Linking Community Profiles, Gene Expression and N-Removal in Anammox Bioreactors Treating Municipal Anaerobic Digestion Reject Water

Park, Hongkeun; Rosenthal, Alex; Ramalingam, K.; Fillos, John; Chandran, Kartik

doi:10.1021/es1002956

Cited by 112 publications

(86 citation statements)

References 42 publications

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“…These results demonstrate that targeting rRNA via RT-qPCR may provide up to 1,000-fold greater sensitivity over corresponding rRNA gene targets. Indeed, the higher sensitivity of RT-qPCR technique compared to qPCR have been reported for quantification of bacteria in natural and engineered systems such as human gut (28), marine sediments and grasslands (50,51), environmental waters (27), and activated sludge processes (21,52). Thus, in our study, the increased detection of fecal bacteria markers via rRNA-based signals suggests that RT-qPCR assays may be better suited for tracking and quantifying active fecal bacteria in environmental waters when the targeted groups are present at relatively low levels.…”

Section: Discussionmentioning

confidence: 99%

Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays

Kapoor

Pitkänen

Ryu

et al. 2015

Appl Environ Microbiol

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The identification of fecal pollution sources is commonly carried out using DNA-based methods. However, there is evidence that DNA can be associated with dead cells or present as "naked DNA" in the environment. Furthermore, it has been shown that rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) assays can be more sensitive than rRNA gene-based qPCR assays since metabolically active cells usually contain higher numbers of ribosomes than quiescent cells. To this end, we compared the detection frequency of host-specific markers and fecal bacteria using RNA-based RT-qPCR and DNA-based qPCR methods for water samples collected in sites impacted by combined sewer overflows. As a group, fecal bacteria were more frequently detected in most sites using RNA-based methods. Specifically, 8, 87, and 85% of the samples positive for general enterococci, Enterococcus faecalis, and Enterococcus faecium markers, respectively, were detected using RT-qPCR, but not with the qPCR assay counterpart. On average, two human-specific Bacteroidales markers were not detected when using DNA in 12% of the samples, while they were positive for all samples when using RNA (cDNA) as the template. Moreover, signal intensity was up to three orders of magnitude higher in RT-qPCR assays than in qPCR assays. The human-specific Bacteroidales markers exhibited moderate correlation with conventional fecal indicators using RT-qPCR results, suggesting the persistence of nonhuman sources of fecal pollution or the presence of false-positive signals. In general, the results from this study suggest that RNA-based assays can increase the detection sensitivity of fecal bacteria in urban watersheds impacted with human fecal sources. Sewage overflows and stormwater runoff introduce high levels of fecal bacteria into surface waters and are considered the primary cause of water quality impairments in urban watersheds, particularly those affected by combined sewer overflows (CSOs) (1, 2). Sewage contamination of surface waters poses a serious risk to human and environmental health via waterborne disease outbreaks (3-5), deterioration of recreational and drinking water quality (6, 7), and degradation of aquatic ecology (8, 9). Hence, identifying the primary source(s) of fecal contamination is imperative to enable best management practices for mitigating pollution and public health risks.Microbial source tracking (MST) methods targeting fecal bacteria have recently been used to identify the sources of fecal contamination impacting water systems (10, 11). Many of these MST methods are based on quantitative PCR (qPCR) assays targeting the bacterial rRNA genes present within water DNA extracts (12, 13). However, the value of DNA-based monitoring in microbial ecology studies is limited by the possibility of DNA being associated with dead cells or the extent to which "naked DNA" may survive in the environment once bacteria are lysed (14-16). These facts pose a significant challenge to the environmental fate and transport of fecal bacteria which are often assess...

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Section: Discussionmentioning

confidence: 99%

Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays

Kapoor

Pitkänen

Ryu

et al. 2015

Appl Environ Microbiol

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“…38 Similar parallels between activity and gene expression are not restricted to AOB and also hold for yeast, anammox, and some heterotrophic bacteria. 39,40 Based on these results, our initial expectation of stable higher emissions from partial nitrification was not entirely satisfied, likely due to the mitigating effect of microbial adaptation at the metabolic, ecological, and gene expression scales. Nevertheless, partial nitrification reactors still have a higher propensity for N 2 O emissions, which municipalities and wastewater utilities need to consider during selection and optimization of low-energy process alternatives for N-removal from centrate or reject water streams.…”

Section: Articlementioning

confidence: 97%

Comparison of Partial and Full Nitrification Processes Applied for Treating High-Strength Nitrogen Wastewaters: Microbial Ecology through Nitrous Oxide Production

Ahn

Kwan

Chandran

2011

Environ. Sci. Technol.

