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  • 1
    Online Resource
    Online Resource
    Reduced and Nonreduced Genomes in Paraburkholderia Symbionts of Social Amoebas
    American Society for Microbiology ; 2022
    In:  mSystems Vol. 7, No. 5 ( 2022-10-26)
    Details
    In: mSystems, American Society for Microbiology, Vol. 7, No. 5 ( 2022-10-26)
    Abstract: The social amoeba Dictyostelium discoideum is a predatory soil protist frequently used for studying host-pathogen interactions. A subset of D. discoideum strains isolated from soil persistently carry symbiotic Paraburkholderia , recently formally described as P. agricolaris , P. bonniea , and P. hayleyella . The three facultative symbiont species of D. discoideum present a unique opportunity to study a naturally occurring symbiosis in a laboratory model protist. There is a large difference in genome size between P. agricolaris (8.7 million base pairs [Mbp]) versus P. hayleyella and P. bonniea (4.1 Mbp). We took a comparative genomics approach and compared the three genomes of D. discoideum symbionts to 12 additional Paraburkholderia genomes to test for genome evolution patterns that frequently accompany host adaptation. Overall, P. agricolaris is difficult to distinguish from other Paraburkholderia based on its genome size and content, but the reduced genomes of P. bonniea and P. hayleyella display characteristics indicative of genome streamlining rather than deterioration during adaptation to their protist hosts. In addition, D. discoideum -symbiont genomes have increased secretion system and motility genes that may mediate interactions with their host. Specifically, adjacent BurBor-like type 3 and T6SS-5-like type 6 secretion system operons shared among all three D. discoideum -symbiont genomes may be important for host interaction. Horizontal transfer of these secretion system operons within the amoeba host environment may have contributed to the unique ability of these symbionts to establish and maintain a symbiotic relationship with D. discoideum . IMPORTANCE Protists are a diverse group of typically single cell eukaryotes. Bacteria and archaea that form long-term symbiotic relationships with protists may evolve in additional ways than those in relationships with multicellular eukaryotes such as plants, animals, or fungi. Social amoebas are a predatory soil protist sometimes found with symbiotic bacteria living inside their cells. They present a unique opportunity to explore a naturally occurring symbiosis in a protist frequently used for studying host-pathogen interactions. We show that one amoeba-symbiont species is similar to other related bacteria in genome size and content, while the two reduced-genome-symbiont species show characteristics of genome streamlining rather than deterioration during adaptation to their host. We also identify sets of genes present in all three amoeba-symbiont genomes that are potentially used for host-symbiont interactions. Because the amoeba symbionts are distantly related, the amoeba host environment may be where these genes were shared among symbionts.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.00562-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2844333-0
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  • 2
    Online Resource
    Online Resource
    Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses
    Elsevier BV ; 2023
    In:  Science of The Total Environment Vol. 889 ( 2023-09), p. 164040-
    Details
    In: Science of The Total Environment, Elsevier BV, Vol. 889 ( 2023-09), p. 164040-
    Type of Medium: Online Resource
    ISSN: 0048-9697
    URL: Article
    DOI: 10.1016/j.scitotenv.2023.164040
    RVK:
    AR 10100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1498726-0
    detail.hit.zdb_id: 121506-1
    SSG: 12
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  • 3
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    Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses
    Annual Reviews ; 2021
    In:  Annual Review of Microbiology Vol. 75, No. 1 ( 2021-10-08), p. 695-718
    Details
    In: Annual Review of Microbiology, Annual Reviews, Vol. 75, No. 1 ( 2021-10-08), p. 695-718
    Abstract: Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations.
