Enrichment and characterization of a bacterial culture that can degrade 4-aminopyridine

Abstract

Background: The agrichemical 4-aminopyridine is used as a bird repellent in crop fields and has an epileptogenic action in a variety of animals, including man and mouse. 4-Aminopyridine is biodegraded in the environment through an unknown mechanism.

Results: A 4-aminopyridine-degrading enrichment culture utilized 4-aminopyridine as a carbon, nitrogen, and energy source, generating 4-amino-3-hydroxypyridine, 3,4-dihydroxypyridine, and formate as intermediates. 4-Amino-3-hydroxypyridine could not be further metabolized and probably accumulated as a dead-end product in the culture. Biodegradability tests and partial sequence analysis of the enrichment culture indicated that 4-aminopyridine was mainly degraded via 3,4-dihydroxypyridine and that the metabolite is probably cleaved by 3-hydroxy-4-pyridone dioxygenase. Seven culturable predominant bacterial strains (strains 4AP-A to 4AP-G) were isolated on nutrient agar plates. Changes in the bacterial populations of 4-aminopyridine, 3,4-dihydroxypyridine, or formate/ammonium chloride enrichment cultures were monitored by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Sequence analysis of the 16S rRNA gene fragments derived from predominant DGGE bands indicated that Pseudomonas nitroreducens 4AP-A and Enterobacter sp. 4AP-G were predominant in the three tested enrichment cultures and that the unculturable strains Hyphomicrobium sp. 4AP-Y and Elizabethkingia sp. 4AP-Z were predominant in 4-aminopyridine and formate/ammonium chloride enrichment cultures and in the 3,4-dihydroxypyridine enrichment culture, respectively. Among the culturable strains, strain 4AP-A could utilize 3,4-dihydroxypyridine as a growth substrate. Although we could not isolate strain 4AP-Y on several media, PCR-DGGE analysis and microscopy indicated that the unique bi-polar filamentous bacterial cells gradually became more dominant with increasing 4-aminopyridine concentration in the medium.

Conclusions: Hyphomicrobium sp. 4AP-Y, P. nitroreducens 4AP-A, and Elizabethkingia sp. 4AP-Z probably play important roles in 4-aminopyridine degradation in crop fields. In the enrichment culture, 3,4-dihydroxypyridine and its metabolites including formate might be shared as growth substrates and maintain the enrichment culture, including these indispensable strains.

Figure 1

Proposed pathway of 4-aminopyridine degradation by the enrichment culture. I, 4-aminopyridine; II, 3,4-dihydroxypyridine; III, 3-(N-formyl)-formiminopyruvate; and IV, 4-amino-3-hydroxypyridine. The ring-cleavage product 3-(N-formyl)-formiminopyruvate from 3,4-dihydroxypyridine was hypothesized from the metabolic pathway of 3,4-dihydroxypyridine in Agrobacterium sp. NCIB 10413 [6,7]. The strains of the enrichment culture probably involved in the steps are indicated.

Figure 2

Growth of the enrichment culture in medium containing 4-aminopyridine. Growth and degradation of 4-aminopyridine. The enrichment culture was cultivated in medium containing 2.13 mM 4-aminopyridine (0.02% wt/vol) at 30°C with shaking. Growth was determined by measuring the optical density at 660 nm (OD₆₆₀) (open squares); the residual 4-aminopyridine (filled triangles, 4-AP) was measured using HPLC as described in the text; the released ammonia (open circles) was measured using the indophenol method [21]; and total protein in the culture (filled circles) was measured using the modified Lowry method, independently performed twice.

Figure 3

DGGE profile of the enrichment culture during cultivation in medium containing 4-aminopyridine. Standard amplified fragments from strains 4AP-A, 4AP-B, 4AP-C, 4AP-D, 4AP-E, 4AP-F, and 4AP-G were loaded in lane M. The enrichment culture grown in medium containing 4-aminopyridine was used to inoculate fresh medium (0.5 ml) containing 2.13 mM 4-aminopyridine (0.02% wt/vol), and the subculture was incubated at 30°C with shaking. The subculture was sampled (0.8 ml) every 12 h, and the harvested cells were used for PCR-DGGE.

Figure 4

DGGE profile of the enrichment culture grown in media containing various concentrations of 4-aminopyridine. The enrichment culture was used to inoculate basal medium without 4-aminopyridine (lane 1) and with 4-aminopyridine (lane 2, 2.13 mM; lane 3, 10.6 mM; and lane 4, 53.2 mM), and the subcultures were incubated at 30°C with shaking. After 4 days of cultivation, the subcultures were sampled for PCR-DGGE analysis. The standard amplified fragments from strains 4AP-A, 4AP-B, 4AP-C, 4AP-D, 4AP-E, 4AP-F, and 4AP-G were loaded in lane M.

Figure 5

DGGE profile of the enrichment cultures from a diluted pre-culture sample. (A) Degradation of 4-aminopyridine by the diluted enrichment culture. The enrichment culture grown in medium containing 4-aminopyridine was diluted 10⁸-fold with 0.8% NaCl solution, and the diluted culture was used to inoculate fresh medium containing 2.13 mM 4-aminopyridine; the subculture was incubated at 30°C with shaking. The remaining 4-aminopyridine (4-AP) was measured using HPLC as described in the text. (Subcultures: a, open triangles; b, open circles; and c, filled squares; d, filled circles). The results of one representative experiment are shown; the residual 4-aminopyridine was measured in triplicate. (B) DGGE profiles of the enrichment culture. Subcultures that degraded 4-aminopyridine in 4 days (a, b, and c) and the subculture that did not degrade 4-aminopyridine (d) were analyzed by PCR-DGGE. The standard amplified fragments from strains 4AP-A, 4AP-B, 4AP-C, 4AP-D, 4AP-E, 4AP-F, and 4AP-G were loaded in lane M. The harvested cells of the enrichment culture were also used for PCR-DGGE (lane KM).

Figure 6

DGGE profiles of the enrichment culture grown in medium containing 4-aminopyridine, 3,4-dihydroxypyridine, or formate. The enrichment culture grown in medium containing 4-aminopyridine was used to inoculate medium containing 0.9 mM 3,4-dihydroxypyridine or 2.13 mM formate and 0.43 mM ammonium chloride. The culture was incubated and subcultured in fresh medium twice before DGGE analysis. (A) The standard amplified fragments from strains 4AP-A, 4AP-B, 4AP-C, 4AP-D, 4AP-E, 4AP-F, and 4AP-G were loaded in lane M. Lane 1, culture grown in medium containing 4-aminopyridine; lane 2, culture grown in medium containing 3,4-dihydroxypyridine. (B) The standard amplified fragments from the seven strains; lane 1, culture grown in medium containing formate and ammonium chloride; lane 2, culture grown in medium in the absence of formate. Extraction of genomic DNA and preparation of DGGE samples were carried out in triplicate. Prominent DNA bands from the DGGE gels were extracted and used as PCR templates as described in the text.