Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation
Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation
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DOI：
10.1111/j.1574-6941.2009.00804.x
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发表时间：
2010-03-01
影响因子：
4.2
通讯作者：
Stoeck, Thorsten
中科院分区：
文献类型：
--
作者：
Jebaraj, Cathrine S.;Raghukumar, Chandralata;Stoeck, Thorsten
为了研究阿拉伯海最低氧带真菌的多样性，用3组不同的聚合酶链式反应(PCR)引物对从环境样品中获得的1440个克隆的小亚基rRNA基因(18S rRNA基因)序列进行了分析。限制性片段长度多态性(RFLP)分析得到549种不同的RFLP图谱，经序列分析，其中268种可归类于真菌(Dikarya和合菌)。剩下的281个RFLP图谱代表了各种非真菌分类群，即使当使用假定的真菌特异性引物时也是如此。相当数量的真菌序列与其他一系列缺氧海洋生境的环境序列密切相关，但与已知的已描述真菌序列关系较远。群落相似性分析表明，真菌群落结构明显不同于常氧区、季节性缺氧区和永久性缺氧区，表明真菌群落对普遍存在的氧气条件有不同的适应策略。此外，我们从研究地点获得了26种真菌培养物，其中大多数与描述良好的Dikarya密切相关(>；97%的序列相似性)。这表明，标准化种植主要生产更多已知的东西。然而，其中两种培养物与已知序列高度分化，似乎在较高的分类水平上代表了新的真菌群。有趣的是，没有一个培养的分离物与获得的任何环境序列都是相同的。我们的研究证明了多重引物法与培养相结合的重要性，以获得对环境样本中真实真菌多样性的更深层次的洞察，并能够对真菌群落进行充分的样本间比较。
In order to study fungal diversity in oxygen minimum zones of the Arabian Sea, we analyzed 1440 cloned small subunit rRNA gene (18S rRNA gene) sequences obtained from environmental samples using three different PCR primer sets. Restriction fragment length polymorphism (RFLP) analyses yielded 549 distinct RFLP patterns, 268 of which could be assigned to fungi (Dikarya and zygomycetes) after sequence analyses. The remaining 281 RFLP patterns represented a variety of nonfungal taxa, even when using putatively fungal-specific primers. A substantial number of fungal sequences were closely related to environmental sequences from a range of other anoxic marine habitats, but distantly related to known sequences of described fungi. Community similarity analyses suggested distinctively different structures of fungal communities from normoxic sites, seasonally anoxic sites and permanently anoxic sites, suggesting different adaptation strategies of fungal communities to prevailing oxygen conditions. Additionally, we obtained 26 fungal cultures from the study sites, most of which were closely related (> 97% sequence similarity) to well-described Dikarya. This indicates that standard cultivation mainly produces more of what is already known. However, two of these cultures were highly divergent to known sequences and seem to represent novel fungal groups on high taxonomic levels. Interestingly, none of the cultured isolates is identical to any of the environmental sequences obtained. Our study demonstrates the importance of a multiple-primer approach combined with cultivation to obtain deeper insights into the true fungal diversity in environmental samples and to enable adequate intersample comparisons of fungal communities.