Advances in monitoring soil microbial community dynamic and function
Tóm tắt
Từ khóa
Tài liệu tham khảo
Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770
Adam B, Klawonn I, Svedén JB et al (2016) N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community. ISME J 10:450–459
Alquezar-Planas DE, Mourier T, Bruhn CAW et al (2013) Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. Sci Rep 3. https://doi.org/10.1038/srep02468
Anderson OR (2011) Soil respiration, climate change and the role of microbial communities. Protist 162:679–690
Angel R, Panhölzl C, Gabriel R et al (2018) Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 20:44–61
Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168
Bardgett RD, Saggar S (1994) Effects of heavy metal contamination on the short-term decomposition of labelled [14C] glucose in a pasture soil. Soil Biol Biochem 26:727–733
Bardgett RD, Bowman WD, Kaufmann R, Schmidt SK (2005) A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol 20:634–641
Bartram AK, Lynch MDJ, Stearns JC et al (2011) Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol 77:3846–3852
Beirn LA, Hempfling JW, Schmid CJ et al (2017) Differences among soil-inhabiting microbial communities in turf throughout the growing season. Crop Sci 57:S262–S273
Belyaeva ON, Haynes RJ, Birukova OA (2005) Barley yield and soil microbial and enzyme activities as affected by contamination of two soils with lead, zinc or copper. Biol Fertil Soils 41:85–94
Bloem J, Schouten AJ, Sørensen SJ et al (2006) Monitoring and evaluating soil quality. In: Bloem J, Hopkins DW, Benedetti A (eds) Microbiological methods for assessing soil quality. CABI, Wallingford, pp 23–49
Boxer SG, Kraft ML, Weber PK (2009) Advances in imaging secondary ion mass spectrometry for biological samples. Annu Rev Biophys 38:53–74
Breure AM (2004) Soil biodiversity: measurements, indicators, threats and soil functions. In: International conference - soil and compost eco-biology. Leon, Spain, pp 1–14
Brown SP, Callaham MA, Oliver AK, Jumpponen A (2013) Deep ion torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiol Ecol 86:557–566
Burns RG (1977) Soil enzymology. Sci Prog 64:275–285
Buyer JS, Sasser M (2012) High throughput phospholipid fatty acid analysis of soils. Appl Soil Ecol 61:127–130
Buyer JS, Teasdale JR, Roberts DP et al (2010) Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol Biochem 42:831–841
Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Caporaso JG, Lauber CL, Walters WA et al (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624
Choi S, Song H, Tripathi BM et al (2017) Effect of experimental soil disturbance and recovery on structure and function of soil community: a metagenomic and metagenetic approach. Sci Rep 7:1–15
Clarke J, Wu HC, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270. https://doi.org/10.1038/nnano.2009.12
Coleman DC (1973) Compartmental analysis of total soil respiration: an exploratory study. Oikos 24:361
Cong J, Liu X, Lu H et al (2015) Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0. Genomics Data 5:397–398
Cook FJ, Orchard VA (2008) Relationships between soil respiration and soil moisture. Soil Biol Biochem 40:1013–1018
Davidson E, Savage K, Bolstad P et al (2002) Belowground carbon allocation in forests estimated from litterfall and IRGA-based soil respiration measurements. Agric For Meteorol 113:39–51
de Gannes V, Bekele I, Dipchansingh D et al (2016) Microbial community structure and function of soil following ecosystem conversion from native forests to teak plantation forests. Front Microbiol 7:1–13
De Mandal S, Panda AK, Lalnunmawii E, et al (2015) Illumina-based analysis of bacterial community in Khuangcherapuk cave of Mizoram, Northeast India
Doolette CL, Gupta VVSR, Lu Y et al (2016) Quantifying the sensitivity of soil microbial communities to silver sulfide nanoparticles using metagenome sequencing. PLoS One 11:1–20
Doran J, Kettler T, Tsivou M (1997) Field and laboratory Solvita soil test evaluation. Lincoln, USA
