Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain

Boyang Ji (1) , Sheng-Da Zhang (1) , Pascal Arnoux (2, 3) , Zoe Rouy (4) , François Alberto (1) , Nadège Philippe (5) , Dorothée Murat (1) , Wei-Jia Zhang (1) , Jean-Baptiste Rioux (3) , Nicolas Ginet (3, 1) , Monique Sabaty (2, 3) , Sophie Mangenot (6) , Nathalie Pradel (7) , Jiesheng Tian , Jing Yang (8) , Lichen Zhang (9) , Wenyan Zhang (10) , Hongmiao Pan (10) , Bernard Henrissat (11) , Pedro M Coutinho (11) , Ying Li (12) , Tian Xiao (13) , Claudine Médigue (14) , Valérie Barbe (6) , David Pignol (2, 3) , Emmanuel Talla (1) , Long-Fei Wu (1)

1 LCB - Laboratoire de chimie bactérienne
2 BIAM - Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB)
3 MEM - Microbiologie Environnementale et Moléculaire
4 UMR 8030 - Génomique métabolique
5 LAPM - Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble]
6 IG - Institut de Génomique d'Evry
7 MIO - Institut méditerranéen d'océanologie
8 Institute of Computing Technology
9 CIML - Centre d'Immunologie de Marseille - Luminy
10 Chinese Academy of Sciences [Qingdao]
11 AFMB - Architecture et fonction des macromolécules biologiques
12 SDAU - Shandong Agricultural University
13 IOCAS - CAS Institute of Oceanology
14 INSB-CNRS - Institut des sciences biologiques

Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.

Domains: Life Sciences [q-bio]

Boyang Ji, Sheng-Da Zhang, Pascal Arnoux, Zoe Rouy, François Alberto, et al.. Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain. Environmental Microbiology, 2014, 16 (2), pp.525-544. ⟨10.1111/1462-2920.12180⟩. ⟨hal-02463127⟩