Graves Christopher J, Makrides Elizabeth J, Schmidt Victor T, Giblin Anne E, Cardon Zoe G, Rand David M
Brown University, Department of Ecology and Evolutionary Biology, Providence, Rhode Island, USA.
Brown University, Division of Applied Mathematics, Providence, Rhode Island, USA.
Appl Environ Microbiol. 2016 Apr 18;82(9):2862-2871. doi: 10.1128/AEM.03990-15. Print 2016 May.
Environmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.
In this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.
人类农业和废水径流造成的环境养分富集可能会导致微生物群落发生变化，使其能够利用新获得的资源。目前，微生物群落对养分富集的反应仍知之甚少，虽然一些研究表明，在高养分负荷下群落组成没有明显变化，但其他针对特定基因的研究已证明有明显影响。在本研究中，我们比较了沿两条盐沼小溪采集的沉积物样本的功能宏基因组图谱，其中一条小溪的源头已暴露于经处理的污水排放40多年。我们发现在富集位点，与反硝化途径中每个生化步骤相关的微生物基因相对丰度有强烈且一致的增加。尽管反硝化相关基因的丰度在局部有细微增加，但基于广泛定义的功能组和分类注释的整体群落结构相似，并随其他环境因素（如两条小溪共有的盐度）而变化。我们数据中一氧化二氮还原酶序列基于同源性的分类归属表明，增加分布在广泛的分类范围内，因此仅从分类数据中难以检测到。这些结果共同说明了微生物群落对人为养分负荷的功能靶向但分类广泛的反应，为现有关于沉积物群落中养分负荷影响的研究中明显相互矛盾的结果提供了一些解释。
在本研究中，我们使用环境宏基因组学来评估河口沉积物中微生物群落对长期富含养分的污水排放的反应。与以往主要基于分类数据或基于引物的特定靶基因扩增来表征群落的研究不同，我们的全基因组宏基因组学方法能够对整个群落中与反硝化相关的基因丰度进行无偏评估。我们发现在长期添加养分的位点，跨广泛系统发育范围与反硝化途径相关的基因序列相对丰度有强烈且一致的增加。虽然需要进一步的工作来确定这些群落反应在调节环境养分循环中的后果，但含有反硝化基因的细菌丰度增加表明此类过程可能在局部上调。此外，我们的结果说明了全基因组宏基因组学与靶向假设检验相结合如何能够揭示微生物群落对环境干扰的精细反应。
