Trichlorobacter thiogenes Should Be Renamed as aGeobacter Species
Trichlorobacter thiogenes Should Be Renamed as aGeobacter Species
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硫代三氯杆菌应更名为地杆菌属
DOI：
10.1128/aem.67.2.1020-1022.2001
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发表时间：
2001
影响因子：
4.4
通讯作者：
D. Lovley
中科院分区：
文献类型：
--
作者：
O. Snoeyenbos;Catherine Gaw Van Praagh;D. Lovley
在De Wever等人最近的一篇论文中。(2)提出将新分离的微生物菌株K1归属于三角洲变形杆菌中的一个新属。这些作者指出，菌株K1的16S核糖体DNA(RDNA)序列将其置于三角洲变形杆菌的“混合分类关系簇”中。从这一声明中可以明显看出，De Wever等人。(2)不知道以前在三角洲变形杆菌中对这一组进行的几次系统发育分析，最引人注目的是Lonergan等人的一项研究。(5)。正如De Wever等人所说。(2)请注意，菌株K1的16S rDNA序列与从生物反应器中提取的16S rDNA序列几乎相同(99%的序列同源性)，他们错误地将其识别为“环境假单胞菌”。但这实际上是一种环境序列，最初被描述为种群类型1序列(类硫磺单胞菌)(1)，并被GenBank和核糖体数据库项目(RDP)II(9)版本7.1列为硫磺单胞菌。(GenBank登录号：{“type”：“Entrez-核苷酸”，“attrs”：{“Text”：“M80618”，“Term_id”：“174326”，“Term_Text”：“M80618”}M80618)。如果De Wever等人。(2)了解Lonergan等人的研究。(5)，他们会意识到，对该序列的详细分析表明，它正好位于地杆菌科地杆菌群内(5)。我们自己对菌株K1序列的分析不仅证实了菌株K1的总序列与地杆菌群中的生物密切相关(图2)。(图1)1)，而且该序列还包含具有地杆菌簇特征的签名二级结构(5)。
图1
根据16S rRNA序列构建的系统发育树显示了硫化毛杆菌K1菌株的系统发育位置。用邻接法和木村双参数遗传法推断了系统发育关系.
目前，地杆菌群只包含一种微生物，丙酸杆菌，它没有被命名为地杆菌(图3)。(图1)1)。在地杆菌科中还有四个种，但这些其他种分布在地杆菌聚类群之外的另外两个属中。因此，很明显，Pelbacter属在系统发育上不是一致的，Gebacter类群中的生物不能被重新命名为Pelbacter，因为这将导致不同系统发生类群的生物被归入同一属。有人建议，避免与系统发育混淆的最简单的方法是将丙酸杆菌归入地质杆菌属(5)。
因此，按照De Wever等人的建议，将菌株K1命名为地杆菌集群中的一个新属。(2)，在原本合乎逻辑的有机体群体内造成严重破坏，该群体主要由系统发育上连贯的集群中的单一属组成。如果菌株K1具有一些独特的生理特征，使其有别于先前描述的地质杆菌物种，则可能有理由指定一个新属，但情况似乎并非如此。菌株K1以乙酸盐为电子供体，还原S0和富马酸，也可能以Fe(III)为电子受体(2)。醋酸盐氧化结合S0和Fe(III)的还原是地杆菌的生理特性之一，许多地杆菌也可以利用富马酸作为醋酸盐氧化的电子受体(6，7，8)。菌株K1能够还原脱氯三氯乙酸，这种生理能力以前没有报道过。然而，据我们所知，还没有对地杆菌集群中的其他生物进行这种反应的能力进行评估。因此，目前还不清楚菌株K1在地杆菌群中的这种能力是独一无二的。此外，De Wever et al.(2)表明菌株K1的还原脱氯作用至少有一部分是菌株K1将S0还原为硫化物，然后三氯乙酸被硫化物还原的结果。由于地杆菌群中的所有生物都具有将S0还原为硫化物的能力，因此很可能所有的地杆菌都具有通过这种电子穿梭机制脱氯三氯乙酸的能力。
此外，即使发现除菌株K1以外的所有地细菌群中的生物都不能还原脱氯三氯乙酸，优先顺序也表明没有必要指定一个新的属。当描述地细菌科中发现的第一个具有还原脱氯能力的硫磺单胞菌(4)时，它没有被归入一个新属，而是被指定为硫磺单胞菌属(3)中的一个新种。这与不混杂具有多个属名称的系统发育相关群的概念是一致的。
综上所述，此时将菌株K1指定为地杆菌群中的一个新属，既不能提高系统发育的清晰度，也不能加深对生理学的理解。建议一旦完成对菌株K1的生理特征描述，即可将其命名为地杆菌属的一个新种。
In a recent paper by De Wever et al. (2), it is proposed that the recently isolated microorganism strain K1 be assigned to a new genus within the delta Proteobacteria. Those authors state that the 16S ribosomal DNA (rDNA) sequence of strain K1 places it within a “cluster of mixed taxonomic affiliation” within the delta Proteobacteria. From this statement it is apparent that De Wever et al. (2) are unaware of several previous phylogenetic analyses of this group within the delta Proteobacteria, most notably, a study by Lonergan et al. (5). As De Wever et al. (2) note, the 16S rDNA sequence of strain K1 is nearly identical (99% sequence identity) to a 16S rDNA sequence recovered from a bioreactor that they misidentify as “environmental sp. 2” but that is actually an environmental sequence first described as a population type 1 sequence (Desulfuromonas-like sp.) (1) and listed by both GenBank and the Ribosomal Database Project (RDP) II (9) release 7.1 as Desulfuromonas sp. (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"M80618","term_id":"174326","term_text":"M80618"}}M80618). If De Wever et al. (2) had known about the study by Lonergan et al. (5), they would have realized that detailed analysis of this sequence has demonstrated that it rests squarely within the Geobacter cluster of the family Geobacteraceae (5). Our own analysis of the strain K1 sequence confirms not only that the overall sequence of strain K1 is closely related to organisms in the Geobacter cluster (Fig. (Fig.1)1) but also that the sequence contains the signature secondary structures characteristic of the Geobacter cluster (5).
FIG. 1