    Type of Medium: Online Resource
    ISSN: 0066-4227 , 1545-3251
    URL: Issue
    URL: Article
    DOI: 10.1146/micro.2021.75.issue-1
    DOI: 10.1146/annurev-micro-051021-123130
    RVK:
    WA 15000
    Language: English
    Publisher: Annual Reviews
    Publication Date: 2021
    detail.hit.zdb_id: 1470471-7
    SSG: 12
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  • 4
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    Genome-Scale Metabolic Modelling of Lifestyle Changes in Rhizobium leguminosarum
    American Society for Microbiology ; 2022
    In:  mSystems Vol. 7, No. 1 ( 2022-02-22)
    Details
    In: mSystems, American Society for Microbiology, Vol. 7, No. 1 ( 2022-02-22)
    Abstract: Biological nitrogen fixation in rhizobium-legume symbioses is of major importance for sustainable agricultural practices. To establish a mutualistic relationship with their plant host, rhizobia transition from free-living bacteria in soil to growth down infection threads inside plant roots and finally differentiate into nitrogen-fixing bacteroids. We reconstructed a genome-scale metabolic model for Rhizobium leguminosarum and integrated the model with transcriptome, proteome, metabolome, and gene essentiality data to investigate nutrient uptake and metabolic fluxes characteristic of these different lifestyles. Synthesis of leucine, polyphosphate, and AICAR is predicted to be important in the rhizosphere, while myo- inositol catabolism is active in undifferentiated nodule bacteria in agreement with experimental evidence. The model indicates that bacteroids utilize xylose and glycolate in addition to dicarboxylates, which could explain previously described gene expression patterns. Histidine is predicted to be actively synthesized in bacteroids, consistent with transcriptome and proteome data for several rhizobial species. These results provide the basis for targeted experimental investigation of metabolic processes specific to the different stages of the rhizobium-legume symbioses. IMPORTANCE Rhizobia are soil bacteria that induce nodule formation on plant roots and differentiate into nitrogen-fixing bacteroids. A detailed understanding of this complex symbiosis is essential for advancing ongoing efforts to engineer novel symbioses with cereal crops for sustainable agriculture. Here, we reconstruct and validate a genome-scale metabolic model for Rhizobium leguminosarum bv. viciae 3841. By integrating the model with various experimental data sets specific to different stages of symbiosis formation, we elucidate the metabolic characteristics of rhizosphere bacteria, undifferentiated bacteria inside root nodules, and nitrogen-fixing bacteroids. Our model predicts metabolic flux patterns for these three distinct lifestyles, thus providing a framework for the interpretation of genome-scale experimental data sets and identifying targets for future experimental studies.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.00975-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2844333-0
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  • 5
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    Online Resource
    Sea Cucumber Body Vesicular Syndrome Is Driven by the Pond Water Microbiome via an Altered Gut Microbiota
    American Society for Microbiology ; 2022
    In:  mSystems Vol. 7, No. 3 ( 2022-06-28)
    Details
    In: mSystems, American Society for Microbiology, Vol. 7, No. 3 ( 2022-06-28)
    Abstract: Apostichopus japonicus (sea cucumber) is one of the most valuable aquaculture species in China; however, different diseases can limit its economic development. Recently, a novel disease, body vesicular syndrome (BVS), was observed in A. japonicus aquaculture. Diseased animals displayed no obvious phenotypic characteristics; however, after boiling at the postharvest stage, blisters, lysis, and body ruptures appeared. In this study, a multiomics strategy incorporating analysis of the gut microbiota, the pond microbiome, and A. japonicus genotype was established to investigate BVS. Detailed analyses of differentially expressed proteins (DEPs) and metabolites suggested that changes in cell adhesion structures, caused by disordered fatty acid β-oxidation mediated by vitamin B5 deficiency, could be a putative BVS mechanism. Furthermore, intestinal dysbacteriosis due to microbiome variations in pond water was considered a potential reason for vitamin B5 deficiency. Our BVS index, based on biomarkers identified from the A. japonicus gut microbiota, was a useful tool for BVS diagnosis. Finally, vitamin B5 supplementation was successfully used to treat BVS, suggesting an association with BVS etiology. IMPORTANCE Body vesicular syndrome (BVS) is a novel disease in sea cucumber aquaculture. As no phenotypic features are visible, BVS is difficult to confirm during aquaculture and postharvest activities, until animals are boiled. Therefore, BVS could lead to severe economic losses compared with other diseases in sea cucumber aquaculture. In this study, for the first time, we systematically investigated BVS pathogenesis and proposed an effective treatment for the condition. Moreover, based on the gut microbiota, we established a noninvasive diagnostic method for BVS in sea cucumber.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.01357-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