Earl JP, Adappa ND, Krol J et al (2018) Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific biosciences sequencing of full-length 16S rRNA genes 06 Biological Sciences 0604 Genetics 06 Biological Sciences 0605 Microbiology. Microbiome 6. https://doi.org/10.1186/s40168-018-0569-2
Edwards NT, Sollins P (1973) Continuous measurement of carbon dioxide evolution from partitioned forest floor components. Ecology 54:406–412
Effron D, de la Horra AM, Defrieri RL et al (2004) Effect of cadmium, copper, and lead on different enzyme activities in a native forest soil. Commun Soil Sci Plant Anal 35:1309–1321
Evanylo G (2009) Agricultural management practices and soil quality: measuring, assessing, and comparing laboratory and field test kit indicators of soil quality attributes. Virginia State Univ, Petersburg
Fierer N, Leff JW, Adams BJ et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 109:21390–21395
Finzi-Hart JA, Pett-Ridge J, Weber PK et al (2009) Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry. Proc Natl Acad Sci U S A 106:6345–6350
Fliebach A, Martens R, Reber HH (1994) Soil microbial biomass and microbial activity in soils treated with heavy metal contaminated sewage sludge. Soil Biol Biochem 26:1201–1205
Foster RA, Sztejrenszus S, Kuypers MMM (2013) Measuring carbon and N2 fixation in field populations of colonial and free-living unicellular cyanobacteria using nanometer-scale secondary ion mass spectrometry (1). J Phycol 49:502–516
Frostegard A, Baath E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22:59–65
Frostegard A, Tunlid A, Baath E (1993) Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59:3605–3617
Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625
Fujimoto M, Moyerbrailean GA, Noman S et al (2014) Application of Ion Torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity. PLoS One 9:1–8
Gahan J, Schmalenberger A (2014) The role of bacteria and mycorrhiza in plant sulfur supply. Front Plant Sci 5:723
Gao C, Ren X, Mason AS et al (2014) Horizontal gene transfer in plants. Funct Integr Genomics 14:23–29
Garrett HE, Cox GS (1973) Carbon dioxide evolution from the floor of an Oak-Hickory forests. Soil Sci Soc Am J 37:641
Gołębiewski M, Deja-Sikora E, Cichosz M et al (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol 67:635–647
González-Pérez JA, González-Vila FJ, Almendros G, Knicker H (2004) The effect of fire on soil organic matter - a review. Environ Int 30:855–870
Goupil K, Nkongolo K (2014) Assessing soil respiration as an indicator of soil microbial activity in reclaimed metal contaminted lands. Am J Environ Sci 10:403–411
Goupil K, Nkongolo KK, Nasserulla S (2015) Characterization of fungal communities in limed and unlimed lands contaminated with metals: phospholipid fatty acid (PLFA) analysis and soil respiration. Am J Biochem Biotechnol 11:45–56
Hagmann DF, Goodey NM, Mathieu C et al (2015) Effect of metal contamination on microbial enzymatic activity in soil. Soil Biol Biochem 91:291–297
He Z, Xu M, Deng Y et al (2010) Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett 13:564–575
He Z, Van Nostrand JD, Zhou J (2012) Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 23:460–466
He Z, Van Nostrand JD, Zhou J (2013) GeoChip-based metagenomic technologies for analyzing microbial community functional structure and activities. https://doi.org/10.1007/978-1-4614-6418-1_760-4
Herrick JE, Hefin J (2013) Soil ecology and ecosystem services. OUP Oxford, Oxford
Hinojosa MB, García-Ruiz R, Carreira JA (2010) Utilizing microbial community structure and function to evaluate the health of heavy metal polluted soils. In: Sherameti I, Varma A (eds) Soil heavy metals. Springer, Berlin, pp 185–224
Hiraoka S, Machiyama A, Ijichi M et al (2016a) Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. BMC Genomics 17. https://doi.org/10.1186/s12864-016-2380-4
Hiraoka S, Yang CC, Iwasaki W (2016b) Metagenomics and bioinformatics in microbial ecology: current status and beyond. Microbes Environ 31:204–212
Hodkinson BP, Grice EA (2015) Next-generation sequencing: a review of technologies and tools for wound microbiome research. Adv Wound Care 4:50–58. https://doi.org/10.1089/wound.2014.0542
