Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

doi:10.1264/jsme2.me13066

Cited by 32 publications

(20 citation statements)

References 65 publications

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“…5a; see also Table S5 in the supplemental material). Although the sequences affiliated with this marine AOA-associated lineage have been obtained from neutral or only slightly acidic environments (43)(44)(45), the evidence directly linking this group to ammonia oxidation was missing. Thus, a greater physiological versatility of this marine lineage was observed in this study, despite reduced labeling compared to that of AOA associated with soil group 1.1b.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

Zhao

Wang

Jia

2015

Appl Environ Microbiol

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Paddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using highthroughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaeal amoA gene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance of Nitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), and Nitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of 13 C-labeled DNA further revealed that 13 CO 2 was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA and Nitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated with Nitrosospira sp. strain L115 and the Nitrosospira multiformis lineage and that the 13 C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic "Candidatus Nitrososphaera gargensis," uncultured fosmid 29i4, and acidophilic "Candidatus Nitrosotalea devanaterra" lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields. Rice feeds over half of the world's population and is usually considered the most important food source in Asia (1). China has approximately 29.2 million ha of rice fields, accounting for 35.8% of the grain-sowing area (2, 3). China is indeed the largest producer of rice on the planet, and the yield production of rice accounts for 43.7% of the total national grain production (4). The growth and production of rice crops depend heavily on anthropogenic management such as irrigation and fertilization. The intensified application of synthetic N fertilizers has increased significantly over the past decades to meet the demand for food productivity in China (5). The excessively high load often leads to the saturation of nitrogen nutrients in paddy soils and causes severe environmental pollution (6).Flood management is the most dominant regime for growing semiaquatic rice plants (7). Irrigated paddy fields thus may serve as a model system for studying the microbial ecology of nitrifying communities in terrestrial environments (8). Nitrification is executed by functional microbial guilds, including ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively), as well as nitrite-oxidizing bacteria...

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Section: Discussionmentioning

confidence: 99%

Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

Zhao

Wang

Jia

2015

Appl Environ Microbiol

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“…The distribution of sediment ammonia-oxidizing archaeal and bacterial populations has been investigated in a variety of freshwater ecosystems, such as river (Reis et al 2015;Sonthiphand et al 2013;Sun et al 2013;Xie et al 2014), reservoir , lake (Bollmann et al 2014;Hou et al 2013;Liu et al 2015;Mukherjee et al 2016;Zhao et al 2013Zhao et al , 2014, wetland (Liu et al 2014a;Wang et al 2013;Yang et al 2014), and pond (Lu et al 2015), yet the relative importance of AOA and AOB to nitrification process in freshwater sediments remains under debate. Several previous studies indicated that AOA amoA gene abundance was usually greater than AOB in lake sediments (Herrmann et al 2009;Hou et al 2013;Zhao et al 2014), while the numerical dominance of AOB over AOA amoA gene abundance was observed in sediments of many freshwater lakes on the Yunnan Plateau (Liu et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake

Yang

Zhao

et al. 2016

Environ Sci Pollut Res

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Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.

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“…pH significantly affected the AOA community in river sediments [20]. Elevated temperature increased AOA abundance, whereas it decreased AOB abundance [30].…”

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confidence: 98%

“…It has been found that AOA dominated in marine sediments [1,17], indicated by its better adaptation to anaerobic, low pH, and low ammonia habitats than AOB [18][19], whereas higher nutrients in the freshwater sediments promoted AOB dominance, such as river sediments [20], mangrove sediments [16,21], and shore side wetlands [22]. Zhao et al [13] found that the abundance of archaeal amoA in lake sediment was higher than bacterial amoA, whereas Moiser and Francis [23] found that bacterial amoA copy numbers were greater than archaeal amoA in most of the estuary.…”

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confidence: 99%