title: Identification and targeted cultivation of abundant novel freshwater sphingomonads and analysis of their population substructure.
abstract: Little is known with respect to bacterial population structures in freshwater environments. Using complementary culture-based, cloning, and high-throughput Illumina sequencing approaches, we investigated microdiverse clusters of bacteria that comprise members with identical or very similar 16S rRNA gene sequences. Two 16S rRNA phylotypes could be recovered by cultivation in low-nutrient-strength liquid media from two lakes of different trophic status. Both phylotypes were found to be physiologically active in situ throughout most of the year, as indicated by the presence of their rRNA sequences in the samples. Analyses of internal transcribed spacer (ITS1) sequences revealed the presence of seven different sequence types among cultured representatives and the cloned rrn fragments. Illumina sequencing yielded 8,576 ITS1 sequences that encompassed 15 major and numerous rare sequence types. The major ITS1 types exhibited distinct temporal patterns, suggesting that the corresponding Sphingomonadaceae lineages occupy different ecological niches. However, since strains of the same ITS1 type showed highly variable substrate utilization patterns, the potential mechanism of niche separation in Sphingomonadaceae cannot be explained by substrate utilization alone and may be related to other traits.
authors.affiliation: Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany.
authors.forename: Mareike
authors.initials: M
authors.lastname: Jogler
authors.forename: Helge
authors.initials: H
authors.lastname: Siemens
authors.forename: Hong
authors.initials: H
authors.lastname: Chen
authors.forename: Boyke
authors.initials: B
authors.lastname: Bunk
authors.forename: Johannes
authors.initials: J
authors.lastname: Sikorski
authors.forename: Jörg
authors.initials: J
authors.lastname: Overmann
mesh_terms: D044822:Biodiversity; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D021901:DNA, Intergenic / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005618:Fresh Water / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D042301:Sphingomonadaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S