Skip to main content Accessibility help
×
Hostname: page-component-8448b6f56d-gtxcr Total loading time: 0 Render date: 2024-04-18T05:52:37.360Z Has data issue: false hasContentIssue false

1 - General Geochemistry and Microbiology Techniques

from Part I - Standard Techniques in Geomicrobiology

Published online by Cambridge University Press:  06 July 2019

Janice P. L. Kenney
Affiliation:
MacEwan University, Edmonton
Harish Veeramani
Affiliation:
Carleton University, Ottawa
Daniel S. Alessi
Affiliation:
University of Alberta
Get access

Summary

Geomicrobiological investigations benefit from knowledge of geochemical and biological systems at different scales, including information about both the abiotic and the biotic components. Gathering this information requires analysis and characterization of both abiotic and biotic components of the target system. The techniques presented in this chapter were selected to cover a variety of needs in geomicrobiological studies, including general sample collection and storage, organic and inorganic compound quantification, and best practices for cultivation, observation, and analysis of microorganisms and microbial communities. In this chapter, introductions and discussions for common techniques provide the reader with a basic understanding of the technique itself, which samples can be analyzed using the technique, and how to prepare samples for analysis. Detailed methods are provided for select techniques, and citations to standard methods are provided for techniques whenever available. For techniques that are rapidly evolving, recent developments and applications are discussed.

Type
Chapter
Information
Analytical Geomicrobiology
A Handbook of Instrumental Techniques
, pp. 3 - 60
Publisher: Cambridge University Press
Print publication year: 2019

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

1.5 References

Amann, RI, Ludwig, W and Schleifer, KH 1995, ‘Phylogenetic identification and in situ detection of individual microbial cells without cultivation’, Microbiological Reviews, vol. 59, no. 1, pp. 143169.Google Scholar
Anderson, TH and Domsch, KH, 1993, ‘The metabolic quotient for CO2 (qCO2) as a specific activity parameter to assess the effects of environmental conditions, such as pH, on the microbial biomass of forest soils’, Soil Biology and Biochemistry, vol. 25, no. 3, pp. 393395.Google Scholar
Atlas, RM 2010, Handbook of microbiological media, CRC Press, Florida.Google Scholar
Barnes, MA, Turner, CR, Jerde, CL, et al. 2014, ‘Environmental conditions influence eDNA persistence in aquatic systems’, Environmental Science & Technology, vol. 48, no. 3, pp. 18191827.Google Scholar
Bates, TE 1993, ‘Soil handling and preparation’, in Carter, MR, (ed), Soil sampling and methods of analysis, CRC Press, Florida.Google Scholar
Batley, GE (ed) 1989, Trace element speciation analytical methods and problems, CRC Press, Florida.Google Scholar
Benndorf, D, Balcke, GU, Harms, H and von Bergen, M 2007, ‘Functional metaproteome analysis of protein extracts from contaminated soil and groundwater’, The ISME Journal, vol. 1, no. 3, pp. 224234.Google Scholar
Blakemore, LC 1968, ‘Determination of iron and aluminum in Tamm’s soil extracts’, New Zealand Journal of Agricultural Research, vol. 11, no. 2, pp. 515520.Google Scholar
Böhme, L, Langer, W and Böhme, F 2005, ‘Microbial biomass, enzyme activities and microbial community structure in two European long-term field experiments’, Agriculture, Ecosystems & Environment, vol. 109, no. 1, pp. 141152.Google Scholar
Bradford, MM 1976, ‘A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding’, Analytical Geochemistry, vol. 72, no. 1–2, pp. 248254.Google Scholar
