Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov.
A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585(T), was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585(T) was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis. Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T). The polar lipids of strain G1A_585(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585(T) was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585(T) ( = DSM 25081(T)  = LMG 26646(T)). Because Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T) form a phylogenetic group together with strain G1A_585(T) that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151(T) = DSM 16223(T) = KCTC 12232(T)), Sphingorhabdus marina comb. nov. (type strain FR1087(T) = DSM 22363(T) = IMSNU 14132(T) = KCTC 12763(T) = JCM 14161(T)) and Sphingorhabdus litoris comb. nov. (type strain FR1093(T) = DSM 22379(T) = IMSNU 14133(T) = KCTC 12764(T) = JCM 14162(T)).
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.|Bereich Mikrobiologie, Biologie I, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany.
Mareike
M
Jogler
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.|Bereich Mikrobiologie, Biologie I, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany.
Hong
H
Chen
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.
Julia
J
Simon
Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany.
Manfred
M
Rohde
Institute of Bacteriology, Mycology and Hygiene (IBMH), University of Veterinary Medicine Vienna, Austria.
Hans-Jürgen
HJ
Busse
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.
Hans-Peter
HP
Klenk
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.
Brian J
BJ
Tindall
Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.|Bereich Mikrobiologie, Biologie I, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany.
Jörg
J
Overmann
D015373:Bacterial Typing Techniques; D001482:Base Composition; D004269:DNA, Bacterial / Q000235:genetics; D005227:Fatty Acids / Q000032:analysis; D005618:Fresh Water / Q000032:analysis*; D005858:Germany; D060106:Lakes / Q000382:microbiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013095:Spermidine / Q000032:analysis; D042301:Sphingomonadaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D014451:Ubiquinone / Q000032:analysis; D014871:Water Microbiology
D004269:DNA, Bacterial; D005227:Fatty Acids; D012336:RNA, Ribosomal, 16S; D014451:Ubiquinone; C025204:Ubiquinone Q2; D013095:Spermidine