Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment

Lee, Ruth D.; Jospin, Guillaume; Lang, Jenna M.; Eisen, Jonathan A.; Coil, David A.

doi:10.1128/genomea.01769-15

Cited by 3 publications

(3 citation statements)

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“…Since we were using antibiotics, we do not expect these isolates to be representative of the true diversity of the culturable bacterial community associated with Z. marina, just the subset of the community naturally resistant to the antibiotics used here. Most of the bacterial isolates we obtained are from known ubiquitous marine lineages (Vibrio, Pseudoalteromonas, Pseudomonas, Shewanella, and Bacillus) which are likely habitat generalists and have all been previously cultured from Z. marina from Bodega Bay, CA [18,20,[22][23][24][25]. We also isolated several bacterial isolates that may represent rare or slow-growing taxa with interesting ecological implications for the seagrass ecosystem.…”

Section: Plos Onementioning

confidence: 99%

“…Previous work has characterized the composition and structure of the bacterial community associated with Z. marina and found the community to be distinct for different seagrass tissues (e.g., roots, leaves, rhizomes) [8][9][10]. Many of the abundant bacteria found associated with Z. marina are thought to have important functions related to nitrogen and sulfur cycling [10][11][12][13][14][15] and several culture-dependent studies have obtained bacterial isolates associated with Z. marina, ranging from ubiquitous marine lineages to putative sulfate-reducers [16][17][18][19][20][21][22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

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Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Ettinger

Eisen

2020

PLoS ONE

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Fungi in the marine environment are often neglected as a research topic, despite that fungi having critical roles on land as decomposers, pathogens or endophytes. Here we used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, also obtaining bacteria and oomycete isolates in the process. A total of 108 fungi, 40 bacteria and 2 oomycetes were isolated. These isolates were then taxonomically identified using a combination of molecular and phylogenetic methods. The majority of the fungal isolates were classified as belonging to the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes. Most fungal isolates were habitat generalists like Penicillium sp. and Cladosporium sp., but we also cultured a diverse set of rare taxa including possible habitat specialists like Colletotrichum sp. which may preferentially associate with Z. marina leaf tissue. Although the bulk of bacterial isolates were identified as being from known ubiquitous marine lineages, we also obtained several Actinomycetes isolates and a Phyllobacterium sp. We identified two oomycetes, another understudied group of marine microbial eukaryotes, as Halophytophthora sp. which may be opportunistic pathogens or saprophytes of Z. marina. Overall, this study generates a culture collection of fungi which adds to knowledge of Z. marina associated fungi and highlights a need for more investigation into the functional and evolutionary roles of microbial eukaryotes associated with seagrasses.

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Section: Plos Onementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Ettinger

Eisen

2020

PLoS ONE

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“…Advantages of working on this species include that there is a genome now available ( Olsen et al, 2016 ), that there is a large network of collaborating labs focusing on this species (Zostera Experimental Network; http://zenscience.org ), and that it can be used in common garden and reciprocal transplant experiments. Along these lines we have been building a library of cultured isolates associated with this species and sequencing the genomes of many of these ( Lee et al, 2015a ; Lee et al, 2015b ; Lee et al, 2016a ; Lee et al, 2016b ; Alexiev et al, 2016a ; Alexiev et al, 2016b ). There are still areas in need of improvement (e.g., there a limited amount of full length 16S and 18S other reference data; only limited information on the in situ functions of microbes are available, there is a need for more genetic tools for the host), but given the importance of coastal marine systems and seagrasses generally, we believe continued efforts to study the host-microbiome-environment interactions in this and related species are important.…”

Section: Discussionmentioning

confidence: 99%

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

Ettinger

Voerman

Lang

et al. 2017

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138

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BackgroundZostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA.MethodsWe characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites.ResultsMicrobial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism).DiscussionOur results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.

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All small things considered: the diversity of fungi, bacteria and oomycota isolated from the seagrass,Zostera marina

Ettinger¹,

Eisen²

2020

Preprint

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Fungi in the marine environment are often neglected as a research topic, despite that fungi having critical roles on land as decomposers, pathogens or beneficial endophytes. Here we used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, also obtaining bacteria and oomycete isolates in the process. A total of 108 fungi, 41 bacteria and 2 oomycetes were isolated. These isolates were then taxonomically identified using a combination of molecular and phylogenetic methods. The majority of the fungal isolates were classified as belonging to the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes. Most fungal isolates were habitat generalists like Penicillium sp. and Cladosporium sp., but we also cultured a diverse set of rare taxa including possible habitat specialists like Colletotrichum sp. which may preferentially associate with Z. marina leaf tissue. Although the bulk of bacterial isolates were identified as being from known ubiquitous marine lineages, we also obtained several Actinomycetes isolates which might produce interesting secondary metabolites and a Phyllobacterium sp. which may be involved in nitrogen cycling in the seagrass ecosystem. We identified two oomycetes, another understudied group of marine microbial eukaryotes, as Halophytophthora sp. which may be opportunistic pathogens of Z. marina. Overall, this study generates a culture collection of fungi, bacteria and oomycetes which expands knowledge of the diversity of Z. marina associated microbes and highlights a need for more investigation into the functional and evolutionary roles of microbial eukaryotes associated with seagrasses.

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Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment

Cited by 3 publications

References 11 publications

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge

All small things considered: the diversity of fungi, bacteria and oomycota isolated from the seagrass,Zostera marina

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