien; Sara Lazar, Cassandre; Sarrazin, Jozée

    2012-09-01

    Recently, small Idas-like mussels have been discovered living on carbonate crusts associated with cold-seeps in the Marmara Sea. These mussels, here referred to as Idas-like nov. sp., differ morphologically and genetically from another species identified as Idas aff. modiolaeformis, living in the same type of ecosystem in the Nile Deep-Sea Fan (eastern Mediterranean Sea). A phylogenetic analysis confirms the distinction between the two species, which belong to highly divergent lineages. Carbon stable isotope values, as well as the detection of thiotroph-related bacteria in the gill tissue, support the presence of a symbiotic, thiotroph-derived nutrition. In contrast, Idas aff. modiolaeformis displays six different types of symbionts. Finally our size-frequency data suggest that the recruitment is continuous in the examined area. The present study extends the documented distribution of symbiont-bearing mussels to the Marmara Sea, and contributes to the characterisation of biological communities in this recently explored area.

  6. The chloroplast genome of a symbiodinium sp. clade C3 isolate

    KAUST Repository

    Barbrook, Adrian C.

    2014-01-01

    Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as \\'minicircles\\'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any \\'empty\\' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic. © 2013 Adrian C. Barbrook.

  7. Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography

    Energy Technology Data Exchange (ETDEWEB)

    Normand, Philippe; Lapierre, Pascal; Tisa, Louis S.; Gogarten, J.Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A.; Berry,Alison; Bickhart, Derek M.; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, M. Pilar; Ggoltsman, Eugene; Huang, Ying; Kopp, Olga; Labarre,Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez,Michele; Mastronunzio, Juliana E.; Mullin, Beth; Niemann, James; Pujic,Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt,Anita; Tavares, Fernando; Tomkins, Jeffrey P.; Vallenet, David; Valverde,Claudio; Wall, Luis; Wang, Ying; Medigue, Claudine; Benson, David R.

    2006-02-01

    Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenome contraction, whereas host plant diversification favored genomeexpansion. The results support the idea that major genome reductions aswell as expansions can occur in facultatively symbiotic soil bacteria asthey respond to new environments in the context of theirsymbioses.

  8. The Population Structure of Antibiotic-Producing Bacterial Symbionts of Apterostigma dentigerum Ants: Impacts of Coevolution and Multipartite Symbiosis

    OpenAIRE

    Caldera, Eric J.; Currie, Cameron R

    2012-01-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to n...

  9. Potential costs of acclimatization to a warmer climate: growth of a reef coral with heat tolerant vs. sensitive symbiont types.

    Directory of Open Access Journals (Sweden)

    Alison Jones

    Full Text Available One of the principle ways in which reef building corals are likely to cope with a warmer climate is by changing to more thermally tolerant endosymbiotic algae (zooxanthellae genotypes. It is highly likely that hosting a more heat-tolerant algal genotype will be accompanied by tradeoffs in the physiology of the coral. To better understand one of these tradeoffs, growth was investigated in the Indo-Pacific reef-building coral Acropora millepora in both the laboratory and the field. In the Keppel Islands in the southern Great Barrier Reef this species naturally harbors nrDNA ITS1 thermally sensitive type C2 or thermally tolerant type D zooxanthellae of the genus Symbiodinium and can change dominant type following bleaching. We show that under controlled conditions, corals with type D symbionts grow 29% slower than those with type C2 symbionts. In the field, type D colonies grew 38% slower than C2 colonies. These results demonstrate the magnitude of trade-offs likely to be experienced by this species as they acclimatize to warmer conditions by changing to more thermally tolerant type D zooxanthellae. Irrespective of symbiont genotype, corals were affected to an even greater degree by the stress of a bleaching event which reduced growth by more than 50% for up to 18 months compared to pre-bleaching rates. The processes of symbiont change and acute thermal stress are likely to act in concert on coral growth as reefs acclimatize to more stressful warmer conditions, further compromising their regeneration capacity following climate change.

  10. Effects of Light, Food Availability and Temperature Stress on the Function of Photosystem II and Photosystem I of Coral Symbionts

    OpenAIRE

    Hoogenboom, Mia O.; Campbell, Douglas A; Beraud, Eric; DeZeeuw, Katrina; Ferrier-Pagès, Christine

    2012-01-01

    Background Reef corals are heterotrophic coelenterates that achieve high productivity through their photosynthetic dinoflagellate symbionts. Excessive seawater temperature destabilises this symbiosis and causes corals to “bleach,” lowering their photosynthetic capacity. Bleaching poses a serious threat to the persistence of coral reefs on a global scale. Despite expanding research on the causes of bleaching, the mechanisms remain a subject of debate. Methodology/Principal Findings This study ...

  11. Host–symbiont recombination versus natural selection in the response of coral–dinoflagellate symbioses to environmental disturbance

    OpenAIRE

    LaJeunesse, Todd C.; Smith, Robin; Walther, Mariana; Pinzón, Jorge; Daniel T Pettay; McGinley, Michael; Aschaffenburg, Matthew; Medina-Rosas, Pedro; Cupul-Magaña, Amilcar L.; Pérez, Andrés López; Reyes-Bonilla, Hector; Warner, Mark E.

    2010-01-01

    Mutualisms between reef-building corals and endosymbiotic dinoflagellates are particularly sensitive to environmental stress, yet the ecosystems they construct have endured major oscillations in global climate. During the winter of 2008, an extreme cold-water event occurred in the Gulf of California that bleached corals in the genus Pocillopora harbouring a thermally ‘sensitive’ symbiont, designated Symbiodinium C1b-c, while colonies possessing Symbiodinium D1 were mostly unaffected. Certain ...

  12. Host–symbiont recombination versus natural selection in the response of coral–dinoflagellate symbioses to environmental disturbance

    Science.gov (United States)

    LaJeunesse, Todd C.; Smith, Robin; Walther, Mariana; Pinzón, Jorge; Pettay, Daniel T.; McGinley, Michael; Aschaffenburg, Matthew; Medina-Rosas, Pedro; Cupul-Magaña, Amilcar L.; Pérez, Andrés López; Reyes-Bonilla, Hector; Warner, Mark E.

    2010-01-01

    Mutualisms between reef-building corals and endosymbiotic dinoflagellates are particularly sensitive to environmental stress, yet the ecosystems they construct have endured major oscillations in global climate. During the winter of 2008, an extreme cold-water event occurred in the Gulf of California that bleached corals in the genus Pocillopora harbouring a thermally ‘sensitive’ symbiont, designated Symbiodinium C1b-c, while colonies possessing Symbiodinium D1 were mostly unaffected. Certain bleached colonies recovered quickly while others suffered partial or complete mortality. In most colonies, no appreciable change was observed in the identity of the original symbiont, indicating that these partnerships are stable. During the initial phases of recovery, a third species of symbiont B1Aiptasia, genetically identical to that harboured by the invasive anemone, Aiptasia sp., grew opportunistically and was visible as light-yellow patches on the branch tips of several colonies. However, this symbiont did not persist and was displaced in all cases by C1b-c several months later. Colonies with D1 were abundant at inshore habitats along the continental eastern Pacific, where seasonal turbidity is high relative to offshore islands. Environmental conditions of the central and southern coasts of Mexico were not sufficient to explain the exclusivity of D1 Pocillopora in these regions. It is possible that mass mortalities associated with major thermal disturbances during the 1997–1998 El Niño Southern Oscillation eliminated C1b-c holobionts from these locations. The differential loss of Pocillopora holobionts in response to thermal stress suggests that natural selection on existing variation can cause rapid and significant shifts in the frequency of particular coral–algal partnerships. However, coral populations may take decades to recover following episodes of severe selection, thereby raising considerable uncertainty about the long-term viability of these communities

  13. Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes

    OpenAIRE

    Silipo, A.; Vitiello, G.; Gully, Djamel; L. Sturiale; Chaintreuil, Clémence; Fardoux, Joël; Gargani, D.; Lee, H I; Kulkarni, G; Busset, N.; Marchetti, R.; Palmigiano, A.; Moll, H; Engel, R; Lanzetta, R

    2014-01-01

    Lipopolysaccharides (LPSs) are major components of the outer membrane of Gram-negative bacteria and are essential for their growth and survival. They act as a structural barrier and play an important role in the interaction with eukaryotic hosts. Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A. Biophysical analyses of reconstituted liposomes indicate that this hopanoid...

  14. Host-symbiont recombination versus natural selection in the response of coral-dinoflagellate symbioses to environmental disturbance.

    Science.gov (United States)

    LaJeunesse, Todd C; Smith, Robin; Walther, Mariana; Pinzón, Jorge; Pettay, Daniel T; McGinley, Michael; Aschaffenburg, Matthew; Medina-Rosas, Pedro; Cupul-Magaña, Amilcar L; Pérez, Andrés López; Reyes-Bonilla, Hector; Warner, Mark E

    2010-10-01

    Mutualisms between reef-building corals and endosymbiotic dinoflagellates are particularly sensitive to environmental stress, yet the ecosystems they construct have endured major oscillations in global climate. During the winter of 2008, an extreme cold-water event occurred in the Gulf of California that bleached corals in the genus Pocillopora harbouring a thermally 'sensitive' symbiont, designated Symbiodinium C1b-c, while colonies possessing Symbiodinium D1 were mostly unaffected. Certain bleached colonies recovered quickly while others suffered partial or complete mortality. In most colonies, no appreciable change was observed in the identity of the original symbiont, indicating that these partnerships are stable. During the initial phases of recovery, a third species of symbiont B1(Aiptasia), genetically identical to that harboured by the invasive anemone, Aiptasia sp., grew opportunistically and was visible as light-yellow patches on the branch tips of several colonies. However, this symbiont did not persist and was displaced in all cases by C1b-c several months later. Colonies with D1 were abundant at inshore habitats along the continental eastern Pacific, where seasonal turbidity is high relative to offshore islands. Environmental conditions of the central and southern coasts of Mexico were not sufficient to explain the exclusivity of D1 Pocillopora in these regions. It is possible that mass mortalities associated with major thermal disturbances during the 1997-1998 El Niño Southern Oscillation eliminated C1b-c holobionts from these locations. The differential loss of Pocillopora holobionts in response to thermal stress suggests that natural selection on existing variation can cause rapid and significant shifts in the frequency of particular coral-algal partnerships. However, coral populations may take decades to recover following episodes of severe selection, thereby raising considerable uncertainty about the long-term viability of these communities. PMID

  15. Antagonistic bacterial interactions help shape host-symbiont dynamics within the fungus-growing ant-microbe mutualism

    DEFF Research Database (Denmark)

    Poulsen, Michael; Erhardt, Daniel P; Molinaro, Daniel J;

    2007-01-01

    . Here we explore complexity of conflict expression within the ancient and coevolved mutualistic association between attine ants, their fungal cultivar, and actinomycetous bacteria (Pseudonocardia). Specifically, we examine conflict between the ants and their Pseudonocardia symbionts maintained to derive...... was substantially less common between more closely related bacteria associated with Acromyrmex leaf-cutting ants. In both experiments, the observed variation in antagonism across pairings was primarily due to the inhibitory capabilities and susceptibility of individual strains, but also the...

  16. Metabolite profiling of symbiont and host during thermal stress and bleaching in a model cnidarian-dinoflagellate symbiosis.

    Science.gov (United States)

    Hillyer, Katie E; Tumanov, Sergey; Villas-Bôas, Silas; Davy, Simon K

    2016-02-01

    Bleaching (dinoflagellate symbiont loss) is one of the greatest threats facing coral reefs. The functional cnidarian-dinoflagellate symbiosis, which forms coral reefs, is based on the bi-directional exchange of nutrients. During thermal stress this exchange breaks down; however, major gaps remain in our understanding of the roles of free metabolite pools in symbiosis and homeostasis. In this study we applied gas chromatography-mass spectrometry (GC-MS) to explore thermally induced changes in intracellular pools of amino and non-amino organic acids in each partner of the model sea anemone Aiptasia sp. and its dinoflagellate symbiont. Elevated temperatures (32 °C for 6 days) resulted in symbiont photoinhibition and bleaching. Thermal stress induced distinct changes in the metabolite profiles of both partners, associated with alterations to central metabolism, oxidative state, cell structure, biosynthesis and signalling. Principally, we detected elevated pools of polyunsaturated fatty acids (PUFAs) in the symbiont, indicative of modifications to lipogenesis/lysis, membrane structure and nitrogen assimilation. In contrast, reductions of multiple PUFAs were detected in host pools, indicative of increased metabolism, peroxidation and/or reduced translocation of these groups. Accumulations of glycolysis intermediates were also observed in both partners, associated with photoinhibition and downstream reductions in carbohydrate metabolism. Correspondingly, we detected accumulations of amino acids and intermediate groups in both partners, with roles in gluconeogenesis and acclimation responses to oxidative stress. These data further our understanding of cellular responses to thermal stress in the symbiosis and generate hypotheses relating to the secondary roles of a number of compounds in homeostasis and heat-stress resistance. PMID:26685173

  17. Expression patterns of mRNAs for methanotrophy and thiotrophy in symbionts of the hydrothermal vent mussel Bathymodiolus puteoserpentis

    OpenAIRE

    Wendeberg, Annelie; Zielinski, Frank U.; Borowski, Christian; Dubilier, Nicole

    2011-01-01

    The hydrothermal vent mussel Bathymodiolus puteoserpentis (Mytilidae) from the Mid-Atlantic Ridge hosts symbiotic sulfur- and methane-oxidizing bacteria in its gills. In this study, we investigated the activity and distribution of these two symbionts in juvenile mussels from the Logatchev hydrothermal vent field (14°45′N Mid-Atlantic Ridge). Expression patterns of two key genes for chemosynthesis were examined: pmoA (encoding subunit A of the particulate methane monooxygenase) as an indicator...

  18. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

    KAUST Repository

    Bayer, Kristina

    2014-07-09

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. The authors quantified sponge symbionts in eight sponge species from three different locations by real time PCR targetting 16S rRNA genes. Additionally, FISH was performed and diversity and abundance of singularized microbial symbionts from Aplysina aerophoba was determined for a comprehensive quantification work. © 2014 Federation of European Microbiological Societies.

  19. Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change.

    Science.gov (United States)

    Hume, Benjamin C C; Voolstra, Christian R; Arif, Chatchanit; D'Angelo, Cecilia; Burt, John A; Eyal, Gal; Loya, Yossi; Wiedenmann, Jörg

    2016-04-19

    Coral communities in the Persian/Arabian Gulf (PAG) withstand unusually high salinity levels and regular summer temperature maxima of up to ∼35 °C that kill conspecifics elsewhere. Due to the recent formation of the PAG and its subsequent shift to a hot climate, these corals have had only coral reefs may respond to global warming. One key to coral survival in the world's warmest reefs are symbioses with a newly discovered alga,Symbiodinium thermophilum Currently, it is unknown whether this symbiont originated elsewhere or emerged from unexpectedly fast evolution catalyzed by the extreme environment. Analyzing genetic diversity of symbiotic algae across >5,000 km of the PAG, the Gulf of Oman, and the Red Sea coastline, we show thatS. thermophilumis a member of a highly diverse, ancient group of symbionts cryptically distributed outside the PAG. We argue that the adjustment to temperature extremes by PAG corals was facilitated by the positive selection of preadapted symbionts. Our findings suggest that maintaining the largest possible pool of potentially stress-tolerant genotypes by protecting existing biodiversity is crucial to promote rapid adaptation to present-day climate change, not only for coral reefs, but for ecosystems in general. PMID:27044109

  20. Discordant coral-symbiont structuring: factors shaping geographical variation of Symbiodinium communities in a facultative zooxanthellate coral genus, Oculina

    Science.gov (United States)

    Leydet, Karine Posbic; Hellberg, Michael E.

    2016-06-01

    Understanding the factors that help shape the association between corals and their algal symbionts, zooxanthellae ( Symbiodinium), is necessary to better understand the functional diversity and acclimatization potential of the coral host. However, most studies focus on tropical zooxanthellate corals and their obligate algal symbionts, thus limiting our full comprehension of coral-algal symbiont associations. Here, we examine algal associations in a facultative zooxanthellate coral. We survey the Symbiodinium communities associated with Oculina corals in the western North Atlantic and the Mediterranean using one clade-level marker ( psbA coding region) and three fine-scale markers ( cp23S- rDNA, b7sym15 flanking region, and b2sym17). We ask whether Oculina spp. harbor geographically different Symbiodinium communities across their geographic range and, if so, whether the host's genetics or habitat differences are correlated with this geographical variation. We found that Oculina corals harbor different Symbiodinium communities across their geographical range. Of the habitat differences (including chlorophyll a concentration and depth), sea surface temperature is better correlated with this geographical variation than the host's genetics, a pattern most evident in the Mediterranean. Our results suggest that although facultative zooxanthellate corals may be less dependent on their algal partners compared to obligate zooxanthellate corals, the Symbiodinium communities that they harbor may nevertheless reflect acclimatization to environmental variation among habitats.

  1. Carbon translocation from symbiont to host depends on irradiance and food availability in the tropical coral Stylophora pistillata

    Science.gov (United States)

    Tremblay, P.; Grover, R.; Maguer, J. F.; Hoogenboom, M.; Ferrier-Pagès, C.

    2014-03-01

    Reef-building corals live in symbiosis with dinoflagellates that translocate a large proportion of their photosynthetically fixed carbon compounds to their coral host for its own metabolism. The carbon budget and translocation rate, however, vary depending on environmental conditions, coral host species, and symbiont clade. To quantify variability in carbon translocation in response to environmental conditions, this study assessed the effect of two different irradiance levels (120 and 250 μmol photons m-2 s-1) and feeding regimes (fed with Artemia salina nauplii and unfed) on the carbon budget of the tropical coral Stylophora pistillata. For this purpose, H13CO3 --enriched seawater was used to trace the conversion of photosynthetic carbon into symbiont and coral biomass and excrete particulate organic carbon. Results showed that carbon translocation (ca. 78 %) and utilization were similar under both irradiance levels for unfed colonies. In contrast, carbon utilization by fed colonies was dependent on the growth irradiance. Under low irradiance, heterotrophy was accompanied by lower carbon translocation (71 %), higher host and symbiont biomass, and higher calcification rates. Under high irradiance, heterotrophy was accompanied by higher rates of photosynthesis, respiration, and carbon translocation (90 %) as well as higher host biomass. Hence, levels of resource sharing within coral-dinoflagellate symbioses depend critically on environmental conditions.