Hohl H, Varma A (2010) Soil: the living matrix. In: Sherameti I, Varma A (eds) Soil heavy metals. Springer, Berlin, pp 1–18
Hong C, Si Y, Xing Y, Li Y (2015) Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas. Environ Sci Pollut Res 22:10788–10799
Ikuta T, Takaki Y, Nagai Y et al (2016) Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME J 10:990–1001. https://doi.org/10.1038/ismej.2015.176
Jünemann S, Sedlazeck FJ, Prior K et al (2013) Updating benchtop sequencing performance comparison. Nat Biotechnol 31:294–296
Kamal S, Prasad R, Varma A (2010) Soil microbial diversity in relation to heavy metals. In: Sherameti I, Varma A (eds) Soil heavy metals. Springer, Berlin, pp 31–63
Karaca A, Cetin SC, Turgay OC, Kizilkaya R (2010) Effects of heavy metals on soil enzyme activities. In: Sherameti I, Varma A (eds) Soil heavy metals. Springer, Berlin, pp 237–262
Kasuga I, Kurisu F, Furumai H (2016) Identification of bacteria assimilating formaldehyde in a biological activated carbon filter by means of DNA stable isotope probing and next-generation sequencing. Water Sci Technol Water Supply 16:915–921
Kaur A, Chaudhary A, Kaur A et al (2005) Phospholipid fatty acid - a bioindicator of environment monitoring and assessment in soil ecosystem. Curr Sci 89:1103–1112
Kertesz MA, Mirleau P (2004) The role of soil microbes in plant sulphur nutrition. J Exp Bot 55:1939–1945
Khan S, Cao Q, Hesham AE-L et al (2007) Soil enzymatic activities and microbial community structure with different application rates of Cd and Pb. J Environ Sci 19:834–840
Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:1–23. https://doi.org/10.3389/fpls.2014.00216
Knight R, Maxwell P, Birmingham A et al (2007) PyCogent: a toolkit for making sense from sequence. Genome Biol 8:1–16. https://doi.org/10.1186/gb-2007-8-8-r171
Koranda M, Kaiser C, Fuchslueger L et al (2014) Fungal and bacterial utilization of organic substrates depends on substrate complexity and N availability. FEMS Microbiol Ecol 87:142–152
Kowalchuk GA, Buma DS, de Boer W et al (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81:509–520
Kuczynski J, Stombaugh J, Walters WA et al (2011) Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics:1–28
Landi L, Renella G, Moreno JL et al (2000) Influence of cadmium on the metabolic quotient, l-:D -glutamic acid respiration ratio and enzyme activity:microbial biomass ratio under laboratory conditions. Biol Fertil Soils 32:8–16
Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120
Laureto LMO, Cianciaruso MV, Samia DSM (2015) Functional diversity: an overview of its history and applicability. Nat Conserv 13:112–116
Li Y, Chen L, Wen H et al (2014) 454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas. J Microbiol Biotechnol 24:313–323
Lim YW, Kim BK, Kim C et al (2010) Assessment of soil fungal communities using pyrosequencing. J Microbiol 48:284–289
Liu L, Li Y, Li S et al (2012, 2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol:1–11
Liu L, Lyu D, Li J et al (2016a) Illumina high-throughput sequencing and comparative analysis of bacterial communities in cherry orchard soil. Toxicol Environ Chem 98:462–478
Liu Q, Qiao N, Xu X et al (2016b) Nitrogen acquisition by plants and microorganisms in a temperate grassland. Sci Rep 6:1–10
Llado S, Baldrian P (2017) Community level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments. PLoS One 12(2):e0171638. https://doi.org/10.1371/journal.pone.0171638
Loman NJ, Constantinidou C, Chan JZM et al (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599–606
Lorenz N, Hintemann T, Kramarewa T et al (2006) Response of microbial activity and microbial community composition in soils to long-term arsenic and cadmium exposure. Soil Biol Biochem 38:1430–1437
Lu Z, He Z, Parisi VA et al (2012) GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ Sci Technol 46:5824–5833
Luo C, Tsementzi D, Kyrpides N et al (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7:e30087
Lv X, Ma B, Yu J et al (2016) Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta. Sci Rep 6:1–10