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  • 6
    Online Resource
    Online Resource
    Finding Needles in Haystacks and Inferring Their Function: Challenges and Successes in Beneficial Symbiosis Research
    American Society for Microbiology ; 2021
    In:  mSystems Vol. 6, No. 2 ( 2021-04-27)
    Details
    In: mSystems, American Society for Microbiology, Vol. 6, No. 2 ( 2021-04-27)
    Abstract: Symbioses between hosts and beneficial microbes are key drivers of biological innovation and diversity. While a range of systems have emerged that provide foundational insights into how symbioses function and evolve, we still have a limited understanding of the vast diversity of organisms that engage in such interactions. Recent advances in molecular tools, theory, and interdisciplinary approaches now permit researchers to expand our knowledge and to press forward the frontiers of symbiosis research. As described in a recent issue of mSystems , Myers and colleagues (K. N. Myers, D. Conn, and A. M. V. Brown, mSystems, 6:e01048-20, 2021, https://doi.org/10.1128/mSystems.01048-20 ) conducted a genome skimming approach to understand the role of obligate beneficial symbionts in plant-parasitic dagger nematodes. Nematodes are extraordinarily abundant and key players in ecosystem function and health. However, they are difficult to harness in the lab. The approach used by Myers et al. ameliorates these challenges to illustrate a relatively complete picture of a poorly understood beneficial symbiosis.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/mSystems.00243-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
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  • 7
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    Editorial: Applying metabolomics to questions in marine ecology and ecophysiology
    Frontiers Media SA ; 2022
    In:  Frontiers in Marine Science Vol. 9 ( 2022-9-27)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 9 ( 2022-9-27)
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    DOI: 10.3389/fmars.2022.1022877
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2757748-X
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  • 8
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    Genomic and Transcriptomic Insights into Salinity Tolerance-Based Niche Differentiation of Synechococcus Clades in Estuarine and Coastal Waters
    American Society for Microbiology ; 2023
    In:  mSystems Vol. 8, No. 1 ( 2023-02-23)
    Details
    In: mSystems, American Society for Microbiology, Vol. 8, No. 1 ( 2023-02-23)
    Abstract: Cluster 5 Synechococcus is one of the most important primary producers on earth. However, ecotypes of this genus exhibit complex geographical distributions, and the genetic basis of niche partitioning is still not fully understood. Here, we report distinct distributions of subcluster 5.1 (SC5.1) and subcluster 5.2 (SC5.2) Synechococcus in estuarine waters, and we reveal that salinity is the main factor determining their distribution. Clade III (belonging to SC5.1) and CB4 (belonging to SC5.2) are dominant clades in the study region, with different ecological distributions. We further conducted physiological, genomic, and transcriptomic studies of Synechococcus strains YX04-3 and HK05, which are affiliated with clade III and CB4, respectively. Laboratory tests showed that HK05 could grow at low salinity (13 ppt), whereas the growth of YX04-3 was suppressed when salinity decreased to 13 ppt. Genomic and transcriptomic analysis suggested that euryhaline clade CB4 is capable of dealing with a sudden drop of salinity by releasing compatible solutes through mechanosensitive channels that are coded by the mscL gene, decreasing biosynthesis of organic osmolytes, and increasing expression of heat shock proteins and high light-inducible proteins to protect photosystem. Furthermore, CB4 strain HK05 exhibited a higher growth rate when growing at low salinity than at high salinity. This