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

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).

本研究针对8个钙质沉积物16S rDNA克隆文库（16S rDNA clone library）中的细菌群落展开调查，旨在评估大堡礁沉积物的细菌多样性，并探究水质下降所引发的群落差异。采样覆盖4个珊瑚礁，每个珊瑚礁分别采集前礁与后礁两处点位的样品：近岸点位为菲茨罗伊岛与海厄特岛（受径流活动增强影响显著），外陆架点位为黑斯廷斯礁与弗林礁（原生未受干扰状态）。
本研究共获得221条非嵌合序列，其中189条（占比85.5%）为独特序列，仅1条序列在多个文库中被检出。通过聚类分析并与已发表序列比对，结果显示所获得的序列隶属于变形菌门（Proteobacteria）的α、γ、δ亚纲、噬纤维菌属-黄杆菌纲-拟杆菌门（Cytophaga, Flavobacteria, Bacteroidetes, CFB）类群、蓝细菌门（Cyanobacteria）、浮霉菌科（Planctomycetaceae）、疣微菌科（Verrucomicrobiaceae）以及酸杆菌科（Acidobacteriaceae）。
另外于每个采样点位采集两份沉积物样品，用于分析碳组分（有机碳、总碳）与氮含量；同时记录了碳酸钙百分比、暴露程度（前礁受波浪作用更强，后礁暴露程度更低）以及平均粒径（单位：mm）。
本研究构建了邻接树（Neighbour-joining tree）以展示8个克隆文库的序列信息。所有序列数据已提交至GenBank数据库，登录号范围为DQ256505至DQ256725。
本研究的核心目标包括：1. 为大堡礁微生物群落的相关研究积累知识储备；2. 首次基于序列数据对大堡礁钙质礁沉积物的细菌群落进行系统性描述；3. 检验该区域细菌群落是否存在可作为陆地径流或珊瑚礁健康下降指示物的特征物种或类群。
本研究获得的序列与以下GenBank登录号标注的菌种相似度最高（括号内为GenBank登录号）：北极海冰细菌（AF468407）、未命名细菌（AY258094）、阿尔卑斯浴杆菌（Balneatrix alpaca，BAY17112）、贝氏硫菌属菌种（Beggiatoa sp.，AF110276）、苯矿化细菌（AF029047）、疑似噬纤维菌属菌种（cf Cytophaga，AF530130、AF530158）、Cryomorphaceae科未命名细菌（AB125062）、发酵噬纤维菌（Cytophaga fermentans，AB125062）、噬纤维菌属菌种（Cytophaga sp.，AB015543、AB015545、AB073572）、Defluvicoccus vanus（AF179678）、酮基脱硫杆菌（Desulfobacterium cetonicum，AJ237603）、腐蚀脱硫杆菌（Desulfobacterium corrodens，AY274450）、普通脱硫弧菌（Desulfovibrio vulgaris，M34399）、内共生体（AF104473）、加拿大柔杆菌（Flexibacter canadensis，AB078046）、玫瑰色柔杆菌（Flexibacter roseolus，AB078061）、柔杆菌属菌种（Flexibacter sp.，AB058906）、发酵地杆菌（Geothrix fermentans，GF41563）、鳃内共生体（AB189713）、Haslea wawrikae（AF514855）、Lewinella persicus（AF039295）、Lyngbya属菌种（Lyngbya sp.，AY049751）、海洋细菌（AF076897、AF406617、AY007676）、海洋γ-变形菌（marine gamma-proteobacterium，AY386339）、海洋雪细菌（AF030776、AF030779）、海洋亚硝化球菌（Nitrosococcus oceani，NOC29872）、恙虫病东方体（Orientia tsutsugamushi，D38625）、玫瑰色颤藻（Oscillatoria rosea，AB003164）、假单胞菌属菌种（Pseudomonas sp.，AB013829）、日本假螺菌（Pseudospirillum japonicum，AB006766）、Reichenbachia agariperforans（AB058919）、Rhodopseudomonas julia（AY428572）、Robiginitalea biformata（AY424900）、Roseobacter属菌种（Roseobacter sp.，AF098494）、大螺旋丝菌（Saprospira grandis，AB088636）、海绵内共生体（AF186415）、硫氧化内共生体（AF165908、AF328856）、硫氧化鳃内共生体（X84984）、硫还原内共生体（AF328857）、未命名共生体（U78037）、Teredinibacter turnerae（AY028398）、Thalasomonas ganghwensis（AY194066）、Trichodesmium thiebautii（AF091321）、未命名酸杆菌科菌种（uncultured Acidobacteriaceae，AY225643）、未命名放线菌（uncultured actinobacterium，AB116464）、未命名α-变形菌（uncultured alpha-bacterium，AB015523、AB015526、AF406524、AF445669、AY225603）、未命名细菌（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）、未命名拟杆菌门菌种（uncultured Bacteroidetes，AB116465、AF507866、AY225659、AY274839、UCY44123）、未命名δ-变形菌（uncultured delta-proteobacterium，AB015243、AB116394、AF424201、AF424227、AF424261、AJ58135、AY217484、AY225608、AY499998）、未命名外硫红螺菌科菌种（uncultured Ectothiorhodospiraceae，AJ567603）、未命名γ-变形菌（uncultured gamma-proteobacterium，AB015252、AB015583、AB116435、AB116469、AF223300、AF351226、AY145601、AY225630、AY225635、U70702）、未命名Holophaga菌（uncultured Holophaga，UHO24100）、未命名海杆菌（uncultured marinobacter，AJ567576）、未命名Pirellula属菌种（uncultured Pirellula sp.，AF029076）、未命名浮霉菌（uncultured planctomycete，AY114326、AY499808、BX294775）、未命名变形菌（uncultured proteobacterium，AJ241015、AY193142）、未命名土壤细菌（uncultured soil bacterium，AJ39044）、未命名疣微菌（uncultured verrucomicrobium，AY114328、AY354864、AY499834、UVE40110、UVE44122）、未鉴定细菌（unidentified bacterium，AB015533、AF317764）、霍乱弧菌（Vibrio cholerae，S0000145）、Vibrio fortis（VSP51491）、Xenococcus属菌种（Xenococcus sp.，AF132783）。