Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora
Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora
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DOI：
10.1128/aem.71.11.7019-7028.2005
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发表时间：
2005-11-01
影响因子：
4.4
通讯作者：
Jensen, PR
中科院分区：
文献类型：
--
作者：
Mincer, TJ;Fenical, W;Jensen, PR
盐孢菌属是放线菌目中第一个专性海洋菌属，也是生物活性次生代谢产物的重要来源。尽管分布于热带或亚热带的海洋沉积物中，但迄今为止只有两种盐孢属植物被栽培，表明物种水平的多样性有限。为了进一步探索盐孢菌的多样性和分布，研究了从巴哈马周围收集的沉积物中分离的350多个菌株的系统发育多样性，包括使用新的富集方法培养的菌株。采用盐孢菌特异性巢式PCR技术，建立了一种不依赖培养的方法，用于从环境DNA中检测盐孢菌并估计其多样性。总的来说，16 S rRNA基因序列的多样性的培养菌株与环境克隆库中检测到的一致。尽管进行了大量的努力，没有发现新的物种水平的多样性，97%的105个菌株的限制性片段长度多态性检查属于一个单一的类型（S。arenicola）。在文库中发现了新的种内多样性，包括一个丰富的新的尚未培养的物种类型，并为该属建立了1,100米的新深度记录。PCR引入的错误，主要是从Taq聚合酶，显着增加克隆库序列的多样性，如果不掩盖的分析，会导致高估的总多样性。一种专门针对营养细胞的环境DNA提取方法提供了海洋沉积物中活跃放线菌生长的证据，同时表明大多数沉积物样品主要含有盐孢属孢子，其浓度在环境克隆文库中无法检测到。直接基于序列的检测孢子形成微生物在环境样品中所面临的挑战进行了讨论。
Salinispora is the first obligate marine genus within the order Actinomycetales and a productive source of biologically active secondary metabolites. Despite a worldwide, tropical or subtropical distribution in marine sediments, only two Salinispora species have thus far been cultivated, suggesting limited species-level diversity. To further explore Salinispora diversity and distributions, the phylogenetic diversity of more than 350 strains isolated from sediments collected around the Bahamas was examined, including strains cultured using new enrichment methods. A culture-independent method, using a Salinispora-specific seminested PCR technique, was used to detect Salinispora from environmental DNA and estimate diversity. Overall, the 16S rRNA gene sequence diversity of cultured strains agreed well with that detected in the environmental clone libraries. Despite extensive effort, no new species level diversity was detected, and 97% of the 105 strains examined by restriction fragment length polymorphism belonged to one phylotype (S. arenicola). New intraspecific diversity was detected in the libraries, including an abundant new phylotype that has yet to be cultured, and a new depth record of 1,100 m was established for the genus. PCR-introduced error, primarily from Taq polymerase, significantly increased clone library sequence diversity and, if not masked from the analyses; would have led to an overestimation of total diversity. An environmental DNA extraction method specific for vegetative cells provided evidence for active actinomycete growth in marine sediments while indicating that a majority of sediment samples contained predominantly Salinispora spores at concentrations that could not be detected in environmental clone libraries. Challenges involved with the direct sequence-based detection of spore-forming microorganisms in environmental samples are discussed.