Ma M (2005) Species richness vs evenness: independent relationship and different responses to edaphic factors. Oikos 111:192–198
Maier MR, Pepper LI, Gerba PC (2009) Environmental microbiology, 2nd edn. Elsevier Academic Press, London
McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ (2015) Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 526:531–535
Mitra S, Förster-Fromme K, Damms-Machado A et al (2013) Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14:1–11
Mühlbachová G, Tlustoš P (2006) Effects of liming on the microbial biomass and its activities in soils long-term contaminated by toxic elements. Plant Soil Environ 52:345–352
Musat N, Foster R, Vagner T et al (2012) Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev 36:486–511
Narendrula R, Nkongolo KK (2015) Fatty acids profile of microbial populations in a mining reclaimed region contaminated with metals: relation with ecological characteristics and soil respiration. J Bioremediation Biodegrad 6:1–9
Narendrula-Kotha R, Nkongolo KK (2017a) Bacterial and fungal resilience to long-term metal exposure in a mining region revealed by metagenomics sequencing. Ecol Genet Genomics 2:12–24
Narendrula-Kotha R, Nkongolo KK (2017b) Changes in enzymatic activities in metal contaminated and reclaimed lands in Northern Ontario (Canada). Ecotoxicol Environ Saf 140:241–248
Narendrula-Kotha R, Nkongolo KK (2017c) Microbial response to soil liming of damaged ecosystems revealed by pyrosequencing and phospholipid fatty acid analyses. PLoS One 12:e0168497
Nielsen MN, Winding A, Binnerup S, et al (2002) Microorganisms as indicators of soil health. NERI technical report no. 388. Denmark
Niu J, Rang Z, Zhang C et al (2016) The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt. BMC Microbiol 16:1–10
Nuñez J, Renslow R, Cliff JB, Anderton CR (2018) NanoSIMS for biological applications: current practices and analyses. Biointerphases 13:03B301
Pennanen T (2001) Microbial communities in boreal coniferous forest humus exposed to heavy metals and changes in soil pH—a summary of the use of phospholipid fatty acids, Biolog® and 3H-thymidine incorporation methods in field studies. Geoderma 100:91–126
Pennanen T, Frostegard A, Fritze H, Baath E (1996) Phospholipid fatty acid composition and heavy metal tolerance of soil microbial communities along two heavy metal-polluted gradients in coniferous forests. Appl Environ Microbiol 62:420–428
Pennanen T, Fritze H, Vanhala P, Kiikkilä O (1998) Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain. Appl Environ Microbiol 64:2173–2180
Petchey OL, Gaston KJ (2006) Functional diversity: back to basics and looking forward. Ecol Lett 9:741–758
Quince C, Lanzén A, Curtis TP et al (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6:639–641
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649
Raich JW, Schlesinger WH (1992) The global carbon dioxide flux in soil respiration and its relationship to vegetation and climate. Tellus B 44:81–99
Rajendhran J, Gunasekaran P (2011) Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res 166:99–110
Renslow RS, Lindemann SR, Cole JK et al (2016) Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. Biointerphases 11:02A322
Richardson AE, Barea J-M, McNeill AM, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321:305–339
Riggs CE, Hobbie SE, Bach EM et al (2015) Nitrogen addition changes grassland soil organic matter decomposition. Biogeochemistry 125:203–219
Rogge A, Vogts A, Voss M et al (2017) Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K and r-strategists. Environ Microbiol 19:2495–2506
Rosselli R, Romoli O, Vitulo N et al (2016) Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon. Sci Rep 6:1–12
Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352
Rousk J, Bååth E, Brookes PC et al (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4:1340–1351
Ryan MG, Law BE (2005) Interpreting, measuring, and modeling soil respiration. Biogeochemistry 73:3–27
Salipante SJ, Kawashima T, Rosenthal C et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol 80:7583–7591