Phylogenetic tree inferred from 16S rRNA sequences showing the phylogenetic placement of “Trichlorobacter thiogenes” strain K1. Phylogenetic relationships shown here were inferred by using neighbor joining and Kimura two-parameter genetic ...
At this time, the Geobacter cluster contains only one organism, Pelobacter propionicus, that does not have the genus designation Geobacter (Fig. (Fig.1).1). There are four more species of Pelobacter within the Geobacteraceae family, but these other Pelobacter species are interspersed throughout two other genera outside the Geobacter cluster. Thus, it is clear that the genus Pelobacter is not phylogenetically coherent and that organisms in the Geobacter cluster cannot be renamed Pelobacter as this would result in organisms of different phylogenetic clusters being placed within the same genus. It has been suggested that the simplest way to avoid confusion with the phylogeny is to place P. propionicus in the genus Geobacter (5).
Therefore, designation of strain K1 as a new genus within the Geobacter cluster, as suggested by De Wever et al. (2), creates havoc within an otherwise logical grouping of organisms, comprised of predominantly a single genus within a phylogenetically coherent cluster. Designation of a new genus might be warranted if strain K1 had some unique physiological characteristics that distinguished it from previously described Geobacter species, but this does not appear to be the case. Strain K1 uses acetate as an electron donor for the reduction of S0 and fumarate, and it has been suggested that it might also use Fe(III) as an electron acceptor (2). The oxidation of acetate coupled to the reduction of S0 and Fe(III) is one of the defining physiological characteristics of Geobacter species, and many Geobacter species can also use fumarate as an electron acceptor for acetate oxidation (6, 7, 8). Strain K1 does reductively dechlorinate trichloroacetic acid, a physiological capacity not previously reported for Geobacter species. However, to our knowledge, no other organisms in the Geobacter cluster have been evaluated for the ability to carry out this reaction. Therefore, it is not clear that strain K1 is unique among organisms in the Geobacter cluster in this ability. Furthermore, De Wever et al. (2) suggest that at least part of the reductive dechlorination observed with strain K1 is the result of strain K1 reducing S0 to sulfide, with the subsequent reduction of the trichloroacetic acid by sulfide. Since all organisms in the Geobacter cluster have the ability to reduce S0 to sulfide, it is likely that all Geobacter species have the ability to dechlorinate trichloroacetic acid via this electron shuttling mechanism.
Furthermore, even if all the organisms in the Geobacter cluster other than strain K1 were found to not be able to reductively dechlorinate trichloroacetic acid, precedence suggests that the designation of a new genus would not be warranted. When the first organism in the Desulfuromonas cluster of the Geobacteraceae found to have the ability to carry out reductive dechlorination was described (4), it was not assigned to a new genus; rather, it was designated a new species in the genus Desulfuromonas (3). This is consistent with the concept of not cluttering phylogenetically coherent groups with multiple genus designations.
In summary, designating strain K1 as a new genus in the Geobacter cluster at this time advances neither clarity in phylogeny or understanding of physiology. It is suggested that, once the characterization of the physiology of strain K1 is completed, it be designated a new species in the genus Geobacter.
影响因子：
14.9
作者：
Maidak, BL;Cole, JR;Woese, CR
通讯作者：
Woese, CR