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Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species

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Abstract

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81T (= DSM 19542T) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81T not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6–96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81T and the animal-associated species Kiloniella majae M56.1T from a spider crab, Kiloniella spongiae MEBiC09566T from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81T contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.

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Acknowledgements

The authors gratefully acknowledge the help of Andrea Schuetze (DSMZ) for growing cells of K. laminariae LD81T (= DSM 19542T) and of Evelyne Brambilla (DSMZ) for DNA extraction and quality control. Financial support of ERA-NET Marine Biotechnology: “ProBone—new tools for prospecting the marine bone-degrading microbiome for new enzymes” (FKZ 031B0570) to U.H. and E.B. is acknowledged. We also thank the Genomics and Proteomics Core Facility (DKFZ) for using their computational resources. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. This study was funded by Horizon 2020 (Grant number ERA-NET FKZ 031B0570).

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Authors and Affiliations

  1. GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105, Kiel, Germany

    Jutta Wiese, Johannes F. Imhoff, Hannes Horn, Erik Borchert & Ute Hentschel

  2. DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA

    Nikos C. Kyrpides & Tanja Woyke

  3. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany

    Markus Göker

  4. School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK

    Hans-Peter Klenk

  5. Christian-Albrechts-University (CAU) of Kiel, Kiel, Germany

    Ute Hentschel

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  1. Jutta Wiese
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  2. Johannes F. Imhoff
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Correspondence to Jutta Wiese.

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Communicated by Erko Stackebrandt.

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Wiese, J., Imhoff, J.F., Horn, H. et al. Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species. Arch Microbiol 202, 815–824 (2020). https://doi.org/10.1007/s00203-019-01791-0

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