is likely achieved by reducing its biosynthesis of organic osmolyte activity and increasing its photosynthetic activity at low salinity, which allowed it to enhance the assimilation of inorganic carbon and nitrogen. Together, these results provide new insights regarding the ecological distribution of SC5.2 and SC5.1 ecotypes and their underlying molecular mechanisms. IMPORTANCE Synechococcus is a group of unicellular Cyanobacteria that are widely distributed in global aquatic ecosystems. Salinity is a factor that affects the distribution of microorganisms in estuarine and coastal environments. In this study, we studied the distribution pattern of Synechococcus community along the salinity gradient in a subtropical estuary. By using omic methods, we unveiled genetic traits that determine the niche partitioning of euryhaline and strictly marine Synechococcus . We also explored the strategies employed by euryhaline Synechococcus to cope with a sudden drop of salinity, and revealed possible mechanisms for the higher growth rate of euryhaline Synechococcus in low salinity conditions. This study provides new insight into the genetic basis of niche partitioning of Synechococcus clades.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.01106-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2844333-0
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  • 9
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    Low salinity activates a virulence program in the generalist marine pathogen Photobacterium damselae subsp. damselae
    American Society for Microbiology ; 2023
    In:  mSystems Vol. 8, No. 3 ( 2023-06-29)
    Details
    In: mSystems, American Society for Microbiology, Vol. 8, No. 3 ( 2023-06-29)
    Abstract: Pathogenic Vibrionaceae species experience continuous shifts of NaCl concentration in their life cycles. However, the impact of salinity changes in gene regulation has been studied in a small number of Vibrio species. In this study, we analyzed the transcriptional response of Photobacterium damselae subsp. damselae ( Pdd ), a generalist and facultative pathogen, to changes in salinity, and demonstrate that growth at 1% NaCl in comparison to 3% NaCl triggers a virulence program of gene expression, with a major impact in the T2SS-dependent secretome. The decrease in NaCl concentration encountered by bacteria on entry into a host is proposed to constitute a regulatory signal that upregulates a genetic program involved in host invasion and tissue damage, nutrient scavenging (notably iron), and stress responses. This study will surely inspire new research on Pdd pathobiology, as well as on other important pathogens of the family Vibrionaceae and related taxa whose salinity regulons still await investigation.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.01253-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2844333-0
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  • 10
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    Sugars dominate the seagrass rhizosphere
    Springer Science and Business Media LLC ; 2022
    In:  Nature Ecology & Evolution Vol. 6, No. 7 ( 2022-05-02), p. 866-877
    Details
    In: Nature Ecology & Evolution, Springer Science and Business Media LLC, Vol. 6, No. 7 ( 2022-05-02), p. 866-877
    Abstract: Seagrasses are among the most efficient sinks of carbon dioxide on Earth. While carbon sequestration in terrestrial plants is linked to the microorganisms living in their soils, the interactions of seagrasses with their rhizospheres are poorly understood. Here, we show that the seagrass, Posidonia oceanica excretes sugars, mainly sucrose, into its rhizosphere. These sugars accumulate to µM concentrations—nearly 80 times higher than previously observed in marine environments. This finding is unexpected as sugars are readily consumed by microorganisms. Our experiments indicated that under low oxygen conditions, phenolic compounds from P. oceanica inhibited microbial consumption of sucrose. Analyses of the rhizosphere community revealed that many microbes had the genes for degrading sucrose but these were only expressed by a few taxa that also expressed genes for degrading phenolics. Given that we observed high sucrose concentrations underneath three other species of marine plants, we predict that the presence of plant-produced phenolics under low oxygen conditions allows the accumulation of labile molecules across aquatic rhizospheres.
    Type of Medium: Online Resource
    ISSN: 2397-334X
    URL: Article
    DOI: 10.1038/s41559-022-01740-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2879715-2
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