Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants

Wang, Dan Qi; Zhou, Chen Hao; Nie, Ming; Gu, Ji Dong; Quan, Zhe

doi:10.1016/j.scitotenv.2021.144993

Cited by 49 publications

(36 citation statements)

References 48 publications

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“…Kinetic and genomic studies showed that comammox Nitrospira was more likely to grow in microaerobic and oligotrophic environments 23 , 24 . Moreover, comammox Nitrospira also exhibited a preference for slightly alkaline environments 53 . In this study, the α-diversity indices of comammox Nitrospira community (either Chao1 index and Observed Species index representing species richness, or Shannon index and 1/Simpson index representing diversity) showed a significant negative correlation with sediment NH 4 + -N content ( P < 0.05, Fig.…”

Section: Discussionmentioning

confidence: 99%

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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Section: Discussionmentioning

confidence: 99%

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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“…Additionally, the absence of comammox Nitrospira in saltwater aquarium biofilters reflects results from other studies showing that comammox Nitrospira are not found within marine environments. Although comammox Nitrospira have been identified in brackish, salt marsh, and estuarine environments (42, 43), it seems that the role of autotrophic ammonia oxidation is occupied by AOA and AOB in fully marine environments, including home marine aquaria.…”

Section: Discussionmentioning

confidence: 99%

“…Although comammox Nitrospira have been identified in brackish, salt marsh, and estuarine environments (42,43), it seems that the role of autotrophic ammonia oxidation is occupied by AOA and AOB in fully marine environments, including home marine aquaria.…”

Section: Abundance Of Ammonia Oxidizers Within Aquarium Biofiltersmentioning

confidence: 99%

Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

McKnight

Neufeld

2021

Preprint

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Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

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“…The tidal cycles in coastal wetlands result in alternating aerobic and anaerobic conditions, which may create an ideal habitat for comammox Nitrospira due to their preference for microaerophilic environments [18,19]. Previous studies reported that the abundance of comammox Nitrospira was similar to or even higher than that of AOA and AOB in some coastal wetlands [7,20]. Despite these efforts [20][21][22], however, niche specialization and environmental determinants of comammox Nitrospira in coastal wetlands remain less understood.…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies reported that the abundance of comammox Nitrospira was similar to or even higher than that of AOA and AOB in some coastal wetlands [7,20]. Despite these efforts [20][21][22], however, niche specialization and environmental determinants of comammox Nitrospira in coastal wetlands remain less understood.…”

Section: Introductionmentioning

confidence: 99%

Plant Species–Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland

Lin

et al. 2022

Microb Ecol

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Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

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Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants

Cited by 49 publications

References 48 publications

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

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

Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

Plant Species–Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland

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