The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling

Plastic is exceedingly abundant in soils, but little is known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio and BI-OPL plastic films buried in alpine soils for 5 months on the genetic potential of the soil microbiome using shotgun metagenomics. The microbiome was more affected by Ecovio and BI-OPL than by polyethylene. Fungi, α- and β-Proteobacteria dominated on the biodegradable films. Ecovio and BI-OPL showed signs of degradation after the incubation, whereas polyethylene did not. Genes involved in cellular processes and signaling (intracellular trafficking, secretion, vesicular transport), as well as metabolism (carbohydrate, lipid and secondary metabolism), were enriched in the plastisphere. Several α/β-hydrolase gene families (cutinase_like, polyesterase-lipase-cutinase, carboxylesterase), which encode enzymes essential to plastic degradation, and carbohydrate-active genes involved in lignin and murein degradation increased on Ecovio and BI-OPL films. Enriched nitrogen fixation and organic N degradation and synthesis genes and decreased nitrification genes on Ecovio altered the biogeochemical cycling, leading to higher ammonium concentrations and depletion of nitrite and nitrate in the soil. Our results indicate that plastics affect the alpine soil microbiome and its functions and suggest that the plastisphere has an untapped microbial potential for plastic biodegradation. + Graphical Abstrac

Can microbes be used to preserve archaeological iron objects?

Can microbes be used to preserve archaeological iron objects? Lucrezia Comensolia, J. Maillardb, P. Juniera and E. Josepha,c a Laboratory of Microbiology, Institute of Biology University of Neuchâtel, Switzerland b Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland c Haute Ecole Arc Conservation-Restauration, Neuchâtel, Switzerland [email protected] Without any conservation-restauration intervention archaeological iron objects are affected by a dramatic corrosion that leads to an irreversible loss of shape. The main issue with this metallic substrate is the chlorine content of the corrosion layers, which, by reaction with H2O and O2, causes an irreversible deterioration of the objects once excavated. Conservation-restauration technics available nowadays are ineffective, too expensive, time consuming and employ toxic substances. Therefore, the “MAIA” project (Microbe for Archaeological Iron Artworks) aims to develop new conservation-restauration methods based on microorganisms. For this purpose, iron reduction and chlorine uptake/volatilization capacities have been studied in selected microorganisms. These two metabolic abilities will allow to actively remove chlorine from the chlorinated iron compounds present in the corrosion layer and also to produce more stable iron minerals. For this aim, two anaerobic bacterial strains of Desulfitobacterium hafniense (strains LBE and TCE1, reported for dehalorespiration) and several fungal strains were studied. Different iron sources were tested either as soluble (iron citrate) or solid-phase iron compounds (powdered iron compounds from real archaeological artefacts). Spectrophotometric analyses were carried out to ascertain iron reduction and the evolution of the bacterial growth was quantified by quantitative Polymerase Chain Reaction (qPCR). Scanning Electronic Microscopy allows studying the fungal absorption of iron and chlorine, Raman Spectroscopy was used to identify the bio-mineral produced and finally we performed the first bacterial treatment of real archaeological iron objects. The results obtained show that microbes have the potential to stabilize iron objects by both reduction into more stable minerals and by removing chlorine from the object

The “Plastisphere” of Biodegradable Plastics Is Characterized by Specific Microbial Taxa of Alpine and Arctic Soils

Plastic pollution poses a threat to terrestrial ecosystems, even impacting soils from remote alpine and arctic areas. Biodegradable plastics are a promising solution to prevent long-term accumulation of plastic litter. However, little is known about the decomposition of biodegradable plastics in soils from alpine and polar ecosystems or the microorganisms involved in the process. Plastics in aquatic environments have previously been shown to form a microbial community on the surface of the plastic distinct from that in the surrounding water, constituting the so-called “plastisphere.” Comparable studies in terrestrial environments are scarce. Here, we aimed to characterize the plastisphere microbiome of three types of plastics differing in their biodegradability in soil using DNA metabarcoding. Polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), and polyethylene (PE) were buried in two different soils, from the Swiss Alps and from Northern Greenland, at 15°C for 8 weeks. While physico-chemical characteristics of the polymers only showed minor (PLA, PBAT) or no (PE) changes after incubation, a considerably lower α-diversity was observed on the plastic surfaces and prominent shifts occurred in the bacterial and fungal community structures between the plastisphere and the adjacent bulk soil not affected by the plastic. Effects on the plastisphere microbiome increased with greater biodegradability of the plastics, from PE to PLA. Copiotrophic taxa within the phyla Proteobacteria and Actinobacteria benefitted the most from plastic input. Especially taxa with a known potential to degrade xenobiotics, including Burkholderiales, Caulobacterales, Pseudomonas, Rhodococcus, and Streptomyces, thrived in the plastisphere of the Alpine and Arctic soils. In addition, Saccharimonadales (superphylum Patescibacteria) was identified as a key taxon associated with PLA. The association of Saccharibacteria with plastic has not been reported before, and pursuing this finding further may shed light on the lifestyle of this obscure candidate phylum. Plastic addition affected fungal taxa to a lesser extent since only few fungal genera such as Phlebia and Alternaria were increased on the plastisphere. Our findings suggest that the soil microbiome can be strongly influenced by plastic pollution in terrestrial cryoenvironments. Further research is required to fully understand microbial colonization on plastic surfaces and the biodegradation of plastic in soils

