scholarly journals Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

2010 ◽  
Vol 4 (4) ◽  
pp. 498-508 ◽  
Author(s):  
Janine Kamke ◽  
Michael W Taylor ◽  
Susanne Schmitt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Sponge Associated Bacteria

scholarly journals Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

2011 ◽  
Vol 77 (20) ◽  
pp. 7207-7216 ◽  
Author(s):  
Naomi F. Montalvo ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Associated Bacteria ◽  
Content Type ◽  
Key Species ◽  
Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

scholarly journals Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths

Marine Drugs ◽  
2019 ◽  
Vol 17 (10) ◽  
pp. 578 ◽  
Author(s):  
Anak Indraningrat ◽  
Sebastian Micheller ◽  
Mandy Runderkamp ◽  
Ina Sauerland ◽  
Leontine Becking ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponges ◽  
Plate Count ◽  
Rrna Gene ◽  
Depth Range ◽  
Prokaryotic Community ◽  
Associated Bacteria ◽  
Xestospongia Muta ◽  
Sponge Associated Bacteria

Sponge-associated bacteria have been mostly cultured from shallow water (≤30 m) sponges, whereas only few studies targeted specimens from below 30 m. This study assessed the cultivability of bacteria from two marine sponges Xestospongia muta and Agelas sventres collected from shallow (<30 m), upper mesophotic (30–60 m), and lower mesophotic (60–90 m) reefs. Sponge-associated bacteria were cultivated on six different media, and replicate plates were used to pick individual colonies or to recover the entire biomass. Prokaryotic community analysis was conducted using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 144 bacterial isolates were picked following a colony morphology coding scheme and subsequently identified by 16S rRNA gene sequence analysis. Sponge individuals at each depth-range harboured specific cultivable bacteria that were not retrieved from specimens collected at other depths. However, there were substantial differences in the number of colonies obtained for replicate sponges of the same species. In addition, source of inoculum and cultivation medium had more impact on the cultured prokaryotic community than sample collection depth. This suggests that the “plate count anomaly” is larger than differences in sponge-associated prokaryotic community composition related to depth.

scholarly journals Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia

2011 ◽  
Vol 61 (2) ◽  
pp. 330-333 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Duck-Chul Oh
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
The Family ◽  
Major Respiratory Quinone

A Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, oxidase- and catalase-positive, marine bacterium, designated A2T, was isolated from a marine sponge, Hymeniacidon flavia, collected from the coast of Jeju Island, South Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A2T was a member of the family Flavobacteriaceae. Its closest relatives were Formosa agariphila KMM 3901T and Formosa algae KMM 3553T (96.99 and 96.98 % 16S rRNA gene sequence similarity, respectively). DNA–DNA relatedness between strain A2T and F. agariphila KMM 3901T and F. algae KMM 3553T was 14.1 and 26.8 %, respectively. The dominant fatty acids (>5 %) of strain A2T were iso-C15 : 0 (33.9 %), iso-C17 : 0 3-OH (20.8 %), iso-C15 : 1 G (10.5 %) and iso-C15 : 0 3-OH (6.1 %). The DNA G+C content of strain A2T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of phenotypic and phylogenetic analysis, strain A2T represents a novel species of the genus Formosa, for which the name Formosa spongicola sp. nov. is proposed. The type strain is A2T (=KCTC 22662T =DSM 22637T).

scholarly journals Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro

2011 ◽  
Vol 61 (2) ◽  
pp. 417-421 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Han-Su You ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence

A Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive bacterium, designated A6T, was isolated from a marine sponge, Halichondria oshoro, collected on the coast of Jeju Island, South Korea. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that strain A6T was a member of the family Flavobacteriaceae. The closest relatives were Aquimarina intermedia LMG 23204T, A. latercula ATCC 23177T, A. brevivitae SMK-19T and A. muelleri KMM 6020T, with which strain A6T shared 95.7, 95.1, 94.7 and 94.6 % 16S rRNA gene sequence similarity, respectively. The dominant fatty acids of strain A6T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (20.0 %), iso-C15 : 0 3-OH (12.3 %), iso-C15 : 1 G (7.2 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.8 %). The DNA G+C content of strain A6T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of combined phenotypic and phylogenetic analyses, strain A6T represents a novel species of the genus Aquimarina, for which the name Aquimarina spongiae sp. nov. is proposed. The type strain is A6T (=KCTC 22663T =DSM 22623T).

