Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification

Journal of Microbiological Methods - Tập 160 - Trang 49-59 - 2019
Jordan Cannon1, Robert A. Sanford2, Lynn Connor3, Wendy H. Yang1,2, Joanne Chee-Sanford3
1Dept. of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
2Dept. of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
3USDA-ARS, Urbana, IL, USA

Tài liệu tham khảo

Aird, 2011, Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries, Genome Biol., 12, R18, 10.1186/gb-2011-12-2-r18 Aklujkar, 2009, The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens, BMC Microbiol., 9, 109, 10.1186/1471-2180-9-109 Baggs, 2011, Soil microbial sources of nitrous oxide: recent advances in knowledge, emerging challenges and future direction, Curr. Opin. Environ. Sustain., 3, 321, 10.1016/j.cosust.2011.08.011 Ben-Dov, 2015, Inosine at different primer positions to study structure and diversity of prokaryotic populations, Curr. Issues. Mol. Biol., 17, 53 Bernard, 2015, Dissimilatory nitrate reduction to ammonium (DNRA) seasonally dominates NO3− reduction pathways in an anthropogenically impacted sub-tropical coastal lagoon, Biogeochemistry., 125, 47, 10.1007/s10533-015-0111-6 Bernhard, 2016, Editorial: linking ecosystem function to microbial diversity, Front. Microbiol., 7 Berthrong, 2014, Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2, Appl. Environ. Microbiol., 80, 3103, 10.1128/AEM.04034-13 Bhowmik, 2017, Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils, AIMS Microbiol., 3, 826, 10.3934/microbiol.2017.4.826 Bonilla-Rosso, 2016, Design and evaluation of primers targeting genes encoding NO-forming nitrite reductases: implications for ecological inference of denitrifying communities, Sci. Rep., 6, 10.1038/srep39208 Bu, 2017, Dissimilatory nitrate reduction to ammonium in the yellow river estuary: rates, abundance, and community diversity, Sci. Rep., 7, 6830, 10.1038/s41598-017-06404-8 Cannon, 2019, Sequence alignments and validation of PCR primers used to detect phylogenetically diverse nrfA genes associated with dissimilatory nitrate reduction to ammonium (DNRA), Data in Brief., 10.1016/j.dib.2019.104016 Chen, 2015, Importance of heterotrophic nitrification and dissimilatory nitrate reduction to ammonium in a cropland soil: evidences from a N-15 tracing study to literature synthesis, Soil Biol. Biochem., 91, 65, 10.1016/j.soilbio.2015.08.026 Chen, 2015, Relationships between denitrification gene expression, dissimilatory nitrate reduction to ammonium and nitrous oxide and dinitrogen production in montane grassland soils, Soil Biol. Biochem., 87, 67, 10.1016/j.soilbio.2015.03.030 Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004 Decleyre, 2015, Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers, Front. Microbiol., 6, 1124, 10.3389/fmicb.2015.01124 Dieffenbach, 1993, General concepts for PCR primer design, PCR Methods Appl., 3, S30, 10.1101/gr.3.3.S30 Einsle, 2011, Structure and function of formate-dependent cytochrome c nitrite reductase, vol. 496, 399, 10.1016/B978-0-12-386489-5.00016-6 Gao, 2017, Soil dissimilatory nitrate reduction processes in the Spartina alterniflora invasion chronosequences of a coastal wetland of southeastern China: dynamics and environmental implications, Plant Soil, 421, 383, 10.1007/s11104-017-3464-x Gardner, 2006, Nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA) support nitrogen dynamics in Texas estuaries, Limnol. Oceanogr., 51, 558, 10.4319/lo.2006.51.1_part_2.0558 Giacomucci, 2012, A new non-degenerate primer pair for the specific detection of the nitrite reductase gene nrfA in the genus Desulfovibrio, J. Mol. Microbiol. Biotechnol., 22, 345, 10.1159/000345768 Giblin, 2013, The importance of dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen cycle of coastal ecosystems, Oceanography, 26, 124, 10.5670/oceanog.2013.54 Griffiths, 