The Applications of Metagenomics in the Detection of Environmental Microbes Involving in Nitrogen Cycle

doi:10.13560/j.cnki.biotech.bull.1985.2018-0024

Abstract

Abstract: The global nitrogen cycle is one of the most important biogeochemical cycles on earth,which is predominantly driven by a large number of microorganisms in various ecosystems. The application of metagenomics to reveal the total amount and diversity of functional microbial communities involved in nitrogen cycle,is one of the hotspots of environmental microbiology in recent years. In this paper,we briefly summarized the recent discovery on the functional microorganisms involved in nitrogen cycle. In addition,we focused on the selection of functional genes that could indicate certain nitrogen biological processes（including nitrogen fixation,nitrification,denitrification,anammox,assimilatory/dissimilatory nitrogen reduction,ammonification and assimilation）,and also highlighted the applications of these functional genes to detect the distribution of functional microbial communities in natural environments. Finally,we pointed out the importance of molecular detection techniques and data analysis platforms for future functional microbiological studies.

Key words: metagenomics, functional genes, nitrogen cycle, molecular detection techniques, functional microbes

WANG Zhu-jun, WANG Shang, LIU Yang-ying, FENG Kai, DENG Ye. The Applications of Metagenomics in the Detection of Environmental Microbes Involving in Nitrogen Cycle[J]. Biotechnology Bulletin, 2018, 34(1): 1-14.

References

[1] Canfield DE, Glazer AN, Falkowski PG. The evolution and future of earth’s nitrogen cycle[J]. Science, 2010, 330：192-196.
[2] Nelson MB, Martiny AC, Martiny JB. Global biogeography of microbial nitrogen-cycling traits in soil[J]. Proc Natl Acad Sci USA, 2016, 113：8033-8040.
[3] Jetten MS. The microbial nitrogen cycle[J]. Environ Microbiol, 2008, 10（11）：2903-2909.
[4] Venter JC RK, Heidelberg JF, Halpern AL, et al. Environmental genome shotgun sequencing of the sargasso sea[J]. Science, 2004, 304：66-74.
[5] Konneke M, Bernhard AE, de la Torre JR, et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon[J]. Nature, 2005, 437：543-546.
[6] He JZ, Zhang LM. Advances in ammonia-oxidizing microorganisms and global nitrogen cycle[J]. Acta Ecologica Sinica, 2009, 29：406-415.
[7] Monteiro M, Seneca J, Magalhaes C. The history of aerobic ammonia oxidizers：from the first discoveries to today[J]. J Microbiol, 2014, 52：537-47.
[8] Daims H, Lebedeva EV, Pjevac P, et al. Complete nitrification by nitrospira bacteria[J]. Nature, 2015, 528：504-509.
[9] van Kessel MA, Speth DR, Albertsen M, et al. Complete nitrification by a single microorganism[J]. Nature, 2015, 528：555-559.
[10] Baptista JD, Lunn M, Davenport RJ, et al. Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge[J]. Appl Environ Microbiol, 2014, 80：5901-5910.
[11] Deng Y, Feng K, Wei ZY, et al. Recent studies and applications of metagenomics in environmental engineering[J]. Chinese Journal of Environmental Engineering, 2016, 10：3373-3382.
[12] Liu YY, Wang S, Li SZ, et al. Advances in molecular ecology on microbial functional genes of carbon cycle[J]. Microbiology China, 2017, 44：1676-1689.
[13] Bustin S, Benes V, Garson J, et al. The miqe guidelines：minimum information for publication of quantitative real-time pcr experiments[J]. Clinical Chemistry, 2009, 55：611-622.
[14] Jia ZJ. Principle and application of DNA-based stable isotope Probing—A review[J]. Acta Microbiologica Sinica, 2011, 51：1585-1594.
[15] Ge Y, He JZ, Zheng YM, et al. Stable isotope probing and its applications in microbial ecology[J]. Acta Ecologica Sinica, 2006, 26：1574-1582.
[16] He SB, Chai LQ, Tan JJ, et al. Rencent advance in fluorescence in situ hybridization[J]. Plant Science Journal, 2014, 32：199-204.
[17] Lin H, Fang SG. Genomic library construction and perspectives on applications in conservation genetics[J]. Acta Theriologica Sinica, 2005, 25：86-90.
[18] Zhu ZX, Chen X. Single cell sequencing technology and its applications progress[J]. Genomics and Applied Biology, 2015, 34：000902-908.