Brodie, EL, DeSantis, TZ, Joyner, DC, et al. 2006, ‘Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation’, Applied and Environmental Microbiology, vol. 72, no. 9, pp. 62886298.Google Scholar
Brown, CT, Hug, LA, Thomas, BC, et al. 2015, ‘Unusual biology across a group comprising more than 15% of domain Bacteria’, Nature, vol. 523, no. 7559, pp. 208211.Google Scholar
Burns, RG 1982, ‘Enzyme activity in soil: location and a possible role in microbial ecology’, Soil Biology and Biochemistry, vol. 14, no. 5, pp. 423427.Google Scholar
Bustin, SA 2000, ‘Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays’, Journal of Molecular Endocrinology, vol. 25, no. 2, pp. 169193.CrossRefGoogle ScholarPubMed
Bustin, SA, Benes, V, Garson, JA, et al. 2009, ‘The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments’, Clinical Chemistry, vol. 55, no. 4, pp. 611622.Google Scholar
Caldwell, HD, Kromhout, J and Schachter, J 1981, ‘Purification and partial characterization of the major outer membrane protein of Chlamydia trachomatis’, Infection and Immunity, vol. 31, no. 3, pp. 11611176.Google Scholar
Cardenas, E and Tiedje, JM 2008, ‘New tools for discovering and characterizing microbial diversity’, Current Opinion in Biotechnology, vol 19, no. 6, pp. 544549.Google Scholar
Carrigg, C, Rice, O, Kavanagh, S, Collins, G and O’Flaherty, V 2007, ‘DNA extraction method affects microbial community profiles from soils and sediment’, Applied Microbiology and Biotechnology, vol. 77, no. 4, pp. 955964.CrossRefGoogle ScholarPubMed
Casida, LE 1977, ‘Microbial metabolic activity in soil as measured by dehydrogenase determinations’, Applied and Environmental Microbiology, vol. 34, no. 6, pp. 630636.Google Scholar
Choi, KH and Dobbs, FC 1999, ‘Comparison of two kinds of Biolog microplates (GN and ECO) in their ability to distinguish among aquatic microbial communities’, Journal of Microbiological Methods, vol. 36, no. 3, pp. 203213.Google Scholar
Chourey, K, Jansson, J, VerBerkmoes, N, et al. 2010, ‘Direct cellular lysis/protein extraction protocol for soil metaproteomics’, Journal of Proteome Research, vol. 9, no. 12, pp. 66156622.CrossRefGoogle ScholarPubMed
Ciardi, C and Nannipieri, P 1990, ‘A comparison of methods for measuring ATP in soil’, Soil Biology and Biochemistry, vol. 22, no. 5, pp. 725727.Google Scholar
Critter, SAM, Freitas, SS and Airoldi, C 2004, ‘Comparison of microbial activity in some Brazilian soils by microcalorimetric and respirometric methods’, Thermochimica Acta, vol. 410, no. 1, pp. 3546.Google Scholar
Crompton, TR 2001, Determination of metals and anions in soils, sediments and sludges, Spon Press, London.CrossRefGoogle Scholar
Daniel, R 2005, ‘The metagenomics of soil’, Nature Reviews Microbiology, vol. 3, no. 6, pp. 470478.Google Scholar
DeSantis, TZ, Brodie, EL, Moberg, JP, et al. 2007, ‘High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment’, Microbial Ecology, vol. 53, no. 3, pp. 371383.Google Scholar
Dinsdale, EA, Edwards, RA, Hall, D, et al. 2008, ‘Functional metagenomic profiling of nine biomes’, Nature, vol. 452, no. 7187, pp. 629632.Google Scholar
ECS 2001, ‘EN 13137:2001 Characterization of waste: determination of total organic carbon (TOC) in waste, sludges and sediments’, European Committee for Standardization.Google Scholar
Feinstein, LM, Sul, WJ and Blackwood, CB 2009, ‘Assessment of bias associated with incomplete extraction of microbial DNA from soil’, Applied and Environmental Microbiology, vol. 75, no. 16, pp. 54285433.Google Scholar
Filip, C, Fletcher, G, Wulff, JL and Earhart, CF 1973, ‘Solubilization of the cytoplasmic membrane of Escherichia coli by the ionic detergent sodium-lauryl sarcosinate’, Journal of Bacteriology, vol. 115, no. 3, pp. 717722.Google Scholar
Fontaine, S, Barot, S, Barré, P, et al. 2007, ‘Stability of organic carbon in deep soil layers controlled by fresh carbon supply’, Nature, vol. 450, no. 7167, pp. 277280.Google Scholar
