Key Laboratory of Marine Biogenetic Resources, The Third Institute of Oceanography, State of Oceanic Administration, Xiamen, China.
FEMS Microbiol Ecol. 2012 Jun;80(3):523-33. doi: 10.1111/j.1574-6941.2012.01322.x. Epub 2012 Mar 8.
Many bacteria have been reported as degraders of long-chain (LC) n-alkanes, but the mechanism is poorly understood. Flavin-binding monooxygenase (AlmA) was recently found to be involved in LC-alkane degradation in bacteria of the Acinetobacter and Alcanivorax genera. However, the diversity of this gene and the role it plays in other bacteria remains unclear. In this study, we surveyed the diversity of almA in marine bacteria and in bacteria found in oil-enrichment communities. To identify the presence of this gene, a pair of degenerate PCR primers were was designed based on conserved motifs of the almA gene sequences in public databases. Using this approach, we identified diverse almA genes in the hydrocarbon-degrading bacteria and in bacterial communities from the surface seawater of the Xiamen coastal area, the South China Sea, the Indian Ocean, and the Atlantic Ocean. As a result, almA was positively detected in 35 isolates belonging to four genera, and a total of 39 different almA sequences were obtained. Five isolates were confirmed to harbor two to three almA genes. From the Xiamen coastal area and the Atlantic Ocean oil-enrichment communities, a total of 60 different almA sequences were obtained. These sequences mainly formed two clusters in the phylogenetic tree, named Class I and Class II, and these shared 45-56% identity at the amino acid level. Class I contained 11 sequences from bacteria represented by the Salinisphaera and Parvibaculum genera. Class II was larger and more diverse, and it was composed of 88 sequences from Proteobacteria, Gram-negative bacteria, and the enriched bacterial communities. These communities were represented by the Alcanivorax and Marinobacter genera, which are the two most popular genera hosting the almA gene. AlmA was also detected across a wide geographical range, as determined by the origin of the bacterial host. Our results demonstrate the diversity of almA and confirm its high rate of occurrence in hydrocarbon-degrading bacteria, indicating that this gene plays an important role in the degradation of LC alkanes in marine environments.
许多细菌已被报道为长链（LC）正烷烃的降解菌，但降解机制尚不清楚。黄素结合单加氧酶（AlmA）最近被发现参与了不动杆菌属和Alcanivorax 属细菌的 LC-烷烃降解。然而，该基因的多样性及其在其他细菌中的作用尚不清楚。在本研究中，我们调查了海洋细菌和石油富集群落中细菌的 almA 多样性。为了鉴定该基因的存在，根据公共数据库中 almA 基因序列的保守基序设计了一对简并 PCR 引物。使用这种方法，我们在烃类降解细菌和来自厦门沿海、南海、印度洋和大西洋的表层海水的细菌群落中鉴定出了不同的 almA 基因。结果，在属于四个属的 35 个分离物中检测到 almA 呈阳性，共获得了 39 个不同的 almA 序列。五个分离物被证实含有 2 到 3 个 almA 基因。从厦门沿海和大西洋的石油富集群落中，共获得了 60 个不同的 almA 序列。这些序列在系统发育树中主要形成两个聚类，命名为 I 类和 II 类，它们在氨基酸水平上的同源性为 45-56%。I 类包含 11 个序列，来自 Salinisphaera 和 Parvibaculum 属的细菌。II 类更大，更具多样性，由来自变形菌门、革兰氏阴性菌和富集细菌群落的 88 个序列组成。这些群落由 Alcanivorax 和 Marinobacter 属代表，它们是宿主 almA 基因最流行的两个属。AlmA 也在很宽的地理范围内被检测到，这是由细菌宿主的来源决定的。我们的结果表明了 almA 的多样性，并证实了它在烃类降解细菌中的高发生率，表明该基因在海洋环境中 LC 烷烃的降解中起着重要作用。
