Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.
Five isolates that were related phylogenetically to members of the genus Pedobacter were isolated from freshwater of the hard-water creek Westerhöfer Bach, North Germany. The five strains (WB 2.1-25(T), WB 2.3-71(T), WB 3.3-3(T), WB 3.3-22(T) and WB 2.3-45(T)) were Gram-negative and chemoheterotrophic, with rod-shaped cells. Most of their metabolic properties matched those given in the description of the genus Pedobacter. Consistent with the genus description, their fatty acids included mainly iso-C(15 : 0) and summed feature 3 (C(16 : 1)omega7c, iso-C(15 : 0) 2-OH or both); C(16 : 1)omega5c, C(16 : 0), iso-C(15 : 0) 3-OH, C(16 : 0) 3-OH and iso-C(17 : 0) 3-OH were present in smaller amounts. The major isoprenoid quinone was menaquinone 7. With one exception, binary similarity values of the almost complete 16S rRNA gene sequences determined among the isolates as well as between the isolates and type strains of Pedobacter species were lower than 98.5 %. The only exception was the close relationship between Pedobacter caeni DSM 16990(T) and strain WB 2.3-45(T) (99.2 % similarity). DNA-DNA reassociation values determined for this pair of strains was 29.8 %, indicating that strain WB 2.3-45(T) represents a unique genospecies. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WB 2.1-25(T) and WB 2.3-71(T) form a group that is moderately related to P. caeni and strain WB 2.3-45(T) (98.5 % similarity). Strains WB 3.3-3(T) and WB 3.3-22(T) (98.5 % similarity) branched separately from these four organisms. The five phylogenetically isolated strains differed from each other as well as from the type strain of the type species (Pedobacter heparinus DSM 2366(T)) and some related representatives of the genus in several metabolic reactions and cultural parameters. On the basis of phenotypic and phylogenetic distinctiveness, five novel species are proposed: Pedobacter duraquae sp. nov., with WB 2.1-25(T) (=DSM 19034(T)=CIP 109481(T)) as the type strain; Pedobacter westerhofensis sp. nov., with WB 3.3-22(T) (=DSM 19036(T)=CIP 109479(T)) as the type strain; Pedobacter metabolipauper sp. nov., with WB 2.3-71(T) (=DSM 19035(T)=CIP 109480(T)) as the type strain; Pedobacter hartonius sp. nov., with WB 3.3-3(T) (=DSM 19033(T)=CIP 109468(T)) as the type strain; and Pedobacter steynii sp. nov., with WB 2.3-45(T) (=DSM 19110(T)=CIP 109507(T)) as the type strain.
Muurholm
Sören
S
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany.
Cousin
Sylvie
S
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany.
Päuker
Orsola
O
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany.
Brambilla
Evelyne
E
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany.
Stackebrandt
Erko
E
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany.
D000818:Animals; D015373:Bacterial Typing Techniques; D041963:Bacteroidetes / Q000737:chemistry / Q000145:classification* / Q000302:isolation & purification*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005227:Fatty Acids / Q000032:analysis; D005618:Fresh Water / Q000382:microbiology*; D020459:Genes, rRNA; D005858:Germany; D008969:Molecular Sequence Data; D009930:Organic Chemicals / Q000378:metabolism; D010802:Phylogeny; D011809:Quinones / Q000032:analysis; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D005227:Fatty Acids; D009930:Organic Chemicals; D011809:Quinones; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S