2000, Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition, Appl. Environ. Microbiol., 66, 5488, 10.1128/AEM.66.12.5488-5491.2000 Head, 2014, Library construction for next-generation sequencing: overviews and challenges, Biotechniques, 56 Jahangir, 2017, In situ denitrification and DNRA rates in groundwater beneath an integrated constructed wetland, Water Res., 111, 254, 10.1016/j.watres.2017.01.015 Jensen, 2011, Intensive nitrogen loss over the Omani shelf due to anammox coupled with dissimilatory nitrite reduction to ammonium, Isme J., 5, 1660, 10.1038/ismej.2011.44 Jones, 2013, The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink, ISME J., 7, 417, 10.1038/ismej.2012.125 Jones, 2014, Recently identified microbial guild mediates soil N2O sink capacity, Nat. Clim. Chang., 4, 801, 10.1038/nclimate2301 Kalle, 2014, Multi-template polymerase chain reaction, Biomol. Detect Quantif., 2, 11, 10.1016/j.bdq.2014.11.002 Koop-Jakobsen, 2010, The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments, Limnol. Oceanogr., 55, 789, 10.4319/lo.2010.55.2.0789 Kuypers, 2018, The microbial nitrogen-cycling network, Nat. Rev. Microbiol., 16, 263, 10.1038/nrmicro.2018.9 Lam, 2009, Revising the nitrogen cycle in the Peruvian oxygen minimum zone, Proc. Natl. Acad. Sci. U. S. A., 106, 4752, 10.1073/pnas.0812444106 Lindemann, 2016, Effect of eastern oysters (Crassostrea virginica) and seasonality on nitrite reductase gene abundance (nirS, nirK, nrfA) in an urban estuary, Estuar. Coasts, 39, 218, 10.1007/s12237-015-9989-4 Mania, 2014, The nitrate-ammonifying and nosZ-carrying bacterium Bacillus vireti is a potent source and sink for nitric and nitrous oxide under high nitrate conditions, Environ. Microbiol., 16, 3196, 10.1111/1462-2920.12478 Minick, 2016, Dissimilatory nitrate reduction to ammonium and N2O flux: effect of soil redox potential and N fertilization in loblolly pine forests, Biol. Fertil. Soils, 52, 601, 10.1007/s00374-016-1098-4 Mohan, 2004, Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification, FEMS Microbiol. Ecol., 49, 433, 10.1016/j.femsec.2004.04.012 Nelson, 2016, Global biogeography of microbial nitrogen-cycling traits in soil, Proc. Natl. Acad. Sci. U. S. A., 113, 8033, 10.1073/pnas.1601070113 Orellana, 2014, Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle, Mbio., 5, 10.1128/mBio.01193-14 Orellana, 2017, Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization, Appl. Environ. Microbiol., 84, 10.1128/AEM.01646-17 Pandey, 2018, Nitrogen addition decreases dissimilatory nitrate reduction to ammonium in rice paddies, Appl. Environ. Microbiol., 84, 10.1128/AEM.00870-18 Qiu, 2001, Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning, Appl. Environ. Microbiol., 67, 880, 10.1128/AEM.67.2.880-887.2001 Roberts, 2014, Increased rates of dissimilatory nitrate reduction to ammonium (DNRA) under oxic conditions in a periodically hypoxic estuary, Geochim. Cosmochim. Acta, 133, 313, 10.1016/j.gca.2014.02.042 Roling, 2014, The family Geobacteraceae, 157 Rutting, 2008, Process-specific analysis of nitrite dynamics in a permanent grassland soil by using a Monte Carlo sampling technique, Eur. J. Soil Sci., 59, 208, 10.1111/j.1365-2389.2007.00976.x Rutting, 2011, Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle, Biogeosciences., 8, 1779, 10.5194/bg-8-1779-2011 Sanford, 2012, Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils, Proc. Natl. Acad. Sci. U. S. A., 109, 19709, 10.1073/pnas.1211238109 SantaLucia, 1998, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc. Natl. Acad. Sci. U. S. A., 95, 1460, 10.1073/pnas.95.4.1460 Shan, 2016, Dissimilatory nitrate reduction processes in typical Chinese Paddy soils: rates, relative contributions, and influencing factors, Environ. Sci. Technol., 50, 9972, 10.1021/acs.est.6b01765 Silver, 2001, Dissimilatory nitrate reduction to ammonium