Abstract
The earth contains a huge number of largely uncharacterized Bacteria and Archaea. Microbiologists are struggling to summarize their genetic diversity and classify them, which has resulted in heated debates on methods for defining species, mechanisms that lead to speciation and whether microbial species even exist. New molecular microbiological techniques allow for environmental screening to determine the presence of nucleic acids in environmental samples. These molecular genetic techniques allow screening for organisms that could be maintained in culture along with those that cannot be identified by standard non molecular means as they cannot be cultured. Although not allowing the description of specific organisms, this technique permits determining numbers and lineages of microorganisms in environmental samples, notably phylogenetic relationships and genetic similarity to sequences in established databases. Recent progress has revealed that the capture of genetic resources from complex microbial communities allows the discovery of a richness of new enzymatic diversity that had not previously been imagined. This new diversity, constitutes a large potential of new and improved applications in industry, medicine, agriculture, bioenergy etc., and promises to facilitate in a significant manner, our transition to a sustainable society, by contributing to the transition to renewable sources of energy, chemicals and materials, the reduction of pollutant burdens. Hiding within the as-yet-undiscovered microorganisms are cures for diseases, means to clean polluted environments, new food sources, and better ways to manufacture products daily used in modern society. This chapter focuses on the structural and functional diversity of the microbes around the globe, which are the primary and richest source of natural genetic resources that can be utilized for the improvement of agriculture, food production, and human health as well as for the welfare of the environment and ecosystems.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bathe S, Schwarzenbeck N, Hausner M (2009) Bioaugmentation of activated sludge towards 3-chloroaniline removal with a mixed bacterial population carrying a degradative plasmid. Bioresour Technol 100:2902–2909
Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Javanovich SB, Feldman RA, Delong EF (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2:516–529
Bent SJ, Pierson JD, Forney LJ, Danovaro R, Luna GM, Dell’anno A, Pietrangeli B (2007) Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol 73:2399–2401
Bridge PD, Roberts PJ, Spooner BM, Panchal G (2003) On the unreliability of published DNA sequences. New Phytol 160:43–48
Carballa M, Smits M, Etcherbehere C et al (2011) Correlations between molecular and operational parameters in continuous lab scale anaerobic reactors. Appl Microbiol Biotechnol 89:303–314
Crab R, Kochva M, Verstraete W, Avnimelech Y (2009) Bio-flocs technology application in over-wintering of tilapia. Aquacult Eng 40:105–112
De Schryver P, Sinha AK, Kunwar PS, Baruah K, Verstraete W, Boon N, De Boeck G, Bossier P (2010) Poly-beta-hydroxybutyrate (PHB) increases growth performance and intestinal bacterial range weighted richness in juvenile European sea bass, Dicentrarchus labrax. Appl Microbiol Biotechnol 86:1535–1541
De Schryver P, Dierckens K, Thi QQ, Amalia R, Marzorati M, Bossier P, Boon N, Verstraete W (2011) Convergent dynamics of the juvenile European sea bass gut microbiota induced by poly-beta-hydroxybutyrate. Environ Microbiol 13:1042–1051
de Wildeman S, Verstraete W (2003) The quest for microbial reductive dechlorination of C2 to C4 chloroalkanes is warranted. Appl Microbiol Biotechnol 61:94–102
Denef V, Park J, Tsoi T, Rouillard J, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM (2004) Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70:4961–4970
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC Jr, Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57
Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270
Gilbert JA, Hill PJ, Dodd CER, Laybourn-Parry J (2004) Demonstration of antifreeze protein activity in Antarctic lake bacteria. Microbiology 150:171–180
Grootaert C, van den Abbeele P, Marzorati M, Broekaert WF, Courtin CM, Delcour JA, Verstraete W, van de Wiele T (2009) Comparison of prebiotic effects of arabinoxylan oligosaccharides and inulin in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 69:231–242
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Handelsman J, Rondon MR, Brady SP, Clady J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:245–249
Lakó J, Hancsók J, Yuzhakova T, Marton G, Utasi A, Rédey Á (2008) Biomass – a source of chemicals and energy for sustainable development. Environ Eng Manag J 7:499–509
Lautenschlager K, Boon N, Wang Y, Egli T, Hammes F (2010) Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition. Water Res 44:4868–4877
Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691
Kamm B, Kamm M (2004) Principles of biorefineries. Appl Microbiol Biotechnol 64:137–145
Margesin R, Gander S, Zacke G, Gounot AM, Schinner F (2003) Hydrocarbon degradation and enzyme activities of cold adapted bacteria and yeast. Extremophiles 7:451–458
Marzorati M, Wittebolle L, Boon N, Daffonchio D, Verstraete W (2008) How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ Microbiol 10:1571–1581
