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Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

ABSTRACT: The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7078480 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

Yang Yuchun Y Daims Holger H Liu Yang Y Herbold Craig W CW Pjevac Petra P Lin Jih-Gaw JG Li Meng M Gu Ji-Dong JD

mBio 20200317 2

The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and <i>in situ</i> transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surpri ...[more]

PMID: 32184251

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Project description:The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.

Project description:The aim of the study was enrichment of nitrifying bacteria and to investigate the potential of autotrophic fixed-film and hybrid bioreactors to treat high strength ammonia wastewater (up to 1,000 mg N/L). Two types of fixed-film systems [moving bed biofilm reactor (MBBR) and BioCordTM] in two different configurations [sequencing batch reactor (SBR) and a continuous stirred tank reactor (CSTR)] were operated for 306 days. The laboratory-scale bioreactors were seeded with activated sludge from a municipal wastewater treatment plant and fed synthetic wastewater with no organics. Strategies for acclimation included biomass reseeding (during bioreactor start-up), and gradual increase in the influent ammonia concentration [from 130 to 1,000 mg N/L (10% every 5 days)]. Stable ammonia removal was observed up to 750 mg N/L from 45 to 145 days in the MBBR SBR (94-100%) and CSTR (72-100%), and BioCordTM SBR (96-100%) and CSTR (92-100%). Ammonia removal declined to 87% ± 6, in all bioreactors treating 1,000 mg N/L (on day 185). Following long-term operation at 1,000 mg N/L (on day 306), ammonia removal was 93-94% in both the MBBR SBR and BioCordTM CSTR; whereas, ammonia removal was relatively lower in MBBR CSTR (20-35%) and BioCordTM SBR (45-54%). Acclimation to increasing concentrations of ammonia led to the enrichment of nitrifying (Nitrosomonas, Nitrospira, and Nitrobacter) and denitrifying (Comamonas, OLB8, and Rhodanobacter) bacteria [16S rRNA gene sequencing (Illumina)] in all bioreactors. In the hybrid bioreactor, the nitrifying and denitrifying bacteria were relatively more abundant in flocs and biofilms, respectively. The presence of dead cells (in biofilms) suggests that in the absence of an organic substrate, endogenous decay is a likely contributor of nutrients for denitrifying bacteria. The nitrite accumulation and abundance of denitrifying bacteria indicate partial denitrification in fixed-film bioreactors operated under limited carbon conditions. Further studies are required to assess the contribution of organic material produced in autotrophic biofilms (by endogenous decay and soluble microbial products) to the overall treatment process. Furthermore, the possibility of sustaining autotrophic nitrogen in high strength waste-streams in the presence of organic substrates warrants further investigation.

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Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

Publications

Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.

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