Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

Zhu, Guibing; Wang, Xiaomin; Wang, Shanyun; Yu, Longbin; Armanbek, Gawhar; Yu, Jie; Jiang, Liping; Yuan, Dongdan; Guo, Zhongrui; Zhang, Hanrui; Zheng, Lei; Schwark, Lorenz; Jetten, Mike S. M.; Yadav, Asheesh Kumar; Zhu, Yan

doi:10.1016/j.scitotenv.2022.154590

Cited by 78 publications

(36 citation statements)

References 91 publications

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“…In this study, our phylogenetic tree showed that the comammox bacteria in the sample fell into three branches, namely, comammox clade A.1, comammox clade A.2, and comammox clade B. Comammox clade A was more widely distributed than comammox clade B, but the distribution difference was not signi cant, which might be due to the scouring of the middle and lower reaches of the riverbed and the coarsening of particles, which affects the microbial niche and diversity 13,26 , so that comammox clade A and comammox clade B could coexist in large quantities. Consistently, many studies have also found that comammox clade A is more widely distributed than comammox clade B, and that comammox clade A.1 clades are more widespread than comammox Clade A 10,27 .…”

Section: Comammox Nitrospira Clade Differentiationsupporting

confidence: 62%

Effects of dam building on Niche differentiation of Comammox Nitrospira in the main stream of the Three Gorges Reservoir area

Liu

Zhang

et al. 2022

Preprint

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Comammox Nitrospira can completely oxidize ammonia nitrogen to nitrate, and the various habitats of comammox Nitrospira are an important guarantee for its survival. This study investigated comammox in river sediments in the Three Gorges Reservoir area. Comammox clade A and comammox clade B were detected in all samples, in which comammox clade A was dominant, and the OUTs detected from comammox clade B (14 OTUs) were more than those detected from comammox clade A. 1 (11 OTUs) and comammox clade A.2 (4 OTUs). The abundance of comammox Nitrospira clade A and clade B amoA genes in the main stream of the Three Gorges Reservoir indicated an increasing trend along the river stream, and reached the maximum in the of the reservoir area. The highest abundance of AOA amoA genes appeared in the upper stream section of the reservoir area. Comammox Nitrospira clade A exhibited the highest abundance (3.00×104±8782.37 copies/g), followed by comammox Nitrospira clade B (1.83×103±1019.82 copies/g), AOB (1.28×103±574.69 copies/g), AOA (1.73 ×102±48.05 copies/g). Both the abundances of comammox clade A and B were positively correlated with sediment pH, indicating that pH was an important environmental factor affecting the growth of comammox bacteria. The Mantel test chart indicated that overlying water dissolved oxygen (DO) in the reservoir area had a significant effect on the differentiation of comammox clade A into comammox clade A.1 and comammox clade A.2. This study confirms that the construction of the Three Gorges Dam has an impact on the niche differentiation of comammox Nitrospira in the main stream of the Three Gorges Reservoir area.

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Section: Comammox Nitrospira Clade Differentiationsupporting

confidence: 62%

Effects of dam building on Niche differentiation of Comammox Nitrospira in the main stream of the Three Gorges Reservoir area

Liu

Zhang

et al. 2022

Preprint

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“…The soil oxygen content in the WLF zone, especially in the topsoil, drastically during the floodingexposure period, thus inevitably affecting the growth of CMX NB. Previous studies showed that clade A had higher metabolic diversity than clade B [39], and clade A not only used ammonia as a metabolic substrate but also utilized urea, cyanate, and hydrogen as substrates for nitrification [6,18,40]. However, the evolution rate of ammonia oxidation-related proteins was faster in clade B genomes than in clade A genomes [18].…”

Section: Effect Of Vertical Depth Of Soil On Abundance Of CMX Nbmentioning

confidence: 97%

Vertical niche differentiation of comammox Nitrospira in water-level fluctuation zone of the Three Gorges Reservoir, China

Ding

Zhou

et al. 2022

Environ Sci Eur

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Comammox (CMX) Nitrospira bacteria (NB) can accomplish ammonia oxidation independently, and their niche differentiation holds promise for their ecological and survival functions. In this work, the vertical niche differentiation of CMX NB was investigated in the soils of 6 water-level fluctuation (WLF) zones (both natural and artificial) in the Three Gorges Reservoir (TGR) region. The results demonstrated that the level of clade A amoA was obviously reduced with increasing soil depth in the natural WLF zones and one of the artificial WLF zones. However, in the other two artificial WLF zones, the abundance of this gene was not dramatically reduced with depth. The level of clade B amoA did not markedly decrease with increasing soil depth in most WLF zones and remained stable in the three WLF zones. Total nitrogen (TN) had the most significant effect on the abundance of CMX NB. Clade A.1, clade A.2.1, clade A.2.2, clade A.3, and clade B of CMX NB co-occurred simultaneously in all WLF zones. The number of operational taxonomic units (OTUs) of clade A in the two types of WLF zones first increased and then decreased with increasing depth, whereas the number of OTUs of clade B continuously increased with depth in the artificial WLF zone. Total carbon (TC) and pH, as environmental factors, affected the community structure of CMX NB. This study confirmed the vertical differentiation of the abundance and diversity of CMX NB in the WLF zones of the TGR region, and the artificial restoration of the WLF zones affected the niche differentiation of CMX NB to a certain degree.

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“…Clade A.1 is the main lineage in mudflat sediments 19 , while clade A.2 and clade B are abundant in agricultural soils 20 , 21 . Clade A.1 is more widely distributed than clade A.2 in natural aquatic ecosystems 22 . Moreover, Ca.…”

Section: Introductionmentioning

confidence: 98%

Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

Zhang

Zhao

et al. 2022

Sci Rep

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Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 103 − 5.06 × 104 copies g−1 dry sediment) was higher than that of clade B (6.26 × 102 − 6.27 × 103 copies g−1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 102 − 6.89 × 103 copies g−1 dry sediment) and AOB (1.44 × 102 − 1.46 × 103 copies g−1 dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.

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Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

Cited by 78 publications

References 91 publications

Effects of dam building on Niche differentiation of Comammox Nitrospira in the main stream of the Three Gorges Reservoir area

Effects of dam building on Niche differentiation of Comammox Nitrospira in the main stream of the Three Gorges Reservoir area

Vertical niche differentiation of comammox Nitrospira in water-level fluctuation zone of the Three Gorges Reservoir, China

Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

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