Bacterial communities in natural ecosystems: groundwater, soil, earthworm casts and burrows
Furlong, Michelle Ann
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Bacterial isolates from fresh earthworm casts were phenotypically and taxonomically different than isolates from soil and earthworm burrows. While most of the cast isolates grew on MacConkey media, reduced nitrate and utilized acetate and Casamino acids for carbon, the majority of the soil and burrow isolates did not. The majority of the soil and burrow isolates belonged to the high G + C gram-positive bacteria (54% and 48%, respectively). The other isolates were distributed among the low G + C gram positives and ?-, ?- and ?- proteobacteria. The majority of the cast isolates were ?-proteobacteria (78%). The remainder of them grouped with the high and low G + C gram positive, ?- and ?- proteobacteria and cytophaga/flexibacter groups. The cast isolates were also less diverse than the soil and burrow isolates. The casts contained fewer biotypes (groups of organisms containing the same phenotype), and those biotypes were more similar to each other than were those of the bulk soil or burrow isolates. After standardizing the sample size, soil and burrow isolates each contained twice as many OTUs (operational taxonomic units as defined by rDNA) and had diversity and evenness values that were much greater than the cast isolates. Cloned rDNA from TCE contaminated and uncontaminated groundwater was compared. The uncontaminated groundwater contained one ribotype, which represented 26 clones and was very similar to Pseudomonas gessardii. The contaminated groundwater contained seventeen ribotypes, which represented forty clones. Sixty-five, thirty-three, and three percent of these clones were related to the ?- and ?- proteobacteria and an unknown group, respectively. The majority of the ?- proteobacteria (85%) grouped with the Methylococcaceae family, and the remainder grouped with the pseudomonads. Forty-six percent of the ?-proteobacteria grouped with methylotrophs, and the remainder grouped with various genera in the order Burkholderiales. Archaeal DNA was detected only in the contaminated water. One ribotype, which represented fifteen clones, grouped with the Crenarchaeota.