Environmental health is increasingly compromised by persistent toxic substances, which may have serious implications in food safety and, thus, in human health. Polybrominated diphenyl ethers (PBDEs) are anthropogenic contaminants with endocrine disruption abilities and are commonly found in seafood, the main route of human exposure. Growing evidence points out that the human gut microbiota interacts with xenobiotics, which may lead to impairment of host homeostasis if functions of microbiota become compromised. The aim of this study was to ascertain if the physiological balance of human gut microbiome is affected by the presence and degree of exposure to PBDEs. Fermentation was performed in a batch closed-system using an inoculum made from fresh human stool. The volatolomic profile was analysed by solid-phase microextraction coupled to gas chromatography-mass spectrometry. Mesophilic, Gram-negative bacteria and coliforms were quantified by classic plating methods. Changes in the gut microbiome were evaluated after DNA extraction followed by deep sequencing of the 16S rDNA region. The exposure to PBDEs resulted in an imbalance in sulfur, short-chain fatty acids and aromatic organic compounds, changing the microbial volatolome in a dose- and time-dependent manner. Slight deviations in the microbial structure of human gut occurred in the presence of PBDEs, especially for high doses of exposure. For the first time, the impact of PBDEs on the microbial homeostasis of human gut microbiota was taken into consideration, revealing noteworthy modifications with serious health implications even at oral exposure doses considered as safe by worldwide regulatory entities.

Di-(2-ethylhexyl) phthalate (DEHP) has been classified as a priority pollutant which increased the healthy risk to human and animals dramatically. Hence, a novel biochemical system combined by DEHP-resistant bacterial flora (B) and a green oxidant of persulfate (PS) activated by Nano-Fe₃O₄ was applied to degrade DEHP in contaminated soil. In this study, the resistant bacterial flora was screened from activated sludge and immobilized by sodium alginate (SAB). Nano-Fe₃O₄ was coated on biochar (BC@Fe₃O₄) to prevent agglomerating in soil. X-ray diffraction (XRD) and scanning electron microscope (SEM) were utilized to characterize BC@Fe₃O₄. Results demonstrated that the treatment of biochemical system (SAB + BC@Fe₃O₄ + PS) presented the maximum degradation rate about 92.56% within 24 days of incubation and improved soil microecology. The 16S rDNA sequences analysis of soil microorganisms showed a significantly different abundance and a similar diversity among different treatments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional genes difference analysis showed that some metabolic pathways, such as metabolism of cofactors and vitamins, energy metabolism, cell growth and death, replication and repair, were associated with the biodegradation of DEHP. Besides, DEHP was converted to MEHP and PA by biodegradation, while DEHP was converted to DBP and PA by persulfate and BC@Fe₃O₄, and then ultimately degraded to CO₂ and H₂O.

Zeolite-supported nanoscale zero-valent iron (Z-NZVI) has great potential for metal(loid) removal, but its encapsulation mechanisms and ecological risks in real soil systems are not completely clear. We conducted long-term incubation experiments to gain new insights into the interactions between metal(loid)s (Cd, Pb, As) and Z-NZVI in naturally contaminated farmland soils, as well as the alteration of indigenous bacterial communities during soil remediation. With the pH-adjusting and adsorption capacities, 30 g kg⁻¹ Z-NZVI amendment significantly decreased the available metal(loid) concentrations by 10.2–96.8% and transformed them into strongly-bound fractions in acidic and alkaline soils after 180 d. An innovative magnetic separation of Z-NZVI from soils followed by XRD and XPS characterizations revealed that B-type ternary complexation, heterogeneous coprecipitation, and/or concurrent redox reactions of metal(loid)s, especially the formation of Cd₃(AsO₄)₂, PbFe₂(AsO₄)₂(OH)₂, and As⁰, occurred only under specific soil conditions. Sequencing of 16S rDNA using Illumina MiSeq platform indicated that temporary shifts in iron-resistant/sensitive, pH-sensitive, denitrifying, and metal-resistant bacteria after Z-NZVI addition were ultimately eliminated because soil characteristics drove the re-establishment of indigenous bacterial community. Meanwhile, Z-NZVI recovered the basic activities of bacterial DNA replication and denitrification functions in soils. These results confirm that Z-NZVI is promising for the long-term remediation of metal(loid)s contaminated farmland soil without significant ecotoxicity.

Nonylphenol (NP), ubiquitously detected as the degradation product of nonionic surfactants nonylphenol polyethoxylates, has been reported as an endocrine disrupter. However, most pure microorganisms can degrade only limited species of NP with low degradation efficiencies. To establish a microbial consortium that can effectively degrade different forms of NP, in this study, we isolated a facultative microbial consortium NP-M2 and characterized the biodegradation of NP by it. NP-M2 could degrade 75.61% and 89.75% of 1000 mg/L NP within 48 h and 8 days, respectively; an efficiency higher than that of any other consortium or pure microorganism reported so far. The addition of yeast extract promoted the biodegradation more significantly than that of glucose. Moreover, surface-active compounds secreted into the extracellular environment were hypothesized to promote high-efficiency metabolism of NP. The detoxification of NP by this consortium was determined. The degradation pathway was hypothesized to be initiated by oxidization of the benzene ring, followed by step-wise side-chain biodegradation. The bacterial composition of NP-M2 was determined using 16S rDNA library, and the consortium was found to mainly comprise members of the Sphingomonas, Pseudomonas, Alicycliphilus, and Acidovorax genera, with the former two accounting for 86.86% of the consortium. The high degradation efficiency of NP-M2 indicated that it could be a promising candidate for NP bioremediation in situ.