Fortune, WB and Mellon, MG 1938, ‘Determination of iron with o-phenanthroline: a spectrophotometric study’, Industrial and Engineering Chemistry, Analytical Edition, vol. 10, no. 2, pp. 6064.Google Scholar
Frias-Lopez, J, Shi, Y, Tyson, GW, et al. 2008, ‘Microbial community gene expression in ocean surface waters’, Proceedings of the National Academy of Sciences, vol. 105, no. 10, pp. 38053810.Google Scholar
Fritz, JS and Gjerde, DT 2009, Ion chromatography, 4th completely revised and enlarged ed, Wiley, New Jersey.Google Scholar
Garland, JL and Mills, AL 1991, ‘Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization’, Applied and Environmental Microbiology, vol. 57, no. 8, pp. 23512359.Google Scholar
Girvan, MS, Bullimore, J, Pretty, JN, Osborn, AM and Ball, AS 2003, ‘Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils’, Applied and Environmental Microbiology, vol. 69, no. 3, pp. 18001809.Google Scholar
Goebel-Stengel, M, Stengel, A, Taché, Y and Reeve, JR 2011, ‘The importance of using the optimal plasticware and glassware in studies involving peptides’, Analytical Biochemistry, vol. 414, no. 1, pp. 3846.Google Scholar
Görg, A, Weiss, W and Dunn, MJ 2004, ‘Current two-dimensional electrophoresis technology for proteomics’, Proteomics vol. 4, no. 12, pp. 36653685.Google Scholar
Green, MR and Sambrook, J 2016, ‘Precipitation of DNA with ethanol’, Cold Spring Harbor Protocols, Available from: http://cshprotocols.cshlp.org/content/2016/12/pdb.prot093377.full.pdf+html [August 18, 2017].Google Scholar
Handelsman, J 2004, ‘Metagenomics: application of genomics to uncultured microorganisms’, Microbiology and Molecular Biology Reviews, vol. 68, no. 4, pp. 669685.CrossRefGoogle ScholarPubMed
Hanson, PJ, Edwards, NT, Garten, CT and Andrews, JA 2000, ‘Separating root and soil microbial contributions to soil respiration: a review of methods and observations’, Biogeochemistry, vol. 48, no. 1, pp. 115146.Google Scholar
Hartley, IP, Hopkins, DW, Garnett, MH, Sommerkorn, M and Wookey, PA 2008, ‘Soil microbial respiration in arctic soil does not acclimate to temperature’, Ecology Letters, vol. 11, no. 10, pp. 10921100.CrossRefGoogle Scholar
He, S, Wurtzel, O, Singh, K, et al. 2010, ‘Validation of two ribosomal RNA removal methods for microbial metatranscriptomics’, Nature Methods, vol. 7, no. 10, pp. 807812.Google Scholar
He, Z, Gentry, TJ, Schadt, CW, et al. 2007, ‘GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes’, The ISME Journal, vol. 1, no. 1, pp. 6777.Google Scholar
Heid, CA, Stevens, J, Livak, KJ and Williams, PM 1996, ‘Real time quantitative PCR’, Genome Research, vol. 6, no. 10, pp. 986994.Google Scholar
Higuchi, R, Dollinger, G, Walsh, PS and Griffith, R 1992, ‘Simultaneous amplification and detection of specific DNA sequences’, Nature Biotechnology, vol. 10, no. 4, pp. 413417.CrossRefGoogle ScholarPubMed
Holland, PM, Abramson, RD, Watson, R and Gelfand, DH 1991, ‘Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase’, Proceedings of the National Academy of Sciences, vol. 88, no. 16, pp. 72767280.CrossRefGoogle ScholarPubMed
Horowitz, AJ, Elrick, KA and Colberg, MR 1992, ‘The effect of membrane filtration artifacts on dissolved trace element concentrations’, Water Research, vol. 26, no. 6, pp. 753763.Google Scholar
Hu, S and van Bruggen, AHC 1997. ‘Microbial dynamics associated with multiphasic decomposition of 14C-labeled cellulose in soil’, Microbial Ecology, vol. 33, no. 2, pp. 134143.Google Scholar
Hu, Z and Qi, L 2014, ‘Sample digestion methods’ in Holland, H, and Turekian, K, (eds), Treatise on geochemistry, 2nd ed, Elsevier Science, Amsterdam.Google Scholar
Huang, B, Ying, H, Yang, P, Wang, X and Gu, S 2000, An atlas of high resolution spectra of rare earth elements for ICP-AES, Royal Society of Chemistry, London.Google Scholar
