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Advances in monitoring soil microbial community dynamic and function

  • Microbial Genetics • Review
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Abstract

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.

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References

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Bardgett RD, Bowman WD, Kaufmann R, Schmidt SK (2005) A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol 20:634–641

    PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Google Scholar 

  • Boxer SG, Kraft ML, Weber PK (2009) Advances in imaging secondary ion mass spectrometry for biological samples. Annu Rev Biophys 38:53–74

    CAS  PubMed  Google Scholar 

  • Breure AM (2004) Soil biodiversity: measurements, indicators, threats and soil functions. In: International conference - soil and compost eco-biology. Leon, Spain, pp 1–14

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Burns RG (1977) Soil enzymology. Sci Prog 64:275–285

    CAS  PubMed  Google Scholar 

  • Buyer JS, Sasser M (2012) High throughput phospholipid fatty acid analysis of soils. Appl Soil Ecol 61:127–130

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Coleman DC (1973) Compartmental analysis of total soil respiration: an exploratory study. Oikos 24:361

    Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • Cook FJ, Orchard VA (2008) Relationships between soil respiration and soil moisture. Soil Biol Biochem 40:1013–1018

    CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • Doran J, Kettler T, Tsivou M (1997) Field and laboratory Solvita soil test evaluation. Lincoln, USA

  • Dunford EA, Neufeld JD (2010) DNA stable-isotope probing (DNA-SIP). J Vis Exp

  • 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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625

    Google Scholar 

  • 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

    Google Scholar 

  • Gahan J, Schmalenberger A (2014) The role of bacteria and mycorrhiza in plant sulfur supply. Front Plant Sci 5:723

    PubMed  PubMed Central  Google Scholar 

  • Gao C, Ren X, Mason AS et al (2014) Horizontal gene transfer in plants. Funct Integr Genomics 14:23–29

    CAS  PubMed  Google Scholar 

  • Garrett HE, Cox GS (1973) Carbon dioxide evolution from the floor of an Oak-Hickory forests. Soil Sci Soc Am J 37:641

    Google Scholar 

  • Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • He Z, Van Nostrand JD, Zhou J (2012) Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 23:460–466

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hohl H, Varma A (2010) Soil: the living matrix. In: Sherameti I, Varma A (eds) Soil heavy metals. Springer, Berlin, pp 1–18

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Jünemann S, Sedlazeck FJ, Prior K et al (2013) Updating benchtop sequencing performance comparison. Nat Biotechnol 31:294–296

    PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Kertesz MA, Mirleau P (2004) The role of soil microbes in plant sulphur nutrition. J Exp Bot 55:1939–1945

    CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Laureto LMO, Cianciaruso MV, Samia DSM (2015) Functional diversity: an overview of its history and applicability. Nat Conserv 13:112–116

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Lim YW, Kim BK, Kim C et al (2010) Assessment of soil fungal communities using pyrosequencing. J Microbiol 48:284–289

    PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Liu Q, Qiao N, Xu X et al (2016b) Nitrogen acquisition by plants and microorganisms in a temperate grassland. Sci Rep 6:1–10

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Ma M (2005) Species richness vs evenness: independent relationship and different responses to edaphic factors. Oikos 111:192–198

    Google Scholar 

  • Maier MR, Pepper LI, Gerba PC (2009) Environmental microbiology, 2nd edn. Elsevier Academic Press, London

    Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    CAS  PubMed  Google Scholar 

  • McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ (2015) Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 526:531–535

    CAS  PubMed  Google Scholar 

  • Metzker ML (2010) Sequencing technologies — the next generation. Nat Rev Genet 11:31–46

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Nuñez J, Renslow R, Cliff JB, Anderton CR (2018) NanoSIMS for biological applications: current practices and analyses. Biointerphases 13:03B301

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Petchey OL, Gaston KJ (2006) Functional diversity: back to basics and looking forward. Ecol Lett 9:741–758

    PubMed  Google Scholar 

  • Quince C, Lanzén A, Curtis TP et al (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6:639–641

    CAS  PubMed  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Rajendhran J, Gunasekaran P (2011) Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res 166:99–110

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Riggs CE, Hobbie SE, Bach EM et al (2015) Nitrogen addition changes grassland soil organic matter decomposition. Biogeochemistry 125:203–219

    CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Ryan MG, Law BE (2005) Interpreting, measuring, and modeling soil respiration. Biogeochemistry 73:3–27

    Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145

    CAS  PubMed  Google Scholar 

  • Sherameti I, Varma A (2015) Heavy metal contamination of soils: monitoring and remediation. Springer, New York

    Google Scholar 

  • 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

    Google Scholar 

  • Shukla G, Varma A (2011) Soil enzymology. Springer, Berlin

    Google Scholar 

  • 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

    Google Scholar 

  • Sinsabaugh RL, Lauber CL, Weintraub MN et al (2008) Stoichiometry of soil enzyme activity at global scale. Ecol Lett 11:1252–1264

    PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Solvita (2013) Official solvita guideline soil CO2 respiration test. Woods End Laboratories Inc., Mt Vernon

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Weil R, Brady N (2015) The nature and properties of soils, 15th edn. Pearson Education, New York

    Google Scholar 

  • Weinstock GM (2012) Genomic approaches to studying the human microbiota. Nature 489:250–256

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Campbell CD, Clark L et al (2006) Microbial indicators of heavy metal contamination in urban and rural soils. Chemosphere 63:1942–1952

    CAS  PubMed  Google Scholar 

  • Yiqi L, Zhou X (2010) Soil respiration and the environment. Elsevier Science, San Diego

    Google Scholar 

  • 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

    Google Scholar 

  • Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38:95–109

    PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Zhou J, Deng Y, He Z et al (2010) Applying GeoChip analysis to disparate microbial communities. Microbe 5:60–65

    Google Scholar 

  • 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

    Google Scholar 

  • Ziels RM, Sousa DZ, Stensel HD, Beck DAC (2018) DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies. ISME J 12:112–123

    CAS  PubMed  Google Scholar 

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Acknowledgments

Thanks to Natural Sciences and Engineering Council of Canada (NSERC) for supporting our research program in Environmental Genomics and transcriptomics.

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Authors and Affiliations

  1. Department of Biology, University of Sudbury, Sudbury, Ontario, P3E 2C6, Canada

    K. K. Nkongolo

  2. Biomolecular Sciences Program, Laurentian, University of Sudbury, Sudbury, Ontario, P3E 2C6, Canada

    K. K. Nkongolo & R. Narendrula-Kotha

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  1. K. K. Nkongolo
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Nkongolo, K.K., Narendrula-Kotha, R. Advances in monitoring soil microbial community dynamic and function. J Appl Genetics 61, 249–263 (2020). https://doi.org/10.1007/s13353-020-00549-5

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