Genetic Diversity through the Looking Glass: Effect of Enrichment Bias

Abstract

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D ؉) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burkholderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfdA and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D ؉ populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques.

In situresponse of the linuron degradation potential to linuron application in an agricultural field

“…Otherwise, bacteria belonging to phylotype D may need to be associated with soil particles making it difficult to culture them in liquid. Dunbar et al (1997) previously suggested that enrichment without solid support tends to select for bacteria which grow rapidly and as such outcompete slow-growing microorganisms. Also, Breugelmans observed different compositions of linurondegrading cultures enriched in the presence or absence of soil particles from soil originating from the same field.…”

“…Microbial degradation is considered an important mechanism in the dissipation of crop protection products in the environment. Various bacterial strains and consortia that degrade or mineralize crop protection products such as linuron (Dejonghe et al, 2003;Sorensen et al, 2005;Breugelmans et al, 2007;Satsuma, 2010), atrazine (Topp et al, 2000;Rousseaux et al, 2002;Getenga et al, 2009) and isoproturon (Sorensen et al, 2001) or 2,4-dichlorophenoxyacetic acid (Dunbar et al, 1997) have been isolated from pesticide-treated agricultural soils by means of enrichment in suspended cultures in which the pesticide of interest is provided as sole nutrient and/or energy source. However, little is known about the involvement and contribution of these organisms to the in situ degradation of the respective compounds, and concerns exist about the occurrence of biases during the enrichment process.…”

Diversity of human small intestinalStreptococcusandVeillonellapopulations

“…Although the latter genera were also detected in other ileostoma samples from subject 1, their relative abundance was generally low (< 0.7%; B. van den Bogert et al, unpublished results). The number of obtained Enterococcus isolates might be explained by a cultivation bias resulting from the use of selective media that preferentially allow growth of specific microbial groups and are known to provide a distorted view of bacterial abundances in the original samples (Dunbar et al, 1997; Table 3 and (clockwise) groupings in Fig. S3.…”

Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic

“…This study described as well a succession of different ndo populations responding to different PAH-contaminated environments. However, results from enrichment experiments can introduce a severe bias, as the array of organisms growing under the enrichment conditions defined do not necessarily reflect what occurs in natural environments (Dunbar et al, 1997).…”