Hug, LA, Baker, BJ, Anantharaman, K, et al. 2016, ‘A new view of the tree of life’, Nature Microbiology, vol. 1, no. 16048.Google Scholar
Hurst, CJ, Crawford, RL, Garland, JL and Lipson, DA (eds) 2007, Manual of environmental microbiology, 3rd ed, American Society for Microbiology Press, Washington, DC.Google Scholar
Hurt, RA, Qiu, X, Wu, L, et al. 2001. ‘Simultaneous recovery of RNA and DNA from soils and sediments’, Applied and Environmental Microbiology, vol. 67, no. 10, pp. 44954503.Google Scholar
Isaacson, T, Damasceno, CM, Saravanan, RS, et al. 2006, ‘Sample extraction techniques for enhanced proteomic analysis of plant tissues’, Nature Protocols, vol. 1, no. 2, pp. 769774.Google Scholar
ISO 1995, ‘ISO 10694:1995 Soil quality: Determination of organic and total carbon after dry combustion (elementary analysis)’, International Organization for Standardization.Google Scholar
Jackson, KW and Jackson, E 1999, Electrothermal atomization for analytical atomic spectrometry, Wiley, New Jersey.Google Scholar
Jackson, ML 2005, Soil chemical analysis: advanced course, Parallel Press, Wisconsin.Google Scholar
Jenkinson, DS and Oades, JM 1979, ‘A method for measuring adenosine triphosphate in soil’, Soil Biology and Biochemistry, vol. 11, no. 2, pp. 193199.Google Scholar
Karl, DM and Holm-Hansen, O 1978, ‘Methodology and measurement of adenylate energy charge ratios in environmental samples’, Marine Biology, vol. 48, no. 2, pp. 185197.Google Scholar
Kasibhatla, S, Amarante-Mendes, GP, Finucane, D, et al. 2006, ‘Analysis of DNA fragmentation using agarose gel electrophoresis’, Cold Spring Harbor Protocols, Available from: http://cshprotocols.cshlp.org/content/2006/1/pdb.prot4429.short [August 18, 2017].CrossRefGoogle Scholar
Kaur, K 2007, Handbook of water and wastewater analysis, Atlantic Publishers & Distributors (P) Ltd., New Delhi.Google Scholar
Keiblinger, KM, Wilhartitz, IC, Schneider, T, et al. 2012, ‘Soil metaproteomics–comparative evaluation of protein extraction protocols’, Soil Biology and Biochemistry, vol. 54, pp. 1424.Google Scholar
Kourtev, PS, Ehrenfeld, JG and Häggblom, M 2002, ‘Exotic plant species alter the microbial community structure and function in the soil’, Ecology, vol. 83, no. 11, pp. 31523166.Google Scholar
Kubista, M, Andrade, JM, Bengtsson, M, et al. 2006, ‘The real-time polymerase chain reaction’, Molecular Aspects of Medicine, vol. 27, no. 2, pp. 95125.Google Scholar
Lachat 2008, Data Pack Lachat Applications in Standard Methods 21st Edition, Lachat Instruments, Milwaukee, Wisconsin.Google Scholar
Lee, SC, Knowles, TJ, Postis, VL, et al. 2016, ‘A method for detergent-free isolation of membrane proteins in their local lipid environment’, Nature Protocols, vol. 11, no. 7, pp. 11491162.Google Scholar
Leff, LG, Dana, JR, McArthur, JV and Shimkets, LJ 1995, ‘Comparison of methods of DNA extraction from stream sediments’, Applied and Environmental Microbiology, vol. 61, no. 3, pp. 11411143.Google Scholar
Levy-Booth, DJ, Campbell, RG, Gulden, RH, et al. 2007, ‘Cycling of extracellular DNA in the soil environment’, Soil Biology and Biochemistry, vol. 39, no. 12, pp. 29772991.Google Scholar
Li, H and Homer, N 2010, ‘A survey of sequence alignment algorithms for next-generation sequencing’, Briefings in Bioinformatics, vol. 11, no. 5, pp. 473483.Google Scholar
Liu, F, Ying, GG, Tao, R, et al. 2009, ‘Effects of six selected antibiotics on plant growth and soil microbial and enzymatic activities’, Environmental Pollution, vol. 157, no. 5, pp. 16361642.Google Scholar
Liu, L, Li, Y, Li, S, et al. 2012, ‘Comparison of next-generation sequencing systems’, Journal of Biomedicine and Biotechnology, vol. 2012, no. 251364, pp. 111.Google Scholar
