Data

Bacterial communities using 16S rDNA from calcareous sediments of nearshore and outer shelf reefs, Great Barrier Reef

Australian Institute of Marine Science
Australian Institute of Marine Science (AIMS)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://apps.aims.gov.au/metadata/view/9b6f6c2b-b364-4696-a55f-01619da33fd4&rft.title=Bacterial communities using 16S rDNA from calcareous sediments of nearshore and outer shelf reefs, Great Barrier Reef&rft.identifier=https://apps.aims.gov.au/metadata/view/9b6f6c2b-b364-4696-a55f-01619da33fd4&rft.publisher=Australian Institute of Marine Science (AIMS)&rft.description=Bacterial communities in eight 16S rDNA clone libraries from calcareous sediments were investigated to assess bacterial diversity in sediments of the Great Barrier Reef and to investigate differences due to decreased water quality. Samples were taken from 2 locations (fore and back reefs) on each of 4 coral reefs: nearshore (Fitzroy and High Islands, subject to enhanced runoff) on the outer shelf (Hastings and Flynn Reefs, pristine conditions).Out of 221 non-chimeric sequences, 189 (85.5%) were unique and only one sequence occurred in more than one library. Cluster analyses and comparison to published sequences indicated that sequences retrieved belonged to the alpha, gamma and delta subdivisions of the Proteobacteria; Cytophaga, Flavobacteria, Bacteroidetes (CFB) group; Cyanobacteria; Planctomycetaceae; Verrucomicrobiaceae; and Acidobacteriaceae.Carbon (organic carbon, total carbon) and nitrogen in the sediments were analysed from two additional samples from each location. Calcium carbonate (%), exposure (front=more exposed to wave action; backreef=less exposure) and mean grain size (mm) were also recorded.Neighbour-joining trees were constructed representing sequences from the 8 clone libraries.All data sequence data are deposited on Genbank (DQ256505 to DQ256725). To contribute to the knowledge on microbial communities of the Great Barrier Reef.To provide a first sequence-based description of bacterial communities on calcareous reef sediments of the GBR.To test if these communities harbour characteristic species or groups which could be used as indicators for land runoff or decreased reef health. Closest matches to the Great Barrier Reef samples, GenBank accession numbers in brackets: arctic sea ice bacterium (AF468407); bacterium (AY258094); Balneatrix alpaca (BAY17112); Beggiatoa sp. (AF110276); benzene mineralizing bacterium (AF029047); cf Cytophaga (AF530130, AF530158); Cryomorphaceae bacterium (AB125062); Cytophaga fermentans (AB125062); Cytophaga sp. (AB015543, AB015545, AB073572); Defluvicoccus vanus (AF179678); Desulfobacterium cetonicum (AJ237603); Desulfobacterium corrodens (AY274450); Desulfovibrio vulgaris (M34399); endosymbiont (AF104473); Flexibacter canadensis (AB078046); Flexibacter roseolus (AB078061); Flexibacter sp. (AB058906); Geothrix fermentans (GF41563); gill symbiont (AB189713); Haslea wawrikae (AF514855); Lewinella persicus (AF039295); Lyngbya sp. (AY049751); marine bacterium (AF076897, AF406617, AY007676); marine gamma-proteobacterium (AY386339); marine snow bacterium (AF030776, AF030779); Nitrosococcus oceani (NOC29872); Orientia tsutsugamushi (D38625); Oscillatoria rosea (AB003164); Pseudomonas sp. (AB013829); Pseudospirillum japonicum (AB006766); Reichenbachia agariperforans (AB058919); Rhodopseudomonas julia (AY428572); Robiginitalea biformata (AY424900); Roseobacter sp. (AF098494); Saprospira grandis (AB088636); sponge symbiont (AF186415); sulfur-oxidising endosymbiont (AF165908, AF328856); sulfur-oxidising gill symbiont (X84984); sulfur-reducing endosymbiont (AF328857); symbiont (U78037); Teredinibacter turnerae (AY028398); Thalasomonas ganghwensis (AY194066); Trichodesmium thiebautii (AF091321); uncultured Acidobacteriaceae (AY225643) ; uncultured actinobacterium (AB116464); uncultured alpha-bacterium (AB015523, AB015526, AF406524, AF445669, AY225603); uncultured bacterium (AF143824, AF317768, AF328183, AF382112, AF382114, AF382143, AY133451, AY171303, AY171323, AY171332, AY171337, AY171357, AY171365, AY172271, AY193132, AY212707, AY216454, AY327875, AY344367, AY373412, AY375053, AY375097, AY500093, UBA56759); uncultured Bacteroidetes (AB116465, AF507866, AY225659, AY274839, UCY44123); uncultured delta-proteobacterium (AB015243, AB116394, AF424201, AF424227, AF424261, AJ58135, AY217484, AY225608, AY499998); uncultured Ectothiorhodospiraceae (AJ567603); uncultured gamma-proteobacterium (AB015252, AB015583, AB116435, AB116469, AF223300, AF351226, AY145601, AY225630, AY225635, U70702); uncultured Holophaga (UHO24100); uncultured marinobacter (AJ567576); uncultured Pirellula sp. (AF029076); uncultured planctomycete (AY114326, AY499808, BX294775); uncultured proteobacterium (AJ241015, AY193142); uncultured soil bacterium (AJ39044); uncultured verrucomicrobium (AY114328, AY354864, AY499834, UVE40110, UVE44122) ; unidentified bacterium (AB015533, AF317764); Vibrio cholerae (S0000145); Vibrio fortis (VSP51491); Xenococcus sp. (AF132783).Maintenance and Update Frequency: notPlannedStatement: Statement: The slightly shortened segment of the gene fragment was selected because of ambiguities in the beginning or end of some sequences.&rft.creator=Australian Institute of Marine Science (AIMS) &rft.date=2025&rft.coverage=westlimit=145.95; southlimit=-17.2; eastlimit=146.3; northlimit=-16.5&rft.coverage=westlimit=145.95; southlimit=-17.2; eastlimit=146.3; northlimit=-16.5&rft_rights=Creative Commons Attribution-NonCommercial 3.0 Australia License http://creativecommons.org/licenses/by-nc/3.0/au/&rft_rights=Use Limitation: All AIMS data, products and services are provided as is and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.&rft_rights=Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: Australian Institute of Marine Science (AIMS). (2009). Bacterial communities using 16S rDNA from calcareous sediments of nearshore and outer shelf reefs, Great Barrier Reef. https://apps.aims.gov.au/metadata/view/9b6f6c2b-b364-4696-a55f-01619da33fd4, accessed[date-of-access].&rft_rights=Resource Usage:Use of the AIMS data is for not-for-profit applications only. All other users shall seek permission for use by contacting AIMS. Acknowledgements as prescribed must be clearly set out in the user's formal communications or publications.Access Constraint: intellectualPropertyRightsUse Constraint: intellectualPropertyRightsSecurity classification code: unclassifiedMetadata Usage:Access Constraint: intellectualPropertyRightsUse Constraint: intellectualPropertyRightsSecurity classification code: unclassified&rft_subject=oceans&rft.type=dataset&rft.language=English Access the data
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Use Limitation: All AIMS data, products and services are provided "as is" and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.

Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "Australian Institute of Marine Science (AIMS). (2009). Bacterial communities using 16S rDNA from calcareous sediments of nearshore and outer shelf reefs, Great Barrier Reef. https://apps.aims.gov.au/metadata/view/9b6f6c2b-b364-4696-a55f-01619da33fd4, accessed[date-of-access]".

Resource Usage:Use of the AIMS data is for not-for-profit applications only. All other users shall seek permission for use by contacting AIMS. Acknowledgements as prescribed must be clearly set out in the user's formal communications or publications.Access Constraint: intellectualPropertyRightsUse Constraint: intellectualPropertyRightsSecurity classification code: unclassifiedMetadata Usage:Access Constraint: intellectualPropertyRightsUse Constraint: intellectualPropertyRightsSecurity classification code: unclassified

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Bacterial communities in eight 16S rDNA clone libraries from calcareous sediments were investigated to assess bacterial diversity in sediments of the Great Barrier Reef and to investigate differences due to decreased water quality. Samples were taken from 2 locations (fore and back reefs) on each of 4 coral reefs: nearshore (Fitzroy and High Islands, subject to enhanced runoff) on the outer shelf (Hastings and Flynn Reefs, pristine conditions).Out of 221 non-chimeric sequences, 189 (85.5%) were unique and only one sequence occurred in more than one library. Cluster analyses and comparison to published sequences indicated that sequences retrieved belonged to the alpha, gamma and delta subdivisions of the Proteobacteria; Cytophaga, Flavobacteria, Bacteroidetes (CFB) group; Cyanobacteria; Planctomycetaceae; Verrucomicrobiaceae; and Acidobacteriaceae.Carbon (organic carbon, total carbon) and nitrogen in the sediments were analysed from two additional samples from each location. Calcium carbonate (%), exposure (front=more exposed to wave action; backreef=less exposure) and mean grain size (mm) were also recorded.Neighbour-joining trees were constructed representing sequences from the 8 clone libraries.All data sequence data are deposited on Genbank (DQ256505 to DQ256725).
To contribute to the knowledge on microbial communities of the Great Barrier Reef.To provide a first sequence-based description of bacterial communities on calcareous reef sediments of the GBR.To test if these communities harbour characteristic species or groups which could be used as indicators for land runoff or decreased reef health.
Closest matches to the Great Barrier Reef samples, GenBank accession numbers in brackets: arctic sea ice bacterium (AF468407); bacterium (AY258094); Balneatrix alpaca (BAY17112); Beggiatoa sp. (AF110276); benzene mineralizing bacterium (AF029047); cf Cytophaga (AF530130, AF530158); Cryomorphaceae bacterium (AB125062); Cytophaga fermentans (AB125062); Cytophaga sp. (AB015543, AB015545, AB073572); Defluvicoccus vanus (AF179678); Desulfobacterium cetonicum (AJ237603); Desulfobacterium corrodens (AY274450); Desulfovibrio vulgaris (M34399); endosymbiont (AF104473); Flexibacter canadensis (AB078046); Flexibacter roseolus (AB078061); Flexibacter sp. (AB058906); Geothrix fermentans (GF41563); gill symbiont (AB189713); Haslea wawrikae (AF514855); Lewinella persicus (AF039295); Lyngbya sp. (AY049751); marine bacterium (AF076897, AF406617, AY007676); marine gamma-proteobacterium (AY386339); marine snow bacterium (AF030776, AF030779); Nitrosococcus oceani (NOC29872); Orientia tsutsugamushi (D38625); Oscillatoria rosea (AB003164); Pseudomonas sp. (AB013829); Pseudospirillum japonicum (AB006766); Reichenbachia agariperforans (AB058919); Rhodopseudomonas julia (AY428572); Robiginitalea biformata (AY424900); Roseobacter sp. (AF098494); Saprospira grandis (AB088636); sponge symbiont (AF186415); sulfur-oxidising endosymbiont (AF165908, AF328856); sulfur-oxidising gill symbiont (X84984); sulfur-reducing endosymbiont (AF328857); symbiont (U78037); Teredinibacter turnerae (AY028398); Thalasomonas ganghwensis (AY194066); Trichodesmium thiebautii (AF091321); uncultured Acidobacteriaceae (AY225643) ; uncultured actinobacterium (AB116464); uncultured alpha-bacterium (AB015523, AB015526, AF406524, AF445669, AY225603); uncultured bacterium (AF143824, AF317768, AF328183, AF382112, AF382114, AF382143, AY133451, AY171303, AY171323, AY171332, AY171337, AY171357, AY171365, AY172271, AY193132, AY212707, AY216454, AY327875, AY344367, AY373412, AY375053, AY375097, AY500093, UBA56759); uncultured Bacteroidetes (AB116465, AF507866, AY225659, AY274839, UCY44123); uncultured delta-proteobacterium (AB015243, AB116394, AF424201, AF424227, AF424261, AJ58135, AY217484, AY225608, AY499998); uncultured Ectothiorhodospiraceae (AJ567603); uncultured gamma-proteobacterium (AB015252, AB015583, AB116435, AB116469, AF223300, AF351226, AY145601, AY225630, AY225635, U70702); uncultured Holophaga (UHO24100); uncultured marinobacter (AJ567576); uncultured Pirellula sp. (AF029076); uncultured planctomycete (AY114326, AY499808, BX294775); uncultured proteobacterium (AJ241015, AY193142); uncultured soil bacterium (AJ39044); uncultured verrucomicrobium (AY114328, AY354864, AY499834, UVE40110, UVE44122) ; unidentified bacterium (AB015533, AF317764); Vibrio cholerae (S0000145); Vibrio fortis (VSP51491); Xenococcus sp. (AF132783).

Lineage

Maintenance and Update Frequency: notPlanned
Statement: Statement: The slightly shortened segment of the gene fragment was selected because of ambiguities in the beginning or end of some sequences.

Notes

Credit
Uthicke, Sven, Dr (Principal Investigator)

Modified: 22 08 2025

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146.3,-16.5 146.3,-17.2 145.95,-17.2 145.95,-16.5 146.3,-16.5

146.125,-16.85

text: westlimit=145.95; southlimit=-17.2; eastlimit=146.3; northlimit=-16.5

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Other Information
Bacterial communities in Great Barrier Reef calcareous sediments: Contrasting 16S rDNA libraries from nearshore and outer shelf reefs: Uthicke S and McGuire K (2007) Bacterial communities in Great Barrier Reef calcareous sediments: Contrasting 16S rDNA libraries from nearshore and outer shelf reefs. Estuarine Coastal and Shelf Science 72: 188-200.

local : articleId=7373

Identifiers
  • global : 9b6f6c2b-b364-4696-a55f-01619da33fd4