Schoch CL, Seifert KA, Huhndorf S et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A 109:6241–6246
Schöler A, Jacquiod S, Vestergaard G et al (2017) Analysis of soil microbial communities based on amplicon sequencing of marker genes. Biol Fertil Soils 53:485–489
Seedorf H, Kittelmann S, Janssen PH (2015) Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle. Appl Environ Microbiol 81:986–995. https://doi.org/10.1128/AEM.03018-14
Seyboldc (1999) Soil Quality Test Kit Guide. United States Dep Agric 1–88
Sheik AR, Brussaard CPD, Lavik G et al (2013) Viral infection of Phaeocystis globosa impedes release of chitinous star-like structures: quantification using single cell approaches. Environ Microbiol 15:1441–1451
Sherameti I, Varma A (2015) Heavy metal contamination of soils: monitoring and remediation. Springer, New York
Shi Z, Yin H, Van Nostrand JD et al (2019) Functional gene array-based ultrasensitive and quantitative detection of microbial populations in complex communities. mSystems 4. https://doi.org/10.1128/msystems.00296-19
Shokralla S, Gibson JF, Nikbakht H et al (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol Ecol Resour 14:1–10
Sinclair L, Osman OA, Bertilsson S et al (2015) Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the Illumina platform. PLoS One 10:1–18
Sinsabaugh RL, Lauber CL, Weintraub MN et al (2008) Stoichiometry of soil enzyme activity at global scale. Ecol Lett 11:1252–1264
Smith JL, Doran JW (1996) Measurement and use of pH and electrical conductivity for soil quality analysis. In: Doran JW, Jones AJ (eds) Methods for assessing soil quality, SSSA spec, Publ, vol 49. Soil Science Society of America, Madison, pp 169–185
Solvita (2013) Official solvita guideline soil CO2 respiration test. Woods End Laboratories Inc., Mt Vernon
Stres B, Danevcic T, Pal L et al (2008) Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms. FEMS Microbiol Ecol 66:110–122
Sulzman EW, Brant JB, Bowden RD, Lajtha K (2005) Contribution of aboveground litter, belowground litter, and rhizosphere respiration to total soil CO2 efflux in an old growth coniferous forest. Biogeochemistry 73:231–256
Taubert M, Grob C, Howat AM et al (2016) Analysis of active methylotrophic communities: when DNA-SIP meets high-throughput technologies. In: Martin F Uroz (ed) microbial environmental genomics (MEG). Humana Press, New York, pp 235–255
Terrado R, Pasulka AL, Lie AA-Y et al (2017) Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis. ISME J 11:2022–2034
Tessler M, Neumann JS, Afshinnekoo E et al (2017) Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing. Sci Rep 7:6589
Tu Q, Yu H, He Z et al (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 14:914–928
Wang FY, Hu JL, Lin XG et al (2011) Arbuscular mycorrhizal fungal community structure and diversity in response to long-term fertilization: a field case from China. World J Microbiol Biotechnol 27:67–74
Weil R, Brady N (2015) The nature and properties of soils, 15th edn. Pearson Education, New York
Yang Y, Campbell CD, Clark L et al (2006) Microbial indicators of heavy metal contamination in urban and rural soils. Chemosphere 63:1942–1952
Yiqi L, Zhou X (2010) Soil respiration and the environment. Elsevier Science, San Diego
Youngblut ND, Barnett SE, Buckley DH (2018) SIPSim: a modeling toolkit to predict accuracy and aid design of DNA-SIP experiments. Front Microbiol 9. https://doi.org/10.3389/fmicb.2018.00570
Yu H, Gao Q, Shao Z et al (2016) Decreasing nitrogen fertilizer input had little effect on microbial communities in three types of soils. PLoS One 11:1–12
Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95–109
Zhang X, Qu Y, Ma Q et al (2015) Illumina MiSeq sequencing reveals diverse microbial communities of activated sludge systems stimulated by different aromatics for indigo biosynthesis from Indole. PLoS One 10:1–14
Zhou J, Deng Y, He Z et al (2010) Applying GeoChip analysis to disparate microbial communities. Microbe 5:60–65
Zhou J, He Z, Yang Y et al (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6:1–17