Livak, KJ and Schmittgen, TD 2001, ‘Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method’, Methods, vol. 25, no. 4, pp. 402408.Google Scholar
Lovley, DR and Phillips, EJ 1986, ‘Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River’, Applied and Environmental Microbiology, vol. 52, no. 4, pp. 751757.Google Scholar
Lowry, OH, Rosebrough, NJ, Farr, AL and Randall, RJ 1951, ‘Protein measurement with the Folin phenol reagent’, Journal of Biological Chemistry, vol. 193, no. 1, pp. 265275.CrossRefGoogle ScholarPubMed
Luo, Y and Zhou, X 2010, Soil respiration and the environment, Academic Press, Burlington, Massachusetts.Google Scholar
Madigan, MT, Martinko, JM, Bender, KS, Buckley, DH and Stahl, DA (eds) 2014, Brock biology of microorganisms, 14th ed, Pearson Education, New York.Google Scholar
Magoc, T, Pabinger, S, Canzar, S, et al. 2013, ‘GAGE-B: an evaluation of genome assemblers for bacterial organisms’, Bioinformatics, vol. 29, no. 14, pp. 17181725.CrossRefGoogle ScholarPubMed
Maier, RM, Pepper, IL and Gerba, CP (eds) 2009, Environmental microbiology, 2nd ed, Academic Press, Burlington, MA.Google Scholar
Mardis, ER 2008, ‘Next-generation DNA sequencing methods’, Annual Review of Genomics and Human Genetics, vol. 9, pp. 387402.Google Scholar
Markowitz, VM, Chen, IMA, Palaniappan, K, et al. 2011, ‘IMG: the integrated microbial genomes database and comparative analysis system’, Nucleic Acids Research, vol. 40, no. D1, pp. D115D122.Google Scholar
Martens, R 1995, ‘Current methods for measuring microbial biomass C in soil: potentials and limitations’, Biology and Fertility of Soils, vol. 19, no. 2, pp. 8799.Google Scholar
Martin, JA and Wang, Z 2011, ‘Next-generation transcriptome assembly’, Nature Reviews Genetics, vol. 12, no. 10, pp. 671682.Google Scholar
McKelvie, ID 2000, ‘Phosphates’ in Nollet, LML, (ed), Handbook of water analysis, Marcel Dekker, Inc., New York.Google Scholar
Mehra, OP and Jackson, ML 1960, ‘Iron oxide removal from soils and clays by a dithionite-citrate system buffered with sodium bicarbonate’, Proceedings 7th National Conference on Clays and Clay Minerals, pp. 317327.Google Scholar
Metzker, ML 2010, ‘Sequencing technologies—the next generation’, Nature Reviews Genetics, vol. 11, no. 1, pp. 3146.Google Scholar
Meyer, F, Paarmann, D, D’Souza, M, et al. 2008, ‘The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes’, BMC Bioinformatics, vol. 9, no. 386, pp. 18.Google Scholar
Mikan, CJ, Schimel, JP and Doyle, AP 2002, ‘Temperature controls of microbial respiration in arctic tundra soils above and below freezing’, Soil Biology and Biochemistry, vol. 34, no. 11, pp. 17851795.Google Scholar
Miller, DN, Bryant, JE, Madsen, EL and Ghiorse, WC 1999, ‘Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples’, Applied and Environmental Microbiology, vol. 65, no. 11, pp. 47154724.Google Scholar
Miller, JR, Koren, S and Sutton, G 2010, ‘Assembly algorithms for next-generation sequencing data’, Genomics, vol. 95, no. 6, pp. 315327.Google Scholar
Montgomery, J, Wittwer, CT, Palais, R and Zhou, L 2007, ‘Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis’, Nature Protocols, vol. 2, no. 1, pp. 5966.Google Scholar
Morrison, TB, Weis, JJ and Wittwer, CT 1998, ‘Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification’, Biotechniques, vol. 24, no. 6, pp. 954958.Google Scholar
Nannipieri, P, Ascher, J, Ceccherini, M, et al. 2003, ‘Microbial diversity and soil functions’, European Journal of Soil Science, vol. 54, no. 4, pp. 655670.Google Scholar
Neethirajan, S, Jayas, DS and Sadistap, S 2009, ‘Carbon dioxide (CO2) sensors for the agri-food industry – a review’, Food and Bioprocess Technology, vol. 2, no. 2, pp. 115121.Google Scholar
