Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms
Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms
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DOI：
10.1128/aem.02943-08
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发表时间：
2009-07-01
影响因子：
4.4
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
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作者：
Goltsman, Daniela S. Aliaga;Denef, Vincent J.;Banfield, Jillian F.
我们分析了共存的嗜酸性氧化铁钩端螺旋菌 II 型和 III 型细菌（硝化螺旋门）的近乎完整的群体（复合）基因组序列，以及来自加利福尼亚州铁山里士满矿酸性矿井排水生物膜的染色体外质粒。对基因组特征样本和另外两个生物膜进行群落蛋白质组学分析，分别鉴定出 64.6% 和 44.9% 的钩端螺旋菌 II 组和 III 组预测蛋白，以及 20% 的预测质粒蛋白。这些细菌具有 92% 的 16S rRNA 基因序列同一性和超过 60% 的基因，包括整合的质粒样区域。染色体外质粒携带的接合基因与整合的接合质粒中的基因具有可检测到的序列相似性，但仅通过蛋白质组学鉴定了染色体外元件上的那些基因。两个细菌群都具有群落基本功能的基因，包括碳固定和维生素、脂肪酸和生物聚合物（包括纤维素）的生物合成；蛋白质组分析揭示了这些活动。两种类型的钩端螺旋菌都有多种渗透保护途径。尽管两者都是活动的，但信号转导和甲基接受趋化蛋白在钩端螺旋菌 III 组中更为丰富，与其在生物膜内的梯度分布一致。有趣的是，钩端螺旋菌 II 组使用甲基依赖性反应途径，而钩端螺旋菌 III 组使用甲基独立反应途径。尽管只有 III 族钩端螺旋菌可以固氮，但这些蛋白质并未通过蛋白质组学鉴定。所有群落中核心蛋白的丰度相似，但功能未知的独特和共享蛋白的丰度水平有所不同。一种生物体特有的一些蛋白质高度表达，可能是钩端螺旋菌 II 类和 III 类功能和生态分化的关键。
We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and > 60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.