Abstract
Microorganisms are the ultimate survivalists and account for the major portion of Earth’s biological diversity. They play critical roles in many global biogeochemical cycles (carbon, nitrogen, sulfur, and iron to name but a few). A gram of soil can contain 103–106 different bacterial species, and microorganisms (bacteria as well as archaea and fungi) have been observed in diverse terrestrial and aquatic environments ranging from deep oceanic hydrothermal vents to isolated voids in polar ice sheets. Given this extreme diversity across the globe, attention has been given to the development of techniques to identify and characterize bacterial communities, encouraged also by the prospect to find new species, enzymes, or proteins that can be used in industrial applications. Over the last 20 years, the science and application of molecular-based approaches has evolved from a perspective of determining the biological structure to elucidating the entire genome and its functions. This chapter will focus on discussing different widely used approaches and recent advancements made to detect and quantify “microbial activity” in contaminated environments using biochemical and molecular tools. Understanding how contaminants are biologically influenced in the environment will require a detailed understanding of both chemical and biological function within various environmental compartments. Combined these techniques can be used to address multiple environmental issues and will aid in the development of new remediation technologies.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Mol Biol Rev 59:143–169
Avaniss-Aghajani E, Jones K, Chapman D, Brunk C (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. Biotechniques 17:144–146
Bae S, Wuertz S (2009) Discrimination of viable and dead fecal bacteroidales bacteria by quantitative PCR with propidium monoazide. Appl Environ Microbiol 75:2940–2944
Baldwin AJ, Moss JA, Pakulski JD, Catala P, Joux F, Jeffrey WH (2005) Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles. Aquat Microb Ecol 41:91–102
Bowman JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, Sicheritz-Ponten T (2012) Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J 6:11–20
Brandt KK, Frandsen RJN, Holm PE, Nybroe O (2010) Development of pollution-induced community tolerance is linked to structural and functional resilience of a soil bacterial community following a five-year field exposure to copper. Soil Biol Biochem 42:748–757
Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H (2009) Metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ Microbiol 11:2216–2227
Bull AT, Ward AC, Goodfellow M (2000) Search and discovery strategies for biotechnology: paradigm shift. Microbiol Mol Biol Rev 64:573–606
Cohan FM (2001) Bacterial species and speciation. Syst Biol 50:513–524
Cordova-Kreylos AL, Cao Y, Green PG, Hwang H-M, Kuivila KM, LaMontagne MG, Van De Werfhorst LC, Holden PA, Scow KM (2006) Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments. Appl Environ Microbiol 72:3357–3366
Corsini A, Cavalca L, Zaccheo P, Crippa L, Andreoni V (2011) Influence of microorganisms on arsenic mobilization and speciation in a submerged contaminated soil: effects of citrate. Appl Soil Ecol 49:99–106
Crowe SA, O’Neill AH, Kulczycki E, Weisener CG, Roberts JA, Fowle DA (2007) Reductive dissolution of trace metals from sediments. Geomicrobiol J 24:157–165
Dojka MA, Hugenholtz P, Haackand SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877
Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669
Edwards KJ, McCollom TM, Konishi H, Buseck PR (2003) Seafloor bioalteration of sulfide minerals: results from in situ incubation studies. Geochim Cosmochim Acta 67:2843–2856
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander ECJ, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57
Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive earth’s biogeochemical cycles. Science 320:1034–1039
Farrell M, Griffith GW, Hobbs PJ, Perkins WT, Jones DL (2010) Microbial diversity and activity are increased by compost amendment of metal-contaminated soil. FEMS Microbiol Ecol 71:94–105
Fayek M, Utsunomiya S, Pfiffner SM, White DC, Riciputi LR, Ewing RC, Anovitz LM, Stadermann FJ (2005) The application of HR-TEM techniques and nano SIMS to chemically and isotopically characterize Geobacter sulfurreducens surfaces. Can Mineral 43:1631–1641
Ferris FG (1993) Microbial biomineralization in natural environments. Earth Sci 47:233–250
Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066
Fike DA, Gammon CL, Ziebis W, Orphan VJ (2008) Micron-scale mapping of sulphur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach. ISME J 2:749–759
Fry J (2000) Bacterial diversity and unculturables. Microbiol Today 27:186–188
Fry JC (2004) Culture-dependent microbiology. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC
Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J (2006) Microarray applications in microbial ecology research. Microb Ecol 52:159–175
Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63
Gough HL, Stahl DA (2011) Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient. ISME J 5:543–558
Graveley BR (2008) Power sequencing. Nature 453:1197–1198
Huang WE, Griffiths RI, Thompson IP, Bailey MJ, Whiteley AS (2004) Raman microscopic analysis of single microbial cells. Anal Chem 76:4452–4458
Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M (2007) Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9:1878–1889
Huang L-N, Zhou W-H, Hallberg KB, Wan C-Y, Li J, Shu W-S (2011) Spatial and temporal analysis of the microbial community in the tailings of a Pb-Zn mine generating acidic drainage. Appl Environ Microbiol 77:5540–5544
Hutchens E (2009) Microbial selectivity on mineral surfaces: possible implications for weathering processes. Fungal Biol Rev 23:115–121
Ito T, Nielsen JL, Okabe S, Watanabe Y, Nielsen PH (2002) Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization. Appl Environ Microbiol 68:356–364
Jakobs-Schönwandt D, Mathies H, Abraham W-R, Pritzkow W, Stephan I, Noll M (2010) Biodegradation of a biocide (Cu-N-cyclohexyldiazenium dioxide) component of a wood preservative by a defined soil bacterial community. Appl Environ Microbiol 78:8076–8083
Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 70(8):4831–4839
Jones WJ (2010) High-throughput sequencing and metagenomics. Estuar Coast 33:944–952
Kaeberlein T, Lewis K, Epstein SS (2002) Isolating “uncultivatable” microorganisms in pure culture in a simulated natural environment. Science 296:1127–1129
Kao C-M, Chen CS, Tsa F-Y, Yang K-H, Chien C-C, Liang S-H, Yang C-A, Chen SC (2010) Application of real-time PCR, DGGE fingerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume. J Hazard Mater 178:409–416
Kemp PF, Aller JY (2004) Bacterial Diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47:161–177
Kent AD, Smith DJ, Benson BJ, Triplett EW (2003) Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69:6768–6776
Kim J, Koo S-Y, Kim J-Y, Lee E-H, Lee S-D, Ko K-S, Ko D-C, Cho K-S (2009) Influence of acid mine drainage on microbial communities in stream and groundwater samples at Guryong Mine, South Korea. Environ Geol 58:1567–1574
Kimura S, Bryan CG, Hallberg KB, Johnson DB (2011) Biodiversity and geochemistry of an extremely acidic, low-temperature subterranean environment sustained by chemolithotrophy. Environ Microbiol 13:2092–2104
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809
Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, Zhou J (2009) Microarray-basedanalysis of microbial functional diversityalong an oil contamination gradient in oil field. FEMS Microbiol Ecol 70:324–333
Lindsay MBJ, Wakeman KD, Rowe OF, Grail BM, Ptacek CJ, Blowes DW, Johnson DB (2011) Microbiology and geochemistry of mine tailings amended with organic carbon for passive treatment of pore water. Geomicrobiol J 28:229–241
Logares R, Haverkamp THA, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H (2012) Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. J Microbiol Methods 91:106–113
Lovley DR (2003) Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev 1:35–44
Lu J, Chen T, Wu J, Chris Wilson P, Hao X, Qian J (2011) Acid tolerance of an acid mine drainage bioremediation system based on biological sulfate reduction. Bioresour Technol 102:10401–10406
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402
Martinez-Inigo MJ, Perez-Sanz A, Ortiz I, Alonso J, Alarcon R, Garcia P, Lobo MC (2009) Bulk soil and rhizosphere bacterial community PCR-DGGE profiles and beta-galactosidase activity as indicators of biological quality in soils contaminated by heavy metals and cultivated with Silene vulgaris (Moench) Garcke. Chemosphere 75:1376–1381
Martins M, Faleiro ML, Barros RJ, Veríssimo AR, Barreiros MA, Costa MC (2009) Characterization and activity studies of highly heavy metal resistant sulphate-reducing bacteria to be used in acid mine drainage decontamination. J Hazard Mater 166:706–713
Mielke HW, Gonzales CR, Powell ET, Le B, Quach VN (2004) PAHs and metals in soils of inner city and suburban New Orleans, Louisiana, USA. Environ Toxicol Pharmacol 18:243–247
Mouser PJ, N’Guessan AL, Elifantz H, Holmes DE, Williams KH, Wilkins MJ, Long PE, Lovley DR (2009) Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. Environ Sci Technol 43:4386–4392
Muyzer G (1999) Genetic fingerprinting of microbial communities – present status and future perspectives. In: Proceedings, 8th international symposium on microbial ecology, Atlantic Canada Society for Microbial Ecology, Halifax, Canada
Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Ňancucheo I, Johnson DB (2011) Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria. Microb Biotechnol 5:34–44
Nee S (2003) Unveiling prokaryotic diversity. Trends Ecol Evol 18:62–63
Neu TR, Manz B, Volke F, Dynes JJ, Hitchcock AP, Lawrence JR (2010) Advanced imaging techniques for assessment of structure, composition and function in biofilm systems. FEMS Microbiol Ecol 72:1–21
Neufeld JD, Mohn WW, de Lorenzo V (2006) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ Microbiol 8:126–140
Nielsen JL, Juretschko S, Wagner M, Nielsen PH (2002) Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography. Appl Environ Microbiol 68:4629–4636
Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ Biosafety Res 6:37–53
Nocker A, Camper AK (2009) Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques. FEMS Microbiol Lett 291:137–142
Norlund KI, Southam G, Tyliszczak T, Hu Y, Karunakaran C, Obst M, Hitchcock AP, Warren LA (2009) Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia. Environ Sci Technol 43:8781–8786
