Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland.
Microb Ecol. 2012 Jul;64(1):105-16. doi: 10.1007/s00248-011-0002-x. Epub 2012 Jan 28.
Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location in Irish waters and with ambient seawater. To date, little is known about the microbial ecology of sponges of these genera. Culture isolation grossly underestimated sponge-associated bacterial diversity. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were represented amongst ~200 isolates, compared with ten phyla found using pyrosequencing. Long average read lengths of ~430 bp (V1-V3 region of 16S rRNA gene) allowed for robust resolution of sequences to genus level. Bacterial OTUs (2,109 total), at 95% sequence similarity, from ten bacterial phyla were recovered from R. ramosa, 349 OTUs were identified in S. stuposa representing eight phyla, while 533 OTUs from six phyla were found in surrounding seawater. Bacterial communities differed significantly between sponge species and the seawater. Analysis of the data for sponge-specific taxa revealed that 2.8% of classified reads from the sponge R. ramosa can be defined as sponge-specific, while 26% of S. stuposa sequences represent sponge-specific bacteria. Novel sponge-specific clusters were identified, whereas the majority of previously reported sponge-specific clusters (e.g. Poribacteria) were absent from these sponge species. This deep and robust analysis provides further evidence that the microbial communities associated with marine sponge species are highly diverse and divergent from one another and appear to be host-selected through as yet unknown processes.
海洋海绵是数量庞大且系统多样的细菌群落的宿主，迄今为止，全球已发现 26 个主要门与海绵物种密切相关。对这些微生物群落的分析揭示了许多海绵特有的新属和种。这些内共生微生物被认为在海绵生理学中发挥着重要作用，包括产生一系列生物活性次生代谢物。在这里，我们报告了使用基于培养和非培养（焦磷酸测序）技术来阐明与从爱尔兰水域单一地理位置采集的海洋海绵 Raspiila ramosa 和 Stelligera stuposa 以及环境海水相关的细菌群落谱。迄今为止，关于这些属的海绵微生物生态学知之甚少。培养分离法大大低估了海绵相关细菌的多样性。在大约 200 个分离株中，有 4 个细菌门（放线菌门、拟杆菌门、厚壁菌门、变形菌门），而使用焦磷酸测序法发现了 10 个门。平均读取长度约为 430bp（16S rRNA 基因 V1-V3 区），可将序列准确解析到属水平。从 Raspiila ramosa 中回收了来自十个细菌门的 2109 个细菌 OTU（总），在 95%序列相似性下，在 S. stuposa 中鉴定了 349 个 OTU，代表 8 个门，而在周围海水中发现了 533 个 OTU，来自六个门。海绵物种和海水之间的细菌群落差异显著。对海绵特有分类群的数据进行分析表明，海绵 Raspiila ramosa 中 2.8%的分类读数可定义为海绵特有，而海绵 S. stuposa 中有 26%的序列代表海绵特有细菌。鉴定出了新的海绵特有类群，而以前报道的大多数海绵特有类群（例如 Poribacteria）在这些海绵物种中不存在。这项深入而稳健的分析进一步证明，与海洋海绵物种相关的微生物群落具有高度的多样性和差异性，并且似乎通过尚未可知的过程被宿主选择。
