Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

Zhao, Jun; Rodriguez, Jonathan; Martens-Habbena, Willm

doi:10.3389/fmicb.2023.1140487

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

Journal Article · Thu Feb 23 00:00:00 EST 2023 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2023.1140487· OSTI ID:2422814

Zhao, Jun ^[1]; Rodriguez, Jonathan ^[1]; Martens-Habbena, Willm ^[1]

Univ. of Florida, Davie, FL (United States). Fort Lauderdale Research and Education Center

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

View Accepted Manuscript (DOE)

Research Organization:: USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2422814

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 14; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (78)

Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships Tolar, Bradley B.; Reji, Linta; Smith, Jason M. Limnology and Oceanography, Vol. 65, Issue 9 https://doi.org/10.1002/lno.11436	journal	March 2020
ggplot2 Wickham, Hadley Use R! https://doi.org/10.1007/978-3-319-24277-4	book	January 2016
Ecophysiology of an Ammonia-Oxidizing Archaeon Adapted to Low-Salinity Habitats Mosier, Annika C.; Lund, Marie B.; Francis, Christopher A. Microbial Ecology, Vol. 64, Issue 4 https://doi.org/10.1007/s00248-012-0075-1	journal	May 2012
Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories Zhao, Jun; Wang, Baozhan; Zhou, Xue Microbial Ecology, Vol. 83, Issue 2 https://doi.org/10.1007/s00248-021-01763-2	journal	May 2021
Microbial diversity and function in soil: from genes to ecosystems Torsvik, Vigdis; Øvreås, Lise Current Opinion in Microbiology, Vol. 5, Issue 3, p. 240-245 https://doi.org/10.1016/S1369-5274(02)00324-7	journal	June 2002
Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils Toole, David R.; Zhao, Jun; Martens-Habbena, Willm Applied Soil Ecology, Vol. 168 https://doi.org/10.1016/j.apsoil.2021.104129	journal	December 2021
Di-(2-ethylhexyl) phthalate (DEHP) exposure suppressed the community diversity and abundance of ammonia-oxidizers and mitigated N2O emissions in an alkaline soil Tao, Rui; Zhang, Hanjie; Gu, Xiuping Ecotoxicology and Environmental Safety, Vol. 227 https://doi.org/10.1016/j.ecoenv.2021.112910	journal	December 2021
Mitigating N2O emission by synthetic inhibitors mixed with urea and cattle manure application via inhibiting ammonia-oxidizing bacteria, but not archaea, in a calcareous soil Tao, Rui; Li, Jun; Hu, Baowei Environmental Pollution, Vol. 273 https://doi.org/10.1016/j.envpol.2021.116478	journal	March 2021
Ammonia-oxidizing bacteria are sensitive and not resilient to organic amendment and nitrapyrin disturbances, but ammonia-oxidizing archaea are resistant Tao, Rui; Li, Jun; Hu, Baowei Geoderma, Vol. 384 https://doi.org/10.1016/j.geoderma.2020.114814	journal	February 2021
A fast and direct spectrophotometric method for the sequential determination of nitrate and nitrite at low concentrations in small volumes García-Robledo, Emilio; Corzo, Alfonso; Papaspyrou, Sokratis Marine Chemistry, Vol. 162 https://doi.org/10.1016/j.marchem.2014.03.002	journal	May 2014
Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems Sun, Xiangxin; Zhao, Jun; Zhang, Liyan Science of The Total Environment, Vol. 835 https://doi.org/10.1016/j.scitotenv.2022.155568	journal	August 2022
Micromanaging the nitrogen cycle in agroecosystems Klimasmith, Isaac M.; Kent, Angela D. Trends in Microbiology, Vol. 30, Issue 11 https://doi.org/10.1016/j.tim.2022.04.006	journal	November 2022
Examining the global distribution of dominant archaeal populations in soil Bates, Scott T.; Berg-Lyons, Donna; Caporaso, J. Gregory The ISME Journal, Vol. 5, Issue 5 https://doi.org/10.1038/ismej.2010.171	journal	November 2010
Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms Verhamme, Daniel T.; Prosser, James I.; Nicol, Graeme W. The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.191	journal	January 2011
Soil bacterial and fungal communities across a pH gradient in an arable soil Rousk, Johannes; Bååth, Erland; Brookes, Philip C. The ISME Journal, Vol. 4, Issue 10 https://doi.org/10.1038/ismej.2010.58	journal	May 2010
Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei The ISME Journal, Vol. 6, Issue 5 https://doi.org/10.1038/ismej.2011.168	journal	December 2011
Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils Wang, Baozhan; Zhao, Jun; Guo, Zhiying The ISME Journal, Vol. 9, Issue 5 https://doi.org/10.1038/ismej.2014.194	journal	October 2014
Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W. The ISME Journal, Vol. 10, Issue 1 https://doi.org/10.1038/ismej.2015.101	journal	July 2015
A communal catalogue reveals Earth’s multiscale microbial diversity Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24621	journal	November 2017
DADA2: High-resolution sample inference from Illumina amplicon data Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J. Nature Methods, Vol. 13, Issue 7 https://doi.org/10.1038/nmeth.3869	journal	May 2016
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N.; Woyke, Tanja Nature Microbiology, Vol. 1, Issue 4 https://doi.org/10.1038/nmicrobiol.2015.32	journal	February 2016
A new view of the tree of life Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik Nature Microbiology, Vol. 1, Issue 5 https://doi.org/10.1038/nmicrobiol.2016.48	journal	April 2016
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar Nature Reviews Microbiology, Vol. 12, Issue 9 https://doi.org/10.1038/nrmicro3330	journal	August 2014
Ecology and exploration of the rare biosphere Lynch, Michael D. J.; Neufeld, Josh D. Nature Reviews Microbiology, Vol. 13, Issue 4 https://doi.org/10.1038/nrmicro3400	journal	March 2015
The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions Hink, Linda; Gubry-Rangin, Cécile; Nicol, Graeme W. The ISME Journal, Vol. 12, Issue 4 https://doi.org/10.1038/s41396-017-0025-5	journal	January 2018
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria Tripathi, Binu M.; Stegen, James C.; Kim, Mincheol The ISME Journal, Vol. 12, Issue 4 https://doi.org/10.1038/s41396-018-0082-4	journal	March 2018
Temperature and soil moisture control microbial community composition in an arctic–alpine ecosystem along elevational and micro-topographic gradients Frindte, K.; Pape, R.; Werner, K. The ISME Journal, Vol. 13, Issue 8 https://doi.org/10.1038/s41396-019-0409-9	journal	April 2019
Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution Ren, Minglei; Feng, Xiaoyuan; Huang, Yongjie The ISME Journal, Vol. 13, Issue 9 https://doi.org/10.1038/s41396-019-0418-8	journal	April 2019
Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons Wang, Baozhan; Qin, Wei; Ren, Yi The ISME Journal, Vol. 13, Issue 12 https://doi.org/10.1038/s41396-019-0493-x	journal	August 2019
Salt tolerance-based niche differentiation of soil ammonia oxidizers Sun, Xiangxin; Zhao, Jun; Zhou, Xue The ISME Journal, Vol. 16, Issue 2 https://doi.org/10.1038/s41396-021-01079-6	journal	August 2021
Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes Alves, Ricardo J. Eloy; Minh, Bui Quang; Urich, Tim Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03861-1	journal	April 2018
Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes Bickel, Samuel; Or, Dani Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-13966-w	journal	January 2020
Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality Zhou, Zhenghu; Wang, Chuankuan; Luo, Yiqi Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16881-7	journal	June 2020
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota Sheridan, Paul O.; Raguideau, Sebastien; Quince, Christopher Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19132-x	journal	October 2020
Diversity, ecology and evolution of Archaea Baker, Brett J.; De Anda, Valerie; Seitz, Kiley W. Nature Microbiology, Vol. 5, Issue 7 https://doi.org/10.1038/s41564-020-0715-z	journal	May 2020
Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil Huang, Laibin; Chakrabarti, Seemanti; Cooper, Jennifer ISME Communications, Vol. 1, Issue 1 https://doi.org/10.1038/s43705-021-00020-4	journal	June 2021
Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence Domeignoz-Horta, Luiz A.; Shinfuku, Melissa; Junier, Pilar ISME Communications, Vol. 1, Issue 1 https://doi.org/10.1038/s43705-021-00071-7	journal	November 2021