Nilsen, TW 2013, ‘Gel purification of RNA’, Cold Spring Harbor Protocols, Available from: http://cshprotocols.cshlp.org/content/2013/2/pdb.prot072942.full.pdf [August 18, 2017].Google Scholar
Nollet, LML (ed) 2000, Handbook of water analysis, Marcel Dekker, Inc., New York.Google Scholar
O’Connor, JT, Komolrit, K and Engelbrecht, RS 1965, ‘Evaluation of the orthophenanthroline method for ferrous-iron determination’, American Water Works Association, vol. 57, no. 7, pp. 926934.Google Scholar
O’Farrell, PH 1975, ‘High resolution two-dimensional electrophoresis of proteins’, Journal of Biological Chemistry, vol. 250, no. 10, pp. 40074021.Google Scholar
Ozsolak, F and Milos, PM 2011, ‘RNA sequencing: advances, challenges and opportunities’, Nature Reviews Genetics, vol. 12, no. 2, pp. 8798.CrossRefGoogle ScholarPubMed
Pansu, M and Gautheyrou, J 2006, Handbook of soil analysis: mineralogical, organic and inorganic methods, Springer-Verlag, Berlin, Heidelberg, New York.Google Scholar
Patel, RK and Jain, M 2012, ‘NGS QC Toolkit: a toolkit for quality control of next generation sequencing data’, PloS One, vol. 7, no. 2, pp. e30619.Google Scholar
Pfaffl, MW 2001, ‘A new mathematical model for relative quantification in real-time RT-PCR’, Nucleic Acids Research, vol. 29, no. 9, pp. 20022007.Google Scholar
Pham, VH and Kim, J 2012, ‘Cultivation of unculturable soil bacteria’, Trends in Biotechnology, vol. 30, no. 9, pp. 475484.Google Scholar
Quail, MA, Smith, M, Coupland, P, et al. 2012, ‘A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers’, BMC Genomics, vol. 13, no. 1, p. 341.Google Scholar
Rice, EW, Baird, RB and Eaton, AD 2017, Standard methods for the examination of water and wastewater, 23rd ed, American Public Health Association, American Water Works Association, Water Environment Federation, Maryland.Google Scholar
Rio, DC, Ares, M, Hannon, GJ and Nilsen, TW 2010, ‘Polyacrylamide gel electrophoresis of RNA’, Cold Spring Harbor Protocols, Available from: http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5444.full.pdf+html [August 18, 2017].Google Scholar
Ririe, KM, Rasmussen, RP and Wittwer, CT 1997, ‘Product differentiation by analysis of DNA melting curves during the polymerase chain reaction’, Analytical Biochemistry, vol. 245, no. 2, pp. 154160.Google Scholar
Salter, SJ, Cox, MJ, Turek, EM, et al. 2014, ‘Reagent and laboratory contamination can critically impact sequence-based microbiome analyses’, BMC Biology, vol. 12, no. 1, p. 87.Google Scholar
Sambrook, J and Russell, DW (eds) 2001, Molecular cloning: a laboratory manual, 3rd ed, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
Schena, M, Shalon, D, Davis, RW and Brown, PO 1995, ‘Quantitative monitoring of gene expression patterns with a complementary DNA microarray’, Science, vol. 270, no. 5235, pp. 467470.Google Scholar
Schilt, AA and Hoyle, WC 1967, ‘Improved sensitivity and selectivity in the spectrophotometric determination of iron by use of a new Ferroin-type reagent’, Analytical Chemistry, vol. 39, no. 1, pp. 114117.Google Scholar
Schmittgen, TD and Livak, KJ 2008, ‘Analyzing real-time PCR data by the comparative CT method’, Nature Protocols, vol. 3, no. 6, pp. 11011108.Google Scholar
Schneider, T and Riedel, K 2010, ‘Environmental proteomics: analysis of structure and function of microbial communities’, Proteomics, vol. 10, no. 4, pp. 785798.Google Scholar
Schnürer, J and Rosswall, T 1982, ‘Fluorescein diacetate hydrolysis as a measure of total microbial activity in soil and litter’, Applied and Environmental Microbiology, vol. 43, no. 6, pp. 12561261.Google Scholar
Schuster, SC 2008, ‘Next-generation sequencing transforms today’s biology’, Nature Methods, vol. 5, no. 1, pp. 1618.Google Scholar
Scopes, RK 1993, Protein purification: principles and practice, 3rd ed, Springer, New York.Google Scholar
