Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group Vitaly V. Kadnikov 1 , Andrey V. Mardanov 1 , Olga A. Podosokorskaya 2 , Sergey N. Gavrilov 2 , Ilya V. Kublanov 2 , Alexey V. Beletsky 1 , Elizaveta A. Bonch-Osmolovskaya 2 , Nikolai V. Ravin 1 * 1 Centre ‘Bioengineering’, Russian Academy of Sciences, Moscow, Russia, 2 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia Abstract Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2 T . A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi. Citation: Kadnikov VV, Mardanov AV, Podosokorskaya OA, Gavrilov SN, Kublanov IV, et al. (2013) Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group. PLoS ONE 8(1): e53047. doi:10.1371/journal.pone.0053047 Editor: Celine Brochier-Armanet, Universite ´ Claude Bernard - Lyon 1, France Received August 7, 2012; Accepted November 23, 2012; Published January 2, 2013 Copyright: ß 2013 Kadnikov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was performed using the scientific equipment of Core Research Facility of Centre ‘Bioengineering’ RAS and supported by Ministry of Education and Sciences of Russia (contract 11.519.11.2029). The work of V.V.K., A.V.M. and N.V.R. was supported by the Program ‘‘The origin and evolution of biosphere’’ of the Russian Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: nravin@biengi.ac.ru Introduction Members of the phylum Chlorobi, also known as green sulfur bacteria, are strictly anaerobic obligately photoautotrophic Bac- teria, which obtain electrons for anaerobic photosynthesis from sulfide and other reduced sulfur compounds [1;2]. The specific light-harvesting complexes, or chlorosomes, of these bacteria are large structures, consisting of bacteriochlorophylls and carotenoids [3]. Other characteristic properties of Chlorobi are their ability to fix nitrogen via molybdenum-containing nitrogenase [4], and to fix CO 2 via the reverse tricarboxylic acid (TCA) cycle [5;6]. Bacteria from the phylum Chlorobi occupy a narrow environmental niche in anoxic aquatic or terrestrial environments where both sulfide and light occur, such as chemocline regions in stratified lakes [1]. Phylogenetically cultured representatives of Chlorobi phylum form one distinct monophyletic group that shares a common root with the Bacteroidetes [7]. Currently, Bacteroidetes and Chlorobi are recognised as two different phyla, but they are closely related in phylogenetic trees based on 16S rRNA as well as other gene sequences [8;9;10]. Conserved indels in several conserved proteins (FtsK, UvrB and ATP synthase a subunit) also strongly indicate that these two phyla shared a common ancestor distinguished from other bacteria [10;11]. Unlike Chlorobi, bacteria from the Bacteroidetes phylum (previ- ously known as the Cytophaga-Flavobacteria-Bacteroides) are metabolically diverse chemoorganotrophes that are able to grow on a variety of complex biopolymers, such as cellulose, chitin and agar [12;13]. Bacteroidetes inhabit diverse habitats including the oral cavity and gastrointestinal tract of humans, where they represent one of the major components of its microbiome. Some species are parasites or sybmionts of humans, animals, algae and protozoa. The free-living Bacteroidetes inhabit soils, fresh and marine water, sediments, and a number of other mostly mesophilic environments [13]. Recently, two non-photosynthetic bacteria related to the Chlorobi phylum were described, - the Ignavibacterium album strain Mat9-16 T [14] and the Melioribacter roseus strain P3M-2 T [15]. The strains were isolated from microbial mats developing in streams of hydrothermal water at Yumata, Japan, and the Tomsk region of PLOS ONE | www.plosone.org 1 January 2013 | Volume 8 | Issue 1 | e53047