[19] Blainey PC. The future is now：single-cell genomics of bacteria and archaea[J]. FEMS Microbiol Rev, 2013, 37：407-427.
[20] Tu Q, Yu H, He Z, et al. Geochip 4：A functional gene-array-based high-throughput environmental technology for microbial community analysis[J]. Mol Ecol Resour, 2014, 14：914-928.
[21] Spencer SJ, Tamminen MV, Preheim SP, et al. Massively parallel sequencing of single cells by epicpcr links functional genes with phylogenetic markers[J]. ISME J, 2016, 10：427-436.
[22] Schmidt TM, Delong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing[J]. Journal of Bacteriology, 1991, 173：4371.
[23] Manz W, Szewzyk U, Ericsson P, et al. In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-Directed fluorescent oligonucleotide probes[J]. Applied & Environmental Microbiology, 1993, 59：2293-2298.
[24] Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA[J]. Appl Environ Microbiol, 1993, 59：695-700.
[25] Liu WT, Marsh TL, Cheng H, et al. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA[J]. Applied & Environmental Microbiology, 1997, 63：4516-4522.
[26] Radajewski S, Ineson P, Parekh NR, et al. Stable-isotope probing as a tool in microbial ecology[J]. Nature, 2000, 403：646-649.
[27] Chandler DP, Stults JR, Cebula S, et al. Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps[J]. Applied & Environmental Microbiology, 2000, 66：3438-3445.
[28] Wu L, Thompson DK, et al. Development and evaluation of functi- onal gene arrays for detection of selected genes in the environment [J]. Appl Environ Microbiol, 2001, 67：5780-5790.
[29] Poinar HN, Schwarz C, Qi J, et al. Metagenomics to paleogenomics：Large-scale sequencing of mammoth DNA[J]. Science, 2006, 311：392-394.
[30] Edwards RA, Rodriguez-Brito B, Wegley L, et al. Using pyrosequencing to shed light on deep mine microbial ecology[J]. BMC Genomics, 2006, 7：57.
[31] Yoon HS, Price DC, Stepanauskas R, et al. Single-cell genomics reveals organismal interactions in uncultivated marine protists[J]. Science, 2011, 332：714-717.
[32] Novak R, Zeng Y, Shuga J, et al. Single-cell multiplex gene detection and sequencing with microfluidically generated agarose emulsions[J]. Angew Chem Int Ed Engl, 2011, 50：390-395.
[33] Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker：molecular fine-scale analysis of natural ammonia-oxidizing populations[J]. Applied & Environmental Microbiology, 1997, 63：4704.
[34] Purkhold U, Pommereningröser A, Juretschko S, et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis：implications for molecular diversity surveys[J]. Applied & Environmental Microbiology, 2000, 66：5368-5382.
[35] Horz HP, Rotthauwe JH, Lukow T, et al. Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products[J]. Journal of Microbiological Methods, 2000, 39：197-204.
[36] Oved T, Shaviv A, Goldrath T, et al. Influence of effluent irrigation on community composition and function of ammonia-oxidizing bacteria in soil[J]. Appl Environ Microbiol, 2001, 67：3426-3433.
[37] Harms G, Layton AC, Dionisi HM, et al. Real-Time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant[J]. Environmental Science & Technology, 2003, 37：343-351.
[38] Freitag TE, Chang L, Prosser JI. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient[J]. Environ Microbiol, 2006, 8：684-696.
[39] Yergeau E, Hogues H, Whyte LG, et al. The functional potential of high arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses[J]. ISME J, 2010, 4：1206-1214.
[40] Gaby JC, Buckley DH. A Comprehensive aligned nifh gene database：a multipurpose tool for studies of nitrogen-fixing bacteria[J]. Database（Oxford）, 2014, 2014：bau001.
[41] Raymond J, Siefert JL, Staples CR, et al. The natural history of nitrogen fixation[J]. Mol Biol Evol, 2004, 21：541-554.
[42] Soni R, Suyal DC, Sai S, et al. Exploration of nifh gene through soil metagenomes of the western indian himalayas[J]. Biotech, 2016, 6：1-4.
[43] Chien Y T, Zinder SH. Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD1 from the eubacterium Clostridium pasteurianum[J]. Journal of Bacteriology, 1994, 176：6590-6598.
