Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands Institute of Biology, Leiden University, Leiden, the Netherlands Department of Plant Pathology, University of California, Davis, CA 95616, USA.
Environ Microbiol Rep. 2012 Aug;4(4):424-32. doi: 10.1111/j.1758-2229.2012.00336.x. Epub 2012 Mar 19.
Collimonas is a genus of soil bacteria comprising three recognized species: C. fungivorans, C. pratensis and C. arenae. Collimonads share the ability to degrade chitin (chitinolysis), feed on living fungal hyphae (mycophagy), and dissolve minerals (weathering), but vary in their inhibition of fungi (fungistasis). To better understand this phenotypic variability, we analysed the genomic content of four strains representing three Collimonas species (Ter14, Ter6, Ter91 and Ter10) by hybridization to a microarray based on reference strain C. fungivorans Ter331. The analysis revealed genes unique to strain Ter331 (e.g. those on the extrachromosomal element pTer331) and genes present in some but not all of the tested strains. Among the latter were several candidates that may contribute to fungistasis, including genes for the production and secretion of antifungals. We hypothesize that differential possession of these genes underlies the specialization of Collimonas strains towards different fungal hosts. We identified a set of 136 genes that were common in all tested Collimonas strains, but absent from the genomes of three other members of the family Oxalobacteraceae. Predicted products of these 'Collimonas core' genes include lytic, secreted enzymes such as chitinases, peptidases, nucleases and phosphatases with a putative role in mycophagy and weathering.
生金单胞菌是土壤细菌的一个属，包含三个已被认可的种：C. 腐生菌、C. 草地生菌和 C. 砂生菌。生金单胞菌具有降解几丁质（几丁质分解）、以活真菌菌丝为食（真菌噬食）和溶解矿物质（风化）的能力，但在抑制真菌（抗真菌作用）方面有所不同。为了更好地理解这种表型变异性，我们通过杂交分析了代表三种生金单胞菌（Ter14、Ter6、Ter91 和 Ter10）的四个菌株的基因组内容，该杂交实验使用了基于参考菌株 C. 腐生菌 Ter331 的微阵列。分析结果揭示了 Ter331 菌株特有的基因（例如染色体外元件 pTer331 上的基因）和存在于一些但不是所有测试菌株中的基因。在后者中，有几个候选基因可能有助于抗真菌作用，包括抗真菌剂的产生和分泌基因。我们假设这些基因的差异存在是生金单胞菌菌株对不同真菌宿主的特化的基础。我们确定了一组在所有测试的生金单胞菌菌株中都共有的 136 个基因，但在其他三个 Oxalobacteraceae 家族成员的基因组中不存在。这些“生金单胞菌核心”基因的预测产物包括裂解、分泌的酶，如几丁质酶、肽酶、核酸酶和磷酸酶，它们可能在真菌噬食和风化中发挥作用。