scholarly journals Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1158-1164 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Duck-Chul Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sponge ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, yellow-pigmented rod, designated A11T, was isolated from a marine sponge, Halichondria oshoro, collected on the coastline of Jeju Island, Republic of Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A11T was a member of the family Flavobacteriaceae . Its closest relatives were members of the genera Muricauda , Flagellimonas and Croceitalea (94.4–94.8 % 16S rRNA gene sequence similarity). The only polar lipid detected in strain A11T was phosphatidylethanolamine. The dominant fatty acids were iso-C15 : 0 (30.4 %), iso-C15 : 1 G (26.7 %), iso-C17 : 0 3-OH (12.4 %) and iso-C15 : 0 3-OH (7.3 %). The DNA G+C content of strain A11T was 41.7 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A11T represents a novel genus and species within the family Flavobacteriaceae , for which the name Spongiibacterium flavum gen. nov., sp. nov. is proposed. The type strain of the type species is A11T ( = KCTC 22665T = DSM 22638T). Emended descriptions of the genera Croceitalea and Flagellimonas are also given.

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

Antipathogenic Activity of Acroporid Bacterial Symbionts Against Brown Band Disease-Associated Bacteria

2021 ◽  
Vol 16 (2) ◽  
pp. 65-74
Author(s):  
Rosa Amalia ◽  
Diah Ayuningrum ◽  
Agus Sabdono ◽  
Ocky Karna Radjasa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
16S Rrna Gene Sequences ◽  
Coral Diseases ◽  
Associated Bacteria ◽  
Brown Band ◽  
The 16S Rrna Gene ◽  
Brown Band Disease

The coral reefs’ condition in most regions in Indonesia has been declining due to coral diseases, such as Brown Band Disease (BrBD). A treatment for BrBD involves the use of biological control agents that have antagonistic properties against disease-causing agents. This study aimed to isolate bacteria from healthy hard coral, those associated with BrBD, and those that had bioactivities against BrBD. Sampling and identification of corals and BrBD were carried out in March 2015 at the Marine National Park of Karimunjawa. Bacteria from healthy and infected corals were isolated and purified. The isolates were subjected to antipathogenic assay using overlay and agar diffusion methods. Finally, molecular identification of active bacteria was carried out using the 16S rRNA gene amplification. As many as 57 bacterial isolates were obtained from healthy coral, as well as four bacterial isolates from coral with BrBD symptoms. A total of 15 bacterial isolates (26%) showed antipathogenic activity against BrBD-associated bacteria. Three isolates with the strongest antipathogenic activities, i.e., GAMSH 3, KASH 6, and TAPSH 1 were identified by 16S rRNA gene sequences. The results showed that they were aligned to Virgibacillus marismortui (97%), Oceanobacillus iheyensis (97%), and Bacillus cereus (96%), respectively.

scholarly journals Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

2009 ◽  
Vol 75 (11) ◽  
pp. 3492-3501 ◽  
Author(s):  
Jean-Baptiste Raina ◽  
Dianne Tapiolas ◽  
Bette L. Willis ◽  
David G. Bourne
Keyword(s):  
16S Rrna ◽  
Acrylic Acid ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sulfur Compounds ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Coral Mucus ◽  
Associated Bacteria ◽  
Cooling Effects

ABSTRACT Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coral-associated bacteria. Two coral species, Montipora aequituberculata and Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera, Roseobacter, Spongiobacter, Vibrio, and Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with Roseobacter sp. constituted 28% of the M. aequituberculata tissue libraries, while 59% of the clones from the A. millepora libraries were affiliated with sequences related to the Spongiobacter genus. Vibrio spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under “normal” environmental conditions, they are a natural component of coral-associated communities. Genes homologous to dddD, and dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.

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