Degenerate PCR primers for assays to track steps of nitrogen metabolism by taxonomically diverse microorganisms in a variety of environments

Keeley, Ryan F.; Rodríguez-González, Laura; Class, U.S.F. Genomics; Briggs, Gemma E.; Frazier, Victoria E.; Mancera, Paola A.; Manzer, Haider S; Ergas, Sarina J.; Scott, Kathleen M.

doi:10.1016/j.mimet.2020.105990

Cited by 8 publications

(2 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The nxrB gene is a key gene involved in nitrite oxidation and works with amoA to complete the nitrification reaction [25]. In this study, nxrB in WD and CY exhibited a synergistic trend with that of amoA, which might be caused by the synergistic changes in ammonia-oxidizing bacteria and nitrite-oxidizing bacteria [58].…”

Section: Correlations Between Nitrogen Cycling Genes and Environmenta...mentioning

confidence: 61%

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Shan,

Du,

et al. 2024

JMSE

View full text Add to dashboard Cite

Industrial farming is one of the main farming systems used for L. vannamei, and it is also the main direction of development in the future. To investigate the role of the bacterial community in nitrogen transformation in industrial L. vannamei farming systems, we studied the concentration of nitrogen compounds, the bacterial community using 16S rRNA sequencing, and nitrogen cycling genes’ abundance using absolute quantitative PCR in aquaculture water (using seawater (WD) and groundwater mixed with seawater (CY)) and analyzed the correlations between them using a person analysis. The results showed that the bacterial α-diversity index (ACE, Shannon, and Sobs) significantly changed during culture in WD but not in CY. Bacterial community species composition analysis and linear discriminant analysis effect size (LEfSe analysis) revealed that Cyanobiaceae and Microbacteriaceae were the dominant bacteria and biomarkers in WD. Vibrionaceae, Ateromonadaceae, Microbacteriaceae, Saprospiraceae, and Cryomorphaceae were the dominant bacteria and biomarkers in CY. A functional annotation of procaryotic taxa (FAPROTAX) analysis revealed that the bacterial community in WD exhibited a greater phototrophic activity at early culture stages, while at the same stage, CY exhibited strong nitrate reduction. A correlation analysis of nitrogen cycling genes and environmental factors revealed that napA, narG, ureC, amoA, and nirK were significantly correlated with the concentrations of total ammonia nitrogen (TAN), nitrite (NO2−-N), nitrate (NO3−-N), and total nitrogen (TN) in WD. In CY, amoA was positively correlated and napA and nirK were negatively correlated with TAN and TN concentrations. A correlation analysis between bacterial abundance and environmental factors revealed that Flavobacteriaceae, Saprospiraceae, Cryomorphaceae, Cyanobiaceae, Halieaceae, and Cyclobacteriaceae were significantly correlated with the concentrations of TAN and NO2−-N. The above results indicated that the bacterial community in industrial shrimp farming systems changed under different conditions, with consequent changes in the abundance of genes being involved in the nitrogen cycle and in this biogeochemical process in the water. Our study facilitates further understanding of microbes and their functions in nitrogen cycling in industrial shrimp farming systems.

show abstract

Section: Correlations Between Nitrogen Cycling Genes and Environmenta...mentioning

confidence: 61%

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Shan,

Du,

et al. 2024

JMSE

View full text Add to dashboard Cite

show abstract

“…Excessive reactive nitrogen contents from industrial, agricultural and domestic sewage activities caused an unprecedented increase in the water with negative effects on the aquatic species, human health and ecological environments (Keeley et al, 2020;Ksenofontov, 2020). Therefore, the elimination of active nitrogen in wastewater is essential and urgent due to these adverse effects.…”

Section: Introductionmentioning

confidence: 99%

Enhanced Nitrogen Removal of Wastewater at Low Temperature by Iterative Screening of Cold-Tolerant Denitrifying Bacteria

Jin

Zheng

Zhao³

et al. 2021

Preprint

View full text Add to dashboard Cite

The biological denitrification for wastewater treatment in winter is often seriously compromised due to the effects of low-temperature (<13 °C) on metabolic activity of microorganism. In this study, an excellent cold-tolerant denitrifying bacterium, Moraxella osloensis LT-01 was isolated by iterative domestication. The strain LT-01 retained about 60% maximal growth activity at 10 °C. Under initial concentrations of 100 mg/L, average ammonium, nitrate and nitrite removal efficiencies for domestic wastewater (C/N 4:1) at 10 °C were 70.35%, 65.39% and 61.74% in 24 h, respectively. Nitrogen balance analysis showed that about 46% of TN was directed toward in the dissimilation form of gas, and 16% of TN was assimilated for cell growth. Key genes hydroxylamine reductase gene (HAO) and nitrite reductase (NirS) involved in nitrification and denitrification processes were identified by gene-specific PCR, indicating that strain LT-01 perform nitrogen removal efficiently via unique simultaneous nitrification and denitrification. These results suggest the bacterium LT-01 has great potential as an effective performer for treating domestic wastewater in winter.

show abstract

Chlorine conversion impact on activated carbon block filters: Water quality and nitrification risk in chloraminated water

Jakpa,

Alfredo

2024

AWWA Water Science

View full text Add to dashboard Cite

The effectiveness of a periodic free chlorine conversion period (FClP) as a nitrification mitigation measure has been scrutinized in chloraminated distribution systems, and knowledge about the response of activated carbon block (ACB) point‐of‐use (POU) filters to this practice is unknown. In this study, three similar filters were monitored bracketing three successive FClPs in the laboratory, aimed at studying the response of ACB POU filters to FClP and the occurrence of nitrification. Results indicate that stagnating filters fostered biofilm growth and increased nitrite concentration (2.5 mg/L‐N) above the EPA maximum contaminant level (MCL). Despite FClP being effective at mitigating nitrification and reducing nitrite concentration far below EPA MCL, this was only temporary. Filters that were microbially seeded before an FClP event re‐nitrified immediately after chloramination resumed. Successive FClPs induced a microbial community change and failed at controlling nitrification, resulting in elevated nitrite and microbial exposure.

show abstract

Degenerate PCR primers for assays to track steps of nitrogen metabolism by taxonomically diverse microorganisms in a variety of environments

Cited by 8 publications

References 54 publications

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Enhanced Nitrogen Removal of Wastewater at Low Temperature by Iterative Screening of Cold-Tolerant Denitrifying Bacteria

Chlorine conversion impact on activated carbon block filters: Water quality and nitrification risk in chloraminated water

Contact Info

Product

Resources

About