  2. Coral bleaching under thermal stress: putative involvement of host/symbiont recognition mechanisms

    Directory of Open Access Journals (Sweden)

    Tambutte Sylvie

    2009-08-01

    Full Text Available Abstract Background Coral bleaching can be defined as the loss of symbiotic zooxanthellae and/or their photosynthetic pigments from their cnidarian host. This major disturbance of reef ecosystems is principally induced by increases in water temperature. Since the beginning of the 1980s and the onset of global climate change, this phenomenon has been occurring at increasing rates and scales, and with increasing severity. Several studies have been undertaken in the last few years to better understand the cellular and molecular mechanisms of coral bleaching but the jigsaw puzzle is far from being complete, especially concerning the early events leading to symbiosis breakdown. The aim of the present study was to find molecular actors involved early in the mechanism leading to symbiosis collapse. Results In our experimental procedure, one set of Pocillopora damicornis nubbins was subjected to a gradual increase of water temperature from 28°C to 32°C over 15 days. A second control set kept at constant temperature (28°C. The differentially expressed mRNA between the stressed states (sampled just before the onset of bleaching and the non stressed states (control were isolated by Suppression Subtractive Hybridization. Transcription rates of the most interesting genes (considering their putative function were quantified by Q-RT-PCR, which revealed a significant decrease in transcription of two candidates six days before bleaching. RACE-PCR experiments showed that one of them (PdC-Lectin contained a C-Type-Lectin domain specific for mannose. Immunolocalisation demonstrated that this host gene mediates molecular interactions between the host and the symbionts suggesting a putative role in zooxanthellae acquisition and/or sequestration. The second gene corresponds to a gene putatively involved in calcification processes (Pdcyst-rich. Its down-regulation could reflect a trade-off mechanism leading to the arrest of the mineralization process under stress

  3. Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

    Energy Technology Data Exchange (ETDEWEB)

    McNulty, Nathan [Washington University, St. Louis; Wu, Meng [Washington University, St. Louis; Erickson, Alison L [ORNL; Pan, Chongle [ORNL; Erickson, Brian K [ORNL; Martens, Eric C [University of Michigan; Pudlo, Nicholas A [University of Michigan; Muegge, Brian [Washington University, St. Louis; Henrissat, Bernard [Universite d' Aix-Marseille I & II; Hettich, Robert {Bob} L [ORNL; Gordon, Jeffrey [Washington University, St. Louis

    2013-01-01

    The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising .90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism s 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight

  4. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia.

    Science.gov (United States)

    Bayer, Kristina; Scheuermayer, Matthias; Fieseler, Lars; Hentschel, Ute

    2013-02-01

    Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions. PMID:22562484

  5. Linking eye design with host symbiont relationships in pontoniine shrimps (Crustacea, Decapoda, Palaemonidae.

    Directory of Open Access Journals (Sweden)

    Nicola C Dobson

    Full Text Available Symbiosis is prevalent in the marine environment with many studies examining the effects of such interactions between host and symbiont. Pontoniine shrimps are a group whose ecology is characterised by symbiotic interactions. This investigation examines the gross morphology of Pontoniinae compound eyes and superficial optical parameters with reference to their symbiotic relationship or lifestyle category; free-living, ectosymbiont, endosymbiont (bivalves or endosymbiont (non-bivalves. The eye morphologies of free-living and ectosymbiotic species are very similar, yet differ from both forms of endosymbiotic species. Endosymbionts have significantly smaller and simpler eyes with larger facets and bigger interommatidial angles and eye parameters for increased sensitivity levels. However bivalve endosymbionts form an intermediary group between non-bivalve endosymbionts and ectosymbionts as a result of their more active lifestyle. The accessory eye or "nebenauge", although of uncertain function, commonly occurs in free-living Pontoniinae species but rarely in endosymbionts apart from in more primitive species. The variation in morphology reflects tensions between functional requirements and ecological pressures that have strongly influenced eye design in Pontoniinae.

  6. Identification of Methanotrophic Biomarker Lipids in the Symbiont-Containing Gills of Seep Mussels

    Science.gov (United States)

    Jahnke, L. L.; Zahiralis, K. D.; Klein, H. P.; Morrison, David (Technical Monitor)

    1994-01-01

    Mussels collected from hydrocarbon seeps in the Gulf of Mexico grow with methane as sole carbon and energy source due to a symbiotic association with methane-oxidizing bacteria. Transmission electron micrographs of mussel gills show cells with stacked intracytoplasmic membranes similar to type I methanotrophic bacteria. Methanotrophs are known to synthesize several types of cyclic triterpenes, hopanoids and methyl sterols, as well as unique monounsaturated fatty acid, double bond positional isomers that serve as biomarkers for this group. Lipid analysis of dissected mussels demonstrated the presence of these biomarkers predominantly in the gill tissue with much smaller amounts in mantle and remaining body tissues. Gill tissue contained 1150 micrograms/g dry wt. of hopanepolyol derivatives and diplopterol while the mantle tissue contained only 17 micrograms/g. The C16 monounsaturated fatty acids (16:1) characteristic of type I methanotrophic membranes dominated the gill tissue making up 53% of the total while only 5% 16:1 was present in the mantle tissue. The methyl sterol distribution was more dispersed. The predominant sterol in all tissues was cholesterol with lesser amounts of other desmethyl and 4-methyl sterols. The gill and mantle tissues contained 3461 micrograms (17% methyl) and 2750 micrograms (5% methyl) sterol per gm dry wt., respectively. Methyl sterol accounted for 44% of the sterol esters isolated from the gill, suggesting active demethylation of the methanotrophic sterols in this tissue. The use of lipid biomarkers could provide an effective means for identifying host-symbiont relationships.

  7. Effects of large mammalian herbivores and ant symbionts on condensed tannins of Acacia drepanolobium in Kenya.

    Science.gov (United States)

    Ward, David; Young, Truman P

    2002-05-01

    Condensed tannins have been considered to be important inducible defenses against mammalian herbivory. We tested for differences in condensed tannin defenses in Acacia drepanolobium in Kenya over two years among different large mammalian herbivore treatments [total exclusion, antelope only, and megaherbivore (elephants and giraffes) + antelope] and with four different ant symbiont species on the trees. We predicted that (1) condensed tannin concentrations would be lowest in the mammal treatment with the lowest level of herbivory (total exclusion), (2) trees occupied by mutualist ants that protect the trees most aggressively would have lower levels of tannins, and (3) if chemical defense production is costly, there would be a trade-off between tannin concentrations, growth, and mechanical defenses. Mean tannin concentrations increased from total exclusion treatments to wildlife-only treatments to megaherbivore + antelope treatments. In 1997, condensed tannin concentrations were significantly lower in trees occupied by the ant Crematogaster nigriceps, the only ant species that actively removed axillary buds. Contrary to our prediction, trees occupied by ant species that protect the trees more aggressively against mammalian herbivores did not have lower overall levels of condensed tannins. There was no consistent evidence of a trade-off between tannin concentrations and growth rate, but there was a positive correlation between mean thorn length and mean tannin concentrations across species of ant inhabitants and across herbivore treatments in 1997. Contrary to our expectation, trees had higher tannin concentrations in the upper parts of the canopy where there is little herbivory by mammals. PMID:12049231

  8. Mesophotic coral depth acclimatization is a function of host-specific symbiont physiology

    Directory of Open Access Journals (Sweden)

    Maren eZiegler

    2015-02-01

    Full Text Available Mesophotic coral ecosystems receive increasing attention owing to their potential as deep coral refuges in times of global environmental change. Here, the mechanisms of coral holobiont photoacclimatization over a 60 m depth gradient in the central Red Sea were examined for the four coral genera Porites, Leptoseris, Pachyseris, and Podabacia. General acclimatization strategies were common to all host-symbiont combinations, e.g. Symbiodinium cell densities and photoprotective to light-harvesting pigment ratios both significantly decreased with water depth. Porites harboured Symbiodinium type C15 over the whole 60 m depth range, while Pachyseris and Podabacia had limited vertical distributions and hosted mainly Symbiodinium type C1. Symbiodinium type C15 had generally higher xanthophyll de-epoxidation rates and lower maximum quantum yields than C1, and also exhibited a strong photoacclimatory signal over depth that relates to the large distribution range of Porites. Interestingly, the coral host had an effect on Symbiodinium pigment composition. When comparing Symbiodinium type C1 in Podabacia and Pachyseris, the ß-carotene chl a-1, the peridinin chl a-1, and diadinoxanthin chl a-1 ratios were significantly different between host species. Our data support a view that depth acclimatization of corals in the mesophotics is supported by Symbiodinium physiology, which in turn is host-specific.

  9. Mosaic origins of Bradyrhizobium legume symbionts on the Caribbean island of Guadeloupe.

    Science.gov (United States)

    Parker, Matthew A; Rousteau, Alain

    2014-08-01

    To analyze geographic affinities of Bradyrhizobium sp. symbionts associated with the diverse legume flora on the Caribbean island of Guadeloupe, 39 isolates from 18 legume genera were compared to a reference set of 269 Bradyrhizobium strains from North America, Central America, Puerto Rico and the Philippines. A multilocus sequence analysis (4192 bp) showed that nucleotide diversity in Guadeloupe equaled or exceeded that found in all other regional Bradyrhizobium populations examined. Bayesian phylogenetic tree analysis grouped the Guadeloupe Bradyrhizobium strains into clades with at least 20 distinct sets of non-Guadeloupe relatives, implying that the island was colonized numerous times from multiple source regions. However, for 18% of the Guadeloupe isolates, inferred geographic affinities for the nifD locus, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted with the source region deduced from a tree based on six concatenated housekeeping genes. Geographic mosaic ancestry was therefore evident among Guadeloupe bradyrhizobia. Horizontal gene transfer subsequent to island colonization appears to have generated strains that carry combinations of genes from disparate source regions. PMID:24747127

  10. Mesophotic coral depth acclimatization is a function of host-specific symbiont physiology

    KAUST Repository

    Ziegler, Maren

    2015-02-06

    Mesophotic coral ecosystems receive increasing attention owing to their potential as deep coral refuges in times of global environmental change. Here, the mechanisms of coral holobiont photoacclimatization over a 60 m depth gradient in the central Red Sea were examined for the four coral genera Porites, Leptoseris, Pachyseris, and Podabacia. General acclimatization strategies were common to all host-symbiont combinations, e.g., Symbiodinium cell densities and photoprotective (PP) to light-harvesting pigment ratios both significantly decreased with water depth. Porites harbored Symbiodinium type C15 over the whole 60 m depth range, while Pachyseris and Podabacia had limited vertical distributions and hosted mainly Symbiodinium type C1. Symbiodinium type C15 had generally higher xanthophyll de-epoxidation rates and lower maximum quantum yields than C1, and also exhibited a strong photoacclimatory signal over depth that relates to the large distribution range of Porites. Interestingly, the coral host had an effect on Symbiodinium pigment composition. When comparing Symbiodinium type C1 in Podabacia and Pachyseris, the ß-carotene chl a−1, the peridinin chl a−1, and diadinoxanthin chl a−1 ratios were significantly different between host species. Our data support a view that depth acclimatization of corals in the mesophotics is facilitated by Symbiodinium physiology, which in turn is host-specific.

  11. Purification and partial genome characterization of the bacterial endosymbiont Blattabacterium cuenoti from the fat bodies of cockroaches

    Directory of Open Access Journals (Sweden)

    Yamada Akinori

    2008-11-01

    Full Text Available Abstract Background Symbiotic relationships between intracellular bacteria and eukaryotes are widespread in nature. Genome sequencing of the bacterial partner has provided a number of key insights into the basis of these symbioses. A challenging aspect of sequencing symbiont genomes is separating the bacteria from the host tissues. In the present study, we describe a simple method of endosymbiont purification from complex environment, using Blattabacterium cuenoti inhabiting in cockroaches as a model system. Findings B. cuenoti cells were successfully purified from the fat bodies of the cockroach Panesthia angustipennis by a combination of slow- and fast-speed centrifugal fractionations, nylon-membrane filtration, and centrifugation with Percoll solutions. We performed pulse-field electrophoresis, diagnostic PCR and random sequencing of the shoutgun library. These experiments confirmed minimal contamination of host and mitochondrial DNA. The genome size and the G+C content of B. cuenoti were inferred to be 650 kb and 32.1 ± 7.6%, respectively. Conclusion The present study showed successful purification and characterization of the genome of B. cuenoti. Our methodology should be applicable for future symbiont genome sequencing projects. An advantage of the present purification method is that each step is easily performed with ordinary microtubes and a microcentrifuge, and without DNase treatment.

  12. Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

    Energy Technology Data Exchange (ETDEWEB)

    Stackebrandt, Erko [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Chang, Yun-Juan [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2013-01-01

    Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci.

    OpenAIRE

    Santos-Garcia, Diego; Rollat-Farnier, Pierre-Antoine; Beitia, Francisco; Zchori-Fein, Einat; Vavre, Fabrice; Mouton, Laurence; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

    2014-01-01

    Many insects harbor inherited bacterial endosymbionts. Although some of them are not strictly essential and are considered facultative, they can be a key to host survival under specific environmental conditions, such as parasitoid attacks, climate changes, or insecticide pressures. The whitefly Bemisia tabaci is at the top of the list of organisms inflicting agricultural damage and outbreaks, and changes in its distribution may be associated to global warming. In this work, we have sequenced ...

  14. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying;

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  15. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.

    Science.gov (United States)

    Linard, Benjamin; Crampton-Platt, Alex; Gillett, Conrad P D T; Timmermans, Martijn J T N; Vogler, Alfried P

    2015-06-01

    Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics. PMID:25979752

  16. Microbial symbionts in insects influence down-regulation of defense genes in maize.

    Directory of Open Access Journals (Sweden)

    Kelli L Barr

    Full Text Available Diabrotica virgifera virgifera larvae are root-feeding insects and significant pests to maize in North America and Europe. Little is known regarding how plants respond to insect attack of roots, thus complicating the selection for plant defense targets. Diabrotica virgifera virgifera is the most successful species in its genus and is the only Diabrotica beetle harboring an almost species-wide Wolbachia infection. Diabrotica virgifera virgifera are infected with Wolbachia and the typical gut flora found in soil-living, phytophagous insects. Diabrotica virgifera virgifera larvae cannot be reared aseptically and thus, it is not possible to observe the response of maize to effects of insect gut flora or other transient microbes. Because Wolbachia are heritable, it is possible to investigate whether Wolbachia infection affects the regulation of maize defenses. To answer if the success of Diabrotica virgifera virgifera is the result of microbial infection, Diabrotica virgifera virgifera were treated with antibiotics to eliminate Wolbachia and a microarray experiment was performed. Direct comparisons made between the response of maize root tissue to the feeding of antibiotic treated and untreated Diabrotica virgifera virgifera show down-regulation of plant defenses in the untreated insects compared to the antibiotic treated and control treatments. Results were confirmed via QRT-PCR. Biological and behavioral assays indicate that microbes have integrated into Diabrotica virgifera virgifera physiology without inducing negative effects and that antibiotic treatment did not affect the behavior or biology of the insect. The expression data and suggest that the pressure of microbes, which are most likely Wolbachia, mediate the down-regulation of many maize defenses via their insect hosts. This is the first report of a potential link between a microbial symbiont of an insect and a silencing effect in the insect host plant. This is also the first expression

  17. A carnivorous plant fed by its ant symbiont: a unique multi-faceted nutritional mutualism.

    Science.gov (United States)

    Bazile, Vincent; Moran, Jonathan A; Le Moguédec, Gilles; Marshall, David J; Gaume, Laurence

    2012-01-01

    Scarcity of essential nutrients has led plants to evolve alternative nutritional strategies, such as myrmecotrophy (ant-waste-derived nutrition) and carnivory (invertebrate predation). The carnivorous plant Nepenthes bicalcarata grows in the Bornean peatswamp forests and is believed to have a mutualistic relationship with its symbiotic ant Camponotus schmitzi. However, the benefits provided by the ant have not been quantified. We tested the hypothesis of a nutritional mutualism, using foliar isotopic and reflectance analyses and by comparing fitness-related traits between ant-inhabited and uninhabited plants. Plants inhabited by C. schmitzi produced more leaves of greater area and nitrogen content than unoccupied plants. The ants were estimated to provide a 200% increase in foliar nitrogen to adult plants. Inhabited plants also produced more and larger pitchers containing higher prey biomass. C. schmitzi-occupied pitchers differed qualitatively in containing C. schmitzi wastes and captured large ants and flying insects. Pitcher abortion rates were lower in inhabited plants partly because of herbivore deterrence as herbivory-aborted buds decreased with ant occupation rate. Lower abortion was also attributed to ant nutritional service. The ants had higher δ(15)N values than any tested prey, and foliar δ(15)N increased with ant occupation rate, confirming their predatory behaviour and demonstrating their direct contribution to the plant-recycled N. We estimated that N. bicalcarata derives on average 42% of its foliar N from C. schmitzi wastes, (76% in highly-occupied plants). According to the Structure Independent Pigment Index, plants without C. schmitzi were nutrient stressed compared to both occupied plants, and pitcher-lacking plants. This attests to the physiological cost of pitcher production and poor nutrient assimilation in the absence of the symbiont. Hence C. schmitzi contributes crucially to the nutrition of N. bicalcarata, via protection of assimilatory

  18. Interaction of arbuscular mycorrhizal symbionts with arsenic and other potentially toxic elements

    International Nuclear Information System (INIS)

    The response of arbuscular mycorrhizal (AM) symbionts to arsenic, and arsenic interactions with phosphorus and potentially toxic elements (PTEs) in soils from a former arsenic mine, the Devon Great Consols, were investigated. The objective was to determine whether AM associations ameliorate arsenic toxicity in Plantago lanceolata and Agrostis capillaris, plants commonly found at abandoned mines. An exploratory investigation indicated the richness in biodiversity of AMF that colonised plants growing at the site. Arsenic was found at high concentrations and was strongly associated with copper and iron. P. lanceolata was always colonised by AMF, while colonisation of A. capillaris was variable. There was no evidence in the field of soil pH or PTEs influencing AMF colonisation and spore density. There was no strong correlation between arsenic content in plant and available arsenic, obtained through various extraction methods. Spore germination and infectivity in the mine soils were strongly influenced by the AMF genotype and to a lesser extent by the soil environment. P. lanceolata and A. capillaris root growth was inhibited at arsenic concentrations of ≥50 μg g-1 in agar. Bioavailability experiments using mine soils and Terra-GreenTM (calcined attapulgite) spiked with sodium arsenate gave no evidence that AMF-colonised plants translocated less arsenic to the shoots. Plants accumulated more arsenic in their roots than in their shoots, whether they were colonised by AMF or not. The A. capillaris genotype used in the present study translocated less of both arsenic and phosphorus to its shoots than P. lanceolata. High available phosphorus in Terra-GreenTM protected plants against arsenic toxicity, at -1 As. There was evidence for inhibition by arsenic in AMF colonisation of roots. For quantifying AMF extra radical hyphae contribution to arsenic transportation from growth medium to plant using a compartmented pot system, the use of low phosphorus medium and a longer

  19. Impact of light and temperature on the uptake of algal symbionts by coral juveniles.

    Directory of Open Access Journals (Sweden)

    David Abrego

    Full Text Available The effects of temperature and light on the breakdown of the coral-Symbiodinium symbiosis are well documented but current understanding of their roles during initial uptake and establishment of symbiosis is limited. In this study, we investigate how temperature and light affect the uptake of the algal symbionts, ITS1 types C1 and D, by juveniles of the broadcast-spawning corals Acropora tenuis and A. millepora. Elevated temperatures had a strong negative effect on Symbiodinium uptake in both coral species, with corals at 31 °C showing as little as 8% uptake compared to 87% at 28 °C. Juveniles in high light treatments (390 µmol photons m(-2 s(-1 had lower cell counts across all temperatures, emphasizing the importance of the light environment during the initial uptake phase. The proportions of the two Symbiodinium types taken up, as quantified by a real time PCR assay using clade C- and D-specific primers, were also influenced by temperature, although variation in uptake dynamics between the two coral species indicates a host effect. At 28 °C, A. tenuis juveniles were dominated by C1 Symbiodinium, and while the number of D Symbiodinium cells increased at 31 °C, they never exceeded the number of C1 cells. In contrast, juveniles of A. millepora had approximately equal numbers of C1 and D cells at 28 °C, but were dominated by D at 30 °C and 31 °C. This study highlights the significant role that environmental factors play in the establishment of coral-Symbiodinium symbiosis and provides insights into how potentially competing Symbiodinium types take up residence in coral juveniles.

