Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico
Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico
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DOI：
10.1128/aem.69.6.3549-3560.2003
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发表时间：
2003-06-01
影响因子：
4.4
通讯作者：
Zhou, JZ
中科院分区：
文献类型：
--
作者：
Liu, XD;Tiquia, SM;Zhou, JZ
为了了解墨西哥太平洋沿岸缺氧区反硝化群落的组成和结构，采用基于pcr的克隆方法对四个站点沉积物中nir基因的分子多样性进行了研究。所有样品共获得50个nir和82个nir操作分类单位（otu）。对44个nirS克隆和31个nirK克隆进行了测序；近红外无性系的相似度为52 ~ 92%，近红外无性系的相似度为50 ~ 99%。nirS和nirK站点之间重叠otu的百分比分别为18 ~ 30%和5 ~ 8%。序列分析结果显示，26%的nirS克隆与粪碱性单胞菌（80 ~ 94%）和stutzeri假单胞菌（80 ~ 99%）的nirS基因相似，而3 ~ 31%的nirK克隆与G-179假单胞菌（98 ~ 99%）、日本慢根瘤菌（91%）、反硝化芽孢杆菌（83%）和木氧碱性单胞菌（96%）的nirK基因密切相关。然而，其余克隆与序列数据库中可用的nirS和nirK序列的相似性不到80%。基于otu百分比和生物地球化学数据的主成分分析（PCA）结果表明，硝酸盐浓度和氧气对反硝化群落有影响。缺氧区各站点的群落特征比富氧区各站点的群落特征更为相似。反硝化群落在距离较近且硝酸盐水平相似的站点中更为相似。基于生物地球化学性质的主成分分析结果表明，地理位置和生物地球化学条件，特别是硝酸盐和氧气水平，是控制反硝化群落结构的关键因素。
understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the Pacific coast of Mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a PCR-based cloning approach. A total of 50 operational taxonomic units (OTUs) for nirK and 82 OTUs for nirS were obtained from all samples. Forty-four of the nirS clones and 31 of the nirK clones were sequenced; the levels of similarity of the nirS clones were 52 to 92%, and the levels of similarity of the nirS clones were 50 to 99%. The percentages of overlapping OTUs between stations were 18 to 30% for nirS and 5 to 8% for nirK. Sequence analysis revealed that 26% of the nirS clones were related to the nirS genes of Alcaligenes faecalis (80 to 94% similar) and Pseudomonas stutzeri (80 to 99%), whereas 3 to 31% of the nirK clones were closely related to the nirK genes of Pseudomonas sp. strain G-179 (98 to 99%), Bradyrhizobium japonicum (91%), Blastobacter denitrificans (83%), and Alcaligenes xylosoxidans (96%). The rest of the clones, however, were less than 80% similar to nirS and nirK sequences available in sequence databases. The results of a principal-component analysis (PCA) based on the percentage of OTUs and biogeochemical data indicated that the nitrate concentration and oxygen have an effect on the denitrifying communities. The communities at the stations in oxygen-deficient zones were more similar than the communities at the stations in the oxygenated zone. The denitrifying communities were more similar at the stations that were closer together and had similar nitrate levels. Also, the results of PCA based on biogeochemical properties suggest that geographic location and biogeochemical conditions, especially the nitrate and oxygen levels, appear to be the key factors that control the structure of denitrifying communities.