Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

Xu, Shaoyi; Wang, Baozhan; Li, Yong; Jiang, Daqian; Zhou, Yuting; Ding, Aqiang; Zong, Yuxiao; Xin, Ling; Zhang, Senyin; Lü, Huijie

doi:10.1016/j.scitotenv.2019.135684

Cited by 120 publications

(65 citation statements)

References 49 publications

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“…Here, comammox Nitrospira amoA sequences obtained from the estuarine tidal flat wetland of China were affiliated with those previously identified in terrestrial sources from China ( Yu et al, 2018 ; Zhao et al, 2019 ). Comammox Nitrospira clade A1 mainly found in fresh water, and engineered ecosystems ( Pjevac et al, 2017 ; Zhao et al, 2019 ) was more abundant and widely distributed than clade A2 that mainly occupies agriculture soils ( Xu et al, 2020 ). The lower abundance of comammox Nitrospira clade B compared comammox Nitrospira clade A observed in this study was also in line with previous studies ( Pjevac et al, 2017 ; Xu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…Comammox Nitrospira clade A1 mainly found in fresh water, and engineered ecosystems ( Pjevac et al, 2017 ; Zhao et al, 2019 ) was more abundant and widely distributed than clade A2 that mainly occupies agriculture soils ( Xu et al, 2020 ). The lower abundance of comammox Nitrospira clade B compared comammox Nitrospira clade A observed in this study was also in line with previous studies ( Pjevac et al, 2017 ; Xu et al, 2020 ). Overall, this indicates that the main source of comammox Nitrospira in the estuarine tidal flat wetland ecosystem is upstream river runoff input with only minor contributions from soil and sediments (clade A2 and clade B).…”

Section: Discussionmentioning

confidence: 99%

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Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

et al. 2020

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Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 5.19 × 10 3 to 8.33 × 10 4 copies/g, 2.21 to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene ( amoA ) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira , whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

et al. 2020

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“…However, reported that the abundance of comammox bacteria was positively related to the amount of N fertilizer along a fertilization gradient in soil, and the two monophyletic clades (clade A and clade B) showed opposite responses to nutrient input. Recent studies also suggested the distinct distribution of clade A and clade B in different environments (Xia et al, 2018;Xu S. et al, 2020), which might be determined by multiple environmental factors (Hu and He, 2017;Shi et al, 2018;Roots et al, 2019;.…”

Section: Introductionmentioning

confidence: 99%

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary

Wang

Zhou

et al. 2021

Front. Microbiol.

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The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.

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“…Comparison of the bacterial OTUs shared among CK and three environmental materials at nine levels showed that the unique OTUs of different treatments in CK, E1, E2, E3, E4, E5, E6, E7, E8, and E9 were 20,19,21,21,24,15,18,18,21, and 12 respectively. The hierarchical clustering analysis showed strong similarities between CK, E1, and E5, and the bacterial communities of E2, E3, and E7.…”

Section: Fig 3 Hierarchical Clustering Tree Of the Bacterial Communmentioning

confidence: 99%

“…Although there are many studies on the improvement of surface soils with amendments, it is rare to improve the poor soils, such as guest soils for ex-situ remediation and deep tillage for in-situ remediation [16][17][18]. At the same time, little research has been done on the combination of humic acid, super absorbent polymer and biochar to improve soil and examine the relationship of these materials with the microbial community response [19][20][21].…”

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confidence: 99%

Responses of Low-Quality Soil Microbial Community Structure and Activities to Application of a Mixed Material of Humic Acid, Biochar, and Super Absorbent Polymer

Li¹,

Men²,

Zhang³

et al. 2020

J. Microbiol. Biotechnol.

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Low-quality soil with little human disturbance is used in mine soil reclamation in China, such as in deep tillage and soil replacement operations [1]. However, it has extreme texture with high density, low porosity, low water capacity, and poor fertilizer conservation [2]. The low-quality of guest soil is closely related to soil microbial diversity and activity [3, 4]. In recent years, more attention has been paid to the use of organic materials like humic acid, biochar, and super absorbent polymer for mine soil reclamation. Humic acid could effectively improve the physical, chemical, and biological properties of soil and promote plant growth. Maji et al. [5] found that humic acid could promote plant growth and increase available nutrient content, while dry weight increased 59.49% as compared to control. Super absorbent polymer could increase soil water retention, which could in turn promote fertilizer conservation, improve plant supply capacity, and increase crop yield [6, 7]. Moreover, super absorbent polymers with high water absorption and water retention ability could also promote aggregate formation [8]. Biochar application in soil is beneficial for carbon (C) sequestration, soil fertility, and ecosystem functioning [9, 10]. Lehmann et al. [11] and Zhu et al. [12] found that the addition of biochar benefited soil microorganisms that play important roles in soil nutrient cycling, carbon exchanges, soil buffering capacity, and soil ecosystem stability. A recent study showed that biochar could improve soil microbial activity, nutrient availability, and plant growth in arid soil [13]. Madhavi et al. [14] found that the combined application of humic acid, biochar, and some chemical fertilizers could significantly enhance acid phosphatase activity. Microorganisms regulate several characteristics like soil organic matter, soil nutrient cycle, soil ecosystem Low-quality soil for land reuse is a crucial problem in vegetation quality and especially to waste disposal sites in mining areas. It is necessary to find suitable materials to improve the soil quality and especially to increase soil microbial diversity and activity. In this study, pot experiments were conducted to investigate the effect of a mixed material of humic acid, super absorbent polymer and biochar on low-quality soil indexes and the microbial community response. The indexes included soil physicochemical properties and the corresponding plant growth. The results showed that the mixed material could improve chemical properties and physical structure of soil by increasing the bulk density, porosity, macro aggregate, and promote the mineralization of nutrient elements in soil. The best performance was achieved by adding 3 g•kg-1 super absorbent polymer, 3 g•kg-1 humic acid, and 10 g•kg-1 biochar to soil with plant total nitrogen, dry weight and height increased by 85.18%, 266.41% and 74.06%, respectively. Physicochemical properties caused changes in soil microbial diversity. Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae,...

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Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

Cited by 120 publications

References 49 publications

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary

Responses of Low-Quality Soil Microbial Community Structure and Activities to Application of a Mixed Material of Humic Acid, Biochar, and Super Absorbent Polymer

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