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Abstract
16S ribosomal RNA (rRNA)gene clone libraries were constructed from the casts of the earthworm Lumbricus rubellus and the agricultural soil it inhabits.Both samples were very diverse and contained a large number of bacterial taxa.However,increased numbers of sequences belonging to the Actinobacteria,Firmicutes,and Pseudomonas taxa,in addition to decreased numbers of one phylogenetically deep unknown taxon were found in the cast library.To examine if these differences were statistically significant,a novel method of comparing 16S rRNA clone libraries was developed (LIBSHUFF).This analysis showed that the cast sample was significantly different from the soil sample,and that the differences in abundance of all four of the previously named taxa were responsible for the difference.The analysis also suggested that the cast bacterial population was derived from the soil population.Archaeal diversity was low in both the soil and cast samples and consisted of sequences from a common soil archaeal lineage.|To examine the possibility of an indigenous intestinal community,earthworms were collected,the intestines dissected and washed,and 16S rRNA clone libraries constructed from DNA extracted from the intestinal material.A significant number of prokaryotes remained attached to the intestine after washing.At least three taxa, belonging to the Acidobacteria,Firmicutes,and one deep Mycoplasma -associated lineage were found in high numbers in the intestine libraries,and were not found in clone libraries made from the cast material or the surrounding soil.An additional taxon, belonging to the -proteobacteria was also detected in signficant numbers in the intestine of earthworms as well as cast material.With the exception of the -proteobacteria,none of the taxa were found in all of the earthworms screened,suggesting that while these sequences may represent intestine-associated organisms,they are not necessarily stable in the L.rubellus population.|An organism isolated from the burrow of an earthworm,which represents the type strain in a novel genus (Solirubrobacter )was characterized.This organism represents only the third cultured species in the Rubrobacteridae subclass of the Actinobacteria phylum and bears similarity to a number of clones recovered from soils around the world.