Microbial diversity

Von Wintzingerode F., Landt O., Ehrlich A., Gobel U. B. Peptide nucleic acid-mediated PGR clamping as a useful supplement in the determination of microbial diversity. Appl. Environ. Microbiol. 2000 66 549-557. 

Dojka MA, P Hugenholtz, SK Haack, NR Pace (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64 3869-3877. 

Teske A, K-U Hinrichs, V Edgcomb, A de Vera Gomez, D Lysela, SP Sulva, ML Sogin, HW Jannach (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin evidence for anaerobic methano-trophic communities. Appl Environ Microbiol 68 1994-2007. 

J. S. Buyer and D. D. Kaufman, Microbial diversity in the rhizosphere of corn grown under conventional and low input systems. Applied Soil Ecology 5 21 (1996). 

There are indications that the variety of C substrates in the rhizosphere soil is basically too wide to be significantly affected by changes in quality of plant residues from the previous crop. For example, legumes as preceding crop were shown to increase significantly microbial diversity in the bulk soil, as estimated by Biolog assay, whereas in the rhizosphere soil this effect of legumes could not be detected (145). 

N. Z. Lupwayi, W. A. Rice, and G. W. Clayton, Soil microbial diversity and community structure under wheat as influenced by tillage and crop rotation. Soil Biol. Biochem. 30 1733 (1998). 

A. C. Kennedy and V. L. Gewin, Soil microbial diversity present and future considerations. Soil. Sci. 162 607 (1997). 

The previous biomarkers relate to phenotypic assessments of microbial diversity and most will probably measure a restricted part of the total microbial pool, since not alt markers will be expressed uniformly by every cell. In contrast, methods involving the detection of nucleic acids may be directly applicable to all microorganisms provided that the complete extraction of DNA (lysis of cells) or permea-bilization of cells can be achieved. 

Pace, N.R. (1997). A molecular view of microbial diversity and the biosphere. Science, 276,... 

Alabouvette C, Backhouse D, Steinberg C, Donovan N J, Edel-Hermann V and Burgess L W (2004), Microbial diversity in soil - effects on crop health , in Schjpnning P, Elmholt S and Christensen B T, Managing Soil Quality - Challenges in Modem Agriculture, CAB International, Wallingford, 121-138. 

Doelman P, Jansen E, Michels M, Van-Til M (1994) Effects of heavy metals in soil on microbial diversity and activity as shown by the sensitivity-resistance index, an ecological relevant parameter. Biol Fertil Soils 17 177-184... 

The links between microbial diversity and soil functioning are unknown because it is difficult to measure microbial diversity. In addition, we generally measure soil functions by determining the rates of microbial processes, without knowing the microbial species effectively involved in the measured process (Nannipieri et al. 2003). The central problem of the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. 

Carbon substrate utilization (BIOLOG) Incubation of soil with substrates color development Indicates functional microbial diversity determined in nonstandard laboratory with specialized equipment produces large quantities of data complex interpretation Dick et al. (1996)... 

Table 10.2 Summary of the effects of organic farming vis-a-vis conventional farming on different microbial diversity and soil functions... 

There is a need to measure the activities of enzymes and to correlate these measured activities with microbial diversity in soil. It is conceptually wrong to assume a simple relationship between a single enzyme activity and microbiological activity in soil (Nannipieri et al. 2003). Most of the assays used to determine microbiological activities in soil present the same problem measuring potential rather than real activities (Nannipieri et al. 1990). Indeed, assays are generally made at optimal pH and temperature and at saturating concentration of substrate. Furthermore, synthetic rather than natural substrates are often used, and soil is incubated as a slurry (Nannipieri et al. 1990). 

The relation between microbial diversity and soil functions is poorly understood because we cannot measure easily the microbial diversity, even if we can detect unculturable microorganisms by molecular techniques (Nannipieri et al. 2003). In addition, the present assays for measuring microbial functions determine the overall rate of entire metabolic processes, such as respiration, or specific enzyme activities, without identifying the active microbial species involved. The recent advances in RNA extraction from soil might permit us to determine active species in soil (Griffiths et al. 2000 Hurt et al. 2001). Further advances in understanding require us to determine the composition of microbial communities and microbial functions in microhabitats. 

Organic management currently provides a clear advantage over conventional farming as a whole with respect to microbial diversity. This review indicates that organic farming has the potential to help in achieving the conservation of soil... 

Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63 4516 1522... 

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