Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae.
Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae.
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DOI：
10.3390/genes9080389
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发表时间：
2018-08-01
期刊：
影响因子：
3.5
通讯作者：
James EK
中科院分区：
文献类型：
--
作者：
Estrada-de Los Santos P;Palmer M;Chávez-Ramírez B;Beukes C;Steenkamp ET;Briscoe L;Khan N;Maluk M;Lafos M;Humm E;Arrabit M;Crook M;Gross E;Simon MF;Dos Reis Junior FB;Whitman WB;Shapiro N;Poole PS;Hirsch AM;Venter SN;James EK
广义伯克霍尔德菌是一个庞大而复杂的类群，包含来自非常广泛的环境（土壤、水、植物、真菌）和临床（动物、人类）栖息地的致病性、植物致病性、共生性和非共生性菌株。它的分类已通过分析16 S rRNA序列，concatenated 4-7管家基因序列，最近通过基因组序列进行了几次评估。目前，将这一类群划分为伯克霍尔德氏菌属、Caballeronia、副伯克霍尔德氏菌属和罗布斯氏菌属得到了基因组分析的有力支持。这些新属广泛对应于伯克霍尔德氏菌s.l.的各种生境/生活方式，例如，在一个实施例中，所有的植物有益和环境（PBE）菌株都包括在副伯克霍尔德氏菌（Paraburkholderia）（其也包括所有的固氮豆科共生体）和卡巴雷氏菌（Caballeronia）中，而大多数人类和动物病原体保留在狭义伯克霍尔德氏菌中。然而，这些属中没有一个能容纳两个重要的物种群。其中之一包括密切相关的Paraburkholderia rhizoxinica和Paraburkholderia endofungorum，它们都是真菌植物病原体小孢根霉的共生体。第二组包括含羞草分解细菌共生副伯克霍尔德氏菌、植物病原体卡氏副伯克霍尔德氏菌、土壤细菌大宝山伯克霍尔德氏菌和土壤副伯克霍尔德氏菌。为了阐明它们在广义伯克霍尔德氏菌中的位置，进行了基于来自100多种广义伯克霍尔德氏菌物种的保守基因的最大似然分析的基因组学方法。此外，计算平均核苷酸同一性（ANI）和氨基酸同一性（AAI）。这些数据有力地支持了两个不同而独特的分支的存在，这实际上支持了两个新属Mycetohabitans gen. nov.和Trinickia gen. nov.的描述。新提出的组合是Mycetohabitans endofungorum comb. nov.，Rhizoxinica comb. nov.，Trinickia carbilli comb. nov.，大宝山三齿藓，Trinickia soli comb. nov.，和Trinickia symbiotica comb. nov.在他们的生活方式往往是复杂的，这些新的组合的基因组的差异特征进行了研究。此外，还深入分析了两个重要的生活方式决定性状-固氮和/或共生共生，以及发病机制，即，确定了Trinickia via-α-维斯其他伯克霍尔德氏菌科的固氮和固氮酶基因的系统发育位置，并通过对植物和线虫Caelophabditis elegans进行感染实验来测试Mycetohabitans和Trinickia中致病的可能性。结果表明：（1）T.共生真菌nif和nod基因适合于更广泛的含羞草-分枝伯克霍尔德菌科，但出现在不同的分支中，而T.卡氏伯克霍尔德氏菌nif基因是自由生活的伯克霍尔德氏菌s.l.菌株，而关于致病性（2）除了已知的植物病原体T之外，测试的Mycetohabitans和Trinickia菌株都不可能是致病性的。卡布里。
Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitans rhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickia dabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickia symbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits—diazotrophy and/or symbiotic nodulation, and pathogenesis—were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophylli nif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.
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影响因子：
3.7
作者：
Angus AA;Agapakis CM;Fong S;Yerrapragada S;Estrada-de los Santos P;Yang P;Song N;Kano S;Caballero-Mellado J;de Faria SM;Dakora FD;Weinstock G;Hirsch AM
通讯作者：
Hirsch AM
DOI：
10.1099/ijsem.0.001065
发表时间：
2016-08-01
影响因子：
2.8
作者：
Dobritsa, Anatoly P.;Samadpour, Mansour
通讯作者：
Samadpour, Mansour
影响因子：
--
作者：
Eberl, Leo;Vandamme, Peter
通讯作者：
Vandamme, Peter
影响因子：
3.7
作者：
Bournaud C;de Faria SM;dos Santos JM;Tisseyre P;Silva M;Chaintreuil C;Gross E;James EK;Prin Y;Moulin L
通讯作者：
Moulin L
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.