Diversity and abundance of comammox bacteria in the sediments of an urban lake

Xu, Yangfan; Lü, Junchang; Liu, Guanglong; Wan, Xiaoliang; Yue, Hua; Zhu, Duanwei; Zhao, Jin

doi:10.1111/jam.14593

Cited by 33 publications

(12 citation statements)

References 57 publications

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“…For example, a study of multiple groundwater-fed sand filters recovered 12 comammox MAGs (5 clade A and 7 clade B) and revealed the co-occurrence of at least five comammox species (10 on average) per system (34). Other studies in soils, sediments, lakes, drinking water, groundwater, and estuaries have also reported the co-existence of multiple comammox species (9,73,93,94 while the three systems in this study have influent ammonia concentrations between 2 and 3 mM.…”

Section: Microdiversity Of Nitrifying Bacteriamentioning

confidence: 99%

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster

Cotto¹,

Vilardi²,

Huo

et al. 2022

Preprint

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Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare population-level (i.e., species) diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether these observations were consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that while Nitrosomonas-like bacteria exhibited higher population-level diversity, the effective microdiversity of most Nitrospira-like bacteria were comparatively higher except for one Nitrospira Lineage II population. Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between comammox bacterial MAGs (93%) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73%) and the Nitrospira-like nitrite oxidizer MAGs (75), suggesting that the same comammox population was detected in all systems. Comammox bacteria and some ammonia oxidizers MAGs were significantly less microdiverse than most ammonia and nitrite oxidizers. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.

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Section: Microdiversity Of Nitrifying Bacteriamentioning

confidence: 99%

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster

Cotto¹,

Vilardi²,

Huo

et al. 2022

Preprint

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show abstract

“…In addition, OTU 7 and OTU 124 in the same lineage (clade A.1) had high homology with the sequences of comammox Nitrospira from wetland soil of Qinghai-Tibetan plateau and lake sediment, respectively 9 , 48 . The sequences of OTU 49, OTU 44, and OTU 11 in clade A.2 had high homology with the sequences of comammox Nitrospira from estuary tidal flat wetland, alpine glacier-forefield soil and lake sediment, respectively 10 . The sequences of OTU 4 in clade B had high similarity with the sequences of comammox Nitrospira from forest soils (> 95%, 1000 replicates) 57 .…”

Section: Discussionmentioning

confidence: 91%

“…Many studies have revealed a wide existence of comammox Nitrospira in freshwater and terrestrial ecosystems such as basin 9 , lake 10 , riparian ecosystem 11 , coastal wetland 12 , agricultural soil 13 , and forest soil 14 . Comammox Nitrospira have also been found in engineering environments including drinking water systems 6 , 15 , wastewater treatment systems 16 , 17 and activated sludge 18 .…”

Section: Introductionmentioning

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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“…In the Rifle soils, AOA was 3.8‐ to 10.5‐fold higher than comammox Nitrospira , as revealed through metagenomic studies [13,91]. Three species of clade A comammox Nitrospira were detected from urban lake sediments in China, This study demonstrates the role of comammox bacteria in the nitrification of the urban lake and the inverse relationship between the growth of comammox and eutrophication [92]. For better management of the nitrification process, it is necessary to know the ecophysiological parameters that are controlling the function of comammox Nitrospira .…”

Section: Ecophysiologymentioning

confidence: 89%

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

et al. 2021

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The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammoniaoxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

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Diversity and abundance of comammox bacteria in the sediments of an urban lake

Cited by 33 publications

References 57 publications

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster

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

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

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