Shendure, J and Ji, H 2008, ‘Next-generation DNA sequencing’, Nature Biotechnology, vol. 26, no. 10, pp. 11351145.Google Scholar
Shimadzu 2013, TOC Application Handbook: Document SCA-130–101-604, Shimadzu Europa GmbH, Duisburg, Germany. <www.shimadzu.eu>>Google Scholar
Shokralla, S, Spall, JL, Gibson, JF and Hajibabaei, M 2012, ‘Next-generation sequencing technologies for environmental DNA research’, Molecular Ecology, vol. 21, no. 8, pp. 17941805.Google Scholar
Smith, PK, Krohn, RI, Hermanson, GT, et al. 1985, ‘Measurement of protein using bicinchoninic acid’, Analytical Biochemistry, vol. 150, no. 1, pp. 7685.Google Scholar
Stookey, LL 1970, ‘Ferrozine – a new spectrophotometric reagent for iron’, Analytical Chemistry, vol. 42, no. 7, pp. 779781.Google Scholar
Tabatabai, MA 1994, ‘Soil enzymes’ in Weaver, RW, Angel, JS and Bottomley, PS, (eds), Methods of soil analysis: Part 2 – microbiological and biochemical properties, pp. 775834. Soil Science Society of America, Wisconsin.Google Scholar
Tabatabai, MA and Bremner, JM 1969, ‘Use of p-nitrophenyl phosphate for assay of soil phosphatase activity’, Soil Biology and Biochemistry, vol. 1, no. 4, pp. 301307.Google Scholar
Tabatabai, MA and Frankenberger, WT Jr. 1996, ‘Liquid chromatography’ in Sparks, DL, Page, AL, Helmke, PA, and Loeppert, RH, (eds), Methods of soil analysis: Part 3 – chemical methods, Soil Science Society of America, Wisconsin.Google Scholar
Taberlet, P, Prud’homme, SM, Campione, E, et al. 2012, ‘Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies’, Molecular Ecology, vol. 21, no. 8, pp. 18161820.Google Scholar
Tan, KH 1996, Soil sampling, preparation, and analysis, Marcel Dekker, Inc., New York.Google Scholar
Tan, SC and Yiap, BC 2009, ‘DNA, RNA, and protein extraction: the past and the present’, Journal of Biomedicine and Biotechnology, vol. 2009, no. 574398, pp. 110.Google Scholar
Taylor, JP, Wilson, B, Mills, MS and Burns, RG 2002, ‘Comparison of microbial numbers and enzymatic activities in surface soils and subsoils using various techniques’, Soil Biology and Biochemistry, vol. 34, no. 3, pp. 387401.Google Scholar
Thomas, T, Gilbert, J and Meyer, F 2012, ‘Metagenomics – a guide from sampling to data analysis’, Microbial Informatics and Experimentation, vol. 2, no. 3, pp. 112.Google Scholar
Thompson, M 2008, ‘CHNS elemental analysers’, Royal Society of Chemistry Analytical Methods Committee, no. 29.Google Scholar
Thompson, M and Walsh, JN 1989, Handbook of inductively coupled plasma spectrometry, 2nd ed, Springer US, New York.CrossRefGoogle Scholar
Thompson, SK 2012, Sampling, 3rd ed, Wiley, New Jersey.Google Scholar
Tringe, SG, von Mering, C, Kobayashi, A, et al. 2005, ‘Comparative metagenomics of microbial communities’, Science, vol. 308, no. 5721, pp. 554557.Google Scholar
Tyson, GW, Chapman, J, Hugenholtz, P and Allen, EE 2004, ‘Community structure and metabolism through reconstruction of microbial genomes from the environment’, Nature, vol. 428, no. 6978, pp. 3743.Google Scholar
Urich, T, Lanzén, A, Qi, J, et al. 2008, ‘Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome’, PloS One, vol. 3, no. 6, pp. e2527.Google Scholar
US EPA 1978, ‘Method 365.3: Phosphorous, All Forms (Colorimetric, Ascorbic Acid, Two Reagent)’, United States Environmental Protection Agency, Washington, DC.Google Scholar
US EPA 1995, ‘Method 7196A: Chromium, hexavalent (colorimetric)’, Test methods for evaluating solid waste, physical/chemical methods. SW-846, 3rd ed, US Environmental Protection Agency, Washington, DC.Google Scholar
US Food and Drug Administration, Laboratory Methods. <www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm062229.htm>..>Google Scholar
Uzoukwu, BA 2000, ‘Methods of water preservation’ in Nollet, LML, (ed), Handbook of water analysis, Marcel Dekker, Inc., New York.Google Scholar