The Potential of Microorganisms for the Conservation- Restoration of Iron Artworks

Archaeological iron artefacts encounter serious post-excavation problems when contaminated with salts. Once excavated, exposure to a higher oxygen concentration and lower relative humidity renders the corrosion crust formed during burial no longer stable. In particular, the process is induced by chloride ions and leads to flaking, cracking and the final loss of shape of the object. The MAIA project (Microbes for Archaeological Iron Artefacts) studied microbial metabolisms to explore their potential for the development of innovative and sustainable methods for the stabilisation of corroded iron archaeological objects. Two different approaches were investigated. First, bacterial reduction of iron solid-phases and biogenic mineral formation were studied as a way to replace unstable corrosion products. Several bacterial strains were compared. Spectroscopic investigations with Raman and Fourier transform infrared spectroscopy on iron coupons, nail surfaces and cross sections demonstrated the conversion of the outermost part of the corrosion layer into more stable biogenic minerals, such as vivianite and siderite. The second approach was to study fungi and their metabolic ability with iron. In particular, alkaliphile fungi that tolerate chlorine were studied for their ability to produce biogenic minerals and to adsorb metals in their biomass. Colorimetric investigation and evaluation of the thickness of the corrosion layer demonstrated that fungi are good candidates for developing bio-cleaning methods for corroded iron, permitting the selective removal of the unstable and powdery corrosion layer without damaging the original metal surface. This study details these approaches and explores the possibilities of their exploitation for development of innovative and more sustainable treatments for the conservation-restoration of corroded iron

Investigation of biogenic passivating layers on corroded iron

This study evaluates mechanisms of biogenic mineral formation induced by bacterial iron reduction for the stabilization of corroded iron. As an example, the Desulfitobacterium hafniense strain TCE1 was employed to treat corroded coupons presenting urban natural atmospheric corrosion, and spectroscopic investigations were performed on the samples’ cross-sections to evaluate the corrosion stratigraphy. The treated samples presented a protective continuous layer of iron phosphates (vivianite Fe2+3(PO4)2·8H2O and barbosalite Fe2+Fe3+2(PO4)2(OH)2), which covered 92% of the surface and was associated with a decrease in the thickness of the original corrosion layer. The results allow us to better understand the conversion of reactive corrosion products into stable biogenic minerals, as well as to identify important criteria for the design of a green alternative treatment for the stabilization of corroded iron

Investigation of Biogenic Passivating Layers on Corroded Iron

This study evaluates mechanisms of biogenic mineral formation induced by bacterial iron reduction for the stabilization of corroded iron. As an example, the Desulfitobacterium hafniense strain TCE1 was employed to treat corroded coupons presenting urban natural atmospheric corrosion, and spectroscopic investigations were performed on the samples' cross-sections to evaluate the corrosion stratigraphy. The treated samples presented a protective continuous layer of iron phosphates (vivianite Fe-3(2+)(PO4)(2)8H(2)O and barbosalite Fe2+Fe23+(PO4)(2)(OH)(2)), which covered 92% of the surface and was associated with a decrease in the thickness of the original corrosion layer. The results allow us to better understand the conversion of reactive corrosion products into stable biogenic minerals, as well as to identify important criteria for the design of a green alternative treatment for the stabilization of corroded iron

Bacterial iron reduction and biogenic mineral formation for the stabilisation of corroded iron objects

Exploiting bacterial metabolism for the stabilisation of corroded iron artefacts is a promising alternative to conventional conservation-restoration methods. Bacterial iron reduction coupled to biogenic mineral formation has been shown to promote the conversion of reactive into stable corrosion products that are integrated into the natural corrosion layer of the object. However, in order to stabilise iron corrosion, the formation of specific biogenic minerals is essential. In this study, we used the facultative anaerobe Shewanella loihica for the production of stable biogenic iron minerals under controlled chemical conditions. The biogenic formation of crystalline iron phosphates was observed after iron reduction in a solution containing Fe(III) citrate. When the same biological treatment was applied on corroded iron plates, a layer composed of iron phosphates and iron carbonates was formed. Surface and cross-section analyses demonstrated that these two stable corrosion products replaced 81% of the reactive corrosion layer after two weeks of treatment. Such results demonstrate the potential of a biological treatment in the development of a stabilisation method to preserve corroded iron objects

Microbial Depolymerization of Epoxy Resins: A Novel Approach to a Complex Challenge

The objective of this project is evaluating the potential of microbes (fungi and bacteria) for the depolymerization of epoxy, aiming at the development of a circular management of natural resources for epoxy in a long-term prospective. For depolymerization, epoxy samples were incubated for 1, 3, 6 and 9 months in soil microcosms inoculated with Ganoderma adspersum. Contact angle data revealed a reduction in the hydrophobicity induced by the fungus. Environmental scanning electron microscopy on epoxy samples incubated for more than 3 years in microbiological water revealed abundant microbiota. This comprised microbes of different sizes and shapes. The fungi Trichoderma harzianum and Aspergillus calidoustus, as well as the bacteria Variovorax sp. and Methyloversatilis discipulorum, were isolated from this environment. Altogether, these results suggest that microbes are able to colonize epoxy surfaces and, most probably, also partially depolymerize them. This could open promising opportunities for the study of new metabolisms potentially able depolymerize epoxy materials.ISSN:2076-341