Department of Civil Engineering, Nagaoka National College of Technology, 888 Nishikatakaimachi, Niigata 060-8628, Japan.
Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido 940-8532, Japan.
Environ Microbiol Rep. 2017 Oct;9(5):550-561. doi: 10.1111/1758-2229.12586. Epub 2017 Oct 6.
Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca. S. japonica' genome were detected. Based on the genomic and proteomic data, the core anammox process and carbon fixation of 'Ca. S. japonica' were further investigated. Additionally, the present study provides the first detailed insights into the genetic background responsible for iron acquisition and menaquinone biosynthesis in anammox bacterial cells. Comparative analysis of the 'Ca. Scalindua' genomes revealed that the 1502 genes found in the 'Ca. S. japonica' genome were not present in the 'Ca. S. profunda' and 'Ca. S. rubra' genomes, showing a high genomic diversity. This result may reflect a high phylogenetic diversity of the genus 'Ca. Scalindua'.
厌氧氨氧化（anammox）细菌隶属于浮霉菌属，它们在海洋中的氮损失中起着重要作用，因此其生理生态学具有重要意义。在这里，我们从日本广岛湾沉积物中富集了一种海洋厌氧氨氧化细菌“Ca. S. japonica”，并对其进行了比较基因组和蛋白质组学分析。该细菌的基因组大小为 4.81Mb，包含 4019 个编码基因（CDS），由 47 个连续序列组成。在蛋白质组中，检测到了 4019 个 CDS 中的 1762 个。基于基因组和蛋白质组数据，进一步研究了“Ca. S. japonica”的核心厌氧氨氧化过程和碳固定。此外，本研究首次详细了解了厌氧氨氧化菌细胞中铁获取和甲萘醌生物合成的遗传背景。“Ca. Scalindua”基因组的比较分析表明，在“Ca. S. japonica”基因组中发现的 1502 个基因不存在于“Ca. S. profunda”和“Ca. S. rubra”基因组中，显示出很高的基因组多样性。这一结果可能反映了浮霉菌属的高度系统发育多样性。