Microbial carbonate precipitation is known as an efficient process for the remediation of heavy metals from contaminated soils. In the present study, a urease positive bacterial isolate, identified as Bacillus cereus NS4 through 16S rDNA sequencing, was utilized on a large scale to remove nickel from industrial soil contaminated by the battery industry. The soil was highly contaminated with an initial total nickel concentration of approximately 900 mg kg−1. The soluble-exchangeable fraction was reduced to 38 mg kg−1 after treatment. The primary objective of metal stabilization was achieved by reducing the bioavailability through immobilizing the nickel in the urease-driven carbonate precipitation. The nickel removal in the soils contributed to the transformation of nickel from mobile species into stable biominerals identified as calcite, vaterite, aragonite and nickelous carbonate when analyzed under XRD. It was proven that during precipitation of calcite, Ni2+ with an ion radius close to Ca2+ was incorporated into the CaCO3 crystal. The biominerals were also characterized by using SEM-EDS to observe the crystal shape and Raman-FTIR spectroscopy to predict responsible bonding during bioremediation with respect to Ni immobilization. The electronic structure and chemical-state information of the detected elements during MICP bioremediation process was studied by XPS. This is the first study in which microbial carbonate precipitation was used for the large-scale remediation of metal-contaminated industrial soil.

Plant establishment, presence of arbuscular mycorrhizal fungi (AMF) and other rhizospheric fungi were studied in mine wastes from Zimapan, Hidalgo state, Mexico, using a holistic approach. Two long-term afforested and three non-afforested mine tailings were included in this research. Fifty-six plant species belonging to 29 families were successfully established on the afforested sites, while unmanaged tailings had only a few native plant species colonizing the surrounding soils. Almost all plant roots collected were associated to AMF in these sites. The genus Glomus was the most abundant AMF species found in their rhizosphere; however, the Acaulospora genus was also observed. Other rhizospheric fungi were identified by 18S rDNA sequencing analysis. Their role in these substrates, i.e. biocontrol, pollutant- and organic matter-degradation, and aides that increase plant metal tolerance is discussed. Our results advance the understanding of fungal diversity in sites polluted with metals and present alternative plants for remediation use.

Microbial mercury (Hg) methylation transforms inorganic mercury to neurotoxic methylmercury (MeHg) mainly in aquatic anoxic environments. Sampling challenges in marine ecosystems, particularly in submarine canyons, leads to a lack of knowledge about the Hg methylating microbia in marine sediments. A previous study showed an enrichment of mercury species in sediments from the Capbreton Canyon where both geochemical parameters and microbial activities constrained the net MeHg production. In order to characterize Hg-methylating microbial communities from coastal to deeper sediments, we analysed the diversity of microorganisms’ (16S rDNA-based sequencing) and Hg methylators (hgcA based cloning and sequencing). Both, 16S rDNA and hgcA gene analysis demonstrated that the putative Hg-methylating prokaryotes were likely within the Deltaproteobacteria, dominated by sulfur-compounds based reducing bacteria (mainly sulfate reducers). Additionally, others clades were also identified as carrying HgcA gene, such as, Chloroflexi, Spirochaetes, Elusimicrobia, PVC superphylum (Plantomycetes, Verrucomicrobia and Chlamydiae) and Euryarchaea. Nevertheless, 61% of the hgcA sequences were not assigned to specific clade, indicating that further studies are needed to understand the implication of new microorganisms carrying hgcA in the Hg methylation in marine environments. These first results suggest that sulfur cycle drives the Hg-methylation in marine ecosystem.

Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH₄⁺ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO₃⁻ showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH₄⁺/NO₃⁻ being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.

The potential impacts of mining activities on tropical coastal ecosystems are poorly understood. In particular, limited information is available on the effects of metals on scleractinian corals which are foundation species that form vital structural habitats supporting other biota. This study investigated the effects of dissolved nickel and copper on the coral Acropora muricata and its associated microbiota. Corals collected from the Great Barrier Reef were exposed to dissolved nickel (45, 90, 470, 900 and 9050 μg Ni/L) or copper (4, 11, 32 and 65 μg Cu/L) in flow through chambers at the National Sea Simulator, Townsville, Qld, Australia. After a 96-h exposure DNA metabarcoding (16S rDNA and 18S rDNA) was undertaken on all samples to detect changes in the structure of the coral microbiome. The controls remained healthy throughout the study period. After 36 h, bleaching was only observed in corals exposed to 32 and 65 μg Cu/L and very high nickel concentrations (9050 μg Ni/L). At 96 h, significant discolouration of corals was only observed in 470 and 900 μg Ni/L treatments, the highest concentrations tested. While high concentrations of nickel caused bleaching, no changes in the composition of their microbiome communities were observed. In contrast, exposure to copper not only resulted in bleaching, but altered the composition of both the eukaryote and bacterial communities of the coral's microbiomes. Our findings showed that these effects were only evident at relatively high concentrations of nickel and copper, reflecting concentrations observed only in extremely polluted environments. Elevated metal concentrations have the capacity to alter the microbiomes which are inherently linked to coral health.

Pollution is a growing environmental problem throughout the world, and the impact of human activities on biodiversity and the genetic variability of natural populations is increasingly preoccupying, given that adaptive processes depend on this variability, in particular that found in the repetitive DNA. In the present study, the mitochondrial DNA (COI) and the distribution of repetitive DNA sequences (18S and 5S rDNA) in the fish genome were analysed in fish populations inhabiting both polluted and unpolluted waters in the northern Amazon basin. The results indicate highly complex ribosomal sequences in the fish genome from the polluted environment because these sequences are involved primarily in the maintenance of genome integrity, mediated by a systematic increase in the number of copies of the ribosomal DNA in response to changes in environmental conditions.