Abstract:Soil microorganisms surviving in mining sites have developed metalresistance mechanisms to biotransform metals. Their use as biofertilizers can improve phytoremediation efficiency in contaminated soils by reducing metal toxicity while promoting plant growth. We analysed through wholemetagenome shotgun sequencing the composition, diversity and function of microbial communities present in a contaminated mine soil along a gradient of metals (As, Cu, Fe, Mn, Pb, Zn) to identify tolerant species carrying metal-resi… Show more
“…By cooperating or cross-feeding with other soil bacterial species, Actinobacteria are able to continue their metabolic activities even at low temperatures 53 . According to a study by Navas et al 54 , Actinobacteria are widely distributed in soils with low metal(loid) contamination. Figure 6 Heatmap presenting differences in the relative abundance of particular sequences among all obtained sequences between the not enriched (control) and the halloysite-enriched soil samples, respectively (class level Euclidean distance measure, Ward algorithm used for clustering).…”
Section: Resultsmentioning
confidence: 99%
“…and Sphingomonas sp. thrive in PTE-contaminated soils 54 , 59 , likely due to their PTE resistance genes 61 , 62 .…”
The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing–thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing–thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT’s role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC’s negative effect on microbial diversity and increased Planctomycetia abundance.
“…By cooperating or cross-feeding with other soil bacterial species, Actinobacteria are able to continue their metabolic activities even at low temperatures 53 . According to a study by Navas et al 54 , Actinobacteria are widely distributed in soils with low metal(loid) contamination. Figure 6 Heatmap presenting differences in the relative abundance of particular sequences among all obtained sequences between the not enriched (control) and the halloysite-enriched soil samples, respectively (class level Euclidean distance measure, Ward algorithm used for clustering).…”
Section: Resultsmentioning
confidence: 99%
“…and Sphingomonas sp. thrive in PTE-contaminated soils 54 , 59 , likely due to their PTE resistance genes 61 , 62 .…”
The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing–thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing–thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT’s role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC’s negative effect on microbial diversity and increased Planctomycetia abundance.
“…In freeze–thaw-exposed samples, abundances of Gammmaproteobacteria and Alphaprotepbacteria significantly increased, the abundance of Betaproteobacteria did not change and the average abundance of Deltaproteobacteria decreased. A study by Navas et al [ 95 ] has shown that Proteobacteria predominated in soil with a high content of metal(-loid)s while Actinobacteria were more abundant in soil with low content of metal(-loid)s. The higher resilience of Proteobacteria to high content of metal(-loid)s can be related to the fact that they are Gram-negative bacteria and possess an outer lipopolysaccharide layer in their cell wall that sequestrates metals extracellularly conferring adaptation to harsh contaminated environments [ 96 ]. Actinobacteria are an important member of soil microbiome participating in carbon cycling and production of soil organic matter [ 94 , 97 ].…”
Section: Resultsmentioning
confidence: 99%
“…Both genera were reported in soils contaminated with potentially toxic elements. Navas, et al [ 95 ] identified Mycobacterium sp. as a predominant genus in soil from mining sites but with a low content of potentially toxic elements while Sphingomonas sp.…”
In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing–thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing–thawing in a glass greenhouse, followed by 64 days under freezing-–thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze–thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing–thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing–thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing–thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing–thawing. Moreover, exposure to freezing–thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing–thawing greatly affected soil microbiome composition, biochar reduced the freeze–thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing–thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.
“…Arsenic is typically present as arsenite (As(III)) in soils, and bacteria can pump out As(III) via an efflux pump, or reduce less common forms of arsenic to As(III) [ 66 ]. Furthermore, another study showed that the most abundant metal-resistance genes in soils from an abandoned copper mine were associated with Cu, As, and Fe resistance [ 67 ]. Nonetheless, a silver-lead–zinc mine also reported the soil bacterial community to vary with As concentrations [ 55 ].…”
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield—a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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