Genetic population structures and biogeography of the cyanobacterium Microcoleus chthonoplastes

In dieser Arbeit wurden die genetische und geographische Diversität sowie das mögliche Vorkommen von Rekombination (der Austausch genetischen Materials zwischen den Individuen) innerhalb und zwischen Populationen des benthisch-marinen, weltweit vorkommenden Cyanobakterium Microcoleus chthonoplastes untersucht. Zu diesem Zweck wurden die Nukleotidsequenzen dreier Genloci (rDNA-ITS Region, kaiC, petB/D) für 310 Proben, die aus verschiedenen Regionen der Erde stammten, analysiert. Neben der Verwendung von Kulturen wurde ein kulturunabhängiger Ansatz entwickelt, mit dem einzelne Filamente direkt amplifiziert und sequenziert werden konnten. Es konnte festgestellt werden, dass Microcoleus chthonoplastes eine hohe, vormals unentdeckte, innerartliche Variabilität auf genetischer Ebene aufweist. Das wurde besonders beim Vergleich der ITS-Region und der Haushaltsgene deutlich. Phylogenetische Bäume, die auf der Grundlage der Nukleotidsequenzen erstellt wurden, ließen bis auf wenige Ausnahmen eine Gruppierung der Organismen hinsichtlich ihrer geographischen Lage auf globaler Ebene erkennen. Auf kleinräumigerer Ebene (z.B. beim Vergleich von Proben aus der Nordsee- und Ostseeregion) konnte dagegen keine Gruppierung hinsichtlich des Herkunftsortes erkannt werden. Im Gegensatz dazu konnte an einzelnen Standorten eine hohe genetische Diversität entdeckt werden. Beim Vergleich entlang eines ökologischen Gradienten, in diesem Fall entlang eines Salinitätsgradienten, konnte eine Anordnung der Proben in Abhängigkeit von der Salinität des Standortes beobachtet werden. Rekombination wurde für M. chthonoplastes in einzelnen geographischen Regionen festgestellt. Untersuchungen von 133 Proben aus der Nordsee- und Ostseeregion ließen auf das häufige Vorkommen von Rekombination schließen.The goal of this project was to gain insight into the genetic diversity and biogeography within and between populations of the marine cyanobacterium Microcoleus chthonoplastes, which can be found in microbial mats worldwide. Additionally, the presence of recombination (that is, the exchange of genetic material between two individuals) within this species was investigated. I analysed the nucleotide sequences from three gene loci (rDNA-ITS region, kaiC, petB/D) for 310 samples. The samples originated from several locations worldwide. Next to analysing cultures, a culture independent method was developed for amplifying and sequencing single filaments directly without the need of growing cultures first. A high, previously undetected sequence diversity could be found within Microcoleus chthonoplastes. Especially the ITS region and the housekeeping genes showed a high resolution on the level of nucleotide sequences. The comparison of phylogenetic trees for the three genes showed that the samples clustered with regard to their geographic origin on a global level. Within single regions, eg. the North Sea and Baltic Sea region, the clustering of the samples seemed not to correlate with the sampling locations. On the other hand, a high genetic diversity within single locations could be detected. Comparing the genetic diversity along a salinity gradient it could be observed that the samples were distributed along the gradient in dependence of the salinity. Frequent recombination could be detected for 133 filaments and cultures sampled from intertidal sand flats of the North Sea and Baltic Sea

Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov.

The genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0% similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T=JCM 12381T=IMSNU 14040T=KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T=JCM 12382T=IMSNU 14049T=KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T=KCCM 42689T=NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data

Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium.

A collection of eight strains, NF 1366(T), NF 450, NF 1101, NF 1107, NF 1123, NF 1413, CCUG 15260 and CCUG 15624, from various clinical origins, were characterized biochemically as similar to Kaistella koreensis and Chryseobacterium haifense. They differed from K. koreensis, which is unable to alkalinize acetate, and from C. haifense, which is ONPG-positive (beta-galactosidase) and acidifies sucrose, fructose and lactose. Based on 16S rRNA gene sequence comparisons, this collection of strains was most closely related to the type strains of K. koreensis (97.3-97.5 %) and C. haifense (99.1 %). Representative strain NF 1366(T) showed only 41.8 % DNA-DNA relatedness with K. koreensis DSM 12107(T) and only 51.9 % with C. haifense DSM 19056(T). DNA-DNA hybridization of strains NF 450 and CCUG 15624 to strain NF 1366(T) was 41.7 and 74.6 %, respectively, and relatedness of these strains with C. haifense DSM 19056(T) was 72.6 and 70.2 %. With the present information, these two strains must be classified as intermediate between C. haifense and strain NF 1366(T). The fatty acid composition and polar lipid profile of strain NF 1366(T) were similar to those reported for other Chryseobacterium species. Like other chryseobacteria, strain NF 1366(T) exhibited a polyamine pattern with the predominant compound sym-homospermidine and a quinone system consisting of menaquinone MK-6 only. For this collection of clinical strains, the name Chryseobacterium anthropi sp. nov. is proposed, with NF 1366(T) (=CCUG 52764(T) =CIP 109762(T)) as the type strain. K. koreensis was shown to be very similar genotypically and phenotypically to Chryseobacterium. Its polar lipid profile exhibited the major characteristics shown for recently described Chryseobacterium species and the fatty acid profile of K. koreensis was also very similar to those of the Chryseobacterium species. Hence, no striking genotypic or phenotypic differences could be found that could justify the classification of this species into a separate genus, and we therefore propose to reclassify Kaistella koreensis in the genus Chryseobacterium as Chryseobacterium koreense comb. nov. (type strain Chj707(T) =IAM 15050(T) =JCM 21512(T) =KCTC 12107(T) =NBRC 103027(T)). An emended description of the genus Chryseobacterium is also proposed