  20. Additive pressures of elevated sea surface temperatures and herbicides on symbiont-bearing foraminifera.

    Directory of Open Access Journals (Sweden)

    Joost W van Dam

    Full Text Available Elevated ocean temperatures and agrochemical pollution individually threaten inshore coral reefs, but these pressures are likely to occur simultaneously. Experiments were conducted to evaluate the combined effects of elevated temperature and the photosystem II (PSII inhibiting herbicide diuron on several types of symbiotic algae (diatom, dinoflagellate or rhodophyte of benthic foraminifera in hospite. Diuron was shown to evoke a direct effect on photosynthetic efficiency (reduced effective PSII quantum yield ΔF/F'(m, while elevated temperatures (>30 °C, only 2 °C above current average summer temperatures were observed to impact photosynthesis more indirectly by causing reductions in maximum PSII quantum yield (F(v/F(m, interpreted as photodamage. Additionally, elevated temperatures were shown to cause bleaching through loss of chlorophyll a in foraminifera hosting either diatoms or dinoflagellates. A significant linear correlation was found between reduced F(v/F(m and loss of chlorophyll a. In most cases, symbionts within foraminifera proved more sensitive to thermal stress in the presence of diuron (≥ 1 µg L(-1. The mixture toxicity model of Independent Action (IA described the combined effects of temperature and diuron on the photosystem of species hosting diatoms or dinoflagellates convincingly and in agreement with probabilistic statistics, so a response additive joint action can be assumed. We thus demonstrate that improving water quality can improve resilience of symbiotic phototrophs to projected increases in ocean temperatures. As IA described the observed combined effects from elevated temperature and diuron stress it may therefore be employed for prediction of untested mixtures and for assessing the efficacy of management measures.

  1. Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals

    Science.gov (United States)

    La Rivière, Marie; Garrabou, Joaquim; Bally, Marc

    2015-12-01

    Gorgonian corals serve as key engineering species within Mediterranean rocky-shore communities that have recently suffered from repeated mortality events during warm temperature anomalies. Among the factors that may link thermal conditions with disease outbreaks, a number of bacterial pathogens have been implicated; they may take advantage of decreases in the defenses and/or overall health of the gorgonian hosts. Considering the beneficial role of the resident bacteria in tropical coral holobionts, a detailed characterization of the gorgonian-associated microbial populations is required to better understand the relationships among native microbiota, host fitness, and pathogen susceptibility. In this study, the bacterial communities associated with three sympatric gorgonian species, Eunicella singularis, Eunicella cavolini, and Corallium rubrum, were investigated to provide insight into the stability and the specificity of host-microbe interactions. Natural variations in bacterial communities were detected using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal DNA. No major differences were identified between individual colonies sampled in winter or in summer within each gorgonian species. Although hierarchical cluster analysis of the T-RFLP profiles revealed that the three species harbor distinct communities, comparison of the T-RFLP peaks indicated the presence of common bacterial ribotypes. From phylogenetic analysis of 16S rDNA clone libraries, we identified a bacterial lineage related to the Hahellaceae family within the Oceanospirillales that is shared among E. singularis, E. cavolini, and C. rubrum and that dominates the communities of both species of Eunicella. However, distinct clades of Hahellaceae are harbored by various gorgonian species from Mediterranean and tropical waters, suggesting that these bacteria have formed host-specific symbiotic relationships with gorgonian octocorals. In addition, the relatedness of symbionts

  2. Tsetse immune system maturation requires the presence of obligate symbionts in larvae.

    Directory of Open Access Journals (Sweden)

    Brian L Weiss

    2011-05-01

    Full Text Available Beneficial microbial symbionts serve important functions within their hosts, including dietary supplementation and maintenance of immune system homeostasis. Little is known about the mechanisms that enable these bacteria to induce specific host phenotypes during development and into adulthood. Here we used the tsetse fly, Glossina morsitans, and its obligate mutualist, Wigglesworthia glossinidia, to investigate the co-evolutionary adaptations that influence the development of host physiological processes. Wigglesworthia is maternally transmitted to tsetse's intrauterine larvae through milk gland secretions. We can produce flies that lack Wigglesworthia (Gmm(Wgm- yet retain their other symbiotic microbes. Such offspring give rise to adults that exhibit a largely normal phenotype, with the exception being that they are reproductively sterile. Our results indicate that when reared under normal environmental conditions Gmm(Wgm- adults are also immuno-compromised and highly susceptible to hemocoelic E. coli infections while age-matched wild-type individuals are refractory. Adults that lack Wigglesworthia during larval development exhibit exceptionally compromised cellular and humoral immune responses following microbial challenge, including reduced expression of genes that encode antimicrobial peptides (cecropin and attacin, hemocyte-mediated processes (thioester-containing proteins 2 and 4 and prophenoloxidase, and signal-mediating molecules (inducible nitric oxide synthase. Furthermore, Gmm(Wgm- adults harbor a reduced population of sessile and circulating hemocytes, a phenomenon that likely results from a significant decrease in larval expression of serpent and lozenge, both of which are associated with the process of early hemocyte differentiation. Our results demonstrate that Wigglesworthia must be present during the development of immature progeny in order for the immune system to function properly in adult tsetse. This phenomenon provides

  3. The high cost of mutualism: effects of four species of East African ant symbionts on their myrmecophyte host tree.

    Science.gov (United States)

    Stanton, Maureen L; Palmer, Todd M

    2011-05-01

    Three recent meta-analyses of protective plant-ant mutualisms report a surprisingly weak relationship between herbivore protection and measured demographic benefits to ant-plants, suggesting high tolerance for herbivory, substantial costs of ant-mediated defense, and/or benefits that are realized episodically rather than continuously. Experimental manipulations of protective ant-plant associations typically last for less than a year, yet virtually all specialized myrmecophytes are long-lived perennials for which the costs and benefits of maintaining ant symbionts could accrue at different rates over the host's lifetime. To complement long-term monitoring studies, we experimentally excluded each of four ant symbionts from their long-lived myrmecophyte host trees (Acacia drepanolobium) for 4.5 years. Ant species varied in their effectiveness against herbivores and in their effects on intermediate-term growth and reproduction, but the level of herbivore protection provided was a poor predictor of the net impact they had on host trees. Removal of the three Crematogaster species resulted in cumulative gains in host tree growth and/or reproduction over the course of the experiment, despite the fact that two of those species significantly reduce chronic herbivore damage. In contrast, although T. penzigi is a relatively poor defender, the low cost of maintaining this ant symbiont apparently eliminated negative impacts on overall tree growth and reproduction, resulting in enhanced allocation to new branch growth by the final census. Acacia drepanolobium is evidently highly tolerant of herbivory by insects and small browsers, and the costs of maintaining Crematogaster colonies exceeded the benefits received during the study. No experimental trees were killed by elephants, but elephant damage was uniquely associated with reduced tree growth, and at least one ant species (C. mimosae) strongly deterred elephant browsing. We hypothesize that rare but catastrophic damage by

  4. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.

    Directory of Open Access Journals (Sweden)

    Liang Ran

    Full Text Available BACKGROUND: An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts and subsequently to the origin of the plant kingdom. The underlying mechanism and the identities of the partners in this monophyletic event remain elusive. METHODOLOGY/PRINCIPAL FINDINGS: To shed light on this evolutionary process, we sequenced the genome of a cyanobacterium residing extracellularly in an endosymbiosis with a plant, the water-fern Azolla filiculoides Lam. This symbiosis was selected as it has characters which make it unique among extant cyanobacterial plant symbioses: the cyanobacterium lacks autonomous growth and is vertically transmitted between plant generations. Our results reveal features of evolutionary significance. The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2% and a high frequency of transposable elements (approximately 600 scattered throughout the genome. Pseudogenization is found in genes such as the replication initiator dnaA and DNA repair genes, considered essential to free-living cyanobacteria. For some functional categories of genes pseudogenes are more prevalent than functional genes. Loss of function is apparent even within the 'core' gene categories of bacteria, such as genes involved in glycolysis and nutrient uptake. In contrast, serving as a critical source of nitrogen for the host, genes related to metabolic processes such as cell differentiation and nitrogen-fixation are well preserved. CONCLUSIONS/SIGNIFICANCE: This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla

  5. Two species of the Asian endemic genus Keteleeria form ectomycorrhizas with diverse fungal symbionts in southwestern China.

    Science.gov (United States)

    Ge, Zai-Wei; Smith, Matthew E; Zhang, Qing-Ying; Yang, Zhu L

    2012-07-01

    The ectomycorrhizal status of Keteleeria species is reported for the first time based on morphological and molecular analyses of root tips from southwestern China. Based on internal transcribed spacer rDNA sequences, we detected 26 ectomycorrhizal (ECM) fungal species on roots of Keteleeria evelyniana and Keteleeria davidiana collected from natural sites and a botanical garden in Kunming, China. These ECM symbionts represent six fungal lineages, including /russula-lactarius, /inocybe, /sebacina, /tomentella-thelephora, /wilcoxina, and /cenococcum. Our results provide the first evidence of ECM formation by Keteleeria and also supply ecologically important information for conservation and restoration efforts to recover populations of Keteleeria. PMID:21997220

  6. Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change

    OpenAIRE

    Hume, Benjamin C C; VOOLSTRA, CHRISTIAN R.; Arif, Chatchanit; D'Angelo, Cecilia; Burt, John A.; Eyal, Gal; Loya, Yossi; Wiedenmann, Jörg

    2016-01-01

    Coral communities in the Persian/Arabian Gulf (PAG) withstand unusually high salinity levels and regular summer temperature maxima of up to ?35 °C that kill conspecifics elsewhere. Due to the recent formation of the PAG and its subsequent shift to a hot climate, these corals have had only 5,000 km of the PAG, the Gulf of Oman, and the Red Sea coastline, we show that S. thermophilum is a member of a highly diverse, ancient group of symbionts cryptically distributed outside the PAG. We argue th...

  7. The light organ symbiont Vibrio fischeri possesses a homolog of the Vibrio cholerae transmembrane transcriptional activator ToxR.

    OpenAIRE

    Reich, K A; Schoolnik, G K

    1994-01-01

    A cross-hybridizing DNA fragment to Vibrio cholerae toxR was cloned from the nonpathogenic light organ symbiont Vibrio fischeri, and three proteins homologous to V. cholerae ToxR, ToxS, and HtpG were deduced from its DNA sequence. V. fischeri ToxR was found to activate a V. cholerae ToxR-regulated promoter, and an antiserum raised against the amino-terminal domain of V. cholerae ToxR cross-reacts V. fischeri ToxR.

  8. Variable interaction specificity and symbiont performance in Panamanian Trachymyrmex and Sericomyrmex fungus-growing ants

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Boomsma, Jacobus Jan

    2014-01-01

    cultivar symbiont-specificity varied from almost full symbiont sharing to one-to-one specialization, suggesting that trade-offs between enzyme activity spectra and life-history traits such as desiccation tolerance, disease susceptibility and temperature sensitivity may apply in some combinations but not in......Background Cooperative benefits of mutualistic interactions are affected by genetic variation among the interacting partners, which may have consequences for interaction-specificities across guilds of sympatric species with similar mutualistic life histories. The gardens of fungus-growing (attine...

  9. Verminephrobacter aporrectodeae sp. nov. subsp. tuberculatae and subsp. caliginosae; the specific nephridial symbionts of the earthworms Aporrectodea tuberculata and A. caliginosa

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Schätzle, Sarah; Schramm, Andreas; Kjeldsen, Kasper Urup

    2012-01-01

    , the specific symbiont of the earthworm Eisenia fetida. In this study two novel rod-shaped, non-endosporeforming, betaproteobacterial symbionts were isolated from the nephridia of two closely related earthworm species. Both isolates were affiliated with the genus Verminephrobacter by 16S rRNA gene......Clone library-based studies have shown that almost all lumbricid earthworm species harbour host-specific symbiotic bacteria belonging to the novel genus Verminephrobacter in their nephridia (excretory organs). To date the only described representative from this genus is Verminephrobacter eiseniae...

  10. Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.

    Science.gov (United States)

    Galán-Vásquez, Edgardo; Sánchez-Osorio, Ismael; Martínez-Antonio, Agustino

    2016-01-01

    The description of transcriptional regulatory networks has been pivotal in the understanding of operating principles under which organisms respond and adapt to varying conditions. While the study of the topology and dynamics of these networks has been the subject of considerable work, the investigation of the evolution of their topology, as a result of the adaptation of organisms to different environmental conditions, has received little attention. In this work, we study the evolution of transcriptional regulatory networks in bacteria from a genome reduction perspective, which manifests itself as the loss of genes at different degrees. We used the transcriptional regulatory network of Escherichia coli as a reference to compare 113 smaller, phylogenetically-related γ-proteobacteria, including 19 genomes of symbionts. We found that the type of regulatory action exerted by transcription factors, as genomes get progressively smaller, correlates well with their degree of conservation, with dual regulators being more conserved than repressors and activators in conditions of extreme reduction. In addition, we found that the preponderant conservation of dual regulators might be due to their role as both global regulators and nucleoid-associated proteins. We summarize our results in a conceptual model of how each TF type is gradually lost as genomes become smaller and give a rationale for the order in which this phenomenon occurs. PMID:26766575

  11. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence...... increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  12. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus;

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in...

  13. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  14. Reciprocal immune benefit based on complementary production of antibiotics by the leech Hirudo verbana and its gut symbiont Aeromonas veronii

    Science.gov (United States)

    Tasiemski, Aurélie; Massol, François; Cuvillier-Hot, Virginie; Boidin-Wichlacz, Céline; Roger, Emmanuel; Rodet, Franck; Fournier, Isabelle; Thomas, Frédéric; Salzet, Michel

    2015-01-01

    The medicinal leech has established a long-term mutualistic association with Aeromonas veronii, a versatile bacterium which can also display free-living waterborne and fish- or human-pathogenic lifestyles. Here, we investigated the role of antibiotics in the dynamics of interaction between the leech and its gut symbiont Aeromonas. By combining biochemical and molecular approaches, we isolated and identified for the first time the antimicrobial peptides (AMPs) produced by the leech digestive tract and by its symbiont Aeromonas. Immunohistochemistry data and PCR analyses evidenced that leech AMP genes are induced in the gut epithelial cells when Aeromonas load is low (starved animals), while repressed when Aeromonas abundance is the highest (post blood feeding). The asynchronous production of AMPs by both partners suggests that these antibiotic substances (i) provide them with reciprocal protection against invasive bacteria and (ii) contribute to the unusual simplicity of the gut microflora of the leech. This immune benefit substantially reinforces the evidence of an evolutionarily stable association between H. verbana and A. veronii. Altogether these data may provide insights into the processes making the association with an Aeromonas species in the digestive tract either deleterious or beneficial. PMID:26635240

  15. Mycorrhizal symbionts of Pisonia grandis and P. sechellarum in Seychelles: identification of mycorrhizal fungi and description of new Tomentella species.