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125

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The increasing regulatory demands to achieve greater nutrient removal from wastewater treatment plant effluents, while minimizing infrastructure investments and operating costs, has resulted in the development of several innovative biological nitrogen removal (BNR) processes. Partial nitrification based processes such as the single reactor system for high ammonium removal over nitrite (SHARON 1 ) and its variants are attractive for treating high-strength nitrogen waste streams such as anaerobic digestion reject water or centrate, owing to their reduced consumption of energy (for aeration) and organic carbon (for denitrification). Indeed, separate treatment of centrate via partial nitrification is one of the options for limiting nitrogen discharges to Jamaica Bay in New York City 2 and is part of PlaNYC, a sustainability plan for New York City targeted for 2030.The energy and carbon savings of partial nitrification processes for nitrogen removal are by virtue of restricting ammonia oxidation to nitrite rather than to nitrate. On the other hand, nitrite is a known trigger for nitrous oxide (N 2 O) and nitric oxide (NO) production via nitrification 3,4 and denitrification 5,6 pathways. Full-scale measurements also point to nitrite as a factor in N 2 O production.7,8 Low (but not zero) dissolved oxygen concentrations were initially implicated as a significant factor for N 2 O and NO emissions from nitrification.9-11 However, the production of N 2 O by nitrifying bacteria under aerobic conditions has also been shown. 3,4,12,13 Recent reports suggest that N 2 O and NO emissions by ammonia oxidizing bacteria are related to imbalances in their metabolism and gene-expression patterns. 14,15 Given that the greenhouse impact of N 2 O is about three hundred times that of carbon dioxide 16 and both N 2 O and NO contribute to ozone layer depletion, 17 it needs to be determined whether N-removal processes based on transient nitrite accumulation are systematically greater contributors of N 2 O and NO than full nitrification based processes. The mechanisms of such differential N 2 O production from partial and full-nitrification systems at the microbial level also need to be understood. Therefore, the overarching goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N 2 O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. It was hypothesized that operation in partial nitrification mode would result in higher N 2 O and NO emissions than operation in full nitrification mode. It was additionally hypothesized that the high emissions of the gases would parallel the sustained elevated expression of the genes coding for their production. ABSTRACT: The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N 2 O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) g...

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“…Frequent appearance and development of Chlorobi-like filamentous bacteria in ANAMMOX reactors, was also reported by Li et al [9]. The relation between the filamentous bacteria and ANAMMOX seed could be typically linked to unconfirmed metabolic connection with the involvement of the filamentous bacteria in bestowing structural integrity to the ANAMMOX in both granular and biofilm phase [11,69].…”

Section: Molecular Signaturesmentioning

confidence: 52%

“…A number of specific sequences and primers were developed to amplify the 16S rRNA from the environmental and enrichment samples using the PCR based approach or by FISH analysis, as detailed in 5.2.2 [4,11,37,69].…”

Section: Molecular Signaturesmentioning

confidence: 99%

State of The Art Strategies for Successful ANAMMOX Startup and Development: A Review

Suneethi¹,

S²,

Joseph³

2014

Int J Waste Resources

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ANAMMOX (Anaerobic ammonium oxidation) bacteria, leading proponent of autotrophic ammonia removal, requires dedicated enrichment and cultivation techniques due to its slow growth rate and low biomass yield. Sensitivity to inhibitory concentrations of NO 2 --N, O 2 etc., often present in industrial effluents makes ANAMMOX startup difficult to achieve. In this paper, significant parameters for ANAMMOX startup and development such as source of seed, type of reactors used, one and two stage ANAMMOX process, operational strategies and experimental conditions promoting long term enrichment, cultivation and quantitative analysis with biomass retention are discoursed in detail. Key chemical and molecular signatures including NO 2 --N, Alkalinity, O 2 , Polymerase chain reaction (PCR), Fluorescence in situ hybridization (FISH), Scanning electron microscopy (SEM), inhibitors and affinity factors for ANAMMOX activity are deliberated. Summary of state of the art on ANAMMOX enrichment, recommendations for future research with specific contributions of this paper to scientific community is brought out in conclusion. State of The

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Linking Community Profiles, Gene Expression and N-Removal in Anammox Bioreactors Treating Municipal Anaerobic Digestion Reject Water

Cited by 112 publications

References 42 publications

Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays

Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays

Comparison of Partial and Full Nitrification Processes Applied for Treating High-Strength Nitrogen Wastewaters: Microbial Ecology through Nitrous Oxide Production

State of The Art Strategies for Successful ANAMMOX Startup and Development: A Review

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