Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil

Abstract

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards

“…The calculated sequence coverage values for bacteria (63-68 %) were lower than those found by others (Sun et al 2014b;Uhlik et al 2013;Zhang et al 2013). The lower coverage values are reiterated in the rarefaction curves, which indicate that deeper sequencing would most likely have identified greater diversity.…”

“…Pyrosequencing techniques are capable of providing a more comprehensive picture of all microbes present in a sample, including low-abundance species (La Duc et al 2012). The technique has been used in numerous studies to investigate bacterial communities in soils (Uhlik et al 2013;Xiong et al 2014;Yang et al 2012;Zhang et al 2013), and recently, a study focusing on bacterial communities using high-throughput sequencing to investigating ARD soils in China was published (Sun et al 2014a). However, to our knowledge, no studies exist in which both the bacterial and fungal communities of soils affected by ARD have been investigated by high-throughput sequencing.…”

Chemical and microbiological characterization of an aged PCB-contaminated soil

“…In addition, microcosmbased SIP studies also confirmed that Burkholderia spp. dominated the aerobic degradation of PCB in a biofilm community grown directly on PCB droplets (Tillmann et al, 2005) as well as the degradation process occurring in a PCB-contaminated soil amended with caffeic acid (Uhlik et al, 2013). Table 3 F values and R 2 of tri-, tetra-, penta-, hexa-and hepta-chlorinated biphenyls (tri-CBs, tetraCBs, penta-CBs, hexa-CBs and hepta-CBs) in soils B, T and R. The data (bold figures) are the mean ± standard deviation of five technical replicates.…”

Plant-Microbe Partnerships for Enhanced Biodegradation of Polychlorinated Biphenyls

“…Watanabe and coworkers beautifully exploited the technique to detect and characterize dominant phenol-degrading bacteria in activated sludge (Watanabe et al 1998 ). In a similar technique, single-strand conformational polymorphism (SSCP), the separation of single-stranded Uhlik et al ( 2013 ) DNA is achieved on the polyacrylamide gel and differences in mobility results due to differences in the folded secondary structure. Here no denaturants are used; hence, DNA molecules of equal size fold and hence move differently according to the DNA base sequences (Schiwieger and Tebbe 1998 ).…”