    Science.gov (United States)

    Suvi, Triin; Tedersoo, Leho; Abarenkov, Kessy; Beaver, Katy; Gerlach, Justin; Kõljalg, Urmas

    2010-01-01

    Nyctaginaceae includes species that are predominantly non-mycorrhizal or form arbuscular or ectomycorrhiza. Root-associated fungi were studied from P. grandis and P. sechellarum roots collected respectively on the islands of Cousin and Silhouette in Seychelles. In addition fungal sporocarps were collected from the sampling area. Fungal symbionts were identified from the roots by anatomotyping and rDNA sequencing; sporocarps collected were examined microscopically and sequenced. Three distantly related ectomycorrhizal fungal species belonging to Thelephoraceae were identified from the roots of P. grandis. Sporocarps also were found for two symbionts and described as new Tomentella species. In addition Tomentella species collected from other Seychelles islands were studied and described as new species if there was no close resemblance to previously established species. P. sechellarum was determined to be an arbuscular mycorrhizal plant; three arbuscular mycorrhizal fungal species were detected from the roots. P. grandis is probably associated only with species of Thelephoraceae throughout its area. Only five Tomentella species are known to form ectomycorrhiza with P. grandis and they never have been found to be associated with another host, suggesting adaptation of these fungi to extreme environmental conditions in host's habitat. PMID:20524585

  16. Expulsion of symbiotic algae during feeding by the green hydra--a mechanism for regulating symbiont density?

    Directory of Open Access Journals (Sweden)

    Yelena Fishman

    Full Text Available BACKGROUND: Algal-cnidarian symbiosis is one of the main factors contributing to the success of cnidarians, and is crucial for the maintenance of coral reefs. While loss of the symbionts (such as in coral bleaching may cause the death of the cnidarian host, over-proliferation of the algae may also harm the host. Thus, there is a need for the host to regulate the population density of its symbionts. In the green hydra, Chlorohydra viridissima, the density of symbiotic algae may be controlled through host modulation of the algal cell cycle. Alternatively, Chlorohydra may actively expel their endosymbionts, although this phenomenon has only been observed under experimentally contrived stress conditions. PRINCIPAL FINDINGS: We show, using light and electron microscopy, that Chlorohydra actively expel endosymbiotic algal cells during predatory feeding on Artemia. This expulsion occurs as part of the apocrine mode of secretion from the endodermal digestive cells, but may also occur via an independent exocytotic mechanism. SIGNIFICANCE: Our results demonstrate, for the first time, active expulsion of endosymbiotic algae from cnidarians under natural conditions. We suggest this phenomenon may represent a mechanism whereby cnidarians can expel excess symbiotic algae when an alternative form of nutrition is available in the form of prey.

  17. Invasive symbiont bearing (and other) foraminifera altering the community structure of eastern Mediterranean rocky reefs environments

    Science.gov (United States)

    Hyams-Kaphzan, Orit; Perelis Grossowicz, Lydia; Almogi-Labin, Ahuva

    2015-04-01

    The rocky reefs of the Israeli eastern Mediterranean shelf constitute a highly diverse marine ecosystem rich in macroalgae and calcareous organisms. The benthic foraminiferal community living in this ecosystem is rapidly changing due to massive invasion of symbiont bearing foraminifera (SBF) as well as other foraminiferal species of tropical origin. This trend facilitated by the ongoing increase in temperature enables more tropical species to adjust to the eastern Mediterranean habitats. In order to document the status of the benthic foraminiferal community structure rocky reefs at Akhziv (AK) and Carmel Head (CH), northern Israel were sampled by scuba diving. Different macroalgae species, including invasive ones, accommodating the live epiphytic benthic foraminifera were sampled twice a year at AK and in each season at CH in three depth intervals between 5-20 m, during 2013-4. The numerical abundance of the group ranges between 170-3500 #/10cc (wet macroalgae volume) without any significant difference in standing stocks within regions, water depths or macroalgae preference. In total 77 benthic foraminiferal species were identified 71 in CH and only 43 at AK. Species richness per site varied between 3 and 42 with higher values at CH. 25% of all species were aliens, mostly Lessepsian, that comprise on average 70% - 84% of the numerical abundance of AK and CH respectively. Cluster analysis using benthic foraminifera relative abundance data did not correlate with the different macroalgae species, water depths or seasonality, indicating that the foraminiferal community in the two regions is quite homogenous. Amphistegina lobifera a Lessepsian migrant is by far the most common species on the Israeli rocky reefs occurring in all samples and comprising 18-93% of the foraminiferal community. Heterostegina depressa behaves similarly to A. lobifera though it occurs in lower numbers. Pararotalia calcariformata, a recently arriving SBF occupies mainly shallow water sites at CH

  18. Non-lethal effects of ocean acidification on two symbiont-bearing benthic foraminiferal species

    Directory of Open Access Journals (Sweden)

    A. McIntyre-Wressnig

    2011-09-01

    Full Text Available We conducted experiments to assess the effect of elevated atmospheric carbon dioxide concentrations on survival, fitness, shell microfabric and growth of two species of symbiont-bearing coral-reef benthic foraminifera, using pCO2 Ievels similar to those likely to occur in shallow marine pore waters in the decades ahead. Foraminifera were cultured at constant temperature and controlled pCO2 (385 ppmv, 1000 ppmv, and 2000 ppmv for six weeks, and total alkalinity and dissolved inorganic carbon were measured to characterize the carbonate chemistry of the incubations. Foraminiferal survival and cellular energy levels were assessed using Adenosine Triphosphate (ATP analyses, and test microstructure and growth were evaluated using high resolution SEM and image analysis. Fitness and survival of Amphistegina (A. gibbosa and Archaias (A. angulatus were not directly affected by elevated pCO2 and the concomitant decrease in pH and calcite saturation states (Ωc values of the seawater (pH and Ωc values of 8.12, 7.86, and 7.50, and 5.4, 3.4, and 1.5, for control, 1000 ppmv, and 2000 ppmv, respectively. In A. gibbosa, a species precipitating low-Mg calcite, test growth was not affected by elevated pCO2, but areas of dissolved calcium carbonate were observed even though Ωc was >1 in all treatments; the fraction of test area dissolved increased with decreasing Ωc. Similar dissolution was observed in offspring produced in the 2000 ppmv pCO2 treatments. In A. angulatus, whose tests are more-solubile high-Mg calcite, growth was greatly diminished in the 2000 ppmv pCO2 treatment compared to the control. These non-lethal effects of ocean acidification – reduced growth in A. angulatus, and enhanced dissolution in A. gibbosa – may reflect differences in test mineralogy

  19. Characteristics of the draft genome of "Candidatus Arsenophonus nilaparvatae", a facultative endosymbiont of Nilaparvata lugens.

    Science.gov (United States)

    Fan, Hai-Wei; Lu, Jia-Bao; Ye, Yu-Xuan; Yu, Xiao-Ping; Zhang, Chuan-Xi

    2016-06-01

    There exists a kind of symbiotic bacterium named "Candidatus Arsenophonus nilaparvatae" in the brown planthopper (BPH), Nilaparvata lugens. After being filtered and assembled from the BPH genome sequencing project, the genome sequence of this bacterial symbiont was obtained. After initial analysis based on the genome, we have found its potential role to synthesize B vitamins for the host. In order to better understand the lifestyle and the genomic changes of this symbiotic bacterium after the symbiotic relationship was established, we further report the characteristics of this draft genome. Compared with several other related bacteria, "Candidatus Arsenophonus nilaparvatae" has proven to be a facultative endosymbiont at the genomic level. Concurrently, the presence of fimbriae and flagella formation related genes indicates this maternally transmitted endosymbiont is most likely to retain the capacity to invade new hosts. Through further analysis of annotated gene sets, we also find evidence of genome reduction in its secretion system and metabolic pathways. These findings reflect its evolutionary trend to be an obligate one and enable a deeper study of microbe-insect interactions. PMID:26792263

  20. Influence of CH4 and H2S availability on symbiont distribution, carbon assimilation and transfer in the dual symbiotic vent mussel Bathymodiolus azoricus

    Directory of Open Access Journals (Sweden)

    R. S. Santos

    2008-12-01

    Full Text Available High densities of mussels of the genus Bathymodiolus are present at hydrothermal vents of the Mid-Atlantic Ridge. It was previously proposed that the chemistry at vent sites would affect their sulphide- and methane-oxidizing endosymbionts' abundance. In this study, we confirmed the latter assumption using fluorescence in situ hybridization on Bathymodiolus azoricus specimens maintained in a controlled laboratory environment at atmospheric pressure with one, both or none of the chemical substrates. A high level of symbiosis plasticity was observed, methane-oxidizers occupying between 4 and 39% of total bacterial area and both symbionts developing according to the presence or absence of their substrates. Using H13CO3− in the presence of sulphide, or 13CH4, we monitored carbon assimilation by the endosymbionts and its translocation to symbiont-free mussel tissues. Carbon was incorporated from methane and sulphide-oxidized inorganic carbon at rates 3 to 10 times slower in the host muscle tissue than in the symbiont-containing gill tissue. Both symbionts thus contribute actively to B. azoricus nutrition and adapt to the availability of their substrates. Further experiments with varying substrate concentrations using the same set-up should provide useful tools to study and even model the effects of changes in hydrothermal fluids on B. azoricus' chemosynthetic nutrition.

  1. Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria.

    Science.gov (United States)

    Szafranski, Kamil M; Deschamps, Philippe; Cunha, Marina R; Gaudron, Sylvie M; Duperron, Sébastien

    2015-01-01

    Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean. Wood and alfalfa substrates in colonization devices were deployed for different periods at 8 deep-sea chemosynthesis-based sites in four distinct geographic areas. Pyrosequencing of a fragment of the 16S rRNA-encoding gene was used to describe bacterial communities. Colonization occurred within the first 14 days. The diversity was higher in samples deployed for more than 289 days. After 289 days, no relation was observed between community richness and deployment duration, suggesting that diversity may have reached saturation sometime in between. Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed. Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified. Their potential status as free-living forms of these symbionts was evaluated based on sequence similarity with demonstrated symbionts. Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps. PMID:25774156

  2. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.

    Directory of Open Access Journals (Sweden)

    Pierre-Marc Delaux

    2014-07-01

    Full Text Available Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM, as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales. Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.

  3. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  4. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

    Energy Technology Data Exchange (ETDEWEB)

    Martin, F.; Aerts, A.; Ahren, D.; Brun, A.; Danchin, E. G. J.; Duchaussoy, F.; Gibon, J.; Kohler, A.; Lindquist, E.; Peresa, V.; Salamov, A.; Shapiro, H. J.; Wuyts, J.; Blaudez, D.; Buee, M.; Brokstein, P.; Canback, B.; Cohen, D.; Courty, P. E.; Coutinho, P. M.; Delaruelle, C.; Detter, J. C.; Deveau, A.; DiFazio, S.; Duplessis, S.; Fraissinet-Tachet, L.; Lucic, E.; Frey-Klett, P.; Fourrey, C.; Feussner, I.; Gay, G.; Grimwood, J.; Hoegger, P. J.; Jain, P.; Kilaru, S.; Labbe, J.; Lin, Y. C.; Legue, V.; Le Tacon, F.; Marmeisse, R.; Melayah, D.; Montanini, B.; Muratet, M.; Nehls, U.; Niculita-Hirzel, H.; Secq, M. P. Oudot-Le; Peter, M.; Quesneville, H.; Rajashekar, B.; Reich, M.; Rouhier, N.; Schmutz, J.; Yin, T.; Chalot, M.; Henrissat, B.; Kues, U.; Lucas, S.; Van de Peer, Y.; Podila, G. K.; Polle, A.; Pukkila, P. J.; Richardson, P. M.; Rouze, P.; Sanders, I. R.; Stajich, J. E.; Tunlid, A.; Tuskan, G.; Grigoriev, I. V.

    2007-08-10

    Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants 1, 2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are

  5. The genome of Laccaria bicolor provides insights into

    Energy Technology Data Exchange (ETDEWEB)

    Martin, F [UMR, France; Aerts, A. [U.S. Department of Energy, Joint Genome Institute; Ahren, D [Lund University, Sweden; Brun, A [UMR, France; Danchin, E [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Duchaussoy, F [UMR, France; Gibon, J [UMR, France; Kohler, A [UMR, France; Lindquist, E [U.S. Department of Energy, Joint Genome Institute; Pereda, V [UMR, France; Salamov, A. [U.S. Department of Energy, Joint Genome Institute; Shapiro, HJ [U.S. Department of Energy, Joint Genome Institute; Wuyts, J [UMR, France; Blaudez, D. [Institut National de la Recherche Agronomique, France; Buee, M [UMR, France; Brokstein, P [U.S. Department of Energy, Joint Genome Institute; Canbeck, B [Lund University, Sweden; Cohen, D [UMR, France; Courty, PE [UMR, France; Coutinho, PM [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Delaruelle, C [UMR, France; Detter, J C [U.S. Department of Energy, Joint Genome Institute; Deveau, A [UMR, France; DiFazio, Stephen P [West Virginia University; Duplessis, S [UMR, France; Fraissinet-Tachet, L [Universite de Lyon, France; Lucic, E [UMR, France; Frey-Klett, P [UMR, France; Fourrey, C [UMR, France; Feussner, I [Georg-August Universitat Gottingen Germany; Gay, G [Universite de Lyon, France; Grimwood, Jane [Stanford University; Hoegger, P J [Georg-August Universitat Gottingen Germany; Jain, P [University of Alabama, Huntsville; Kilaru, S [Georg-August Universitat Gottingen Germany; Labbe, J [UMR, France; Lin, Y C [Ghent University, Belgium; Legue, V [UMR, France; Le Tacon, F [UMR, France; Marmeisse, R [Universite de Lyon, France; Melayah, D [Universite de Lyon, France; Montanini, B [UMR, France; Muratet, M [University of Alabama, Huntsville; Nehls, U [Eberhard-Karls-Universitat, Tubingen, Germany; Niculita-Hirzel, H [University of Lausanne, Switzerland; Oudot-Le Secq, M P [UMR, France; Peter, M [UMR, France; Quesneville, H [Unite de Recherches en Genomique-Info,Evry Cedex; Rajashekar, B [Lund University, Sweden; Reich, M [UMR, France; Rouhler, N [UMR, France; Schmutz, Jeremy [Stanford University; Yin, Tongming [ORNL; Tuskan, Gerald A [ORNL; Chalot, M [UMR, France; Henrissat, B [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Kues, U [Georg-August Universitat Gottingen Germany; Lucas, S [U.S. Department of Energy, Joint Genome Institute; Van de Peer, Y [Ghent University, Belgium; Podila, G [University of Alabama, Huntsville; Polle, A [Georg-August Universitat Gottingen Germany; Pukkila, P J [University of North Carolina, Chapel Hill; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Rouze, P [Ghent University, Belgium; Sanders, I R [University of Lausanne, Switzerland; Stajich, J E [University of California, Berkeley; Tunlid, A [Lund University, Sweden; Grigoriev, I. [U.S. Department of Energy, Joint Genome Institute

    2008-01-01

    Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are

  6. Citrus Genomics

    OpenAIRE

    Talon, Manuel; Gmitter, Fred G.Jr.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The hist...

  7. Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

    Energy Technology Data Exchange (ETDEWEB)

    Koropatkin, Nicole M.; Martens, Eric C.; Gordon, Jeffrey I.; Smith, Thomas J. (WU); (Danforth)

    2009-01-12

    The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique {alpha}-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.

  8. Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

    Science.gov (United States)

    David, Aaron S; Seabloom, Eric W; May, Georgiana

    2016-05-01

    Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes-fungi living asymptomatically within plants-to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities. PMID:26626912

  9. Seasonal Preservation Success of the Marine Dinoflagellate Coral Symbiont, Symbiodinium sp.

    Directory of Open Access Journals (Sweden)

    Mary Hagedorn

    Full Text Available Coral reefs are some of the most diverse and productive ecosystems on the planet, but are threatened by global and local stressors, mandating the need for incorporating ex situ conservation practices. One approach that is highly protective is the development of genome resource banks that preserve the species and its genetic diversity. A critical component of the reef are the endosymbiotic algae, Symbiodinium sp., living within most coral that transfer energy-rich sugars to their hosts. Although Symbiodinium are maintained alive in culture collections around the world, the cryopreservation of these algae to prevent loss and genetic drift is not well-defined. This study examined the quantum yield physiology and freezing protocols that resulted in survival of Symbiodinium at 24 h post-thawing. Only the ultra-rapid procedure called vitrification resulted in success whereas conventional slow freezing protocols did not. We determined that success also depended on using a thin film of agar with embedded Symbiodinium on Cryotops, a process that yielded a post-thaw viability of >50% in extracted and vitrified Symbiodinium from Fungia scutaria, Pocillopora damicornis and Porites compressa. Additionally, there also was a seasonal influence on vitrification success as the best post-thaw survival of F. scutaria occurred in winter and spring compared to summer and fall (P < 0.05. These findings lay the foundation for developing a viable genome resource bank for the world's Symbiodinium that, in turn, will not only protect this critical element of coral functionality but serve as a resource for understanding the complexities of symbiosis, support selective breeding experiments to develop more thermally resilient strains of coral, and provide a 'gold-standard' genomics collection, allowing for full genomic sequencing of unique Symbiodinium strains.

  10. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

    Science.gov (United States)

    Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Vargas Jentzsch, Iris M.; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  11. Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits.

    Science.gov (United States)

    Hillman, Kai; Goodrich-Blair, Heidi

    2016-06-01

    In defensive symbioses where microbes benefit their host by killing competitors, predators or parasites, natural selection should favor the transmission of microbes with the most beneficial defensive traits. During the initiation of symbiosis, the host's ability to accurately pre-assess a symbiont's beneficial traits would be a selective advantage. We propose that one mechanism by which a host could recognize and select a beneficial partner would be if the latter displayed an honest signal of its defensive or other symbiotic capabilities. As one example, we suggest that polymorphic toxins and their surface receptors, which are involved in inter-microbial competition and predator killing activities, can be honest signals that facilitate partner choice in defensive symbioses. PMID:27128187

  12. Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

    DEFF Research Database (Denmark)

    Liberti, Joanito; Sapountzis, Panagiotis; Hansen, Lars H.;

    2015-01-01

    Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated...... the population-level infection dynamics for Entomoplasmatales and Bartonellaceae in Megalomyrmex symmetochus guest ants and their Sericomyrmex amabilis hosts. We further assessed the stability of the bacterial communities through a diet manipulation experiment and evaluated possible transmission modes...... in shared nests such as consumption of the same fungus garden food, eating of host brood by social parasites, trophallaxis and grooming interactions between the ants, or parallel acquisition from the same nest environment. Our results imply that cohabiting ant social parasites and hosts may obtain...

  13. Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes.

