Distribution, Diversity, and Abundance of Nitrite Oxidizing Bacteria in the Subterranean Estuary of the Daya Bay

Abstract

The oxidation of nitrite to nitrate as the second step of nitrification is vital for the global nitrogen cycle, and the genus Nitrospira is the most widespread nitrite-oxidizing bacteria (NOB) in diverse natural ecosystems. However, our understanding of Nitrospira distribution and their response to dynamic environmental parameters is still limited in the subterranean estuary (STE), a special environment of the mixed zone between land and sea. In this study, Nitrospira communities were collected within 5–10 cm depth intervals of sediments with the physiochemical gradients along the transections of the Daya Bay (DYB) from the landward member to the seaward member. The abundance, community structure of Nitrospira, and their potentially influencing environmental factors were investigated using Q-PCR, the high throughput sequencing targeting Nitrospira nxrB gene, and biostatistics analyses. The abundance of Nitrospira showed uniform distribution along the transections, but significantly decreasing variations were observed from the surface (<20 cm) to the bottom (>20 cm) of sediments. The community diversity and structure of Nitrospira also displayed a remarkable vertical distribution in the DYB (STE), although no significant differences were observed along the transections of STE. Nitrospira marina (N. marina) predominated in the sediments, Candidatus Nitrospira bockiana (Ca. N. bockiana), and Candidatus Nitrospira defluvii (Ca. N. defluvii) were the main Nitrospira species, and Candidatus Nitrospira lenta (Ca. N. lenta) and Nitrospira japonica (N. japonica) also existed with relatively low abundance in the DYB (STE). These findings revealed that Nitrospira species (Ca. N. defluvii, Ca. N. lenta, and N. japonica) derived from activated sludge was also widespread in natural habitats and deduced that the STE may be affected by the pollution derived from terrigenous human activities. The statistical analysis combined with the STE dynamic variation indicated that dissolved organic carbon (DOC), salinity, and ammonium along the sediment depths attributed to the vertical community distribution of the Nitrospira species. In summary, the vertical distribution of Nitrospira and their response to the dynamic physicochemical parameters imply their important role in the nitrite oxidation of the STE and provide insights into the niche differentiation and diversely physiologic metabolism of NOB.

Existence and distribution of novel phylotypes of Nitrospira in water columnsof the South China Sea

“…A steep increase in our knowledge of Nitrospira in various natural and engineered ecosystems has been witnessed with the rapid development of molecular approaches combined with traditional methods ( Watson et al., 1986 ; Lebedeva et al., 2010 ; Ushiki et al., 2013 ; Boris et al., 2015 ; Daims et al., 2016 ; Hong et al., 2021 ; Sun et al., 2022 ). Nitrospira seems to be monophyletic at the phyloevolutionary level, but it consists of six genetic sub-lineages according to the 16S rRNA gene and is the most diversified genus among the known NOB ( Lebedeva et al., 2010 ; Daims et al., 2016 ).…”

“…Nevertheless, all lineages of Nitrospira could not be amplified by the “universal” primers of the 16S rRNA gene ( Hong et al., 2020 ). The phylogenetic features and diversities of functional communities may be investigated by the functional genes as suitable molecular signatures, which code the pivotal units for enzyme catalytic reactions ( Sun et al., 2022 ).…”

“…N. lenta and Ca. N. defluvii were typically found and primarily resided in active sludge of wastewater treatment systems ( Boris et al., 2015 ; Lücker et al., 2010 ), they were generally present in many natural environments, including rivers, universal estuaries, subterranean estuaries (STE), and tropical bays ( Cébron and Garnier, 2005 ; Hou et al., 2018 ; Mao et al., 2020 ; Hong et al., 2021 ; Sun et al., 2022 ). Ca.…”

“…N. marina may be one of the most prevalent NOB species in marine environments ( Watson et al., 1986 ). In recent years, N. marina was reported to be widely distributed in waters of the PRE, sediments of Daya Bay (STE), and intertidal zones of Zhangjiang Bay with many mangrove plants ( Hou et al., 2018 ; Mao et al., 2020 ; Hong et al., 2021 ; Sun et al., 2022 ). The organic matter in STE and Zhanjiang Bay and strong seawater intrusion in the PRE may properly illuminate the wide or dominant distribution of N. marina in these environments ( Hou et al., 2018 ; Mao et al., 2020 ; Hong et al., 2021 ; Sun et al., 2022 ).…”

“…In recent years, N. marina was reported to be widely distributed in waters of the PRE, sediments of Daya Bay (STE), and intertidal zones of Zhangjiang Bay with many mangrove plants (Hou et al, 2018;Mao et al, 2020;Hong et al, 2021;Sun et al, 2022). The organic matter in STE and Zhanjiang Bay and strong seawater intrusion in the PRE may properly illuminate the wide or dominant distribution of N. marina in these environments (Hou et al, 2018;Mao et al, 2020;Hong et al, 2021;Sun et al, 2022). Nevertheless, N. marina-related species accounted for only 1.39% of nxrB sequences in the water columns of the SCS in our study.…”