How can we measure soil biodiversity?

There is consensus among scientists that we need to learn more about how the soil functions. At present, just 1% of bacterial and fungal species have been identified, compared to over 80% of plants. Fewer than 2% of nematode species are known to us, and just 4% of mites. Without knowing what actually lives down there, how can we possibly understand their role in keeping soil healthy?

Whereas the soil macro- and megafauna is visible to the naked eye, and the mesofauna can conveniently be observed and counted using binoculars, soil microbial diversity is not that easily assessed. With more microbial cells living in in one hand of grassland soil than humans on our planet, how can we possibly measure what is there?

There are currently two types of tests that can be performed: Tests that analyse and classify parts of the microbial material itself (‘taxonomic tests’), and tests thatlook at the metabolic products of microbes (‘functional tests’). A common taxonomic test is to extract DNA directly from the soil and make a genetic ‘fingerprint’ of the soil microbial community. To further detect which genes are actively switched on, so-called DNA microarray tests are being used. A DNA microarray is a solid (e.g. glass) surface to which numerous microscopic DNA spots (‘probes’) are attached. These are linked to fluorescent chemicals, and when fragments of soil DNA connect to these probes the matches can be analysed using UV light in fluorescence spectroscopy.
Functional tests aim at analysing the metabolic activities of soil microbes. An example can be found in the graphs section to the right

Having standardized field and laboratory methods for assessing key functional groups of soil organisms is however just the beginning. The challenge in the future will be to establish indicators and critical levels of the soil biotic functional assemblages that are needed to maintain the key soil . This could provide the basis for long-term monitoring, just as the quality of water and air is assessed.

Despite all the research to date, there is no standardised system to allow comparison between different sites and plots, as well as over time. However, some progress is being made: a research programme called ENVASSO (Environmental Assessment of Soil for Monitoring, 2006-2008) has proposed the building blocks for the first comprehensive, harmonised soil information system in Europe. A set of indicators has been suggested that covers all trophic levels, and addresses taxonomic as well as functional aspects.
 
More recently, the ECOFINDERS project (2011-2014) assesses the “normal operating range” of a suite of soil organism s and functions and fills knowledge gaps between soil biodiversity, soil functioning and ecosystem services, as well as the valuation of some of these relationships.
Since 1997, soil biodiversity monitoring is a reality in the Netherlands, where 70% of land is agricultural area and concerns about loss of biodiversity are high. As part of the Netherlands Soil Monitoring Network (NSMN), a “Biological Indicator for Soil Quality” (BISQ) has been developed that contains a wide range of soil biological parameters are being assessed annually in about 300 randomly selected locations.

Pitfall (“barber”) trap for catching epigeic soil macro- and megafauna.
Source: "/en.wikipedia.org/wiki/Earthworm"

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