    Science.gov (United States)

    Silipo, Alba; Vitiello, Giuseppe; Gully, Djamel; Sturiale, Luisa; Chaintreuil, Clémence; Fardoux, Joel; Gargani, Daniel; Lee, Hae-In; Kulkarni, Gargi; Busset, Nicolas; Marchetti, Roberta; Palmigiano, Angelo; Moll, Herman; Engel, Regina; Lanzetta, Rosa; Paduano, Luigi; Parrilli, Michelangelo; Chang, Woo-Suk; Holst, Otto; Newman, Dianne K; Garozzo, Domenico; D'Errico, Gerardino; Giraud, Eric; Molinaro, Antonio

    2014-01-01

    Lipopolysaccharides (LPSs) are major components of the outer membrane of Gram-negative bacteria and are essential for their growth and survival. They act as a structural barrier and play an important role in the interaction with eukaryotic hosts. Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A. Biophysical analyses of reconstituted liposomes indicate that this hopanoid-lipid A structure reinforces the stability and rigidity of the outer membrane. In addition, the bacterium produces other hopanoid molecules not linked to LPS. A hopanoid-deficient strain, lacking a squalene hopene cyclase, displays increased sensitivity to stressful conditions and reduced ability to survive intracellularly in the host plant. This unusual combination of hopanoid and LPS molecules may represent an adaptation to optimize bacterial survival in both free-living and symbiotic states. PMID:25355435

  14. Pederin-type pathways of uncultivated bacterial symbionts: analysis of o-methyltransferases and generation of a biosynthetic hybrid.

    Science.gov (United States)

    Zimmermann, Katrin; Engeser, Marianne; Blunt, John W; Munro, Murray H G; Piel, Jörn

    2009-03-01

    The complex polyketide pederin is a potent antitumor agent isolated from Paederus spp. rove beetles. We have previously isolated a set of genes from a bacterial endosymbiont that are good candidates for pederin biosynthesis. To biochemically study this pathway, we expressed three methyltransferases from the putative pederin pathway and used the partially unmethylated analogue mycalamide A from the marine sponge Mycale hentscheli as test substrate. Analysis by high-resolution MS/MS and NMR revealed that PedO regiospecifically methylates the marine compound to generate the nonnatural hybrid compound 18-O-methylmycalamide A with increased cytotoxicity. To our knowledge, this is the first biochemical evidence that invertebrates can obtain defensive complex polyketides from bacterial symbionts. PMID:19206228

  15. Bonus Organisms in High-Throughput Eukaryotic Whole-Genome Shorgun Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank; Platt, Darren

    2006-02-06

    The DOE Joint Genome Institute has sequenced over 50 eukaryotic genomes, ranging in size from 15 MB to 1.6 GB, over a wide range of organism types. In the course of doing so, it has become clear that a substantial fraction of these data sets contains bonus organisms, usually prokaryotes, in addition to the desired genome. While some of these additional organisms are extraneous contamination, they are sometimes symbionts, and so can be of biological interest. Therefore, it is desirable to assemble the bonus organisms along with the main genome. This transforms the problem into one of metagenomic assembly, which is considerably more challenging than traditional whole-genome shotgun (WGS) assembly. The different organisms will usually be present at different sequence depths, which is difficult to handle in most WGS assemblers. In addition, with multiple distinct genomes present, chimerism can produce cross-organism combinations. Finally, there is no guarantee that only a single bonus organism will be present. For example, one JGI project contained at least two different prokaryotic contaminants, plus a 145 KB plasmid of unknown origin. We have developed techniques to routinely identify and handle such bonus organisms in a high-throughput sequencing environment. Approaches include screening and partitioning the unassembled data, and iterative subassemblies. These methods are applicable not only to bonus organisms, but also to desired components such as organelles. These procedures have the additional benefit of identifying, and allowing for the removal of, cloning artifacts such as E.coli and spurious vector inclusions.

  16. Light-induced dissociation of antenna complexes in the symbionts of scleractinian corals correlates with sensitivity to coral bleaching

    Science.gov (United States)

    Hill, R.; Larkum, A. W. D.; Prášil, O.; Kramer, D. M.; Szabó, M.; Kumar, V.; Ralph, P. J.

    2012-12-01

    Elevated temperatures in combination with moderate to high irradiance are known to cause bleaching events in scleractinian corals, characterised by damage to photosystem II (PSII). Photoprotective mechanisms of the symbiont can reduce the excitation pressure impinging upon PSII. In the bleaching sensitive species, Acropora millepora and Pocillopora damicornis, high light alone induced photoprotection through the xanthophyll cycle, increased content of the antioxidant carotenoid, β-carotene, as well as the dissociation of the light-harvesting chlorophyll complexes. The evidence is compatible with either the membrane-bound chlorophyll a-chlorophyll c 2-peridinin-protein (acpPC) complex or the peripheral peridinin-chlorophyll-protein complex, or both, disconnecting from PSII under high light. The acpPC complex potentially showed a state transition response with redistribution towards photosystem I to reduce PSII over-excitation. This apparent acpPC dissociation/reassociation was promoted by the addition of the xanthophyll cycle inhibitor, dithiothreitol, under high irradiance. Exposure to thermal stress as well as high light promoted xanthophyll de-epoxidation and increased β-carotene content, although it did not influence light-harvesting chlorophyll complex (LHC) dissociation, indicating light, rather than temperature, controls LHC dissociation. Photoinhibition was avoided in the bleaching tolerant species, Pavona decussata, suggesting xanthophyll cycling along with LHC dissociation may have been sufficient to prevent photodamage to PSII. Symbionts of P. decussata also displayed the greatest detachment of antenna complexes, while the more thermally sensitive species, Pocillopora damicornis and A. millepora, showed less LHC dissociation, suggesting antenna movement influences bleaching susceptibility.

  17. Morphogenetic role of F-actin meshwork in chamber formation: immunolabeling results from symbiont bearing benthic foraminifera

    Science.gov (United States)

    Tyszka, Jaroslaw; Raitzsch, Markus; Bijma, Jelle; Höher, Nicole; Bickmeyer, Ulf; Rivera-Ingraham, Georginia; Topa, Paweł; Kaczmarek, Karina; Mewes, Antje; Bowser, Samuel; Travis, Jeffrey

    2015-04-01

    Foraminifera are excellent tracers of palaeoceanographic conditions recorded in their shell (test) morphology and chemical composition. Understanding foraminiferal morphology controlled by chamberwise growth can be reduced to processes of chamber formation. However, little is known about how foraminifera control the shape of the chamber wall to be biosynthesized and precipitated. Searching for fundamental morphogenetic features involved in biomineralization, we focused on foraminifers, which belong to the class Globothalamea. The most critical condition to run experiments was to have convenient access to early stages of chamber formation in any species of cultured benthic foraminifers. We have tested small foraminifers collected from the tidal flats of the North Sea. All species, including Ammonia, Haynesina, and Elphidium, turned out to be unsuitable due to their reproduction seasonality and/or unpredictability. The problem was solved by using symbiont bearing Amphistegina lessonii cultured in small aquaria. In well treated cultures, such foraminifera often reproduce on a glass wall surface, serving as a continuous source of juveniles. They tend to regularly construct chambers. Another important point is that symbiont bearing foraminifers usually do not construct opaque protective cysts from detritus that disturb observations. All these features facilitate immunolabeling experiments observed under confocal microscopy. Therefore, for the first time, we managed to label cytoskeleton proteins during the chamber formation in Foraminifera. The results show that the shape of chamber is predefined by a meshwork of F-actin, which acts as a dynamic organic scaffold most likely responsible for distribution and docking of biomineralizing molecules (glycoproteins). The F-actin meshwork interacts with microtubules and all associated proteins, which are involved in the morphogenesis of biomineralized structures. Foraminifera, like other eukaryotic cells, can form active

  18. Recent Invasion of the Symbiont-Bearing Foraminifera Pararotalia into the Eastern Mediterranean Facilitated by the Ongoing Warming Trend.

    Directory of Open Access Journals (Sweden)

    Christiane Schmidt

    Full Text Available The eastern Mediterranean is a hotspot of biological invasions. Numerous species of Indo-pacific origin have colonized the Mediterranean in recent times, including tropical symbiont-bearing foraminifera. Among these is the species Pararotalia calcariformata. Unlike other invasive foraminifera, this species was discovered only two decades ago and is restricted to the eastern Mediterranean coast. Combining ecological, genetic and physiological observations, we attempt to explain the recent invasion of this species in the Mediterranean Sea. Using morphological and genetic data, we confirm the species attribution to P. calcariformata McCulloch 1977 and identify its symbionts as a consortium of diatom species dominated by Minutocellus polymorphus. We document photosynthetic activity of its endosymbionts using Pulse Amplitude Modulated Fluorometry and test the effects of elevated temperatures on growth rates of asexual offspring. The culturing of asexual offspring for 120 days shows a 30-day period of rapid growth followed by a period of slower growth. A subsequent 48-day temperature sensitivity experiment indicates a similar developmental pathway and high growth rate at 28°C, whereas an almost complete inhibition of growth was observed at 20°C and 35°C. This indicates that the offspring of this species may have lower tolerance to cold temperatures than what would be expected for species native to the Mediterranean. We expand this hypothesis by applying a Species Distribution Model (SDM based on modern occurrences in the Mediterranean using three environmental variables: irradiance, turbidity and yearly minimum temperature. The model reproduces the observed restricted distribution and indicates that the range of the species will drastically expand westwards under future global change scenarios. We conclude that P. calcariformata established a population in the Levant because of the recent warming in the region. In line with observations from other

  19. A GHF7 cellulase from the protist symbiont community of Reticulitermes flavipes enables more efficient lignocellulose processing by host enzymes.

    Science.gov (United States)

    Sethi, Amit; Kovaleva, Elena S; Slack, Jeffrey M; Brown, Susan; Buchman, George W; Scharf, Michael E

    2013-12-01

    Termites and their gut microbial symbionts efficiently degrade lignocellulose into fermentable monosaccharides. This study examined three glycosyl hydrolase family 7 (GHF7) cellulases from protist symbionts of the termite Reticulitermes flavipes. We tested the hypotheses that three GHF7 cellulases (GHF7-3, GHF7-5, and GHF7-6) can function synergistically with three host digestive enzymes and a fungal cellulase preparation. Full-length cDNA sequences of the three GHF7s were assembled and their protist origins confirmed through a combination of quantitative PCR and cellobiohydrolase (CBH) activity assays. Recombinant versions of the three GHF7s were generated using a baculovirus-insect expression system and their activity toward several model substrates compared with and without metallic cofactors. GHF7-3 was the most active of the three cellulases; it exhibited a combination of CBH, endoglucanase (EGase), and β-glucosidase activities that were optimal around pH 7 and 30°C, and enhanced by calcium chloride and zinc sulfate. Lignocellulose saccharification assays were then done using various combinations of the three GHF7s along with a host EGase (Cell-1), beta-glucosidase (β-glu), and laccase (LacA). GHF7-3 was the only GHF7 to enhance glucose release by Cell-1 and β-glu. Finally, GHF7-3, Cell-1, and β-glu were individually tested with a commercial fungal cellulase preparation in lignocellulose saccharification assays, but only β-glu appreciably enhanced glucose release. Our hypothesis that protist GHF7 cellulases are capable of synergistic interactions with host termite digestive enzymes is supported only in the case of GHF7-3. These findings suggest that not all protist cellulases will enhance saccharification by cocktails of other termite or fungal lignocellulases. PMID:24186432

  20. Seasonal Preservation Success of the Marine Dinoflagellate Coral Symbiont, Symbiodinium sp.

    Science.gov (United States)

    Hagedorn, Mary; Carter, Virginia L

    2015-01-01

    Coral reefs are some of the most diverse and productive ecosystems on the planet, but are threatened by global and local stressors, mandating the need for incorporating ex situ conservation practices. One approach that is highly protective is the development of genome resource banks that preserve the species and its genetic diversity. A critical component of the reef are the endosymbiotic algae, Symbiodinium sp., living within most coral that transfer energy-rich sugars to their hosts. Although Symbiodinium are maintained alive in culture collections around the world, the cryopreservation of these algae to prevent loss and genetic drift is not well-defined. This study examined the quantum yield physiology and freezing protocols that resulted in survival of Symbiodinium at 24 h post-thawing. Only the ultra-rapid procedure called vitrification resulted in success whereas conventional slow freezing protocols did not. We determined that success also depended on using a thin film of agar with embedded Symbiodinium on Cryotops, a process that yielded a post-thaw viability of >50% in extracted and vitrified Symbiodinium from Fungia scutaria, Pocillopora damicornis and Porites compressa. Additionally, there also was a seasonal influence on vitrification success as the best post-thaw survival of F. scutaria occurred in winter and spring compared to summer and fall (P coral functionality but serve as a resource for understanding the complexities of symbiosis, support selective breeding experiments to develop more thermally resilient strains of coral, and provide a 'gold-standard' genomics collection, allowing for full genomic sequencing of unique Symbiodinium strains. PMID:26422237

  1. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts

    Directory of Open Access Journals (Sweden)

    Normand Philippe

    2008-01-01

    Full Text Available Abstract Background Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown molecular interactions between Frankia and their host plants. We compared the genome-based secretomes of three Frankia strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core Frankia secretome. Proteins in the core secretome may be involved in the actinorhizal symbiosis. Results The Frankia genomes have conserved Sec (general secretory and Tat (twin arginine translocase secretion systems. The potential secretome of each Frankia strain comprised 4–5% of the total proteome, a lower percentage than that found in the genomes of other actinobacteria, legume endosymbionts, and plant pathogens. Hydrolytic enzymes made up only a small fraction of the total number of predicted secreted proteins in each strain. Surprisingly, polysaccharide-degrading enzymes were few in number, especially in strain CcI3, with more esterolytic, lipolytic and proteolytic enzymes having signal peptides. A total of 161 orthologous proteins belong to the core Frankia secretome. Of these, 52 also lack homologs in closely related actinobacteria, and are termed "Frankia-specific." The genes encoding these conserved secreted proteins are often clustered near secretion machinery genes. Conclusion The predicted secretomes of Frankia sp. are relatively small and include few hydrolases, which could reflect adaptation to a symbiotic lifestyle. There are no well-conserved secreted polysaccharide-degrading enzymes present in all three Frankia

  2. 内生真菌-禾草共生体内生物碱的种类及其生理生态作用%TYPES OF ALKALOIDS IN FUNGAL ENDOPHYTE-GRASS SYMBIONT AND THEIR ECOPHYSIOLOGICAL ROLE

    Institute of Scientific and Technical Information of China (English)

    周芳; 高玉葆

    2003-01-01

    In this review, we summarized recent studies on alkaloids in endophyte - grass symbiont, including detection and classification, effects of environmental factors on concentration of the alkaloids, and their ecophysiological role to the plant host. Tab 1, Ref 49

  3. Whole Genome Sequencing

    Science.gov (United States)

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  4. Genomes on ice.

    Science.gov (United States)

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  5. Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites.

    Directory of Open Access Journals (Sweden)

    Paolo Marinho de Andrade Zanotto

    Full Text Available We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.

  6. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

    Directory of Open Access Journals (Sweden)

    Eric C Martens

    2011-12-01

    Full Text Available Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target

  7. A genomic approach to coral-dinoflagellate symbiosis: Studies of Acropora digitifera and Symbiodinium minutum

    Directory of Open Access Journals (Sweden)

    Chuya eShinzato

    2014-07-01

    Full Text Available Far more intimate knowledge of scleractinian coral biology is essential in order to understand how diverse coral-symbiont endosymbioses have been established. In particular, molecular and cellular mechanisms enabling the establishment and maintenance of obligate endosymbiosis with photosynthetic dinoflagellates require further clarification. By extension, such understanding may also shed light upon environmental conditions that promote the collapse of this mutualism. Genomic data undergird studies of all symbiotic processes. Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. We discuss Acropora genes involved in calcification, embryonic development, innate immunity, apoptosis, autophagy, UV resistance, fluorescence, photoreceptors, circadian clocks, etc. We also detail gene loss in amino acid metabolism that may explain at least part of the Acropora stress-response. Characteristic features of the Symbiodinium genome are also reviewed, focusing on the expansion of certain gene families, the molecular basis for permanently condensed chromatin, unique spliceosomal splicing, and unusual gene arrangement. Salient features of the Symbiodinium plastid and mitochondrial genomes are also illuminated. Although many questions regarding these interdependent genomes remain, we summarize information necessary for future studies of coral-dinoflagellate endosymbiosis.

  8. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  9. Onion Thrips, Thrips tabaci, Have Gut Bacteria That are Closely Related to the Symbionts of the Western Flower Thrips, Frankliniella occidentalis

    OpenAIRE

    Vries, de, P.M.; Wurff, van der, A.W.G.; Jacobs, G.; Breeuwer, J.A.J.

    2008-01-01

    It has been shown that many insects have Enterobacteriaceae bacteria in their gut system. The western flower thrips, Frankliniella occidentalis Pergande [Thysanoptera: Thripidae], has a symbiotic relation with Erwinia species gut bacteria. To determine if other Thripidae species have similar bacterial symbionts, the onion thrips, Thrips tabaci, was studied because, like F. occidentalis, it is phytophagous. Contrary to F. occidentalis, T. tabaci is endemic in Europe and biotypes have been desc...

  10. Evidence for cospeciation events in the host–symbiont system involving crinoids (Echinodermata) and their obligate associates, the myzostomids (Myzostomida, Annelida)

    OpenAIRE

    Lanterbecq, D.; Rouse, G W; Eeckhaut, I

    2010-01-01

    Although molecular-based phylogenetic studies of hosts and their associates are increasingly common in the literature, no study to date has examined the hypothesis of coevolutionary process between hosts and commensals in the marine environment. The present work investigates the phylogenetic relationships among 16 species of obligate symbiont marine worms (Myzostomida) and their echinoderm hosts (Crinoidea) in order to estimate the phylogenetic congruence existing between the two lineages. Th...

  11. Survival to parasitoids in an insect hosting defensive symbionts: a multivariate approach to polymorphic traits affecting host use by its natural enemy.