Autotrophic ammonia oxidation by soil thaumarchaea Zhang, L. -M.; Offre, P. R.; He, J. -Z. Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1004947107	journal	September 2010
Niche specialization of terrestrial archaeal ammonia oxidizers Gubry-Rangin, C.; Hai, B.; Quince, C. Proceedings of the National Academy of Sciences, Vol. 108, Issue 52 https://doi.org/10.1073/pnas.1109000108	journal	December 2011
Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 30 https://doi.org/10.1073/pnas.1419329112	journal	July 2015
Estimating prokaryotic diversity and its limits Curtis, T. P.; Sloan, W. T.; Scannell, J. W. Proceedings of the National Academy of Sciences, Vol. 99, Issue 16, p. 10494-10499 https://doi.org/10.1073/pnas.142680199	journal	July 2002
The vast unknown microbial biosphere Pedrós-Alió, Carlos; Manrubia, Susanna Proceedings of the National Academy of Sciences, Vol. 113, Issue 24 https://doi.org/10.1073/pnas.1606105113	journal	June 2016
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Kopylova, Evguenia; Noé, Laurent; Touzet, Hélène Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts611	journal	October 2012
The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events Yang, Yiyan; Zhang, Chuanlun; Lenton, Timothy M. Molecular Biology and Evolution, Vol. 38, Issue 9 https://doi.org/10.1093/molbev/msab129	journal	May 2021
ARB: a software environment for sequence data Ludwig, W. Nucleic Acids Research, Vol. 32, Issue 4 https://doi.org/10.1093/nar/gkh293	journal	February 2004
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies Parada, Alma E.; Needham, David M.; Fuhrman, Jed A. Environmental Microbiology, Vol. 18, Issue 5 https://doi.org/10.1111/1462-2920.13023	journal	October 2015
Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton: Primer choice effects on populations, communities Wear, Emma K.; Wilbanks, Elizabeth G.; Nelson, Craig E. Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14091	journal	April 2018
Differential response of nonadapted ammonia-oxidising archaea and bacteria to drying-rewetting stress Thion, Cécile; Prosser, James I. FEMS Microbiology Ecology https://doi.org/10.1111/1574-6941.12395	journal	September 2014
Classifying human influences on terrestrial ecosystems Rillig, Matthias C.; Ryo, Masahiro; Lehmann, Anika Global Change Biology, Vol. 27, Issue 11 https://doi.org/10.1111/gcb.15577	journal	March 2021
Archaea rather than bacteria control nitrification in two agricultural acidic soils: Archaeal nitrification in acidic soils Gubry-Rangin, Cécile; Nicol, Graeme W.; Prosser, James I. FEMS Microbiology Ecology, Vol. 74, Issue 3 https://doi.org/10.1111/j.1574-6941.2010.00971.x	journal	October 2010
VEGAN, a package of R functions for community ecology Dixon, Philip Journal of Vegetation Science, Vol. 14, Issue 6 https://doi.org/10.1111/j.1654-1103.2003.tb02228.x	journal	April 2003
The global soil community and its influence on biogeochemistry Crowther, T. W.; van den Hoogen, J.; Wan, J. Science, Vol. 365, Issue 6455 https://doi.org/10.1126/science.aav0550	journal	August 2019
The role of multiple global change factors in driving soil functions and microbial biodiversity Rillig, Matthias C.; Ryo, Masahiro; Lehmann, Anika Science, Vol. 366, Issue 6467 https://doi.org/10.1126/science.aay2832	journal	November 2019
Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil Zhao, Jun; Wang, Baozhan; Jia, Zhongjun Applied and Environmental Microbiology, Vol. 81, Issue 9 https://doi.org/10.1128/AEM.00426-15	journal	May 2015
Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example Bru, D.; Martin-Laurent, F.; Philippot, L. Applied and Environmental Microbiology, Vol. 74, Issue 5 https://doi.org/10.1128/AEM.02403-07	journal	March 2008
A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon Jung, Man-Young; Park, Soo-Je; Kim, So-Jeong Applied and Environmental Microbiology, Vol. 80, Issue 12 https://doi.org/10.1128/AEM.03730-13	journal	April 2014
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys Walters, William; Hyde, Embriette R.; Berg-Lyons, Donna mSystems, Vol. 1, Issue 1 https://doi.org/10.1128/mSystems.00009-15	journal	December 2015
