Nzoué A, Miché L, Klonowska A, Laguerre G, de Lajudie P, Moulin L
IRD, UMR 113, Symbioses Tropicales et Méditerranéennes, F-34398 Montpellier, France.
Syst Appl Microbiol. 2009 Sep;32(6):400-12. doi: 10.1016/j.syapm.2009.06.002. Epub 2009 Jun 24.
This study reports the multilocus sequence analysis (MLSA) of nine house-keeping gene fragments (atpD, dnaK, glnA, glnB, gltA, gyrB, recA, rpoB and thrC) on a collection of 38 Bradyrhizobium isolated from Aeschynomene species in Senegal, which had previously been characterised by several phenotypic and genotypic techniques, allowing a comparative analysis of MLSA resolution power for species delineation in this genus. The nifH locus was also studied to compare house-keeping and symbiotic gene phylogenies and obtain insights into the unusual symbiotic properties of these Aeschynomene symbionts. Phylogenetic analyses (maximum likelihood, Bayesian) of concatenated nine loci produced a well-resolved phylogeny of the strain collection separating photosynthetic bradyrhizobial strains (PB) from non-photosynthetic bradyrhizobial (NPB) ones. The PB clade was interpreted as the remains an expanding ancient species that presently shows high diversification, giving rise to potential new species. B. denitrificans LMG8443 and BTAi1 strains formed a sub-clade that was identified as recently emerging new species. Congruence analyses (by Shimodaira-Hasegawa (S-H) tests) identified three gene-fragments (dnaK, glnB and recA) that should be preferred for MLSA analyses in Bradyrhizobium genus. The nine loci or nifH phylogenies were not correlated with the unusual symbiotic properties of PB (nod-dependent/nod-independent). Advantages and drawbacks of MLSA for species delineation in Bradyrhizobium are discussed.
本研究报告了对从塞内加尔合萌属植物中分离出的38株慢生根瘤菌进行的9个持家基因片段（atpD、dnaK、glnA、glnB、gltA、gyrB、recA、rpoB和thrC）的多位点序列分析（MLSA）。这些慢生根瘤菌此前已通过多种表型和基因型技术进行了表征，从而能够对MLSA在该属物种划分中的分辨能力进行比较分析。还研究了nifH基因座，以比较持家基因和共生基因的系统发育，并深入了解这些合萌共生体不同寻常的共生特性。对串联的9个基因座进行系统发育分析（最大似然法、贝叶斯法），得到了一个分辨率良好的菌株系统发育树，将光合慢生根瘤菌菌株（PB）与非光合慢生根瘤菌（NPB）菌株区分开来。PB分支被解释为一个不断扩展的古老物种的残余，该物种目前表现出高度的多样性，可能会产生新的物种。反硝化慢生根瘤菌LMG8443和BTAi1菌株形成了一个亚分支，被确定为最近出现的新物种。通过Shimodaira-Hasegawa（S-H）检验进行的一致性分析确定了三个基因片段（dnaK、glnB和recA），在慢生根瘤菌属的MLSA分析中应优先选择。9个基因座或nifH基因的系统发育与PB不同寻常的共生特性（依赖结瘤/不依赖结瘤）无关。讨论了MLSA在慢生根瘤菌物种划分中的优缺点。