    Directory of Open Access Journals (Sweden)

    Emilie Bilodeau

    Full Text Available Insect parasitoids and their insect hosts represent a wide range of parasitic trophic relations that can be used to understand the evolution of biotic diversity on earth. Testing theories of coevolution between hosts and parasites is based on factors directly involved in host susceptibility and parasitoid virulence. We used controlled encounters with potential hosts of the Aphidius ervi wasp to elucidate behavioral and other phenotypic traits of host Acyrthosiphon pisum that most contribute to success or failure of parasitism. The host aphid is at an advanced stage of specialization on different crop plants, and exhibits intra-population polymorphism for traits of parasitoid avoidance and resistance based on clonal variation of color morph and anti-parasitoid bacterial symbionts. Randomly selected aphid clones from alfalfa and clover were matched in 5 minute encounters with wasps of two parasitoid lineages deriving from hosts of each plant biotype in a replicated transplant experimental design. In addition to crop plant affiliation (alfalfa, clover, aphid clones were characterized for color morph (green, pink, Hamiltonella defensa and Regiella insecticola symbionts, and frequently used behaviors in encounters with A. ervi wasps. A total of 12 explanatory variables were examined using redundancy analysis (RDA to predict host survival or failure to A. ervi parasitism. Aphid color was the best univariate predictor, but was poorly predictive in the RDA model. In contrast, aphid host plant and symbionts were not significant univariate predictors, but significant predictors in the multivariate model. Aphid susceptibility to wasp acceptance as reflected in host attacks and oviposition clearly differed from its suitability to parasitism and progeny development. Parasitoid progeny were three times more likely to survive on clover than alfalfa host aphids, which was compensated by behaviorally adjusting eggs invested per host. Strong variation of the

  12. Production and Metabolism of Indole Acetic Acid in Root Nodules and Symbiont (Rhizobium undicola Isolated from Root Nodule of Aquatic Medicinal Legume Neptunia oleracea Lour.

    Directory of Open Access Journals (Sweden)

    Pallab Kumar Ghosh

    2015-01-01

    Full Text Available Indole acetic acid is a phytohormone which plays a vital role in plant growth and development. The purpose of this study was to shed some light on the production of IAA in roots, nodules, and symbionts of an aquatic legume Neptunia oleracea and its possible role in nodular symbiosis. The symbiont (N37 was isolated from nodules of this plant and identified as Rhizobium undicola based on biochemical characteristics, 16S rDNA sequence homology, and DNA-DNA hybridization results. The root nodules were found to contain more IAA and tryptophan than root; however, no detectable amount of IAA was found in root. The IAA metabolizing enzymes IAA oxidase, IAA peroxidase (E.C.1.11.1.7, and polyphenol oxidase (E.C.1.14.18.1 were higher in root than nodule but total phenol and IAA content were reversed. The strain N37 was found to produce copious amount of IAA in YEM broth medium with tryptophan and reached its stationary phase at 20 h. An enrichment of the medium with mannitol, ammonium sulphate, B12, and 4-hydroxybenzaldehyde was found to promote the IAA production. The presence of IAA metabolizing enzymes and IAA production with PGPR traits including ACC deaminase activity of the symbionts was essential for plant microbe interaction and nodule function.

  13. Physiological response to elevated temperature and pCO2 varies across four Pacific coral species: Understanding the unique host+symbiont response

    Science.gov (United States)

    Hoadley, Kenneth D.; Pettay, D. Tye; Grottoli, Andréa G.; Cai, Wei-Jun; Melman, Todd F.; Schoepf, Verena; Hu, Xinping; Li, Qian; Xu, Hui; Wang, Yongchen; Matsui, Yohei; Baumann, Justin H.; Warner, Mark E.

    2015-12-01

    The physiological response to individual and combined stressors of elevated temperature and pCO2 were measured over a 24-day period in four Pacific corals and their respective symbionts (Acropora millepora/Symbiodinium C21a, Pocillopora damicornis/Symbiodinium C1c-d-t, Montipora monasteriata/Symbiodinium C15, and Turbinaria reniformis/Symbiodinium trenchii). Multivariate analyses indicated that elevated temperature played a greater role in altering physiological response, with the greatest degree of change occurring within M. monasteriata and T. reniformis. Algal cellular volume, protein, and lipid content all increased for M. monasteriata. Likewise, S. trenchii volume and protein content in T. reniformis also increased with temperature. Despite decreases in maximal photochemical efficiency, few changes in biochemical composition (i.e. lipids, proteins, and carbohydrates) or cellular volume occurred at high temperature in the two thermally sensitive symbionts C21a and C1c-d-t. Intracellular carbonic anhydrase transcript abundance increased with temperature in A. millepora but not in P. damicornis, possibly reflecting differences in host mitigated carbon supply during thermal stress. Importantly, our results show that the host and symbiont response to climate change differs considerably across species and that greater physiological plasticity in response to elevated temperature may be an important strategy distinguishing thermally tolerant vs. thermally sensitive species.

  14. Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins.

    Science.gov (United States)

    Starcevic, Antonio; Akthar, Shamima; Dunlap, Walter C; Shick, J Malcolm; Hranueli, Daslav; Cullum, John; Long, Paul F

    2008-02-19

    The shikimic acid pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the shikimic acid pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a "shared metabolic adaptation" between the partners. PMID:18268342

  15. Evidence for Vertical Transmission of Bacterial Symbionts from Adult to Embryo in the Caribbean Sponge Svenzea zeai

    KAUST Repository

    Lee, O. O.

    2009-07-31

    The Caribbean reef sponge Svenzea zeai was previously found to contain substantial quantities of unicellular photosynthetic and autotrophic microbes in its tissues, but the identities of these symbionts and their method of transfer from adult to progeny are largely unknown. In this study, both a 16S rRNA gene-based fingerprinting technique (denaturing gradient gel electrophoresis [DGGE]) and clone library analysis were applied to compare the bacterial communities associated with adults and embryos of S. zeai to test the hypothesis of vertical transfer across generations. In addition, the same techniques were applied to the bacterial community from the seawater adjacent to adult sponges to test the hypothesis that water column bacteria could be transferred horizontally as sponge symbionts. Results of both DGGE and clone library analysis support the vertical transfer hypothesis in that the bacterial communities associated with sponge adults and embryos were highly similar to each other but completely different from those in the surrounding seawater. Sequencing of prominent DGGE bands and of clones from the libraries revealed that the bacterial communities associated with the sponge, whether adult or embryo, consisted of a large proportion of bacteria in the phyla Chloroflexi and Acidobacteria, while most of the sequences recovered from the community in the adjacent water column belonged to the class Alphaproteobacteria. Altogether, 21 monophyletic sequence clusters, comprising sequences from both sponge adults and embryos but not from the seawater, were identified. More than half of the sponge-derived sequences fell into these clusters. Comparison of sequences recovered in this study with those deposited in GenBank revealed that more than 75% of S. zeai-derived sequences were closely related to sequences derived from other sponge species, but none of the sequences recovered from the seawater column overlapped with those from adults or embryos of S. zeai. In

  16. Comparative genomics of Serratia spp.: two paths towards endosymbiotic life.

    Directory of Open Access Journals (Sweden)

    Alejandro Manzano-Marín

    Full Text Available Symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. Buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, Serratia symbiotica. Of particular interest is the case of the cedar aphid Cinara cedri, where B. aphidicola BCc and S. symbiotica SCc need each other to fulfil their symbiotic role with the insect. Moreover, various features seem to indicate that S. symbiotica SCc is closer to an obligate endosymbiont than to other facultative S. symbiotica, such as the one described for the aphid Acirthosyphon pisum (S. symbiotica SAp. This work is based on the comparative genomics of five strains of Serratia, three free-living and two endosymbiotic ones (one facultative and one obligate which should allow us to dissect the genome reduction taking place in the adaptive process to an intracellular life-style. Using a pan-genome approach, we have identified shared and strain-specific genes from both endosymbiotic strains and gained insight into the different genetic reduction both S. symbiotica have undergone. We have identified both retained and reduced functional categories in S. symbiotica compared to the Free-Living Serratia (FLS that seem to be related with its endosymbiotic role in their specific host-symbiont systems. By means of a phylogenomic reconstruction we have solved the position of both endosymbionts with confidence, established the probable insect-pathogen origin of the symbiotic clade as well as the high amino-acid substitution rate in S. symbiotica SCc. Finally, we were able to quantify the minimal number of rearrangements suffered in the endosymbiotic lineages and reconstruct a minimal rearrangement phylogeny. All these findings provide important evidence for the existence of at least two distinctive S. symbiotica lineages that are characterized by different rearrangements, gene content, genome size and branch lengths.

  17. Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

    Energy Technology Data Exchange (ETDEWEB)

    Hallam, Steven J.; Konstantinidis, Konstantinos T.; Brochier,Celine; Putnam, Nik; Schleper, Christa; Watanabe, Yoh-ichi; Sugahara,Junichi; Preston, Christina; de la Torre, Jose; Richardson, Paul M.; DeLong, Edward F.

    2006-06-24

    Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.

  18. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  19. Microbial genomic taxonomy

    OpenAIRE

    Cristiane C Thompson; Chimetto, Luciane; Edwards, Robert A.; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes,  70% in silico Genome-to-Genome Hybridization similarity (G...

  20. Ebolavirus comparative genomics

    OpenAIRE

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S; Pedersen, Thomas Dybdal; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequen...

  1. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  2. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  3. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  4. Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR.

    Science.gov (United States)

    Bayer, Kristina; Kamke, Janine; Hentschel, Ute

    2014-09-01

    In spite of considerable insights into the microbial diversity of marine sponges, quantitative information on microbial abundances and community composition remains scarce. Here, we established qPCR assays for the specific quantification of four bacterial phyla of representative sponge symbionts as well as the kingdoms Eubacteria and Archaea. We could show that the 16S rRNA gene numbers of Archaea, Chloroflexi, and the candidate phylum Poribacteria were 4-6 orders of magnitude higher in high microbial abundance (HMA) than in low microbial abundance (LMA) sponges and that actinobacterial 16S rRNA gene numbers were 1-2 orders higher in HMA over LMA sponges, while those for Cyanobacteria were stable between HMA and LMA sponges. Fluorescence in situ hybridization of Aplysina aerophoba tissue sections confirmed the numerical dominance of Chloroflexi, which was followed by Poribacteria. Archaeal and actinobacterial cells were detected in much lower numbers. By use of fluorescence-activated cell sorting as a primer- and probe-independent approach, the dominance of Chloroflexi, Proteobacteria, and Poribacteria in A. aerophoba was confirmed. Our study provides new quantitative insights into the microbiology of sponges and contributes to a better understanding of the HMA/LMA dichotomy. PMID:24942664

  5. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  6. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  7. Genome sequence of Candidatus Riesia pediculischaeffi, endosymbiont of chimpanzee lice, and genomic comparison of recently acquired endosymbionts from human and chimpanzee lice.

    Science.gov (United States)

    Boyd, Bret M; Allen, Julie M; de Crécy-Lagard, Valérie; Reed, David L

    2014-11-01

    The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time: faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed phylogenetic history of these endosymbionts with divergence dates for closely related species. This allows for genome evolution to be studied in detail and rates of change to be estimated in a phylogenetic framework. Here, we sequenced the genome of the chimpanzee louse endosymbiont (Candidatus Riesia pediculischaeffi) and compared it with the closely related genome of the human body louse endosymbiont. From this comparison, we found evidence for recent genome erosion leading to gene loss in these endosymbionts. Although gene loss was detected, it was not significantly greater than in older endosymbionts from aphids and ants. Additionally, we searched for genes associated with B-vitamin synthesis in the two louse endosymbiont genomes because these endosymbionts are believed to synthesize essential B vitamins absent in the louse's diet. All of the expected genes were present, except those involved in thiamin synthesis. We failed to find genes encoding for proteins involved in the biosynthesis of thiamin or any complete exogenous means of salvaging thiamin, suggesting there is an undescribed mechanism for the salvage of thiamin. Finally, genes encoding for the pantothenate de novo biosynthesis pathway were located on a plasmid in both taxa along with a heat shock protein. Movement of these genes onto a plasmid may be functionally and evolutionarily significant, potentially increasing production and guarding against the deleterious effects of mutation. These data add to a growing

  8. Insights into archaeal evolution and symbiosis from the genomes of a Nanoarchaeon and its crenarchaeal host from Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Podar, Mircea [ORNL; Graham, David E [ORNL; Reysenbach, Anna-Louise [Portland State University; Koonin, Eugene [National Center for Biotechnology Information; Wolf, Yuri [National Center for Biotechnology Information; Makarova, Kira S. [National Center for Biotechnology Information

    2013-01-01

    A hyperthemophilic member of the Nanoarchaeota from Obsidian Pool, a thermal feature in Yellowstone National Park was characterized using single cell isolation and sequencing, together with its putative host, a Sulfolobales archaeon. This first representative of a non-marine Nanoarchaeota (Nst1) resembles Nanoarchaeum equitans by lacking most biosynthetic capabilities, the two forming a deep-branching archaeal lineage. However, the Nst1 genome is over 20% larger, encodes a complete gluconeogenesis pathway and a full complement of archaeal flagellum proteins. Comparison of the two genomes suggests that the marine and terrestrial Nanoarchaeota lineages share a common ancestor that was already a symbiont of another archaeon. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. The two distinct Nanoarchaeota-host genomic data sets offer insights into the evolution of archaeal symbiosis and parasitism and will further enable studies of the cellular and molecular mechanisms of these relationships.

  9. Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria.

    Science.gov (United States)

    Kešnerová, Lucie; Moritz, Roxane; Engel, Philipp

    2016-01-01

    Here, we report the culture and characterization of an alphaproteobacterium of the order Rhizobiales, isolated from the gut of the honey bee Apis mellifera. Strain PEB0122T shares >95 % 16S rRNA gene sequence similarity with species of the genus Bartonella, a group of mammalian pathogens transmitted by bloodsucking arthropods. Phylogenetic analyses showed that PEB0122T and related strains from the honey bee gut form a sister clade of the genus Bartonella. Optimal growth of strain PEB0122T was obtained on solid media supplemented with defibrinated sheep blood under microaerophilic conditions at 35-37 °C, which is consistent with the cultural characteristics of other species of the genus Bartonella. Reduced growth of strain PEB0122T also occurred under aerobic conditions. The rod-shaped cells of strain PEB0122T had a mean length of 1.2-1.8 μm and revealed hairy surface structures. Strain PEB0122T was positive for catalase, cytochrome c oxidase, urease and nitrate reductase. The fatty acid composition was comparable to those of other species of the genus Bartonella, with palmitic acid (C16 : 0) and isomers of 18- and 19-carbon chains being the most abundant. The genomic DNA G+C content of PEB0122T was determined to be about 45.5 mol%. The high 16S rRNA gene sequence similarity with species of Bartonella and its close phylogenetic position suggest that strain PEB0122T represents a novel species within the genus Bartonella, for which we propose the name Bartonella apis sp. nov. The type strain is PEB0122T ( = NCIMB 14961T = DSM 29779T). PMID:26537852

  10. Glucose and Glycogen Metabolism in Brugia malayi Is Associated with Wolbachia Symbiont Fitness.

    Science.gov (United States)

    Voronin, Denis; Bachu, Saheed; Shlossman, Michael; Unnasch, Thomas R; Ghedin, Elodie; Lustigman, Sara

    2016-01-01

    Wolbachia are endosymbiotic bacteria found in the majority of arthropods and filarial nematodes of medical and veterinary importance. They have evolved a wide range of symbiotic associations. In filarial nematodes that cause human lymphatic filariasis (Wuchereria bancrofti, Brugia malayi) or onchocerciasis (Onchocerca volvulus), Wolbachia are important for parasite development, reproduction and survival. The symbiotic bacteria rely in part on nutrients and energy sources provided by the host. Genomic analyses suggest that the strain of Wolbachia found in B. malayi (wBm) lacks the genes for two glycolytic enzymes--6-phosphofructokinase and pyruvate kinase--and is thus potentially unable to convert glucose into pyruvate, an important substrate for energy generation. The Wolbachia surface protein, wBm00432, is complexed to six B. malayi glycolytic enzymes, including aldolase. In this study we characterized two B. malayi aldolase isozymes and found that their expression is dependent on Wolbachia fitness and number. We confirmed by immuno-transmission electron microscopy that aldolase is associated with the Wolbachia surface. RNAi experiments suggested that aldolase-2 plays a significant role in both Wolbachia survival and embryogenesis in B. malayi. Treatment with doxycycline reduced Wolbachia fitness and increased the amount of both glucose and glycogen detected in the filarial parasite, indicating that glucose metabolism and glycogen storage in B. malayi are associated with Wolbachia fitness. This metabolic co-dependency between Wolbachia and its filarial nematode indicates that glycolysis could be a shared metabolic pathway between the bacteria and B. malayi, and thus a potential new target for anti-filarial therapy. PMID:27078260

  11. Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

    2013-03-11

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

  12. Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.

    Directory of Open Access Journals (Sweden)

    2006-05-01

    Full Text Available The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with DNA transfer, suggesting that ancestral rickettsiae might have been endowed with a conjugation apparatus. Here we present the genome sequence of Rickettsia bellii, the earliest diverging species of known rickettsiae. The 1,552,076 base pair-long chromosome does not exhibit the colinearity observed between other rickettsia genomes, and encodes a complete set of putative conjugal DNA transfer genes most similar to homologues found in Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The genome exhibits many other genes highly similar to homologues in intracellular bacteria of amoebae. We sought and observed sex pili-like cell surface appendages for R. bellii. We also found that R. bellii very efficiently multiplies in the nucleus of eukaryotic cells and survives in the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that amoeba-like ancestral protozoa could have served as a genetic "melting pot" where the ancestors of rickettsiae and other bacteria promiscuously exchanged genes, eventually leading to their adaptation to the intracellular lifestyle within eukaryotic cells.

  13. [The Principle of Genome Complementarity in the Enhancement of Plant Adaptive Capacities].

    Science.gov (United States)

    Tikhonovich, I A; Andronov, E E; Borisov, A Yu; Dolgikh, E A; Zhernakov, A I; Zhukov, V A; Provorov, N A; Roumiantseva, M L; Simarov, B V

    2015-09-01

    In the present work, the potential for the enhancement of the adaptive capacity of microbe-plant systems (MPSs) through the integration of the symbiosis partners' genomes is considered on the example of different types of symbiotic relationships. The accumulated data on the genetic control of interactions for both the plant and microbe, which are discussed in the paper with respect to signaling genes, suggest that it is the complementarity of genetic determinants that underlies the successful formation of MPSs. A eukaryotic genome with limited information content, which is stable throughout a generation, is complemented by a virtually unlimited prokaryotic metagenome. The microsymbiont's ability to adapt to different living conditions is based on the restructuring of the accessory genome by different mechanisms, which are likely to be activated under the influence of plants, although the details of such a regulation remain unknown. Features of the genetic control of the interaction, particularly its universal character for different symbionts, allow us to formulate a principle of genome-complementarity with respect to interacting organisms and consider it an important factor, an adaptation that enhances the abilities of M PSs for their sustainable development in natural ecosystems and for high plant productivity in agrocenoses. PMID:26606794

  14. The coffee genome hub : a resource for coffee genomes

    OpenAIRE

    Dereeper, Alexis; Bocs, Stéphanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaëtan

    2015-01-01

    The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub ( ext-link-type="uri" xlink:href="http://coffee-genome.org/" xlink:type="simple">http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilit...

