Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

Abstract

The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates according to in vitro assays. PGP tested in vivo on tomato plants using eleven selected bacterial isolates, confirmed the promotion and protection potential of the rhizosphere bacteria. Different spontaneous plant species naturally selected in a historical chronically polluted site showed to determine the enrichment of peculiar bacterial communities in the soil fractions associated to the roots. All the rhizosphere communities, nevertheless, hosted bacteria with degradation/detoxification and PGP potential, putatively sustaining the natural attenuation process.

Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils

“…All the isolates, with the exception of one Pseudomonas strain, were affiliated to the phylum Actinobacteria. The phylogenetic composition of this collection differs from a previous bacterial collection isolated from spontaneous plants naturally selected in the same area of the SIN Caffaro, which comprised a higher phylogenetic diversity and, besides Actinobacteria (up to 75% of the isolates obtained from the same plant), contained also Proteobacteria (up to 32%) and Bacilli (up to 13%) [43]. This apparent discrepancy can be explained by the combination of the selective isolation conditions applied in this work, which exploited PSMs as unique carbon source, and the different origin of the root-associated soil, sampled from potted P .…”

“…arundinacea subjected to repeated flooding to induce cyclic redox conditions. Actinobacteria, a significant part of spontaneous plants rhizosphere in the SIN-Brescia Caffaro as also demonstrated by cultivation independent methods [43], showed to be an important potential degradative phylogenetic group in this aged PCB contaminated site, and its dominance in plant soil surrounding root suggests its keystone role, being specifically enriched by rhizo-stimulation. Further experiments are nevertheless needed to sustain this speculation.…”

Climatic impacts on the bacterial community profiles of cork oak soils

“…The cork oak core microbiome was dominated by Proteobacteria (33.2% of core OTUs and 39.7% of total reads assigned), mainly including Alphaproteobacteria (20.5% and 29.8%, respectively), but also Actinobacteria (19.1% and 24.2%, respectively) and Acidobacteria (19.9% and 20%, respectively). From the core bacterial community, several bacterial orders that typically inhabit soil fractions under the influence of plants were detected (Rhizobiales, Burkholderiales, Shingomonadales and Pseudomonadales, all from Proteobacteria; Gaiellales from Actinobacteria; Hayat et al, 2010;Vergani et al, 2017), comprising together > 54% of total bacterial core reads. Although only a part of the studied soil was in direct contact with cork oak roots, this core bacterial community is likely to be modulated by the specific influence of cork oak roots proximity.…”

Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

“…Biphenyl has been widely used as a mineralizable polychlorinated biphenyls (PCBs) analog in biodegradation studies ( Leigh et al, 2006 ; Uhlik et al, 2009 ; Leewis et al, 2016 ; Vergani et al, 2017a ). PCBs are a family of man-made persistent organic chemicals that consist of a biphenyl skeleton where 1–10 hydrogen atoms are substituted by chlorine giving rise to up to 209 congeners.…”