[44] Wang J, Bao JT, Li XR, et al. Molecular ecology of nifh genes and transcripts along a chronosequence in revegetated areas of the tengger desert[J]. Microb Ecol, 2016, 71：150-163.
[45] Wang J, Zhang D, Zhang L, et al. Temporal variation of diazotrophic community abundance and structure in surface and subsoil under four fertilization regimes during a wheat growing season[J]. Agriculture, Ecosystems & Environment, 2016, 216：116-124.
[46] Zhang B, Penton CR, Xue C, et al. Evaluation of the ion torrent personal genome machine for gene-targeted studies using amplicons of the nitrogenase gene nifh[J]. Appl Environ Microbiol, 2015, 81：4536-4545.
[47] Wang L, Yu Z, Yang J, et al. Diazotrophic bacterial community variability in a subtropical deep reservoir is correlated with seasonal changes in nitrogen[J]. Environ Sci Pollut Res Int, 2015, 22：19695-19705.
[48] Xiao P, Jiang Y, Liu Y, et al. Re-evaluation of the diversity and distribution of diazotrophs in the south china sea by pyrosequencing the nifh gene[J]. Marine and Freshwater Research, 2015, 66：681.
[49] Chen CL, Wu MN, Wei WX. Effect of long-term application of nitrogen fertilizer on the diversity of nitrifying genes（amoa and hao）in paddy soil[J]. Environmental Science, 2011, 32：1489-1496.
[50] Wertz S, Poly F, Le Roux X, et al. Development and application of a PCR-denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter-like nxrA sequences in soil[J]. FEMS Microbiol Ecol, 2008, 63：261-271.
[51] Avrahami S, Conrad R. Cold-temperate climate：a factor for selection of ammonia oxidizers in upland soil?[J]Can J Microbiol, 2005, 51：709-714.
[52] Purkhold U, Pommerening-Röser A, Juretschko S, et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis：implications for molecular diversity surveys[J]. Applied & Environmental Microbiology, 2001：5368-5382.
[53] Cubillos AM, Vallejo VE, Arbeli Z, et al. Effect of the conversion of conventional pasture to intensive silvopastoral systems on edaphic bacterial and ammonia oxidizer communities in Colombia[J]. European Journal of Soil Biology, 2016, 72：42-50.
[54] Yang YD, Ren YF, Wang XQ, et al. Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing[J]. Journal of Soils and Sediments, 2017：1-12.
[55] Gao J, Luo X, Wu G, et al. Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten astewater treatment systems[J]. Applied Microbiology & Biotechnology, 2013, 98：3339-3354.
[56] Zhang Y, Tian Z, Liu M, et al. High Concentrations of the antibiotic spiramycin in wastewater lead to high abundance of ammonia-oxidizing archaea in nitrifying populations[J]. Environ Sci Technol, 2015, 49：9124-132.
[57] Vetterli A, Hietanen S, Leskinen E. Spatial and temporal dynamics of ammonia oxidizers in the sediments of the gulf of Finland, Baltic Sea[J]. Mar Environ Res, 2016, 113：153-63.
[58] Bertagnolli AD, Ulloa O. Hydrography shapes amoA containing thaumarcheota in the coastal waters off central chile[J]. Environ Microbiol Rep, 2017, 9（6）：717-728.
[59] Hiroya S MF. Comparison of 16S rRNA, ammonia monooxygenase subunit A and hydroxylamine oxidoreductase gene, in chemolithotrophic ammonia-oxidizing bacteria[J]. Journal of General & Applied Microbiology, 2002, 48：173-176.
[60] Moran MA, Buchan A, González JM, et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment[J]Nature, 2004, 432：910-913.
[61] Poret-Peterson AT, Graham JE, Gulledge J, et al. Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath[J]. ISME J, 2008, 2：1213-1220.
[62] Rani S, Koh HW, Rhee SK, et al. Detection and diversity of the nitrite oxidoreductase alpha subunit（nxrA）gene of nitrospina in marine sediments[J]. Microb Ecol, 2017, 73：111-122.
[63] Shoun H, Fushinobu S, Jiang L, et al. Fungal denitrification and nitric oxide reductase cytochrome P450nor[J]. Philos Trans R Soc Lond B Biol Sci, 2012, 367：1186-1194.
[64] Reyna L, Wunderlin DA, Genti-Raimondi S. Identification and quantification of a novel nitrate-reducing community in sediments of suquia river basin along a nitrate gradient[J]. Environ Pollut, 2010, 158：1608-1614.
