title: Responses of denitrifying bacterial communities to short-term waterlogging of soils.
abstract: Agricultural soil is often subjected to waterlogging after heavy rainfalls, resulting in sharp and explosive increases in the emission of nitrous oxide (N2O), an important greenhouse gas primarily released from agricultural soil ecosystems. Previous studies on waterlogged soil examined the abundance of denitrifiers but not the composition of denitrifier communities in soil. Also, the PCR primers used in those studies could only detect partial groups of denitrifiers. Here, we performed pyrosequencing analyses with the aid of recently developed PCR primers exhibiting high coverage for three denitrification genes, nirK, nirS, and nosZ to examine the effect of short-term waterlogging on denitrifier communities in soil. We found that microbial communities harboring denitrification genes in the top 5 cm of soil distributed according to soil depth, water-soluble carbon, and nitrate nitrogen. Short-term waterlogging scarcely affected abundance, richness, or the alpha-diversities of microbial communities harboring nirK, nirS, and nosZ genes, but significantly affected their composition, particularly in microbial communities at soil depths of 0 to 1 cm. Our results indicated that the composition of denitrifying microbial communities but not the abundance of denitrifiers in soil was responsive to short-term waterlogging of an agricultural soil ecosystem.
authors.affiliation: Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki, 305-8604, Japan. ywangbioinfo@gmail.com.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Uchida
authors.affiliation: Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.|Kyodo Milk Industry Co., Ltd, 20-1, Hirai, Hinode, Nishitama, Tokyo, 190-0182, Japan.
authors.forename: Yumi
authors.initials: Y
authors.lastname: Shimomura
authors.affiliation: Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Akiyama
authors.affiliation: Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 3-1-3, Kannondai, Tsukuba, Ibaraki, 305-8604, Japan. hayatsu@affrc.go.jp.
authors.forename: Masahito
authors.initials: M
authors.lastname: Hayatsu
mesh_terms: D001426:Bacterial Proteins; D058440:Denitrification; D064307:Microbiota; D009572:Nitrite Reductases / Q000378:metabolism; D009609:Nitrous Oxide / Q000032:analysis / Q000378:metabolism*; D011891:Rain; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D012987:Soil; D009572:Nitrite Reductases; D009609:Nitrous Oxide