Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

Abstract

Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 10 4 CFU g of soil ؊1 . The analysis of Sphingomonas population structures of several PAHcontaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

“…Several genera belonging to Acetobacteraceae have been linked with hydrocarbon degradation at moderately low pH levels (Hamamura et al, 2005;Rö ling et al, 2006). Sphingomonadaceae, Burkholderiaceae and Pseudomonadaceae are recognized for their extraordinary catabolic flexibility and are among the most common hydrocarbon degraders in a variety of soils (Leys et al, 2004;Stolz, 2009;Silby et al, 2011;Pérez-Pantoja et al, 2012); however, a thorough knowledge on pH optima of these groups is still lacking. Although these results provide clues about the pH preferences of these bacterial groups in the studied site, it remains to be shown whether they successfully degrade PAH or TPH compounds under these conditions.…”

Diversity of endophytic bacteria in Caragana microphylla grown in the desert grassland of the Ningxia Hui Autonomous Region of China

“…For example, endophytic Burkholderiaceae species have been detected in several crops (Sun et al, 2008). Similarly, members of the Sphingomonadaceae family are widespread in different types of soils, sediments, and pelagic aquatic environments, and are known for their ability to utilize a wide variety of carbon sources; several are in fact renowned degraders of recalcitrant (xenobiotic) molecules (Leys et al, 2004). Additionally, some sphingomonads were also found to play important roles in the mycorrhizosphere (Boersma et al, 2009).…”

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“…These isolated strains, PHPY and SK, are proposed to be new members of Sphingomonadaceae and Rhodobacteraceae, respectively. Several reports have shown the important role of bacteria in Sphingomonadaceae for PAH degradation in soils 16,31,32 , mangrove sediments 33 , and deep subsurface sediments 34 . This study, in accordance with previous reports 35 , also found that sphingomonads with PAH degradation ability can be isolated from seawater, indicating that sphingomonads are found in a wide variety of environments and might play a key role in the degradation of PAHs in various environments, including the marine environment.…”