Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons

Abstract

Fast-growing mycobacteria are considered essential members of the polycyclic aromatic hydrocarbons (PAH) degrading bacterial community in PAH-contaminated soils. To study the natural role and diversity of the Mycobacterium community in contaminated soils, a culture-independent fingerprinting method based on PCR combined with denaturing gradient gel electrophoresis (DGGE) was developed. New PCR primers were selected which specifically targeted the 16S rRNA genes of fast-growing mycobacteria, and single-band DGGE profiles of amplicons were obtained for most Mycobacterium strains tested. Strains belonging to the same species revealed identical DGGE fingerprints, and in most cases, but not all, these fingerprints were typical for one species, allowing partial differentiation between species in a Mycobacterium community. Mycobacterium strains inoculated in soil were detected with a detection limit of 10(6) CFU g(-1) of soil using the new primer set as such, or approximately 10(2) CFU g(-1) in a nested PCR approach combining eubacterial and the Mycobacterium specific primers. Using the PCR-DGGE method, different species could be individually recognized in a mixed Mycobacterium community. This approach was used to rapidly assess the Mycobacterium community structure of several PAH-contaminated soils of diverse origin with different overall contamination profiles, pollution concentrations and chemical-physical soil characteristics. In the non-contaminated soil, most of the recovered 16SrRNA gene sequence did not match with previous described PAH-degrading Mycobacterium strains. In most PAH-contaminated soils, mycobacteria were detected which were closely related to fast-growing species such as Mycobacterium frederiksbergense and Mycobacterium austroafricanum, species that are known to include strains with PAH-degrading capacities. Interestingly, 16S rRNA genes related to M. tusciae sequences, a Mycobacterium species so far not reported in relation to biodegradation of PAHs, were detected in all contaminated soils.

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

“…One was for QZ 50 mg kg À1 pyrenetreated soil (QT) on day 60, the other was for QZ control soil (QC) on day 60. The PCR amplification used the primers Myco66F/Myco600R (Leys et al, 2005) as described in Table 2. A touchdown PCR protocol was used as previously.…”

“…The majority of them are Gram-positive. The fast-growing Mycobacterium spp (Miller et al, 2004;Leys et al, 2005), which play a key role in the degradation of high molecular weight PAH, have received particular attention. In addition, some pyrene-degrading g-Proteobacteria, such as enteric bacterium Leclercia adecarboxylata, has also been isolated (Eriksson et al, 2002;Sarma et al, 2004).…”

Isolation and Identification of Mycobacteria from Soils at an Illegal Dumping Site and Landfills in Japan

“…Yan Wang 1 tion of contaminated sites with other microorganisms (5,10,17,19,22,41,44). Detailed analyses of the interaction between environmental conditions and mycobacteria are needed.…”

“…Fax: ϩ81-93-602-4799. E-mail: hatsumi@med.uoeh-u.ac.jp Abbreviations: ARB, amoeba resistant bacteria; CFU, colony forming unit; DSMZ, the German National Resource Centre for Biological Material; hsp65, heat shock protein gene 65-kilodalton; MOI, multiplicity of infection; PAH, polycyclic aromatic hydrocarbons; PBS, phosphate buffered saline; PCDDS, polychlorinated dibenzo-p-dioxins; PCR, polymerase chain reaction; rpoB, RNA polymerase β-subunit gene; SDS, sodium dodecyl sulfate; Z-N, Ziehl-Neelsen staining; 16S rRNA, 16S ribosomal RNA.tion of contaminated sites with other microorganisms (5,10,17,19,22,41,44). Detailed analyses of the interaction between environmental conditions and mycobacteria are needed.…”

Genotypic responses of bacterial community structure to a mixture of wastewater-borne PAHs and PBDEs in constructed mangrove microcosms

“…These three bacterial groups differ in oxygen requirement, as Sphingomonas is a group of gram-negative, strictly aerobic bacteria, while Mycobacteria are gram-positive, aerobic bacteria. The two genera differ in their degrading preference of types and bioavailability of PAHs in sediments [18][19][20]. Dehalococcoides spp., within the phylum Chloroflexi, is a typical anaerobic halorespirer, which uses only hydrogen as electro donor and halogenated organic compounds as electron acceptors [21].…”