Hahn Martin W, Schmidt Johanna, Asiyo Grace Ssanyu, Kyrpides Nikos C, Woyke Tanja, Whitman William B
Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria.
Department of Biological Sciences, Kyambogo University, P.O Box 1, Kyambogo, Uganda.
Int J Syst Evol Microbiol. 2017 Dec;67(12):5087-5093. doi: 10.1099/ijsem.0.002421. Epub 2017 Oct 25.
The genus Polynucleobacter (family Burkholderiaceae) is phylogenetically subdivided into at least four subclusters. One of those, subcluster PnecC, was recognized as a cryptic species complex. Here we test by comparative genome analyses whether subcluster PnecD, currently solely represented by the species Polynucleobactercosmopolitanus, also represents such a cryptic species complex. The genome sequences of the two P. cosmopolitanus strains, MWH-MoIso2 and MWH-VicM1, were determined. The latter strain was also characterized in the previous description of P. cosmopolitanus. These two strains originate from a temperate lake located in Austria and from the large tropical Lake Victoria located in East Africa, respectively. Strains MWH-MoIso2 and MWH-VicM1 possess quite small genomes of 1.78 and 1.63 Mbp, respectively, and share similar G+C values of 44.1 and 43.1 mol%, respectively. Both strains encode only a single copy of the ribosomal operon, and their 16S rRNA genes differ only in four positions, equalling a sequence similarity of 99.74 %. Both genomes possess characteristics indicating evolutionary genome streamlining, such as high coding densities of 93.9 and 94.6 % of bases, respectively. Average nucleotide identity (ANI) comparisons of the genomes of the two strains resulted in a value of 78.4 %, suggesting that each of the strains represents a separate species. Our investigation suggests that PnecD represents an additional cryptic species complex within the genus Polynucleobacter that was not resolved by 16S rRNA gene sequence analyses. We propose reclassification of strain MWH-VicM1 as Polynucleobacter victoriensis sp. nov., with type strain MWH-VicM1(=DSM 21486=JCM 32005).
多核杆菌属（伯克霍尔德菌科）在系统发育上至少可细分为四个亚群。其中一个亚群，即亚群PnecC，被认为是一个隐性物种复合体。在此，我们通过比较基因组分析来测试目前仅由环球多核杆菌代表的亚群PnecD是否也代表这样一个隐性物种复合体。测定了两株环球多核杆菌菌株MWH-MoIso2和MWH-VicM1的基因组序列。后一株菌株在之前对环球多核杆菌的描述中也有特征描述。这两株菌株分别来自奥地利的一个温带湖泊和东非的大型热带维多利亚湖。菌株MWH-MoIso2和MWH-VicM1的基因组相当小，分别为1.78 Mbp和1.63 Mbp，并且G+C值相似，分别为44.1 mol%和43.1 mol%。两株菌株均仅编码一个核糖体操纵子拷贝，它们的16S rRNA基因仅在四个位置不同，序列相似性为99.74%。两个基因组都具有表明进化基因组精简的特征，例如碱基的编码密度分别高达93.9%和94.6%。对两株菌株基因组的平均核苷酸同一性（ANI）比较得出的值为78.4%，这表明每株菌株都代表一个单独的物种。我们的研究表明，PnecD代表多核杆菌属内另一个未通过16S rRNA基因序列分析解析的隐性物种复合体。我们建议将菌株MWH-VicM1重新分类为新种维多利亚多核杆菌，模式菌株为MWH-VicM1（=DSM 21486=JCM 32005）。