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes Lloyd, Karen G.; Steen, Andrew D.; Ladau, Joshua mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/mSystems.00055-18	journal	September 2018
Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation Zhao, Jun; Meng, Yiyu; Drewer, Julia mSystems, Vol. 5, Issue 3 https://doi.org/10.1128/mSystems.00309-20	journal	June 2020
Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils Wang, Haitao; Bagnoud, Alexandre; Ponce-Toledo, Rafael I. mSystems, Vol. 6, Issue 4 https://doi.org/10.1128/mSystems.00546-21	journal	August 2021
A Salicylate–Hypochlorite Method for Determining Ammonia in Seawater Bower, Carol E.; Holm-Hansen, Thomas Canadian Journal of Fisheries and Aquatic Sciences, Vol. 37, Issue 5 https://doi.org/10.1139/f80-106	journal	May 1980
Archaea in Biogeochemical Cycles Offre, Pierre; Spang, Anja; Schleper, Christa Annual Review of Microbiology, Vol. 67, Issue 1 https://doi.org/10.1146/annurev-micro-092412-155614	journal	September 2013
The Uncultured Microbial Majority Rappé, Michael S.; Giovannoni, Stephen J. Annual Review of Microbiology, Vol. 57, Issue 1 https://doi.org/10.1146/annurev.micro.57.030502.090759	journal	October 2003
Removing Noise From Pyrosequenced Amplicons Quince, Christopher; Lanzen, Anders; Davenport, Russell J. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-38	journal	January 2011
Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis Yang, Bo; Wang, Yong; Qian, Pei-Yuan BMC Bioinformatics, Vol. 17, Issue 1 https://doi.org/10.1186/s12859-016-0992-y	journal	March 2016
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies Brooks, J. Paul; Edwards, David J.; Harwich, Michael D. BMC Microbiology, Vol. 15, Issue 1 https://doi.org/10.1186/s12866-015-0351-6	journal	March 2015
16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform Fouhy, Fiona; Clooney, Adam G.; Stanton, Catherine BMC Microbiology, Vol. 16, Issue 1 https://doi.org/10.1186/s12866-016-0738-z	journal	June 2016
Taxonomic Precision of Different Hypervariable Regions of 16S rRNA Gene and Annotation Methods for Functional Bacterial Groups in Biological Wastewater Treatment Guo, Feng; Ju, Feng; Cai, Lin PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0076185	journal	October 2013
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Apprill, A.; McNally, S.; Parsons, R. Aquatic Microbial Ecology, Vol. 75, Issue 2 https://doi.org/10.3354/ame01753	journal	June 2015
Primer and platform effects on 16S rRNA tag sequencing Tremblay, Julien; Singh, Kanwar; Fern, Alison Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00771	journal	August 2015
Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs Fischer, Martin A.; Güllert, Simon; Neulinger, Sven C. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01297	journal	August 2016
Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys Thijs, Sofie; Op De Beeck, Michiel; Beckers, Bram Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00494	journal	March 2017
Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China Liu, Junjie; Yu, Zhenhua; Yao, Qin Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00023	journal	January 2019
Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment Kerrigan, Zak; Kirkpatrick, John B.; D’Hondt, Steven Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01640	journal	July 2019
Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body Pausan, Manuela R.; Csorba, Cintia; Singer, Georg Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02796	journal	December 2019
Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities Fadeev, Eduard; Cardozo-Mino, Magda G.; Rapp, Josephine Z. Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.637526	journal	February 2021
Evaluation of four primer sets for analysis of comammox communities in black soils Bai, Xin; Hu, Xiaojing; Liu, Junjie Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.944373	journal	July 2022

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16S rRNA gene amplicon Illumina sequencing
59 BASIC BIOLOGICAL SCIENCES
ammonia-oxidizing archaea
land use change
metagenomics
microbial communities
primer evaluation
soil

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

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