Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

Abstract

BackgroundSoil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.MethodsAtrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA.ResultsA total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins.ConclusionsDirect plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0868-3) contains supplementary material, which is available to authorized users.

Colonization of plant roots and enhanced atrazine degradation by a strain of Arthrobacter ureafaciens

“…Grassland soil S1 not adapted to atrazine was collected in East Jinan. Location and history of the site and characteristics of S1 soil were previously reported (Bazhanov et al 2016 ).…”

“…Atrazine-degrading strain A. ureafaciens DnL1-1 harboring the genes trzN and atzBC was earlier isolated from the maize rhizosphere by a direct plating method (Bazhanov et al 2016 ). The strain was deposited in the China General Microbiological Culture Collection Center (CGMCC) under the registration no.…”

“…The type strain A. ureafaciens CGMCC 1.1897 T was obtained from the CGMCC. Mineral media SM and SMY (Bazhanov et al 2016 ) were used to grow atrazine-degrading bacteria. Swimming motility was detected in liquid and semisolid (0.2% agar) medium SA, which contained salts of SM medium and 1 g/L asparagine as sole carbon and nitrogen source.…”

“…Strains belonging to the genus Arthrobacter are one of the most frequently isolated degraders of atrazine (Arbeli and Fuentes 2010 ; Krutz et al 2010 ; Bazhanov et al 2016 ). It is traditionally believed that Arthrobacter bacteria, being typical autochthonous soil microbes (Winogradsky 1925 ) and “K” strategists (Bowen 1980 ), are associated with bulk rather than rhizosphere soil (Cacciari and Lippi 1987 ).…”

“…This suggests that the most successful soil degraders of atrazine are those associated with plant roots and therefore can be expected to actively colonize the rhizoplane and rhizosphere. Our previous research demonstrated that genetically similar atrazine-degrading Arthrobacter ureafaciens strains were ubiquitous in exposed to atrazine agricultural soils of Shandong Province and prevailed among atrazine degraders directly isolated from the maize rhizosphere (Bazhanov et al 2016 ). The present study aimed to assess the root-colonizing capacity of strain A. ureafaciens DnL1-1 applied via inoculation of plant seeds and to evaluate consequent root-associated degradation of atrazine.…”