Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Coyotzi, Sara; Doxey, Andrew C.; Clark, Ian D.; Lapen, David R.; Cappellen, Philippe Van; Neufeld, Josh D.

doi:10.1111/1462-2920.13643

Cited by 59 publications

(39 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…nirK and nirS. This limited coverage has been noted previously (Bonilla-Rosso et al, 2016;Decleyre et al, 2016;Coyotzi et al, 2017). Consistently, 361 nirK nucleotide sequences of Bacteria and Archaea in this study were aligned and clustered into two major clades (Fig.…”

Section: Resultssupporting

confidence: 89%

“…Although some of the existing primers were designed for universal nirK amplification Hallin and Lindgren, 1999;Casciotti and Ward, 2001;Rösch et al, 2002;Chénier et al, 2003;Liu et al, 2003;Henry et al, 2004;Chen et al, 2010), in silico primer tests against the nirK nucleotide sequences indicated that they covered 0.28%-27.4% of the overall nirK sequences (data not shown); they actually only cover clade I (Table 1). This limited coverage has been noted previously (Bonilla-Rosso et al, 2016;Decleyre et al, 2016;Coyotzi et al, 2017). Among all the primers targeting clade I of nirK, nirKC1F/nirKC1R by Wei and colleagues (2015b) had the highest coverage (89.3%, Table 1).…”

Section: Resultsmentioning

confidence: 50%

See 1 more Smart Citation

An evaluation of primers for detecting denitrifiers via their functional genes

Zilles

Kent

2019

Environmental Microbiology

View full text Add to dashboard Cite

Summary Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio‐environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

show abstract

Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 50%

An evaluation of primers for detecting denitrifiers via their functional genes

Zilles

Kent

2019

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…All these products may be released during denitrification. Reactions are regulated by the enzymes nitrate reductase and nitrite reductase ( Figure 9; Coyotzi et al, 2017). The reactions are carried out by denitrifying bacteria that are widely distributed across the bacterial taxa.…”

Section: Biological Denitrificationmentioning

confidence: 99%

Nitrous oxide emission from agricultural soils

Velthof

Rietra

2018

View full text Add to dashboard Cite

2018. Nitrous oxide emission from agricultural soils. Wageningen, Wageningen Environmental Research, Report 2921. 58 pp.; 23 fig.; 19 tab.; 166 ref. Lachgas (N 2 O) is een broeikasgas met op mondiaal niveau een aandeel van 6% in de emissies van broeikasgassen. Bemeste landbouwgronden zijn een belangrijke bron van N 2 O. Er is een literatuurstudie uitgevoerd naar N 2 O-emissie uit landbouwgronden met focus op de emissie uit verschillende typen kunstmest en de mogelijkheden om de emissie uit kunstmest te beperken. De N 2 O-emissie uit kunstmest draagt voor 0,8% bij aan de totale broeikasgasemissie in Nederland. Uit de literatuur volgt dat toediening van kunstmest onder gemiddelde en relatief droge omstandigheden in de bodem leidt tot een beperkt risico op N 2 O-emissie voor zowel grasland als bouwland. Het risico op N 2 O-emissie neemt toe als nitraathoudende kunstmeststoffen, zoals kalkammonsalpeter en urean, onder natte omstandigheden aan grasland (alle grondsoorten) en bouwland (met name klei-en veengrond) worden toegediend. Het toedienen van een ammoniummeststof (eventueel met nitrificatieremmer) of ureum onder natte omstandigheden of het uitstellen van bemesting van de nitraathoudende kunstmest tot drogere omstandigheden zijn mogelijkheden om N 2 O-emissie te beperken. De zogenaamde 4R-strategie om de benutting van nutriënten uit meststoffen te verhogen, kan ook leiden tot een lagere N 2 O-emissie, namelijk N-toediening met het juiste type, juiste hoeveelheid, juiste tijdstip en juiste plaats.Nitrous oxide (N 2 O) is a greenhouse gas contributing to 6% of the global greenhouse effect. Fertilized agricultural soils are a major source of N 2 O. A literature study on N 2 O emission from agricultural soils was carried out focussing on the effect of different types of mineral nitrogen (N) fertilizers and strategies to mitigate N 2 O emission from fertilizers. The N 2 O emission from mineral N fertilizer application contributes to 0.8% of the total greenhouse gas emission in the Netherlands. The study shows that application of mineral N fertilizer under moderate and relatively dry conditions results in a relatively low risk of N 2 O emission from both grassland and arable land. However, during wet conditions, application of nitrate containing mineral fertilizers such as (calcium) ammonium nitrate and urean to grasslands (all soil types) and arable crops on clay and peat soils increases the risk of N 2 O emission. To decrease the risk of N 2 O emission during wet conditions, an ammonium based fertilizer (possibly with a nitrification inhibitor) or urea can be used. Alternatively, the application of nitrate based fertilizer should be postponed until drier periods. The 4R strategy to increase nutrient use efficiency of fertilizers will also reduce N 2 O emission, i.e., N application with the Right type, at the Right rate, at the Right time, and in the Right place.

show abstract

“…Targeted amplicon sequencing of 13 C-enriched DNA provides phylogenetic information about populations of interest ( Neufeld et al, 2007 ). When combined with functional information, DNA-SIP informs the understanding of resource availability and allocation in complex environments ( Li et al, 2011 ; Coyotzi et al, 2017 ). Isothermal calorimetry combined with 13 C-SIP has the potential to provide valuable insight into the simultaneous identity of active members and physiology of the microbial communities, enabling greater understanding of the role community composition plays in soil C dynamics.…”

Section: Introductionmentioning

confidence: 99%

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use

2017

View full text Add to dashboard Cite

Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with 13C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.

show abstract

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Cited by 59 publications

References 99 publications

An evaluation of primers for detecting denitrifiers via their functional genes

An evaluation of primers for detecting denitrifiers via their functional genes

Nitrous oxide emission from agricultural soils

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use

Contact Info

Product

Resources

About