High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Abstract

<jats:title>Abstract</jats:title><jats:p>Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the <jats:italic>Nitrospira</jats:italic> genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of <jats:italic>Nitrospira</jats:italic>, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that <jats:italic>Nitrospira</jats:italic> species strongly dominate RBC biofilm samples and that comammox <jats:italic>Nitrospira</jats:italic> outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox <jats:italic>Nitrospira</jats:italic> with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized <jats:italic>Nitrospira</jats:italic> members. Diverse functional profiles imply a high level of niche heterogeneity among comammox <jats:italic>Nitrospira</jats:italic>, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox <jats:italic>Nitrospira</jats:italic>, suggesting an ability to degrade cyanate, which has not been shown previously for <jats:italic>Nitrospira</jats:italic> that are not strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox <jats:italic>Nitrospira</jats:italic>, and other nitrite oxidizers.</jats:p>

Potential survival strategies of novel comammox and nitrite-oxidizingNitrospirapresent in a reactor treating high-ammonia brackish landfill leachate

“…The relative abundance of AOM in this study was comparable to that in several previous studies reporting that comammox Nitrospira had a lower relative abundance than that of AOA in full-scale WWTPs [14,18,78,79]. On the other hand, there are controversial reports that comammox Nitrospira were dominant in wastewater treatment systems [18,68,[80][81][82]. A unique characteristic of the environment in this study stemmed from the presence of methanol, added as an external electron donor, which was plausibly instrumental in favoring the growth of comammox Nitrospira LAS72.…”

Evaluation of Two Primer Sets for Amplification of Comammox Nitrospira amoA Genes in Wetland Soils

“…They were designed to differentiate between (comaA-244f/659r for) clades A and (comaB-244f/659r for) clade B comammox amoA sequences within the Nitrospira genus ( Table 1), amplifying a comammox amoA gene amplicons with a size of 415 bp at binding regions between positions 244-261 and 643-659 ( Figure 1). This primer set has been used for the detection of comammox amoA genes in nitrification reactors (Roots et al, 2019), agricultural soils (Li et al, 2019;Liu et al, 2019;Wang et al, 2019), wetland (Shah and Wang, 2019), forest soil (Shi et al, 2018) and wastewater treatment plant (Spasov et al, 2019).…”

“…Other newly developed primers only detect a certain fraction of the comammox amoA genes within the clade A (Bartelme et al, 2017;Wang et al, 2018;Xia et al, 2018;Beach and Noguera, 2019;Zheng et al, 2019). Among them, the primer sets of Ntsp-amoA 162F/359R (Fowler et al, 2018) and comaA/B-244f/659r (Pjevac et al, 2017) are the two most widely used primers for studying the environmental distribution of comammox amoA genes (Wang Y. et al, 2017;Fowler et al, 2018;Shi et al, 2018;Roots et al, 2019;Spasov et al, 2019;Wang et al, 2019). An appropriate primer set is crucial for achieving an unbiased representation and efficient assessment of comammox community composition in various environments.…”

Activity-based cell sorting reveals resistance of functionally degenerateNitrospiraduring a press disturbance in nitrifying activated sludge

“…Despite its potential efficacy for supporting mainstream PN, a limited number of studies have further validated the long-term stability of FA-based RAS treatment and assessed its impacts on the structure and activity of the nitrifying microbial community (Duan et al, 2019a;Li et al, 2020). NOB communities in wastewater treatment often display functional degeneracy, wherein the nitrite oxidation process is distributed among several phylogenetically diverse taxa with varying auxiliary metabolic potentials (Daims et al, 2016;Lücker et al, 2015;Spasov et al, 2019). Such degeneracy may enable NOB communities to resist selective pressures imparted by out-selection strategies by recruiting functionally redundant, yet physiologically diverse, NOB members (Duan et al, 2019a;Li et al, 2020;Liu and Wang, 2013).…”