UvA-DARE (Digital Academic Repository) Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium Kuever, J.; Visser, M.; Loeffler, C.; Boll, M.; Worm, P.; Sousa, D.Z.; Plugge, C.M.; Schaap, P.J.; Muyzer, G.; Pereira, I.A.C.; Parshina, S.N.; Goodwin, L.A; Kyrpides, N.C.; Detter, J.; Woyke, T.; Chain, P.; Davenport, K.W.; Rohde, M.; Spring, S.; Klenk, H.-P.; Stams, A.J.M. DOI 10.4056/sigs.5209235 Publication date 2014 Document Version Final published version Published in Standards in Genomic Sciences Link to publication Citation for published version (APA): Kuever, J., Visser, M., Loeffler, C., Boll, M., Worm, P., Sousa, D. Z., Plugge, C. M., Schaap, P. J., Muyzer, G., Pereira, I. A. C., Parshina, S. N., Goodwin, L. A., Kyrpides, N. C., Detter, J., Woyke, T., Chain, P., Davenport, K. W., Rohde, M., Spring, S., ... Stams, A. J. M. (2014). Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram- positive sulfate-reducing bacterium. Standards in Genomic Sciences, 9(3), 821-839. https://doi.org/10.4056/sigs.5209235 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You willUvA-DARE be contacted is a service as provided soon as by possible.the library of the University of Amsterdam (https://dare.uva.nl) Download date:01 Oct 2021 Standards in Genomic Sciences (2014) 9:821-839 DOI:10.4056/sigs.5209235 Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium Jan Kuever1, Michael Visser2, Claudia Loeffler3, Matthias Boll3, Petra Worm2, Diana Z. Sousa2, Caroline M. Plugge2, Peter J. Schaap4, Gerard Muyzer5, Ines A.C. Pereira6, Sofiya N. Parshina7, Lynne A. Goodwin8,9, Nikos C. Kyrpides8, Janine Detter9, Tanja Woyke8, Patrick Chain8,9, Karen W. Davenport8,9, Manfred Rohde10, Stefan Spring11; Hans-Peter Klenk11, Alfons J.M. Stams2,12 1Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany 2Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands 3Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany 4Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands 5Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynam- ics, University of Amsterdam, Amsterdam, The Netherlands 6Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal 7Winogradsky Institute of Microbiology Russian Academy of Sciences, Moscow, Russia 8DOE Joint Genome Institute, Walnut Creek, California, USA 9Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 10HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 11Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 12University of Minho, Centre of Biological Engineering, Braga, Portugal Keywords: spore-forming anaerobes, sulfate reduction, autotrophic, anaerobic degrada- tion of aromatic compounds, complete oxidizer, Peptococcaceae, Clostridiales Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of or- ganic substrates, in particular several aromatic compounds, short-chain and medium- chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduc- tion of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the ab- sence of sulfate. It does not require any vitamins for growth. Here, we describe the fea- tures of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate pro- tein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA path- way, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transfor- mation and degradation of aromatic compounds, which are lacking in the other se- quenced Desulfotomaculum genomes. Introduction Desulfotomaculum gibsoniae strain GrollT (DSM CO2 coupled to sulfate reduction. The strain is 7213) is a mesophilic sulfate-reducing bacte- also able to grow autotrophically with H2/CO2 rium isolated from a freshwater ditch in Bre- and sulfate, and is able to ferment pyruvate and men, Northern Germany [1,2]. It grows with a crotonate. In the absence of sulfate, it grows wide range of substrates, including organic ac- slowly on H2/CO2, formate, and methoxylated ids, such as medium-chain fatty acids, short- aromatic compounds. D. gibsoniae does not re- chain fatty acids, and several aromatic com- quire vitamins for growth. pounds [1]. These substrates are degraded to The Genomic Standards Consortium Desulfotomaculum gibsoniae The genus Desulfotomaculum is a heterogeneous The Desulfotomaculum genus is divided group of anaerobic spore-forming sulfate- phylogenetically into different subgroups [1]. To reducing bacteria, with thermophilic, meso- get a thorough understanding of the evolution- philic, and psychrophilic members that grow at ary relationships of the different neutral or alkaline pH values [3]. Their cell wall Desulfotomaculum subgroups and the physiolo- stains Gram-negative, but the ultrastructure of gy of the individual species, it is important to the cell wall is characteristic of Gram-positive have genome sequence information. Here, we bacteria [4]. They are physiologically very di- present a summary of the features of D. verse. In contrast to Gram-negative sulfate- gibsoniae strain GrollT, together with the de- reducing bacteria and closely related Clostridia, scription of the complete genomic sequencing very little is known about their physiology, but and annotation. A special emphasis is put on the members of this genus are known to play an im- ability of this strain to grow on a large variety of portant role in the carbon and sulfur cycle in di- aromatic compounds and the responsible genes, verse habitats. and its capacity for acetogenic growth in the ab- sence of sulfate. Figure 1. Neighbor joining tree based on 16S rRNA gene sequences showing the phylogenetic affiliations of Desulfotomaculum and related species and highlighted to show the subgroups of Desulfotomaculum cluster 1. D. gibsoniae is printed in bold type. The recently described Desulfotomaculum defluvii (cluster 1a), Desulfotomaculum intricatum (cluster 1f), Desulfotomaculum peckii (cluster 1e), and Desulfotomaculum varum (cluster 1a) and the entire cluster 1g are not included in the tree. A set of Thermotogales species were used as outgroup, but were pruned from the tree. Closed circles represent bootstrap values between 75 and 100%. The scale bar represents 10% sequence difference. 822 Standards in Genomic Sciences Kuever et al. Classification and features D. gibsoniae is a member of the phylum was shown with pyruvate, crotonate, formate, H2 Firmicutes. Phylogenetic analysis of the 16S + CO2, and methoxylated aromatic compounds as rRNA genes of D. gibsoniae shows that it clusters substrates. In the presence of an electron accep- in Desulfotomaculum cluster 1, subgroup b. (Fig- tor it can completely oxidize substrates to CO2. ure 1 [1]). Other species in this subgroup are D. Suitable electron acceptors are sulfate, thiosul- geothermicum, D. arcticum, D. alcoholivorax, D. fate and sulfite. The cells of D. gibsoniae are thermosapovorans, D. sapomandens and the non- straight or slightly curved rods (1.0-2.5 × 4-7 Desulfotomaculum species Sporotomaculum Figure 2). Spores of D. hydroxybenzoicum and S. syntrophicum. gibsoniae are spherical and located in the center D. gibsoniae is a mesophilic sulfate reducer, with ofμm) the with cells, pointed causing ends swelling. ( A summary of the an optimum growth temperature between 35- classification and general features of D. 37°C [1,2]. Fermentative and acetogenic growth gibsoniae is presented in Table 1. Figure 2. Scanning electron micrograph of D. gibsoniae strain GrollT. Genome sequencing and annotation Genome project history The genome project is listed in the Genome D. gibsoniae was selected for sequencing in the OnLine Database (GOLD) [18] as project DOE Joint Genome Institute Community Se- Gi07572, and the complete genome sequence is quencing Program 2009, proposal deposited in Genbank. Sequencing, finishing and 300132_795700 'Exploring the genetic and annotation of the D. gibsoniae genome were per- physiological diversity of Desulfotomaculum