  15. Phytophthora genomics: the plant destroyers' genome decoded

    NARCIS (Netherlands)

    Govers, F.; Gijzen, M.

    2006-01-01

    The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered

  16. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2003-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  17. Genomic Data Commons | Office of Cancer Genomics

    Science.gov (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  18. Comparative genomics explains the evolutionary success of reef-forming corals.

    Science.gov (United States)

    Bhattacharya, Debashish; Agrawal, Shobhit; Aranda, Manuel; Baumgarten, Sebastian; Belcaid, Mahdi; Drake, Jeana L; Erwin, Douglas; Foret, Sylvian; Gates, Ruth D; Gruber, David F; Kamel, Bishoy; Lesser, Michael P; Levy, Oren; Liew, Yi Jin; MacManes, Matthew; Mass, Tali; Medina, Monica; Mehr, Shaadi; Meyer, Eli; Price, Dana C; Putnam, Hollie M; Qiu, Huan; Shinzato, Chuya; Shoguchi, Eiichi; Stokes, Alexander J; Tambutté, Sylvie; Tchernov, Dan; Voolstra, Christian R; Wagner, Nicole; Walker, Charles W; Weber, Andreas Pm; Weis, Virginia; Zelzion, Ehud; Zoccola, Didier; Falkowski, Paul G

    2016-01-01

    Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years. PMID:27218454

  19. Comparative genomics explains the evolutionary success of reef-forming corals

    KAUST Repository

    Bhattacharya, Debashish

    2016-05-24

    Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.

  20. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  1. Effects of antibiotics on hydrogen production and gut symbionts in the Formosan subterranean termite Coptotermes formosanus (Isoptera: Rhinotermitidae)

    Institute of Scientific and Technical Information of China (English)

    Yueqing Cao; Jian-Zhong Sun; Jose M.Rodriguez

    2012-01-01

    Symbiotic microorganisms that inhabit the gut of Coptoterrnes forrnosanus enable this termite to degrade lignocelluloses and further produce hydrogen as an important intermediate to be recycled in its hindgut or as a byproduct to be emitted to the atmosphere.Both symbiotic protists and prokaryotes in the guts of termites demonstrated some different roles with respect to hydrogen production.In this study,the effects of two antibiotics,ampicillin and tetracycline,on hydrogen emission and the gut symbionts of C.formosanus were investigated.Hydrogen emission from termite guts was significantly enhanced when termites fed on wood diets treated with either ampicillin or tetracycline.The greatest H2 emission rates,2519 ± 74 and 2080 ± 377 nmol/h/g body weight,were recorded with the treatments of ampicillin and tetracycline,respectively,which showed 6-7 times more H2 production than that of controls.Antibiotic-treated diets negatively affected the prokaryotic communities and reduced their abundances,particularly on those ectosymbionts inhabiting the gut walls or in the gut fluid of C.formosanus,such as spirochetes.However,no significant reductions in the counts of gut cellulolytic protists,Pseudotrichonympha grassii and Holonastigotoids hartmanni,were recorded; and with a further observation by confocal laser scanning microscopy,the endosymbionts inhabiting P.grassii generally survived the antibiotic treatments.These results suggest that some prokaryotes may serve as the main hydrogen consumers,while P.grassii,together with its endosymbionts,may function as the main contributors for hydrogen production in the hindgut of C.formosanus.

  2. Special structures of hoopoe eggshells enhance the adhesion of symbiont-carrying uropygial secretion that increase hatching success.

    Science.gov (United States)

    Martín-Vivaldi, Manuel; Soler, Juan J; Peralta-Sánchez, Juan M; Arco, Laura; Martín-Platero, Antonio M; Martínez-Bueno, Manuel; Ruiz-Rodríguez, Magdalena; Valdivia, Eva

    2014-11-01

    Animals live in a bacterial world, and detecting and exploring adaptations favouring mutualistic relationships with antibiotic-producing bacteria as a strategy to fight pathogens are of prime importance for evolutionary ecologists. Uropygial secretion of European hoopoes (Upupa epops, Linnaeus) contains antimicrobials from mutualistic bacteria that may be used to prevent embryo infection. Here, we investigated the microscopic structure of hoopoe eggshells looking for special features favouring the adhesion of antimicrobial uropygial secretions. We impeded female access to the uropygial gland and compared microscopic characteristics of eggshells, bacterial loads of eggs and of uropygial secretion, and hatching success of experimental and control females. Then, we explored the link between microbiological characteristics of uropygial secretion and these of eggs of hoopoes, as well as possible fitness benefits. The microscopic study revealed special structures in hoopoes' eggshells (crypts). The experimental prevention of females' gland access demonstrated that crypts are filled with uropygial secretion and that symbiotic enterococci bacteria on the eggshells come, at least partially, from those in the female's uropygial gland. Moreover, the experiment resulted in a higher permeability of eggshells by several groups of bacteria and in elimination of the positive relationships detected for control nests between hatching success and density of symbiotic bacteria, either in the uropygial secretion of females or on the eggshell. The findings of specialized crypts on the eggshells of hoopoes, and of video-recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. Moreover, the detected associations between bacteria and hatching success suggest that crypts enhancing the adhesion of symbiont-carrying uropygial secretion likely protect embryos against infections. PMID

  3. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    Science.gov (United States)

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  4. Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices.

    Science.gov (United States)

    Battini, Fabio; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

    2016-02-01

    Arbuscular Mycorrhizal Fungi (AMF) live in symbiosis with most crop plants and represent essential elements of soil fertility and plant nutrition and productivity, facilitating soil mineral nutrient uptake and protecting plants from biotic and abiotic stresses. These beneficial services may be mediated by the dense and active spore-associated bacterial communities, which sustain diverse functions, such as the promotion of mycorrhizal activity, biological control of soilborne diseases, nitrogen fixation, and the supply of nutrients and growth factors. In this work, we utilised culture-dependent methods to isolate and functionally characterize the microbiota strictly associated to Rhizophagus intraradices spores, and molecularly identified the strains with best potential plant growth promoting (PGP) activities by 16S rDNA sequence analysis. We isolated in pure culture 374 bacterial strains belonging to different functional groups-actinobacteria, spore-forming, chitinolytic and N2-fixing bacteria-and screened 122 strains for their potential PGP activities. The most common PGP trait was represented by P solubilization from phytate (69.7%), followed by siderophore production (65.6%), mineral P solubilization (49.2%) and IAA production (42.6%). About 76% of actinobacteria and 65% of chitinolytic bacteria displayed multiple PGP activities. Nineteen strains with best potential PGP activities, assigned to Sinorhizobium meliloti, Streptomyces spp., Arthrobacter phenanthrenivorans, Nocardiodes albus, Bacillus sp. pumilus group, Fictibacillus barbaricus and Lysinibacillus fusiformis, showed the ability to produce IAA and siderophores and to solubilize P from mineral phosphate and phytate, representing suitable candidates as biocontrol agents, biofertilisers and bioenhancers, in the perspective of targeted management of beneficial symbionts and their associated bacteria in sustainable food production systems. PMID:26805620

  5. Climate-driven variation in the intensity of a host-symbiont animal interaction along a broad elevation gradient.

    Directory of Open Access Journals (Sweden)

    Leandro Meléndez

    Full Text Available Gradients of environmental stress may affect biotic interactions in unpredictable ways responding to climate variation, depending on the abiotic stress tolerance of interacting partners. Here, we study the effect of local climate on the intensity of feather mites in six mountain passerines along a 1400 m elevational gradient characterized by shifting temperature and rainfall. Although obligatory symbionts of warm-blooded organisms are assumed to live in mild and homeothermic environments, those inhabiting external, non-blood-irrigated body portions of the host organism, such as feather mites, are expected to endure exposure to the direct influence of a fluctuating climate. As expected, feather mite intensity declined with elevation in all bird species, a pattern that was also found in cold-adapted passerines that have typical alpine habits. The elevation cline was mainly explained by a positive effect of the average temperature upon mite intensity in five of the six species studied. Precipitation explained less variance in mite intensity than average temperature, and showed a negative correlation in half of the studied species. We found no climate-driven migration of mites along the wings of birds, no replacement of mite species along elevation gradients and no association with available food resources for mites (estimated by the size of the uropygial gland. This study suggests that ectosymbionts of warm-blooded animals may be highly sensitive to climatic variation and become less abundant under stressful environmental conditions, providing empirical evidence of the decline of specialized biotic interactions among animal species at high elevations.

  6. Effects of light, food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts.

    Directory of Open Access Journals (Sweden)

    Mia O Hoogenboom

    Full Text Available BACKGROUND: Reef corals are heterotrophic coelenterates that achieve high productivity through their photosynthetic dinoflagellate symbionts. Excessive seawater temperature destabilises this symbiosis and causes corals to "bleach," lowering their photosynthetic capacity. Bleaching poses a serious threat to the persistence of coral reefs on a global scale. Despite expanding research on the causes of bleaching, the mechanisms remain a subject of debate. METHODOLOGY/PRINCIPAL FINDINGS: This study determined how light and food availability modulate the effects of temperature stress on photosynthesis in two reef coral species. We quantified the activities of Photosystem II, Photosystem I and whole chain electron transport under combinations of normal and stressful growth temperatures, moderate and high light levels and the presence or absence of feeding of the coral hosts. Our results show that PS1 function is comparatively robust against temperature stress in both species, whereas PS2 and whole chain electron transport are susceptible to temperature stress. In the symbiotic dinoflagellates of Stylophora pistillata the contents of chlorophyll and major photosynthetic complexes were primarily affected by food availability. In Turbinaria reniformis growth temperature was the dominant influence on the contents of the photosynthetic complexes. In both species feeding the host significantly protected photosynthetic function from high temperature stress. CONCLUSIONS/SIGNIFICANCE: Our findings support the photoinhibition model of coral bleaching and demonstrate that PS1 is not a major site for thermal damage during bleaching events. Feeding mitigates bleaching in two scleractinian corals, so that reef responses to temperature stresses will likely be influenced by the coinciding availabilities of prey for the host.

  7. Exploiting the genome

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  8. Genomics of Sorghum

    OpenAIRE

    Paterson, Andrew H.

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relatin...

  9. Whole Genome Selection

    Science.gov (United States)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  10. Public Health Genomics

    OpenAIRE

    Lavinha, João

    2012-01-01

    Professional genomic and molecular medicine and consumer genetics. The health field concept and the public health wheel. The enterprise of Public Health Genomics (PHGEN). Genetic exceptionalism. Ethical benchmarks. Introduction and use of genome-based knowledge in the health services. Stakeholder involvement.

  11. Growth dynamics of the threatened Caribbean staghorn coral Acropora cervicornis: influence of host genotype, symbiont identity, colony size, and environmental setting.

    Directory of Open Access Journals (Sweden)

    Diego Lirman

    Full Text Available BACKGROUND: The drastic decline in the abundance of Caribbean acroporid corals (Acropora cervicornis, A. palmata has prompted the listing of this genus as threatened as well as the development of a regional propagation and restoration program. Using in situ underwater nurseries, we documented the influence of coral genotype and symbiont identity, colony size, and propagation method on the growth and branching patterns of staghorn corals in Florida and the Dominican Republic. METHODOLOGY/PRINCIPAL FINDINGS: Individual tracking of> 1700 nursery-grown staghorn fragments and colonies from 37 distinct genotypes (identified using microsatellites in Florida and the Dominican Republic revealed a significant positive relationship between size and growth, but a decreasing rate of productivity with increasing size. Pruning vigor (enhanced growth after fragmentation was documented even in colonies that lost 95% of their coral tissue/skeleton, indicating that high productivity can be maintained within nurseries by sequentially fragmenting corals. A significant effect of coral genotype was documented for corals grown in a common-garden setting, with fast-growing genotypes growing up to an order of magnitude faster than slow-growing genotypes. Algal-symbiont identity established using qPCR techniques showed that clade A (likely Symbiodinium A3 was the dominant symbiont type for all coral genotypes, except for one coral genotype in the DR and two in Florida that were dominated by clade C, with A- and C-dominated genotypes having similar growth rates. CONCLUSION/SIGNIFICANCE: The threatened Caribbean staghorn coral is capable of extremely fast growth, with annual productivity rates exceeding 5 cm of new coral produced for every cm of existing coral. This species benefits from high fragment survivorship coupled by the pruning vigor experienced by the parent colonies after fragmentation. These life-history characteristics make A. cervicornis a successful candidate

  12. Towards a molecular understanding of symbiont function: Identification of a fungal gene for the degradation of xylan in the fungus gardens of leaf-cutting ants

    OpenAIRE

    Lange Lene; De Fine Licht Henrik H; Schiøtt Morten; Boomsma Jacobus J

    2008-01-01

    Abstract Background Leaf-cutting ants live in symbiosis with a fungus that they rear for food by providing it with live plant material. Until recently the fungus' main inferred function was to make otherwise inaccessible cell wall degradation products available to the ants, but new studies have shed doubt on this idea. To provide evidence for the cell wall degrading capacity of the attine ant symbiont, we designed PCR primers from conserved regions of known xylanase genes, to be used in PCR w...

  13. A genome blogger manifesto

    Directory of Open Access Journals (Sweden)

    Corpas Manuel

    2012-10-01

    Full Text Available Abstract Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  14. Statistics of genome architecture

    International Nuclear Information System (INIS)

    The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.

  15. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.;

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of...... tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios....... RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a...

  16. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel;

    2015-01-01

    Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus......, genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other...... chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling...

  17. Development in Rice Genome Research Based on Accurate Genome Sequence

    OpenAIRE

    2008-01-01

    Rice is one of the most important crops in the world. Although genetic improvement is a key technology for the acceleration of rice breeding, a lack of genome information had restricted efforts in molecular-based breeding until the completion of the high-quality rice genome sequence, which opened new opportunities for research in various areas of genomics. The syntenic relationship of the rice genome to other cereal genomes makes the rice genome invaluable for understanding how cereal genomes...

  18. The Genome of Laccaria Bi color Provides Insights into Mycorrhizal Symbiosis

    Energy Technology Data Exchange (ETDEWEB)

    Martin, F [UMR, France; Aerts, A. [U.S. Department of Energy, Joint Genome Institute; Ahren, D [Lund University, Sweden; Brun, A [UMR, France; Duchaussoy, F [UMR, France; Gibon, J [UMR, France; Kohler, A [UMR, France; Lindquist, E [U.S. Department of Energy, Joint Genome Institute; Pereda, V [UMR, France; Salamov, A. [U.S. Department of Energy, Joint Genome Institute; Shapiro, HJ [U.S. Department of Energy, Joint Genome Institute; Wuyts, J [UMR, France; Blaudez, D [UMR, France; Buee, M [UMR, France; Brokstein, P [U.S. Department of Energy, Joint Genome Institute; Canbeck, B [Lund University, Sweden; Cohen, D [UMR, France; Courty, PE [UMR, France; Coutinho, PM [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Danchin, E [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Delaruelle, C [UMR, France; Detter, J C [U.S. Department of Energy, Joint Genome Institute; Deveau, A [UMR, France; DiFazio, Stephen P [West Virginia University; Duplessis, S [UMR, France; Fraissinet-Tachet, L [Universite de Lyon, France; Lucic, E [UMR, France; Frey-Klett, P [UMR, France; Fourrey, C [UMR, France; Feussner, I [Georg-August Universitat Gottingen Germany; Gay, G [Universite de Lyon, France; Grimwood, Jane [Stanford University; Hoegger, P J [Georg-August Universitat Gottingen Germany; Jain, P [University of Alabama, Huntsville; Kilaru, S [Georg-August Universitat Gottingen Germany; Labbe, J [UMR, France; Lin, Y C [Ghent University, Belgium; Legue, V [UMR, France; Le Tacon, F [UMR, France; Marmeisse, R [Universite de Lyon, France; Melayah, D [Universite de Lyon, France; Montanini, B [UMR, France; Muratet, M [University of Alabama, Huntsville; Nehls, U [Eberhard-Karls-Universitat, Tubingen, Germany; Niculita-Hirzel, H [University of Lausanne, Switzerland; Oudot-Le Secq, M P [UMR, France; Peter, M [UMR, France; Quesneville, H [Unite de Recherches en Genomique-Info,Evry Cedex; Rajashekar, B [Lund University, Sweden; Reich, M [UMR, France; Rouhler, N [UMR, France; Schmutz, Jeremy [Stanford University; Yin, Tongming [ORNL; Chalot, M [UMR, France; Henrissat, B [Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS and Unive; Kues, U [Georg-August Universitat Gottingen Germany; Lucas, S [U.S. Department of Energy, Joint Genome Institute; Van de Peer, Y [Ghent University, Belgium; Podila, G [University of Alabama, Huntsville; Polle, A [Georg-August Universitat Gottingen Germany; Pukkila, P J [University of North Carolina, Chapel Hill; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Rouze, P [Ghent University, Belgium; Sanders, I R [University of Lausanne, Switzerland; Stajich, J E [University of California, Berkeley; Tunlid, A [Lund University, Sweden; Tuskan, Gerald A [ORNL; Grigoriev, I. [U.S. Department of Energy, Joint Genome Institute

    2008-01-01

    Mycorrhizal symbioses the union of roots and soil fungi are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate and montane forests all depend on ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and

  19. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.