[65] Zumft WG. Cell biology and molecular basis of denitrification[J]. Microbiology & Molecular Biology Reviews, 1997, 61：533-616.
[66] Philippot L, Kuffner M, et al. Genetic structure and activity of the nitrate-reducers community in the rhizosphere of different cultivars of maize[J]. Plant and Soil, 2006, 287：177-186.
[67] Deiglmayr K, Philippot L, Kandeler E. Functional stability of the nitrate-reducing community in grassland soils towards high nitrate supply[J]. Soil Biology and Biochemistry, 2006, 38：2980-2984.
[68] Bulc TG, Klemenčič AK, Razinger J. Vegetated ditches for treatment of surface water with highly fluctuating water regime. [J]Water Science & Technology, 2011, 63：2353.
[69] Glockner AB, Jüngst A, Zumft WG. Copper-containing nitrite reductase from pseudomonas aureofaciens is functional in a mutationally cytochrome cd1-free background（Nirs-）of Pseudomonas stutzeri[J]. Archives of Microbiology, 1993, 160：18-26.
[70] Yang JK, Cheng ZB, Li J, et al. Community composition of nirS-type denitrifier in a shallow eutrophic lake. [J]Microb Ecol, 2013, 66：796-805.
[71] Lee JA, Francis CA. Spatiotemporal characterization of San Francisco bay denitrifying communities：A comparison of nirK and nirS diversity and abundance[J]. Microb Ecol, 2017, 73：271-284.
[72] Zhou S, Huang T, et al. Illumina Miseq sequencing reveals the community composition of Nirs-Type and Nirk-Type denitrifiers in zhoucun Reservoir - a large shallow eutrophic reservoir in northern China[J]. RSC Adv, 2016, 6：91517-91528.
[73] Fagerstone KD, Quinn JC, Bradley TH, et al. Quantitative measurement of direct nitrous oxide emissions from microalgae cultivation[J]. Environ Sci Technol, 2011, 45：9449-9456.
[74] Kearns PJ, Angell JH, Feinman SG, et al. Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments[J]. Estuarine, Coastal and Shelf Science, 2015, 154：39-47.
[75] Orellana LH, Rodriguez-R LM, Higgins S, et al. Detecting nitrous oxide reductase（Nosz）genes in soil metagenomes：method development and implications for the nitrogen cycle[J]. Mbio, 2014, 5（3）：e01193-14.
[76] Sanford RA, Wagner DD, Wu Q, et al. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils[J]. Proc Natl Acad Sci USA, 2012, 109：19709-19714.
[77] Jones CM, Graf DR, Bru D, et al. The unaccounted yet abundant nitrous oxide-reducing microbial community：A potential nitrous oxide sink[J]. ISME J, 2013, 7：417-426.
[78] Wyman M, Hodgson S, Bird C. Denitrifying alphaproteobacteria from the arabian sea that express nosz, the gene encoding nitrous oxide reductase, in oxic and suboxic waters[J]. Appl Environ Microbiol, 2013, 79：2670-81.
[79] Kartal B, Maalcke WJ, de Almeida NM, et al. Molecular mechanism of anaerobic ammonium oxidation[J]. Nature, 2011, 479：127-30.
[80] Dang H, Zhou H, Zhang Z, et al. Molecular detection of candidatus scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai sea, China[J]. PLoS One, 2013, 8：e61330.
[81] Sun W, Xia C, Xu M, et al. Diversity and distribution of planktonic anaerobic ammonium-oxidizing bacteria in the Dongjiang river, China[J]. Microbiol Res, 2014, 169：897-906.
[82] Harhangi HR, Le Roy M, van Alen T, et al. Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria[J]. Appl Environ Microbiol, 2012, 78：752-758.
[83] Shen LD, Wu HS, Gao ZQ, et al. Evidence for anaerobic ammonium oxidation process in freshwater sediments of aquaculture ponds[J]. Environmental Science and Pollution Research, 2016, 23：1344.
[84] Naeher S, Huguet A, Roose-Amsaleg CL, et al. Molecular and geochemical constraints on anaerobic ammonium oxidation（anammox）in a riparian zone of the Seine Estuary（France）[J]. Biogeochemistry, 2015, 123：237-250.
[85] Russ L, Kartal B, et al. Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin[J]. Front Microbiol, 2013, 4：219.
