Duganella albus sp. nov., Duganella aquatilis sp. nov., Duganella pernnla sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China

Abstract

<jats:p>Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT9W<jats:sup>T</jats:sup>, FT25W, FT26W<jats:sup>T</jats:sup>, FT109W<jats:sup>T</jats:sup>, FT134W and CY42W<jats:sup>T</jats:sup>) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences showed that the six strains shared similarities of less than 98.1 % with other species within the family <jats:italic> <jats:named-content content-type="family"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1699" xlink:type="simple">Oxalobacteraceae</jats:ext-link> </jats:named-content> </jats:italic> and formed two separately distinct clades in phylogenetic trees. The 16S rRNA gene sequence similarities between strains FT9W<jats:sup>T</jats:sup> and FT25W, and between strains FT109W<jats:sup>T</jats:sup> and FT134W were both 99.7 %. The genome sizes of strains FT9W<jats:sup>T</jats:sup>, FT25W, FT26W<jats:sup>T</jats:sup>, FT109W<jats:sup>T</jats:sup>, FT134W and CY42W<jats:sup>T</jats:sup> were 6.45, 6.45, 6.54, 6.43, 6.52 and 6.74 Mbp with G+C contents of 64.0, 64.0, 63.8, 63.2, 63.2 and 62.5 %, respectively. The calculated pairwise average nucleotide (ANI) values among the six strains and other related species were less than 93.9 %, except that the values were 99.9 % between strains FT9W<jats:sup>T</jats:sup> and FT25W, 98.2 % between strains FT109W<jats:sup>T</jats:sup> and FT134W, and 95.0 and 95.1 % between strain FT26W<jats:sup>T</jats:sup> and strains FT9W<jats:sup>T</jats:sup> and FT25W, respectively. However, strain FT26W<jats:sup>T</jats:sup> shared 16S rRNA gene sequence similarities of only 98.3 and 98.2 % with FT9W<jats:sup>T</jats:sup> and FT25W, respectively. The respiratory quinone of the six strains was determined to be Q-8. The major fatty acids were C<jats:sub>16 : 1</jats:sub> <jats:italic>ω</jats:italic>7<jats:italic>c</jats:italic>, C<jats:sub>16 : 0</jats:sub> and C<jats:sub>12 : 0</jats:sub>. The predominant polar lipids included phosphatidylethanolamine and phosphatidylglycerol. Considering the phenotypic, biochemical, genotypic and ANI data, strains FT9W<jats:sup>T</jats:sup> and FT25W, and FT109W<jats:sup>T</jats:sup> and FT134W may belong to the same species, respectively. Although the pairwise ANI values between strain FT26W<jats:sup>T</jats:sup> and each of strains FT9W<jats:sup>T</jats:sup> and FT25W were located in the transition region of species demarcation, the dissimilarities among them indicated that strain FT26W<jats:sup>T</jats:sup> could represent an independent novel species. The reconstructed phylogenomic tree based on a concatenation of 92 core genes showed that the six strains clustered closely with <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.23909" xlink:type="simple">Duganella sacchari</jats:ext-link> </jats:named-content> </jats:italic> Sac-22<jats:sup>T</jats:sup> and <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.23910" xlink:type="simple">Duganella radicis</jats:ext-link> </jats:named-content> </jats:italic> KCTC 22382<jats:sup>T</jats:sup>, and supported that these six strains belong to the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1703" xlink:type="simple">Duganella</jats:ext-link> </jats:named-content> </jats:italic>. The names <jats:italic>Duganella albus</jats:italic> sp. nov. (type strain FT9W<jats:sup>T</jats:sup>=GDMCC 1.1637<jats:sup>T</jats:sup>=KACC 21313<jats:sup>T</jats:sup>), <jats:italic>Duganella aquatilis</jats:italic> sp. nov. (type strain FT26W<jats:sup>T</jats:sup>=GDMCC 1.1641<jats:sup>T</jats:sup>=KACC 21315<jats:sup>T</jats:sup>), <jats:italic>Duganella pernnla</jats:italic> sp. nov. (type strain FT109W<jats:sup>T</jats:sup>=GDMCC 1.1688<jats:sup>T</jats:sup>=KACC 21480<jats:sup>T</jats:sup>) and <jats:italic>Duganella levis</jats:italic> sp. nov. (type strain CY42W<jats:sup>T</jats:sup>=GDMCC 1.1673<jats:sup>T</jats:sup>=KACC 21465<jats:sup>T</jats:sup>) are proposed.</jats:p>

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers

“…Furthermore, carbohydrate assimilative properties and enzyme production abilities were also identifying properties among strain AF9R3 T and closely related species (Table 1). Strain AF9R3 T , D. levis KACC 21465 T , D. margarita KACC 21480 T and D. lactea KACC 21466 T were found to be aerobic in this study while the latter three species were described as facultatively anaerobic by Lu et al [7,23]. On the other hand, the differences between strain GN2-R2 T , and M. arvi KACC 21416 T , M. norwichensis KACC 21420 T and M. putida KACC 21418 T can be observed in terms of nitrate reduction ability, production of oxidase and urease, assimilation patterns of various substrates, and enzymatic activities (Table 2).…”

“…However, strain GN2-R2 T comprised PL as the major polar lipid, which is different from the closely related species [13,47]. Strains AF9R3 T and GN2-R2 T contained ubiquinone 8 (Q-8) as the predominant respiratory quinone, similar Data from: a, Lu et al [23]; b, Lu et al [7].…”

“…margarita FT109W T and D. lactea FT50W T in that these four species commonly had DPG, PG and PE as the major polar lipids [7, 23]. Strain GN2-R2 T comprised DPG, PG, PE, AL, two Ls and phospholipid (PL) (Fig.…”

“…According to the 16S rRNA gene sequence-based phylogenetic tree, the members of the genus Duganella and Massilia were found to be polyphyletic and intermingled with the genera Janthinobacterium , Pesudoduganella and Rugamonas [4–6]. The genus Duganella , including validly and invalidly named species, were isolated from wastewater [3], a maize field [6], subtropical streams [7], sap from Acer pictum [5], zebrafish [4], ginseng soil [8], leaf surface of Trifolium repens [9] and rhizosphere of field-grown sugar cane [10]. The genus Massilia was first proposed for an isolate from a culture of blood from a febrile patient with common variable immunodeficiency [11].…”

Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.

“…in 1997 with the reclassification of Zoogloea ramigera IAM 12670 T (P. R. Dugan 115) as Duganella zoogloeoides [1]. Since then, 11 novel species within this genus were reported, including Duganella phyllosphaerae T54 T , Duganella ginsengisoli DCY83 T , Duganella sacchari Sac-22 T , Duganella radicis Sac-41 T , Duganella albus FT9W T , Duganella aquatilis FT26W T , Duganella pernnla FT109W T , Duganella levis CY42W T , ‘ Duganella rivus FT55W’, ‘ Duganella fentianensis FT93W’ and ‘ Duganella qianjiadongensis CY13W’, and strain Pseudoduganella danionis was reclassified as ‘ Duganella danionis ’ [2–6]. The genus Massilia was proposed by La Scola et al .…”