Valentini, R, Matteucci, G, Dolman, AJ, et al. 2000, ‘Respiration as the main determinant of carbon balance in European forests’, Nature, vol. 404, no. 6780, pp. 861865.Google Scholar
Van Loon, JC and Barefoot, RR 1989, Analytical methods for geochemical exploration, Academic Press, Burlington, Massachusetts.Google Scholar
Vartoukian, SR, Palmer, RM and Wade, WG 2010, ‘Strategies for culture of “unculturable” bacteria’, FEMS Microbiology Letters, vol. 309, no. 1, pp. 17.Google ScholarPubMed
Venter, JC, Remington, K, Heidelberg, JF, et al. 2004, ‘Environmental genome shotgun sequencing of the Sargasso Sea’, Science, vol. 304, no. 5667, pp. 6674.Google Scholar
Verschoor, MJ and Molot, LA 2013, ‘A comparison of three colorimetric methods of ferrous and total reactive iron measurement in freshwaters’, Limnology and Oceanography: Methods, vol. 11, pp. 113125.Google Scholar
Viollier, E, Inglett, PW, Hunter, K, Roychoudhury, AN and Van Cappellen, P 2000, ‘The ferrozine method revisited: Fe(II)/Fe(III) determination in natural waters’, Applied Geochemistry, vol. 15, pp. 785790.Google Scholar
von Mersi, W and Schinner, F 1991, ‘An improved and accurate method for determining the dehydrogenase activity of soils with iodonitrotetrazolium chloride’, Biology and Fertility of Soils, vol. 11, no. 3, pp. 216220.Google Scholar
Wang, Z, Gerstein, M and Snyder, M 2009, ‘RNA-Seq: a revolutionary tool for transcriptomics’, Nature Reviews Genetics, vol. 10, no. 1, pp. 5763.Google Scholar
Ward, DM, Weller, R and Bateson, MM 1990, ‘16S rRNA sequences reveal numerous uncultured microorganisms in a natural community’, Nature, vol. 345, no. 6270, pp. 6365.Google Scholar
Welz, B and Sperling, M 1999, Atomic absorption spectrometry, 3rd ed, Wiley-VCH, Weinheim.Google Scholar
Welz, B, Becker-Ross, H, Florek, S and Heitmann, U 2005, High-resolution continuum source AAS: the better way to do atomic absorption spectrometry, Wiley-VCH, Weinheim.Google Scholar
Willerslev, E, Hansen, AJ and Poinar, HN 2004, ‘Isolation of nucleic acids and cultures from fossil ice and permafrost’, Trends in Ecology & Evolution, vol. 19, no. 3, pp. 141147.Google Scholar
Willner, D, Daly, J, Whiley, D, et al. 2012, ‘Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples’, PloS One, vol. 7, no. 4, pp. e34605.Google Scholar
Wilson, K 1997, ‘Preparation of genomic DNA from bacteria’ in Ausubel, FM, Brent, R, Kimston, RE, Moore, DD, Seidman, JG, Smith, JA and Struhl, K, (eds), Current protocols in molecular biology, pp. 2.4.12.4.5. John Wiley & Sons, Inc., New York, NY.Google Scholar
Wiśniewski, JR, Zougman, A, Nagaraj, N and Mann, M 2009, ‘Universal sample preparation method for proteome analysis’, Nature Methods, vol. 6, no. 5, pp. 359362.CrossRefGoogle ScholarPubMed
Wrighton, KC, Thomas, BC, Sharon, I, et al. 2012, ‘Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla’, Science, vol. 337, no. 6102, pp. 16611665.Google Scholar
Zhang, W, Parker, KM, Luo, Y, et al. 2005, ‘Soil microbial responses to experimental warming and clipping in a tallgrass prairie’, Global Change Biology, vol. 11, no. 2, pp. 266277.Google Scholar
Zhou, J, Bruns, MA and Tiedje, JM 1996, ‘DNA recovery from soils of diverse composition’, Applied and Environmental Microbiology, vol. 62, no. 2, pp. 316322.Google Scholar
Zimmerman, CF, Keefe, CW and Bashe, J 1997, ‘Method 440.0 Determination of carbon and nitrogen in sediments and particulates of estuarine/coastal waters using elemental analysis’, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, Ohio.Google Scholar
Zwietering, MH, Jongenburger, I, Rombouts, FM and van’t Riet, K 1990, ‘Modeling of the bacterial growth curve’, Applied and Environmental Microbiology, vol. 56, no. 6, pp. 18751881.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×