Marzorati M, Balloi A, de Ferra F, Corallo L, Carpani G, Wittebolle L, Verstraete W, Daffonchio D (2010a) Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethanedegrading bacterial consortium enriched from a contaminated aquifer. Microb Cell Fact 19:9–12
Marzorati M, Verhelst A, Luta G, Sinnott R, Verstraete W, Van de Wiele T, Possemiers S (2010b) In vitro modulation of the human gastrointestinal microbial community by plant-derived polysaccharide-rich dietary supplements. Int J Food Microbiol 139:168–176
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2:860–866
Possemiers S, Marzorati M, Verstraete W, Van de Wiele T (2010) Bacteria and chocolate: a successful combination for probiotic delivery. Int J Food Microbiol 141:97–103
Prol-Garcia MJ, Planas M, Pintado J (2010) Different colonization and residence time of Listonella anguillarum and Vibrio splendidus in the rotifer Brachionus plicatilis determined by real-time PCR and DGGE. Aquaculture 302:26–35
Pycke B, Etcherbehere C, Van de Caveye P, Negroni A, Verstraete W, Boon N (2011) A time course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities. Water Sci Technol 63:769–775
Qi ZZ, Dierckens K, Defoirdt T, Sorgeloos P, Boon N, Bao ZM, Bossier P (2009) Analysis of the evolution of microbial communities associated with different cultures of rotifer strains belonging to different cryptic species of the Brachionus plicatilis species complex. Aquaculture 292:23–29
Quaiser A, Ochsenreiter T, Klenk H-P, Kletzin A, Treusch AH, Meurer G, Eck J, Sensen CW, Schleper G (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4:603–611
Reinartz J, Bruyns E, Lin JZ, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R (2002) Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomic Proteomic 1:95–104
Rojas-Oropeza M, Dendooven L, Garza-Avendano L, Souza V, Philippot L, Cabirol N (2010) Effects of biosolids application on nitrogen dynamics and microbial structure in a saline-sodic soil of the former Lake Texcoco (Mexico). Bioresour Technol 101:2491–2498
Rondon MR, Goodman RM, Handelsman J (1999) The earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17:403–409
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547
Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, Longhi C, Maiella G, Cucchiara S, Conte MP (2010) A distinctive ‘microbial signature’ in celiac pediatric patients. BMC Microbiol 17:175
Siddiqui KS, Cavicchioli R (2006) Cold-adapted enzymes. Annu Rev Biochem 75:403–433
Singh BK, Campbell CD, Sorenson SJ, Zhou J (2009) Soil genomics. Nat Rev Microbiol 7:756. doi:10.1038/nrmicro2119-c1
Smidt H, de Vos WM (2004) Anaerobic microbial dehalogenation. Annu Rev Microbiol 58:43–73
Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063
Van den Abbeele P, Grootaert C, Marzorati M, Possemiers S, Verstraete W, Gerard P, Rabot S, Bruneau A, El Aidy S, Derrien M, Zoetendal E, Kleerebezem M, Smidt H, Van de Wiele T (2010) Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium Cluster IX. Appl Environ Microbiol 76:5237–5246
van der Gast CJ, Jefferson B, Reid E (2006) Bacterial diversity is determined by volume in membrane bioreactors. Environ Microbiol 8:1048–1055
van Trappen S, Vandecandelaere I, Mergaert J, Swings J (2005) Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov, novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 55:769–772
Verstraete W, Wittelbolle L, Heylen K, Vanparys B, de Vos P, van de Wiele T, Boon N (2007) Microbial resource management: the road to go for environmental biotechnology. Eng Life Sci 7:117–126
Vlaeminck SE, Terada A, Smets BF, Van der Linden D, Boon N, Verstraete W, Carballa M (2009) Nitrogen removal from digested black water by one-stage partial nitritation and anammox. Environ Sci Technol 43:5035–5041
Whiteford N, Skelly T, Curtis C, Ritchie ME, Lohr A, Zaranek AW, Abnizova I, Brown C (2009) Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics 25:2194–2199
Wittebolle L, Vervaeren H, Verstraete W, Boon N (2008) Quantifying community dynamics of nitrifiers in functionally stable reactors. Appl Environ Microbiol 74:286–293
Wittebolle L, van Vooren N, Verstraete W, Boon N (2009a) High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors. J Appl Microbiol 107:385–394
Wittebolle L, Verstraete W, Boon N (2009b) The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors. Water Res 43:4149–4158
Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R (2001) The European large subunit ribosomal RNA database. Nucleic Acids Res 29:175–177
Wuyts J, Van de Peen Y, Winkelmans T, De Wachter R (2002) The European database on small subunit ribosomal RNA. Nucleic Acids Res 30:183–185
Yamada T, Hiraoka Y, Das Gupta TK, Chakrabarty AM (2004) Rusticyanin, a bacterial electron transfer protein causes G (1) arrest in J774 and apoptosis in human cancer cells. Cell Cycle 3:1182–1187
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Malik, A., Masood, F., Grohmann, E. (2013). Management of Microbial Resources in the Environment: A Broad Perspective. In: Malik, A., Grohmann, E., Alves, M. (eds) Management of Microbial Resources in the Environment. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5931-2_1
Download citation
DOI: https://doi.org/10.1007/978-94-007-5931-2_1
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-5930-5
Online ISBN: 978-94-007-5931-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)