Cleavage of poly(cis-1,4-isoprene) rubber as solid substrate by cultures of Gordonia polyisoprenivorans

An Assessment of Biodegradability and Phytotoxicity of Natural Rubber in a Simulated Soil Condition via CO2 Evolution Measurement

In this study, the biodegradation of various natural rubber (NR) samples, i.e., neat NR and NR filled with two different curative contents was investigated under a long-term simulated soil condition at a temperature of 25 ± 2 °C in accordance with ISO 17556. Natural clay loam soil, with a pH of 7.2 and a water holding capacity of 57.6%, was employed. Under controlled test condition both unvulcanized and vulcanized NR samples having low curative content, respectively designated as UNRL and VNRL, exhibited similar biodegradation behaviors to the neat NR. They showed fast biodegradation at the early stage, and their biodegradation rate did not significantly change throughout the test period (365 days). However, for the NR samples having high curative content, respectively called UNRH and VNRH for the unvulcanized and vulcanized samples, a biodegradation delay was observed within the first 130 days. Surprisingly, the UNRH showed a relatively high biodegradation rate after the induction period. At the end of the test, most of the rubber samples (the neat NR, UNRL, VNRL, and UNRH) showed a comparable degree of biodegradation, with a value ranging from 54-59%. The VNRH, on the other hand, showed the lowest degree of biodegradation (ca. 28%). The results indicate that the number of curatives does not significantly affect the biodegradability of unvulcanized NR in the long term, despite the fact that a high curative content might retard microorganism activity at the beginning of the biodegradation process. Apparently, crosslink density is one of the key factors governing the biodegradability of NR. The phytotoxicity of the soils after the biodegradation test was also assessed and represented in terms of seedling emergence, survival rate, and plant biomass for Sorghum bicolor. The values of seedling emergence (≥80%), survival rate (100%), and plant biomass of all soil samples were not statistically different from those of the blank soil, indicating the low phytotoxicity of the tested soils subjected to the biodegradation of the rubber samples. Taken as a whole, it can be concluded that the CO2 measurement technique is one of the most effective methods to assess the biodegradability of rubbers. The knowledge obtained from this study can also be applied to formulate more environmentally friendly rubber products.

Rubber Oxygenase Degradation Assay by UV-Labeling and Gel Permeation Chromatography

A versatile and robust end-group derivatization approach using oximes has been developed for the detection of oxidative degradation of synthetic polyisoprenes and polybutadiene. This method demonstrates broad applicability, effectively monitoring degradation across a wide molecular weight range through ultraviolet (UV)-detection coupled to gel permeation chromatography. Importantly, it enables the effective monitoring of degradation via derivatization-induced UV-maximum shifts, even in the presence of an excess of undegraded polyene, overcoming limitations previously reported with refractive index detectors. Notably, this oxime-based derivatization methodology is used in enzymatic degradation experiments of synthetic polyisoprenes characterized by a cis: trans ratio with the rubber oxygenase LcpK30. It reveals substantial UV absorption in derivatized enzymatic degradation products of polyisoprene with molecular weights exceeding 1000 g mol-1 - an unprecedented revelation for this enzyme's activity on such synthetic polyisoprenes. This innovative approach holds promise as a valuable tool for advancing research into the degradation of synthetic polyisoprenes and polybutadiene, particularly under conditions of low organocatalytic or enzymatic degradation activity. With its broad applicability and capacity to reveal previously hidden degradation processes, it represents a noteworthy contribution to sustainable polymer chemistry.

Study of sequential abiotic and biotic degradation of styrene butadiene rubber

Styrene butadiene rubber is one of the main constituents of tire tread. During tire life, the tread material undergoes different stresses that impact its structure and chemical composition. Wear particles are then released into the environment as weathered material. To understand their fate, it is important to start with a better characterization of abiotic and biotic degradation of the elastomer material. A multi-disciplinary approach was implemented to study the photo- and thermo- degradation of non-vulcanized SBR films containing 15 w% styrene as well as their potential biodegradation by Rhodoccocus ruber and Gordonia polyisoprenivorans bacterial strains. Each ageing process leads to crosslinking reactions, much surface oxidation of the films and the production of hundreds of short chain compounds. These degradation products present a high level of unsaturation and oxidation and can be released into water to become potential substrates for microorganisms. Both strains were able to degrade from 0.2 to 1.2 % (% ThOD) of the aged SBR film after 30-day incubation while no biodegradation was observed on the pristine material. A 25-75 % decrease in the signal intensity of water extractable compounds was observed, suggesting that biomass production was linked to the consumption of low-molecular-weight degradation products. These results evidence the positive impact of abiotic degradation on the biodegradation process of styrene butadiene rubber.

Methods of Identifying Gordonia Strains in Clinical Samples

Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.