in upland tropical forest soils, Ecology, 82, 2410, 10.1890/0012-9658(2001)082[2410:DNRTAI]2.0.CO;2 Silver, 2005, Nitrogen cycling in tropical plantation forests: potential controls on nitrogen retention, Ecol. Appl., 15, 1604, 10.1890/04-1322 Simon, 2013, Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations, BBA-Bioenergetics, 1827, 114, 10.1016/j.bbabio.2012.07.005 Sipos, 2007, Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis, FEMS Microbiol. Ecol., 60, 341, 10.1111/j.1574-6941.2007.00283.x Smith, 2007, Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments, Appl. Environ. Microbiol., 73, 3612, 10.1128/AEM.02894-06 Smith, 2015, Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient, Front. Microbiol., 6, 10.3389/fmicb.2015.00542 Song, 2014, Linking DNRA community structure and activity in a shallow lagoonal estuarine system, Front. Microbiol., 5, 10.3389/fmicb.2014.00460 Sotta, 2008, Differing N status and N retention processes of soils under old-growth lowland forest in eastern Amazonia, Caxiuanã, Brazil, Soil Biol. Biochem., 40, 740, 10.1016/j.soilbio.2007.10.009 Stein, 2011, Surveying N2O-producing pathways in bacteria. Methods in enzymology: research on nitrification and related processes, Vol 486, Part A, 486, 131 Stein, 2016, The nitrogen cycle, Curr. Biol., 26, R94, 10.1016/j.cub.2015.12.021 Stief, 2018, Freshwater copepod carcasses as pelagic microsites of dissimilatory nitrate reduction to ammonium, FEMS Microbiol. Ecol., 94, 10.1093/femsec/fiy144 Stremińska, 2012, Nitrous oxide production in soil isolates of nitrate-ammonifying bacteria, Environ. Microbiol. Rep., 4, 66, 10.1111/j.1758-2229.2011.00302.x Su, 2012, Dissimilatory nitrate reduction by Pseudomonas alcaliphila with an electrode as the sole electron donor, Biotechnol. Bioeng., 109, 2904, 10.1002/bit.24554 Takeuchi, 2006, Habitat segregation of a functional gene encoding nitrate ammonification in estuarine sediments, Geomicrobiol J., 23, 75, 10.1080/01490450500533866 Tatti, 2017, Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios, Appl. Soil Ecol., 110, 53, 10.1016/j.apsoil.2016.10.014 Templer, 2008, Plant and microbial controls on nitrogen retention and loss in a humid tropical forest, Ecology, 89, 3030, 10.1890/07-1631.1 Tiedje, 1988, 179 Tsai, 1991, Rapid method for direct extraction of DNA from soil and sediments, Appl. Environ. Microbiol., 57, 1070, 10.1128/AEM.57.4.1070-1074.1991 van den Berg, 2016, DNRA and denitrification coexist over a broad range of acetate/N-NO3− ratios, in a chemostat enrichment culture, Front. Microbiol., 7, 10.3389/fmicb.2016.01842 van den Berg, 2017, Role of nitrite in the competition between denitrification and DNRA in a chemostat enrichment culture, AMB Express, 7, 10.1186/s13568-017-0398-x Welsh, 2014, Refined NrfA phylogeny improves PCR-based nrfA gene detection, Appl. Environ. Microbiol., 80, 2110, 10.1128/AEM.03443-13 Wu, 2010, Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method, BMC Microbiol., 10, 255, 10.1186/1471-2180-10-255 Yang, 2017, Cross-biome assessment of gross soil nitrogen cycling in California ecosystems, Soil Biol. Biochem., 107, 144, 10.1016/j.soilbio.2017.01.004 Yin, 2002, Dissimilatory nitrate reduction to ammonium and responsible microorganisms in two Chinese and Australian paddy soils, Soil Biol. Biochem., 34, 1131, 10.1016/S0038-0717(02)00049-4 Yoon, 2015, Nitrite control over dissimilatory nitrate/nitrite reduction pathways in Shewanella loihica strain PV-4, Appl. Environ. Microbiol., 81, 3510, 10.1128/AEM.00688-15 Yu, 2018, Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea, Appl. Microbiol. Biotechnol., 102, 447, 10.1007/s00253-017-8594-9 Zhang, 2015, Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in soil nitrogen conservation in neutral and alkaline but not acidic rice soil, J. Soils Sediments, 15, 523, 10.1007/s11368-014-1037-7