[86] Bale NJ, Villanueva L, Fan H, et al. Occurrence and activity of anammox bacteria in surface sediments of the southern north sea[J]. FEMS Microbiol Ecol, 2014, 89：99-110.
[87] Gardner WS, McCarthy MJ, An S, et al. Nitrogen fixation and dissimilatory nitrate reduction to ammonium（DNRA）support nitrogen dynamics in Texas estuaries[J]. Limnology & Oceanography, 2006, 51：558-568.
[88] Lam P, Lavik G, Jensen MM, et al. Revising the nitrogen cycle in the peruvian oxygen minimum zone[J]. Proceedings of the National Academy of Sciences of the United States of America, 2009, 106：4752-4757.
[89] Jiang X, Dang H, Jiao N. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments[J]. PLoS One, 2015, 10：e0117473.
[90] Rubio LM, Herrero A, Flores E. A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase[J]. Plant Molecular Biology, 1996, 30：845-850.
[91] Feng WW, Liu JF, Gu JD, et al. Nitrate-reducing community in production water of three oil reservoirs and their responses to different carbon sources revealed by nitrate-reductase encoding gene（napA）[J]. International Biodeterioration & Biodegradation, 2011, 65：1081-1086.
[92] Paerl RW, Johnson KS, Welsh RM, et al. Differential distributions of synechococcus subgroups across the california current system[J]. Front Microbiol, 2011, 2：59.
[93] Paerl RW, Turk KA, Beinart RA, et al. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcl and narB quantitative PCR. [J]Environ Microbiol, 2012, 14：580-593.
[94] Buxens M, Llama MJ, Serra JL. Effect of the inorganic nitrogen source in the expression of nitrite reductase（Nira）in Bp-1. [J]Advances in Microbiology, 2014, 4（15）：1044-1056.
[95] Frias JE, Flores E. Induction of the nitrate assimilation nirA operon and protein-protein interactions in the maturation of nitrate and nitrite reductases in the cyanobacterium Anabaena sp. strain PCC 7120. [J]J Bacteriol, 2015, 197：2442-2452.
[96] Suzuki I, Horie N, Sugiyama T, Omata T. Identification and characterization of two nitrogen-regulated genes of the cyanobacterium Synechococcus sp. strain PCC7942 required for maximum efficiency of nitrogen assimilation. [J]Journal of Bacteriology, 1995, 177：290-296.
[97] Frias JE, Flores E. Negative regulation of expression of the nitrate assimilation nirA operon in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. [J]J Bacteriol, 2010, 192：2769-2778.
[98] Alcantara-Hernandez RJ, Valenzuela-Encinas C, Zavala-Diaz de la Serna FJ, et al. Haloarchaeal assimilatory nitrate-reducing communities from a saline alkaline soil[J]. FEMS Microbiol Lett, 2009, 298：56-66.
[99] Boucher DJ, Adler B, Boyce JD. The pasteurella multocida nrfE gene is upregulated during infection and is essential for nitrite reduction but not for virulence[J]. J Bacteriol, 2005, 187：2278-2285.
[100] Song B, Lisa JA, Tobias CR. Linking DNRA community structure and activity in a shallow lagoonal estuarine system[J]. Front Microbiol, 2014, 5：460.
[101] Zhang X, Liu W, Schloter M, et al. Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes[J]. PLoS One, 2013, 8：e76500.
[102] Mobley HL, Island MD, et al. Molecular biology of microbial ure-ases[J]. Microbiological Reviews, 1995, 59（3）：451-480.
[103] Zhao SG, Wang JQ, Bu DP, et al. Biochemistry and molecular biology of bacterial ureases[J]. Microbiology China, 2008, 35：1146-1152.
[104] Berges JA, Contents MM. Enzymes and N cycling[J]. Nitrogen in the Marine Environment, 2008.
[105] Bolster DMWG. Glossary of terms used in bioinorganic chemistry（Iupac Recommendations 1997）[J]. Pure & Applied Chemistry, 1997, 69：1251-1304.
[106] Raghoebarsing AA, Pol A, van de Pas-Schoonen KT, et al. A microbial consortium couples anaerobic methane oxidation to denitrification[J]. Nature, 2006, 440：918-921.
[107] Schmittgen TD. High-throughput real-time PCR[J]. Methods in Molecular Biology, 2008, 429：89.
[108] Wei ZY, Jin DC, Deng Y. Bioinformatics tools and applications in the study of environmental microbial metagenomics[J]. Microbiology China, 2015, 42（5）：890-901.