Effect of soil bacteria on the ability of polycyclic aromatic hydrocarbons (PAHs) removal by Trametes versicolor and Irpex lacteus from contaminated soil

The effect of bacteria represented by indigenous soil microflora or a mixture of soil bacteria Pseudomonas aeruginosa and Rhodococcus erythropolis on fungal growth, extracellular enzyme production and polycyclic aromatic hydrocarbons (PAHs) biodegradation efficiency in soil of white-rot fungi Trametes versicolor and Irpex lacteus was investigated. Both fungi were able to colonize soil. The growth yields measured by ergosterol were about two-fold in I. lacteus after 10 weeks. Laccase was produced in T. versicolor cultures in the presence or absence of bacteria but live bacteria reduced the laccase levels in soil about 5 times. Manganese-dependent peroxidase (MnP) was not detected in T. versicolor cultures. The amounts of MnP and laccase in I. lacteus cultures were not affected by the presence of bacteria. T. versicolor was more efficient in PAH removal for all PAHs tested although its capacity to colonize soil was lower. The removal rates of PAHs by T. versicolor in sterile soil were 1.5-fold, 5.8-fold and 1.8-fold for 2-3-ring, 4-ring and 5-6-ring PAHs, compared to I. lacteus, respectively. I. lacteus showed a low efficiency of removal of pyrene, benzo[a]anthracene and benzo[k]fluoranthene, compared to T. versicolor, whereas chrysene and benzo[b]fluoranthene were degraded by neither fungus. The main effect of the presence of the indigenous microflora or R. erythropolis and P. aeruginosa was a significant decrease of degradation of total PAHs by both T. versicolor and I. lacteus. Weak fungal/bacterial synergistic effects were observed in the case of removal of acenapthylene, benzo[a]pyrene, dibenzo[a,h]anthracene and benzo[g,h,i]perylene by I. lacteus and acenapthylene by T. versicolor. However, the bacterial effects were different in the two fungi. PAH abiotic losses represented 15 and 21% of the total PAHs after 5 and 10 weeks, respectively; naphthalene and acenaphthene were removed from the soil due to volatilization.     

Phylogenetic characterization of dwarf archaea and bacteria from a semiarid soil

Microscopic studies have shown that most microbes exist in soils as dwarf cells that are thought to be an adaptation to nutrient limitation. Most dwarfs are uncultured by current approaches and have not been identified phylogenetically. Only a few dwarf bacteria have been isolated in culture and dwarf archaea have received little study. We selected a semiarid creosotebush shrubland site for studying dwarf microorganisms because arid and semiarid soils are generally nutrient-poor. Soils were collected beneath creosotebush canopies and in open areas between shrubs. Cells were eluted in sodium pyrophosphate and filtered with a 0.45-μm pore-size filter. Filtrate DNA was extracted, PCR-amplified using universal bacterial and archaeal 16S rDNA primers, cloned, RFLP-screened, and sequenced. The eluted cell filtrates were also inoculated into R2B medium. After incubation, cultures were filtered to select against populations of dwarfs that formed large cells in the presence of nutrients (pleomorphic dwarfs) and to select for populations that retained dwarf size (intrinsic dwarfs). Dwarf archaea and bacteria were present in the initial filtrate and in the cultures. A single dwarf archaeon (SevArch-01) that is related to other soil Crenarchaeota sequences was found in the initial filtrates and in subsequent filtrate cultures, indicating an intrinsically dwarf archaeon. Dwarf bacteria fell into four bacterial phyla: Proteobacteria, Firmicutes, Actinobacteria, and the TM-7 group. Intrinsically dwarf bacteria in enrichment cultures were identified as α- and β-Proteobacteria. Dwarf bacteria related to Arthrobacter, Propionibacterium, and other actinobacteria were detected. Several sequences showed no close relationships to any microorganisms that have been grown in culture.