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