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    • There is a fundamental conflict between maintaining soil macrofaunal biodiversity normally extant in naturally-functioning ecosystems, and implementing any type of agriculture requiring a wholesale replacement of the vegetation. I work with earthworms, and the general rule is that habitat conversion wipes out the indigenous species.  There are exceptions.  For example recent sampling in Terra Preta (aka Amazon Dark Earths) shows plenty of earthworms, most of which we believe to be local or regional species, rather than widely-distributed invasive and/or anthropochorous species.  However those sites sample are mostly under secondary forest and we may be seeing a long to medium term recovery of local diversity after site abandonment.  The sites are also embedded in larger areas of agriculturally-converted land, so it is difficult to judge. what the earthworm diversity would have been prior to the relatively recent (last 50 to 100 years) deforestation. 

      Soil genesis is strongly affected by ecosystem engineer soil fauna, earthworms  among them.  The use of soils thus developed typically entails a dramatic reduction in the species richness and functional trait spectrum originally present in that soil.  So while we benefit from the legacy of soil bio-engineers, we do not presently have a good way to maintain those engineers in the soil.  The primary replacements are the widely distributed or invasive species mentioned above; these will be different in different climate regions.  There is a well-characterized tropical set of common replacment species, of which Pontoscolex corethrurus is the best known, and others for temperate zones including higher elevation tropical locations. 

      It is easy to find cases of degradation of earthworm biodiversity, even including our best attempts at sustainable agricultural systems. The longer term question is how soils can be maintained under the new, simplified biotic regime characteristic of all agriculture.