Soil as a Biological System and Omics Approaches

Authors

  • Paolo Nannipieri Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze

DOI:

https://doi.org/10.6092/issn.2281-4485/4541

Abstract

Soil as a biological system is characterized by: i) the presence of a remarkable diversity since thousands of bacterial genomes can be present in one gram of soil. In addition microbial biomass is huge; ii) only a minor proportion of the available space is occupied by microorganisms in soil (microbiological space);  iii) soil colloids can adsorb important biological molecules such as proteins and nucleic acids. Nucleic acids can adsorbed and retain their biological activity; iv). soil components show enzyme-like activities. Unfortunately there is no methods to distinguish enzyme from enzyme-like reactions but these methods are needed to quantify both contributions; v) virus are more abundant than in other systems such as aquatic ones. A book “Omics in Soil Science” (Nannipieri et al 2014) has been recently published; it presents the state-of-the-art of omics in soil science, a field that is advancing rapidly on many fronts. The various omics (mainly metagenomics, metatranscriptomics, proteomics and proteogenomics) approaches hold much promise but also await further refinement before they are ready for widespread adaptation. One way to judge their readiness is to compare them to methods that have become standards for soil microbiology research. Methods become standards because they provide useful information quickly and inexpensively. There is no question that omics can provide useful information, some of which cannot be obtained with traditional techniques, and integration of omics methods may provide insights into ecosystem functioning. In particular, the potential for omics to provide comprehensive coverage of genes and genes products make them well-suited for the study of general soil microbiological phenomena, such as decomposition, response to water stress

References

ARENELLA M., GIAGNONI L., MASCIANDARO G., CECCANTI B., NANNIPIERI P., RENELLA G. (2014) Interactions between proteins and humic substances affect protein identification by mass spectrometry. Biol Fertil Soils, 50:447-454

CLARHOLM M. (1985) Interactions of bacteria, protozoa, and plants leading to mineralization of soil nitrogen. Soil Biol Biochem, 17:181–187.

DELMONT T.O., FRANCIOLI D., JACQUESSON S., LAOUDI S., NESME M.J., CECCHERINI M.T., NANNIPIERI P., SIMONET P., VOGEL T.M. (2014) microbial community development and unseen diversity recovery in inoculated sterile soil. Biol Fertil Soils, 50:1069-1076.

GIANFREDA L., RUGGIERO P. (2006) Enzyme activities in soil. In Nannipieri P, Smalla K (Eds) Nucleic acids and proteins in soil. Springer, Berlin, pp 257-311.

GRIFFITHS B., CLARHOLM M., BONKOWSKI M. (2012) Protozoa. In Huang PM, Li Y, Summer ME (Eds) Handbook of Soil Sciences. Properties and Processes, 2nd Edition, CRC Press, Taylor & Francis Group, Boca Raton, FL, pp 24-11-24-18.

HUANG P.M. (1995) The role of short-range ordered mineral colloids in abiotic transformations of organic compounds in the environment. In Huang PM, Berthelin J, Bollag JM, McGill WB, Page AL (Eds). Environmental impact of soil component interactions: natural and anthropogenic organics, vol I. CRC Press, Boca Raton, FL, pp 135-167.

KIM Y., WEGNER C-E., LIESACK W. (2014) Soil metatranscriptomic. In Nannipieri P, Pietramellara G, Renella G (Eds) Omics in soil Science. Caster Academic Press, Norfolk. UK, pp 63-93.

LIPSON S.M., STOTZKY G. (1986). Effect of kaolinite on the specific infectivity or reovirus. FEMS Microbiological Letters, 37:83-88.

MYROLD D.D., NANNIPIERI P. (2014) Classical techniques versus omics approaches. In Nannipieri P, Pietramellara G, Renella G (Eds) Omics in soil Science. Caster Academic Press, Norfolk. UK, pp 179-187.

NANNIPIERI P., GIAGNONI L., RENELLA G., PUGLISI E., CECCANTI B., MASCIANDARO G., FORNASIER F., MOSCATELLI M.C., MARINARI S. (2012) Soil enzymology: classical and molecular approaches. Biology and Fertility of Soils, 48:743-762.

NANNIPIERI P., PIETRAMELLARA G., RENELLA G. (2014) Soil as a biological system. In Nannipieri P, Pietramellara G, Renella G (Eds) Omics in soil Science. Caster Academic Press, Norfolk. UK, pp 1-7.

NANNIPIERI P., ASCHER J., CECCHERINI M.T., LANDI L., PIETRAMELLARA G., RENELLA G. (2003) Microbial diversity and soil functions. European Journal of Soil Science, 54:655-670.

PIETRAMELLARA G., ASCHER J., BORGOGNI F., CECCHERINI M.T., GUERRI G., NANNIPIERI P. (2009). Extracellular DNA in soil and sediment: fate and ecological relevance. Biology and Fertility of Soils, 45:219-235.

RENELLA G., GIAGNONI L., ARENELLA M., NANNIPIERI P. (2014) Soil proteomics. In Nannipieri P, Pietramellara G, Renella G (Eds) Omics in soil Science. Caster Academic Press, Norfolk. UK, pp 95-125.

RUGGIERO P., DEC J., BOLLAG J.M. (1999) Soil as a catalytic system. In Bollag JM, Stotzky G (eds) Soil Biochemistry. Marcel Dekker, New York, pp 79-122.

VAN ELSAS J.D., CRETOIU M.S., KIELAK A.M., DINI-ANDREOTE F. (2014) Soil metagenomics, potential applications and methodological problems. In Nannipieri P, Pietramellara G, Renella G (Eds) Omics in soil Science. Caster Academic Press, Norfolk. UK, pp 31-44.

VETTORI C., STOTZKY G., YODER M., GALLORI E. (1999) Interaction between bacteriophage PBS1 and clay minerals and transduction of Bacillus subtilis by clay-phage complexes. Environmental Microbiology, 1:347-355.

WILLIAMSON K.E., SRINIVASIAH S., WOMMACK K. E. (2012) Viruses in soil ecosystem. In Huang PM, Li Y, Summer ME (Eds) Handbook of Soil Sciences. Properties and Processes, 2nd Edition, CRC Press, Taylor & Francis Group, Boca Raton, FL, pp 24-1-24-10.

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Published

2014-12-01

How to Cite

Nannipieri, P. (2014). Soil as a Biological System and Omics Approaches. EQA - International Journal of Environmental Quality, 13(13), 61–66. https://doi.org/10.6092/issn.2281-4485/4541

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