title: Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments.
abstract: Nitrite-oxidizing bacteria (NOB) are chemolithoautotrophs that catalyze the oxidation of nitrite to nitrate, which is the second step of aerobic nitrification. In marine ecosystems, Nitrospina is assumed to be a major contributor to nitrification. To date, two strains of Nitrospina have been isolated from marine environments. Despite their ecological relevance, their ecophysiology and environmental distribution are understudied owing to fastidious cultivation techniques and the lack of a sufficient functional gene marker. To estimate the abundance, diversity, and distribution of Nitrospina in various marine sediments, we used nxrA, which encodes the alpha subunit of nitrite oxidoreductase, as a functional and phylogenetic marker. We observed that Nitrospina diversity in polar sediments was significantly lower than that of non-polar samples. Moreover, nxrA-like sequences revealed an unexpected diversity of Nitrospina, with approximately 41,000 different sequences based on a 95% similarity cutoff from six marine sediments. We detected nxrA gene copy numbers of up to 3.57 × 104per gram of marine sediment sample. The results of this study provide insight into the distribution and diversity of Nitrospina, which is fundamentally important for understanding their contribution to the nitrogen cycle in marine sediments.
authors.affiliation: Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
authors.forename: Sundas
authors.initials: S
authors.lastname: Rani
authors.affiliation: Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
authors.forename: Hyeon-Woo
authors.initials: HW
authors.lastname: Koh
authors.affiliation: Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Cheongju, 28644, Republic of Korea.
authors.forename: Sung-Keun
authors.initials: SK
authors.lastname: Rhee
authors.affiliation: Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. fujitani@aoni.waseda.jp.
authors.forename: Hirotsugu
authors.initials: H
authors.lastname: Fujitani
authors.affiliation: Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea. sjpark@jejunu.ac.kr.
authors.forename: Soo-Je
authors.identifier: http://orcid.org/0000-0003-0359-7431
authors.initials: SJ
authors.lastname: Park
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology*; D058465:Nitrification / Q000235:genetics*; D009573:Nitrites / Q000378:metabolism*; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C048879:nitrite dehydrogenase
keywords: Marine sediment; Nitrite-oxidizing bacteria; Nitrospina; Pyrosequencing; nxrA