Okabe S, Kindaichi T, Ito T (2004) MAR-FISH – an ecophysiological approach to link phylogenetic affiliation and In situ metabolic activity of microorganisms at a single-cell resolution. Microbes Environ 19:83–98
Orphan VJ, House CH (2009) Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo microbial processes. Geobiology 7:360–372
Peplies J, Lachmund C, Glöckner FO, Manz W (2006) A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl Environ Microbiol 72:4829–4838
Quiros LM, Parra F, Hardisson C (1989) Structural functional analysis of ribosomal subunits from vegetative Mycelium and spores of Streptomyces antibioticus. J Gen Microbiol 135:1661–1670
Rastogi G, Sani RK (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In: Ahmad I, Ahmad F, Pitchel J (eds) Microbes and microbial technology: agricultural and environmental applications. Springer Science + Business Media, New York, p 516
Röling WFM, Milner MG, Jones DM, Lee K, Daniel F, Swannell RJP, Head IM (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68:5537–5548
Romanowski G, Lorenz MG, Sayler GS, Wackernagel W (1992) Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl Environ Microbiol 58:3012–3019
Ros M, Rodriguez I, Garcia C, Hernandez T (2010) Microbial communities involved in the bioremediation of an aged recalcitrant hydrocarbon polluted soil by using organic amendments. Bioresour Technol 101:6916–6923
Santos Pontes D, Lima-Bittencourt CI, Chartone-Souza E, Amaral Nascimento AM (2007) Molecular approaches: advantages and artifacts in assessing bacterial diversity. J Ind Microbiol Biotechnol 34:463–473
Schippers A, Breuker A, Blazejak A, Bosecker K, Kock D, Wright TL (2010) The biogeochemistry and microbiology of sulfidic mine waste and bioleaching dumps and heaps, and novel Fe(II)-oxidizing bacteria. Hydrometallurgy 104:342–350
Schopf JM (1993) Microfossils of the early archaean apex chart: new evidence of the antiquity of life. Science 260:640–646
Seifert J, Erler B, Seibt K, Rohrbach N, Arnold J, Schlömann M, Kassahun A, Jenk U (2008) Characterization of the microbial diversity in the abandoned uranium mine Königstein. In: Merkel BJ, Hasche-Berger A (eds) Uranium, mining and hydrogeology. Springer, Berlin, pp 733–742
Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805
Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23:249–261
Tan G-L, Shu W-S, Zhou W-H, Li X-L, Lan C-Y, Huang L-N (2009) Seasonal and spatial variations in microbial community structure and diversity in the acid stream draining across an ongoing surface mining site. FEMS Microbiol Ecol 70:277–285
Taskin B, Gozen AG, Duran M (2011) Selective quantification of viable Escherichia coli bacteria in biosolids by quantitative PCR with propidium monoazide modification. Appl Environ Microbiol 77:4329–4335
Thavamani P, Malik S, Beer M, Megharaj M, Naidu R (2012) Microbial activity and diversity in long-term mixed contaminated soils with respect to polyaromatic hydrocarbons and heavy metals. J Environ Manag 99:10–17
Tipayno S, Kim C-G, Sa T (2012) T-RFLP analysis of structural changes in soil bacterial communities in response to metal and metalloid contamination and initial phytoremediation. Appl Soil Ecol 61:137–146
Tischer K, Zeder M, Klug R, Pernthaler J, Schattenhofer M, Harms H, Wendeberg A (2012) Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples. Syst Appl Microbiol 35(8):526–532. doi:10.1016/j.syapm.2012.01.004
Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245
von Wintzingerode F, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229
Wagner M (2009) Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 63:411–429
Wagner M, Haider S (2012) New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol 23:96–102
Wagner M, Loy A (2002) Bacterial community composition and function in sewage treatment systems. Curr Opin Biotechnol 13:218–227
Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6:302–309
Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63–65
Warren LA, Haak EA (2001) Biogeochemicalcontrols on metalbehaviour in freshwater environments. Earth Sci Rev 54:261–320
Weisener CG, Babechuk MG, Fryer BJ, Maunder C (2008) Microbial dissolution of silver jarosite: examining its trace metal behaviour in reduced environments. Geomicrobiol J 25:415–424
Wellington EMH, Berry A, Krsek M (2003) Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr Opin Microbiol 6:295–301
Xiong J, Wu L, Tu S, Van Nostrand JD, He Z, Zhou J, Wang G (2010) Microbial communities and functional genes associated with soil arsenic contamination and the rhizosphere of the arsenic-hyperaccumulating plant pteris vittata L. Appl Environ Microbiol 76:7277–7284
Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS One 7(1):e30058
Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900
Zhou J, Thompson DK (2002) Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 13:204–207
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Loick, N., Weisener, C. (2014). Novel Molecular Tools to Assess Microbial Activity in Contaminated Environments. In: Parmar, N., Singh, A. (eds) Geomicrobiology and Biogeochemistry. Soil Biology, vol 39. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41837-2_2
Download citation
DOI: https://doi.org/10.1007/978-3-642-41837-2_2
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-41836-5
Online ISBN: 978-3-642-41837-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)