Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches
Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches
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DOI：
10.1016/j.syapm.2010.02.005
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发表时间：
2010-06-01
影响因子：
3.4
通讯作者：
Cherif, Ameur
中科院分区：
文献类型：
--
作者：
Ettoumi, Besma;Bouhajja, Emna;Cherif, Ameur
采用依赖培养和独立培养的方法对第勒尼安海沉积物中的细菌多样性进行了评估。从相对于4个海山和非海山站的不同沉积层(长达30厘米)收集的样本，在3425米至3580米的深度进行了DNA提取和针对V3区的165rRNA扩增。变性梯度凝胶电泳法(DGGE)显示了多个异质性图谱，共分离出27条单一条带，并进行了测序。序列分析表明，在26%的DGGE条带中存在菲米库特、放线杆菌和氯杆菌，并且属于可培养和不可培养克隆的序列占优势(55%)。为了证实这些发现，进行了培养尝试，允许分离出87株被归类为蛋白质细菌的菌株。通过自动核糖体基因间隔区分析(ARSA)和165rDNA测序实现鉴定。分离株与变形杆菌的伽马亚类、α亚类和β亚类的亲缘关系分别为77%、17%和6%。最具优势的革马氏蛋白细菌，分属于冷杆菌Marin-cola和P.submarinus分支(n=53)，以及盐生单胞菌(n=14)，表现出巨大的种内多样性，有29个不同的Arisa单倍型。这两种方法对这些嗜冷和中度嗜盐物种及其广泛的微生物多样性的检测表明，它们在第勒尼海沉积物中占优势，在那里它们构成了本土微生物区系。(C)2010年爱思唯尔股份有限公司。版权所有。
Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and independent approaches. Samples collected from the different sediment layers (up to 30 cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580 m, were subjected to DNA extraction and 165 rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 165 rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marin-cola and P. submarinus clade (n = 53) and to Halomonas aquamarina (n = 14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora. (C) 2010 Elsevier GmbH. All rights reserved.