Assessment of Biological Contribution to Natural Recovery of Anthropized Freshwater Sediments From Argentina: Autochthonous Microbiome Structure and Functional Prediction.

Monitored natural recovery (MNR) is an in situ technique of conventional remediation for the treatment of contaminated sediments that relies on natural processes to reduce the bioavailability or toxicity of contaminants. Metabarcoding and bioinformatics approaches to infer functional prediction were applied in bottom sediments of a tributary drainage channel of Río de La Plata estuary, in order to assess the biological contribution to MNR. Hydrocarbon concentration in water samples and surface sediments was below the detection limit. Surface sediments were represented with high available phosphorous, alkaline pH, and the bacterial classes Anaerolineae, Planctomycetia, and Deltaproteobacteria. The functional prediction in surface sediments showed an increase of metabolic activity, carbon fixation, methanogenesis, and synergistic relationships between Archaeas, Syntrophobacterales, and Desulfobacterales. The prediction in non-surface sediments suggested the capacity to respond to different kinds of environmental stresses (oxidative, osmotic, heat, acid pH, and heavy metals), predicted mostly in Lactobacillales order, and the capacity of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinomyces classes to degrade xenobiotic compounds. Canonical correspondence analysis (CCA) suggests that depth, phosphate content, redox potential, and pH were the variables that structured the bacterial community and not the hydrocarbons. The characterization of sediments by metabarcoding and functional prediction approaches, allowed to assess how the microbial activity would contribute to the recovery of the site.

A historical legacy of antibiotic utilization on bacterial seed banks in sediments.

The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.

Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches.

The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).

Remediation of phenanthrene-contaminated soil by simultaneous persulfate chemical oxidation and biodegradation processes.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous compounds with carcinogenic and/or mutagenic potential. To address the limitations of individual remediation techniques and to achieve better PAH removal efficiencies, the combination of chemical and biological treatments can be used. The degradation of phenanthrene (chosen as a model of PAH) by persulfate in freshly contaminated soil microcosms was studied to assess its impact on the biodegradation process and on soil properties. Soil microcosms contaminated with 140 mg/kgDRY SOIL of phenanthrene were treated with different persulfate (PS) concentrations 0.86-41.7 g/kgDRY SOIL and incubated for 28 days. Analyses of phenanthrene and persulfate concentrations and soil pH were performed. Cultivable heterotrophic bacterial count was carried out after 28 days of treatment. Genetic diversity analysis of the soil microcosm bacterial community was performed by PCR amplification of bacterial 16S rDNA fragments followed by denaturing gradient gel electrophoresis (DGGE). The addition of PS in low concentrations could be an interesting biostimulatory strategy that managed to shorten the lag phase of the phenanthrene biological elimination, without negative effects on the physicochemical and biological soil properties, improving the remediation treatment.