    Science.gov (United States)

    Okubo, Takashi; Tsukui, Takahiro; Maita, Hiroko; Okamoto, Shinobu; Oshima, Kenshiro; Fujisawa, Takatomo; Saito, Akihiro; Futamata, Hiroyuki; Hattori, Reiko; Shimomura, Yumi; Haruta, Shin; Morimoto, Sho; Wang, Yong; Sakai, Yoriko; Hattori, Masahira; Aizawa, Shin-Ichi; Nagashima, Kenji V P; Masuda, Sachiko; Hattori, Tsutomu; Yamashita, Akifumi; Bao, Zhihua; Hayatsu, Masahito; Kajiya-Kanegae, Hiromi; Yoshinaga, Ikuo; Sakamoto, Kazunori; Toyota, Koki; Nakao, Mitsuteru; Kohara, Mitsuyo; Anda, Mizue; Niwa, Rieko; Jung-Hwan, Park; Sameshima-Saito, Reiko; Tokuda, Shin-Ichi; Yamamoto, Sumiko; Yamamoto, Syuji; Yokoyama, Tadashi; Akutsu, Tomoko; Nakamura, Yasukazu; Nakahira-Yanaka, Yuka; Takada Hoshino, Yuko; Hirakawa, Hideki; Mitsui, Hisayuki; Terasawa, Kimihiro; Itakura, Manabu; Sato, Shusei; Ikeda-Ohtsubo, Wakako; Sakakura, Natsuko; Kaminuma, Eli; Minamisawa, Kiwamu

    2012-01-01

    Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere. PMID:22452844

  20. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes,  70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  1. Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

    Directory of Open Access Journals (Sweden)

    Xiaoyuan Chi

    2008-01-01

    Full Text Available Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Δ9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution.

  2. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    Directory of Open Access Journals (Sweden)

    Carolyn A. Young

    2015-04-01

    Full Text Available The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization. The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.

  3. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    Science.gov (United States)

    Young, Carolyn A.; Schardl, Christopher L.; Panaccione, Daniel G.; Florea, Simona; Takach, Johanna E.; Charlton, Nikki D.; Moore, Neil; Webb, Jennifer S.; Jaromczyk, Jolanta

    2015-01-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  4. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics.

    Science.gov (United States)

    Duan, Yongping; Zhou, Lijuan; Hall, David G; Li, Wenbin; Doddapaneni, Harshavardhan; Lin, Hong; Liu, Li; Vahling, Cheryl M; Gabriel, Dean W; Williams, Kelly P; Dickerman, Allan; Sun, Yijun; Gottwald, Tim

    2009-08-01

    Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of alpha-Proteobacteria, 'Candidatus Liberibacter asiaticus', 'Ca. L. americanus', and 'Ca. L. africanus'. A complete circular 'Ca. L. asiaticus' genome has been obtained by metagenomics, using the DNA extracted from a single 'Ca. L. asiaticus'-infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. 'Ca. L. asiaticus' appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, 'Ca. L. asiaticus' lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. 'Ca. L. asiaticus' appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed 'Ca. L. asiaticus' as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured alpha-proteobacteria that is both an intracellular plant pathogen and insect symbiont. PMID:19589076

  5. Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

    KAUST Repository

    Tian, Renmao

    2014-08-29

    Sulfur-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) play essential roles in marine sponges. However, the detailed characteristics and physiology of the bacteria are largely unknown. Here, we present and analyse the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy. The loss of transposase and virulence-associated genes and the maintenance of the ancient polyphosphate glucokinase gene suggested a stabilized SOB genome that might have coevolved with the ancient host during establishment of their association. Exclusive distribution in sponge, bacterial detoxification for the host (sulfide oxidation) and the enrichment for symbiotic characteristics (genes-encoding ankyrin) in the SOB genome supported the bacterial role as an intercellular symbiont. Despite possessing complete autotrophic sulfur oxidation pathways, the bacterium developed a much more versatile capacity for carbohydrate uptake and metabolism, in comparison with its closest relatives (Thioalkalivibrio) and to other representative autotrophs from the same order (Chromatiales). The ability to perform both autotrophic and heterotrophic metabolism likely results from the unstable supply of reduced sulfur in the sponge and is considered critical for the sponge-SOB consortium. Our study provides insights into SOB of sponge-specific clade with thioautotrophic and versatile heterotrophic metabolism relevant to its roles in the micro-environment of the sponge body. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat;

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a...... distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae....... Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could...

  7. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  8. Clinical Genomic Database

    OpenAIRE

    Solomon, Benjamin D.; Nguyen, Anh-Dao; Bear, Kelly A.; Wolfsberg, Tyra G.

    2013-01-01

    Technological advances have greatly increased the availability of human genomic sequencing. However, the capacity to analyze genomic data in a clinically meaningful way lags behind the ability to generate such data. To help address this obstacle, we reviewed all conditions with genetic causes and constructed the Clinical Genomic Database (CGD) (http://research.nhgri.nih.gov/CGD/), a searchable, freely Web-accessible database of conditions based on the clinical utility of genetic diagnosis and...

  9. Physician Assistant Genomic Competencies.

    Science.gov (United States)

    Goldgar, Constance; Michaud, Ed; Park, Nguyen; Jenkins, Jean

    2016-09-01

    Genomic discoveries are increasingly being applied to the clinical care of patients. All physician assistants (PAs) need to acquire competency in genomics to provide the best possible care for patients within the scope of their practice. In this article, we present an updated version of PA genomic competencies and learning outcomes in a framework that is consistent with the current medical education guidelines and the collaborative nature of PAs in interprofessional health care teams. PMID:27490287

  10. Integrative Genomics Viewer

    OpenAIRE

    James T Robinson; Thorvaldsdóttir, Helga; Winckler, Wendy; Guttman, Mitchell; Lander, Eric S; Getz, Gad; Mesirov, Jill P.

    2011-01-01

    To the Editor: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Exper...

  11. Chromium and Genomic Stability

    OpenAIRE

    Wise, Sandra S.; Wise, John Pierce

    2011-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as high...

  12. Expectations from structural genomics.

    OpenAIRE

    Brenner, S. E.; Levitt, M.

    2000-01-01

    Structural genomics projects aim to provide an experimental structure or a good model for every protein in all completed genomes. Most of the experimental work for these projects will be directed toward proteins whose fold cannot be readily recognized by simple sequence comparison with proteins of known structure. Based on the history of proteins classified in the SCOP structure database, we expect that only about a quarter of the early structural genomics targets will have a new fold. Among ...

  13. Evolutionary genomics of Entamoeba

    OpenAIRE

    Weedall, Gareth D.; Hall, Neil

    2011-01-01

    Entamoeba histolytica is a human pathogen that causes amoebic dysentery and leads to significant morbidity and mortality worldwide. Understanding the genome and evolution of the parasite will help explain how, when and why it causes disease. Here we review current knowledge about the evolutionary genomics of Entamoeba: how differences between the genomes of different species may help explain different phenotypes, and how variation among E. histolytica parasites reveals patterns of population ...

  14. The Genome Atlas Resource

    OpenAIRE

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik; Hansson, Lena; Ussery, David

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The r...

  15. Comparative genomics of Bifidobacteria

    OpenAIRE

    Bottacini, Francesca

    2013-01-01

    Chapter 2 of this thesis describes the sequence analysis of 14 bifidobacterial genomes from various species of the genus Bifidobacterium, and the determination of their open pan-genome trend. This analysis first determined the total number of genes to be considered as the reservoir of functions available to representatives of this genus. Many identified genes are still uncharacterized, but may be involved in the adaptation to the gut environment. This comparative genomic analysis also determi...

  16. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  17. Genomics of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies. PMID:25638019

  18. Genome of Crocodilepox Virus

    OpenAIRE

    Afonso, C. L.; Tulman, E. R.; Delhon, G.; Lu, Z.; Viljoen, G. J.; Wallace, D. B.; Kutish, G. F.; Rock, D. L.

    2006-01-01

    Here, we present the genome sequence, with analysis, of a poxvirus infecting Nile crocodiles (Crocodylus niloticus) (crocodilepox virus; CRV). The genome is 190,054 bp (62% G+C) and predicted to contain 173 genes encoding proteins of 53 to 1,941 amino acids. The central genomic region contains genes conserved and generally colinear with those of other chordopoxviruses (ChPVs). CRV is distinct, as the terminal 33-kbp (left) and 13-kbp (right) genomic regions are largely CRV specific, containin...

  19. REFORESTATION AND SEEDLING SYMBIONTS

    Science.gov (United States)

    Tree seedlings are dependent on symbiotic associations with microorganisms including bacteria, fungi, and actinomycetes for normal growth and development. itrogen fixing leguminous and non-leguminous trees form symbiotic relationships with Rhizobium (bacteria) and Frankia (actino...

  20. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø;

    2012-01-01

    Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven...... as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casual mutation alleles are reversed across populations, or the actual...... casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...

  1. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory; Detter, Chris [Los Alamos National Laboratory; Bruce, David [Los Alamos National Laboratory; Challacome, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Philippe [CNRS, UNIV LYON; Necsula, Anamaria [CNRS, UNIV LYON; Daubin, Vincent [CNRS, UNIV LYON; Medigue, Claudine [CNRS/GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [DOE JOINT GENOME INST.; Pujic, Pierre [CNRS, UNIV LYON; Richardson, Paul [DOE JOINT GENOME INST; Berry, Alison M [UC DAVIS

    2008-01-01

    We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus lIB, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudogenes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

  2. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory; Detter, John C [Los Alamos National Laboratory; Bruce, David C [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Necsulea, Anamaria [UNIV LYON; Daubin, Vincent [UNIV LYON; Medigue, Claudine [GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [JGI; Pujic, Pierre [UNIV LYON; Berry, Alison M [UC DAVIS; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Phillipe [UNIV LYON

    2009-01-01

    We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus 11B, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudo genes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

  3. Genome-Scale Models

    DEFF Research Database (Denmark)

    Bergdahl, Basti; Sonnenschein, Nikolaus; Machado, Daniel;

    2016-01-01

    An introduction to genome-scale models, how to build and use them, will be given in this chapter. Genome-scale models have become an important part of systems biology and metabolic engineering, and are increasingly used in research, both in academica and in industry, both for modeling chemical...

  4. Human genome I

    International Nuclear Information System (INIS)

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  5. Genomics for Weed Science

    Science.gov (United States)

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  6. Genetics and Genomics

    Science.gov (United States)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  7. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  8. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA...

  9. Unlocking the bovine genome

    Science.gov (United States)

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  10. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  11. Genomic Feature Models

    DEFF Research Database (Denmark)

    Sørensen, Peter; Edwards, Stefan McKinnon; Rohde, Palle Duun

    Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non-additive g......Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non...... sets of genetic variants. We have applied these approaches to whole genome sequences and a complex trait phenotype resistance to starvation collected on inbred lines from the Drosophila Genome Reference Panel population. We identified a number of genomic features classification schemes (e.g. prior QTL...

  12. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from...... Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  13. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  14. Evolution of genome architecture.

    Science.gov (United States)

    Koonin, Eugene V

    2009-02-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome

  15. A Brazilian population of the asexual fungus-growing ant Mycocepurus smithii (Formicidae, Myrmicinae, Attini cultivates fungal symbionts with gongylidia-like structures.

    Directory of Open Access Journals (Sweden)

    Virginia E Masiulionis

    Full Text Available Attine ants cultivate fungi as their most important food source and in turn the fungus is nourished, protected against harmful microorganisms, and dispersed by the ants. This symbiosis evolved approximately 50-60 million years ago in the late Paleocene or early Eocene, and since its origin attine ants have acquired a variety of fungal mutualists in the Leucocoprineae and the distantly related Pterulaceae. The most specialized symbiotic interaction is referred to as "higher agriculture" and includes leafcutter ant agriculture in which the ants cultivate the single species Leucoagaricus gongylophorus. Higher agriculture fungal cultivars are characterized by specialized hyphal tip swellings, so-called gongylidia, which are considered a unique, derived morphological adaptation of higher attine fungi thought to be absent in lower attine fungi. Rare reports of gongylidia-like structures in fungus gardens of lower attines exist, but it was never tested whether these represent rare switches of lower attines to L. gonglyphorus cultivars or whether lower attine cultivars occasionally produce gongylidia. Here we describe the occurrence of gongylidia-like structures in fungus gardens of the asexual lower attine ant Mycocepurus smithii. To test whether M. smithii cultivates leafcutter ant fungi or whether lower attine cultivars produce gongylidia, we identified the M. smithii fungus utilizing molecular and morphological methods. Results shows that the gongylidia-like structures of M. smithii gardens are morphologically similar to gongylidia of higher attine fungus gardens and can only be distinguished by their slightly smaller size. A molecular phylogenetic analysis of the fungal ITS sequence indicates that the gongylidia-bearing M. smithii cultivar belongs to the so-called "Clade 1"of lower Attini cultivars. Given that M. smithii is capable of cultivating a morphologically and genetically diverse array of fungal symbionts, we discuss whether asexuality of

  16. A Brazilian population of the asexual fungus-growing ant Mycocepurus smithii (Formicidae, Myrmicinae, Attini) cultivates fungal symbionts with gongylidia-like structures.

    Science.gov (United States)

    Masiulionis, Virginia E; Rabeling, Christian; De Fine Licht, Henrik H; Schultz, Ted; Bacci, Maurício; Bezerra, Cintia M Santos; Pagnocca, Fernando C

    2014-01-01

    Attine ants cultivate fungi as their most important food source and in turn the fungus is nourished, protected against harmful microorganisms, and dispersed by the ants. This symbiosis evolved approximately 50-60 million years ago in the late Paleocene or early Eocene, and since its origin attine ants have acquired a variety of fungal mutualists in the Leucocoprineae and the distantly related Pterulaceae. The most specialized symbiotic interaction is referred to as "higher agriculture" and includes leafcutter ant agriculture in which the ants cultivate the single species Leucoagaricus gongylophorus. Higher agriculture fungal cultivars are characterized by specialized hyphal tip swellings, so-called gongylidia, which are considered a unique, derived morphological adaptation of higher attine fungi thought to be absent in lower attine fungi. Rare reports of gongylidia-like structures in fungus gardens of lower attines exist, but it was never tested whether these represent rare switches of lower attines to L. gonglyphorus cultivars or whether lower attine cultivars occasionally produce gongylidia. Here we describe the occurrence of gongylidia-like structures in fungus gardens of the asexual lower attine ant Mycocepurus smithii. To test whether M. smithii cultivates leafcutter ant fungi or whether lower attine cultivars produce gongylidia, we identified the M. smithii fungus utilizing molecular and morphological methods. Results shows that the gongylidia-like structures of M. smithii gardens are morphologically similar to gongylidia of higher attine fungus gardens and can only be distinguished by their slightly smaller size. A molecular phylogenetic analysis of the fungal ITS sequence indicates that the gongylidia-bearing M. smithii cultivar belongs to the so-called "Clade 1"of lower Attini cultivars. Given that M. smithii is capable of cultivating a morphologically and genetically diverse array of fungal symbionts, we discuss whether asexuality of the ant host maybe

  17. Genomic instability following irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Hacker-Klom, U.B.; Goehde, W. [Inst. fuer Strahlenbiologie, Muenster Univ. (Germany)

    2001-07-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  18. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  19. 纤毛类原生动物中宿主-共生体系统的研究%Studies on the Host-Symbiont System in Ciliates

    Institute of Scientific and Technical Information of China (English)

    顾福康; 孙军; 何远; 田沁

    2001-01-01

    目前已经在100多种纤毛虫中观察到细菌、藻类和其他微生物等共生体。对纤毛虫中宿主-共生体系统的研究表明,双小核草履虫中卡巴粒的遗传为细胞质遗传理论提供了例证;含细菌共生体的许多厌氧纤毛虫无线粒体,共生体对宿主代谢有重要作用;尾草履虫-钝状全孢螺菌共生作用中,共生菌感染形式的39kDa、15kDa周质蛋白可分别与IF-3-1、IF-3-2两种单抗反应,其共生体早期感染过程中两种抗原的量发生显著变化,并且共生体生殖 形式选择性地合成63kDa蛋白质,该蛋白质可能是与共生作用有联系的关键分子;绿草履虫-小球藻共生系统中,共生藻中存在葡糖胺硬性壁是其与草履虫发生共生关系的基本条件,其中,共生藻参与宿主代谢,与宿主形成相互受益的专一性关系,并且藻类共生体的作用可能影响了宿主草履虫基因组有关结构,改变了其基因表达。作者推测,探索共生体对宿主基因结构及其表达产物的影响可能是对纤毛虫中共生作用研究的主要趋势,这对于深入了 解真核细胞中宿主-共生体双方的相互作用、物质交流在分子水平上的调控机理、细胞结构与功能的关系等细胞生命活动规律是有意义的。%To date, bacterial,algal and other microbial symbionts have been found in more than 100 species of ciliates. The study of the host-symbiont system in ciliates shows that: ( 1 ) The inheritance of kappa particles in the cytoplasm of Paramecium aurelia is a classic example of the cytoplasmic inheritance theory. (2) Bacterial symbionts in some anerobic ciliates that lack mitochondria play the major role in the host's metabolism. (3) In the P. Caudatum-Holospora obtusa system, 39- and 15-kDa periplasmic pro teins of the infectious H. Obtusa reacted with IF-3-1 and IF-3-2 monoclonal antibodies respectively. The amounts of both antigens were reduced during

  20. Genome instability and aging.

    Science.gov (United States)

    Vijg, Jan; Suh, Yousin

    2013-01-01

    Genome instability has long been implicated as the main causal factor in aging. Somatic cells are continuously exposed to various sources of DNA damage, from reactive oxygen species to UV radiation to environmental mutagens. To cope with the tens of thousands of chemical lesions introduced into the genome of a typical cell each day, a complex network of genome maintenance systems acts to remove damage and restore the correct base pair sequence. Occasionally, however, repair is erroneous, and such errors, as well as the occasional failure to correctly replicate the genome during cell division, are the basis for mutations and epimutations. There is now ample evidence that mutations accumulate in various organs and tissues of higher animals, including humans, mice, and flies. What is not known, however, is whether the frequency of these random changes is sufficient to cause the phenotypic effects generally associated with aging. The exception is cancer, an age-related disease caused by the accumulation of mutations and epimutations. Here, we first review current concepts regarding the relationship between DNA damage, repair, and mutation, as well as the data regarding genome alterations as a function of age. We then describe a model for how randomly induced DNA sequence and epigenomic variants in the somatic genomes of animals can result in functional decline and disease in old age. Finally, we discuss the genetics of genome instability in relation to longevity to address the importance of alterations in the somatic genome as a causal factor in aging and to underscore the opportunities provided by genetic approaches to develop interventions that attenuate genome instability, reduce disease risk, and increase life span. PMID:23398157