Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments.
Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments.
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DOI：
10.3389/fmicb.2013.00342
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发表时间：
2013
影响因子：
5.2
通讯作者：
Colaneri C
中科院分区：
文献类型：
--
作者：
Bowen JL;Byrnes JE;Weisman D;Colaneri C
功能基因焦磷酸测序是一个有用的工具，以检查的多样性和丰富的微生物，促进关键的生物地球化学过程。其中一个过程，脱氮，是特别重要的，因为它将固定的硝酸盐（NO−3）转化为N2气体，然后返回大气。在氮限制的盐沼中，在进入邻近沃茨之前去除NO−3有助于防止富营养化。因此，了解盐沼微生物脱氮的动态对于维护健康的沿海生态系统至关重要。我们使用焦磷酸测序的nirS基因，以研究施肥实验丰富的沼泽地的群落反应。焦磷酸测序序列数据分析的一个关键挑战是了解基因序列中的微小差异是否具有生态意义。我们应用了一种来自信息论的新方法来确定将DNA序列聚类为OTU的最佳相似性水平，同时仍然捕获系统的生态复杂性，为88%。系统发育分析得到6个优势类群，其中最大的类群占所有序列的一半以上，但没有近距离的养殖代表。在鉴定的638个OTU中，仅11个存在于所有样地中，并且没有单一OTU占优势。然而，我们确实发现了大量只存在于一个地块中的专业OTU。高度的地方性OTU，而占很大比例的nirS多样性的地块，被发现在较低的丰度比通才类群。专家类群的比例增加，营养供应的增加，这表明，除了肥料可能会创造条件，扩大生态位空间的微生物，并可能提高反硝化的遗传能力。
Functional gene pyrosequencing is emerging as a useful tool to examine the diversity and abundance of microbes that facilitate key biogeochemical processes. One such process, denitrification, is of particular importance because it converts fixed nitrate (NO−3) to N2 gas, which returns to the atmosphere. In nitrogen limited salt marshes, removal of NO−3 prior to entering adjacent waters helps prevent eutrophication. Understanding the dynamics of salt marsh microbial denitrification is thus imperative for the maintenance of healthy coastal ecosystems. We used pyrosequencing of the nirS gene to examine the denitrifying community response to fertilization in experimentally enriched marsh plots. A key challenge in the analysis of sequence data derived from pyrosequencing is understanding whether small differences in gene sequences are ecologically meaningful. We applied a novel approach from information theory to determine that the optimal similarity level for clustering DNA sequences into OTUs, while still capturing the ecological complexity of the system, was 88%. With this clustering, phylogenetic analysis yielded 6 dominant clades of denitrifiers, the largest of which, accounting for more than half of all the sequences collected, had no close cultured representatives. Of the 638 OTUs identified, only 11 were present in all plots and no single OTU was dominant. We did, however, find a large number of specialist OTUs that were present only in a single plot. The high degree of endemic OTUs, while accounting for a large proportion of the nirS diversity in the plots, were found in lower abundance than the generalist taxa. The proportion of specialist taxa increased with increasing supply of nutrients, suggesting that addition of fertilizer may create conditions that expand the niche space for denitrifying organisms and may enhance the genetic capacity for denitrification.
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DOI：
10.1038/ismej.2011.159
发表时间：
2012-05
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
8.8
作者：
Allesina, Stefano;Pascual, Mercedes
通讯作者：
Pascual, Mercedes
影响因子：
4.5
作者：
Bowen, J. L.;Crump, B. C.;Hobbie, J. E.
通讯作者：
Hobbie, J. E.
DOI：
10.1073/pnas.022447299
发表时间：
2002-02-05
影响因子：
11.1
作者：
Bertness, MD;Ewanchuk, PJ;Silliman, BR
通讯作者：
Silliman, BR
影响因子：
4.9
作者：
Duarte, CM;Middelburg, JJ;Caraco, N
通讯作者：
Caraco, N