Biodegradation of rubber in cultures of Rhodococcus rhodochrous and by its enzyme latex clearing protein

The biodegradation of rubber materials is considered as a sustainable recycling alternative, highlighting the use of microorganisms and enzymes in oxidative processes of natural rubber. Currently, the main challenge is the treatment of rubber materials such as waste tyres, where the mixture of rubber polymers with different additives and the cross-linked structure obtained due to the vulcanisation process positions them as highly persistent materials. This study characterises the degradation of different rubber-containing substrates in in vivo and in vitro processes using the bacterium Rhodococcus rhodochrous and the oxygenase latex clearing protein (Lcp) from the same strain. For the first time, the degradation of polyisoprene particles in liquid cultures of R. rhodochrous was analysed, obtaining up to 19.32% mass loss of the polymer when using it as the only carbon source. Scanning electron microscopy analysis demonstrated surface alteration of pure polyisoprene and vulcanised rubber particles after 2 weeks of incubation. The enzyme Lcp_RR was produced in bioreactors under rhamnose induction and its activity characterised in oxygen consumption assays at different enzyme concentrations. A maximum consumption of 28.38 µmol_O2/min was obtained by adding 100 µg/mL Lcp_RR to a 2% (v/v) latex emulsion as substrate. The bioconversion of natural rubber into reaction degradation products or oligoisoprenoids was calculated to be 32.54%. Furthermore, the mass distribution of the oligoisoprenoids was analysed by liquid chromatography coupled to mass spectrometry (LC-MS) and 17 degradation products, ranging from C20 to C100 oligoisoprenoids, were identified. The multi-enzymatic degradation capacity of R. rhodochrous positions it as a model microorganism in complex degradation processes such as in the case of tyre waste.

Biological Process of Alkane Degradation by Gordonia sihwaniensis

With the development of the petroleum industry, oil pollution has become widespread. It is harmful to the digestive, immune, reproductive, and nervous systems of fishes, wild animals, and humans, causing severe threats to ecological safety and human health. Gordonia has increasingly attracted attention in the treatment of alkane pollution for its outstanding performance against hydrophobic refractory substances. However, the lack of knowledge about alkane uptake and degradation restricts the application of gordonia. In this paper, we studied the strain lys1-3 of Gordonia sihwaniensis isolated from coal chemical wastewater, which showed good alkane degradation performance by lys1-3. It is found that stimulated by an alkane, lys1-3 secreted biosurfactants, which emulsified large alkane particles to smaller particles. By active transport, unmodified alkane was transferred into cells and produced a large amount of acid, which was secreted out of the cells.

Assessing the Biodegradation of Vulcanised Rubber Particles by Fungi Using Genetic, Molecular and Surface Analysis

Millions of tonnes of tyre waste are discarded annually and are considered one of the most difficult solid wastes to recycle. A sustainable alternative for the treatment of vulcanised rubber is the use of microorganisms that can biotransform polymers and aromatic compounds and then assimilate and mineralise some of the degradation products. However, vulcanised rubber materials present great resistance to biodegradation due to the presence of highly hydrophobic cross-linked structures that are provided by the additives they contain and the vulcanisation process itself. In this work, the biodegradation capabilities of 10 fungal strains cultivated in PDA and EM solid medium were studied over a period of 4 weeks. The growth of the strains, the mass loss of the vulcanised rubber particles and the surface structure were analysed after the incubation period. With the white rot fungi Trametes versicolor and Pleurotus ostreatus, biodegradation percentages of 7.5 and 6.1%, respectively, were achieved. The FTIR and SEM-EDS analyses confirmed a modification of the abundance of functional groups and elements arranged on the rubber surface, such as C, O, S, Si, and Zn, due to the biological treatment employed. The availability of genomic sequences of P. ostreatus and T. versicolor in public repositories allowed the analysis of the genetic content, genomic characteristics and specific components of both fungal species, determining some similarities between both species and their relationship with rubber biodegradation. Both fungi presented a higher number of sequences for laccases and manganese peroxidases, two extracellular enzymes responsible for many of the oxidative reactions reported in the literature. This was confirmed by measuring the laccase and peroxidase activity in cultures of T. versicolor and P. ostreatus with rubber particles, reaching between 2.8 and 3.3-times higher enzyme activity than in the absence of rubber. The integrative analysis of the results, supported by genetic and bioinformatics tools, allowed a deeper analysis of the biodegradation processes of vulcanised rubber. It is expected that this type of analysis can be used to find more efficient biotechnological solutions in the future.

Bacterial and enzymatic degradation of poly(cis-1,4-isoprene) rubber: Novel biotechnological applications

Poly(cis-1,4-isoprene) rubber is a highly demanded elastomeric material mainly used for the manufacturing of tires. The end-cycle of rubber-made products is creating serious environmental concern and, therefore, different recycling processes have been proposed. However, the current physical-chemical processes include the use of hazardous chemical solvents, large amounts of energy, and possibly generations of unhealthy micro-plastics. Under this scenario, eco-friendly alternatives are needed and biotechnological rubber treatments are demonstrating huge potential. The cleavage mechanisms and the biochemical pathways for the uptake of poly(cis-1,4-isoprene) rubber have been extensively reported. Likewise, novel bacterial strains able to degrade the polymer have been studied and the involved structural and functional enzymes have been analyzed. Considering the fundamentals, biotechnological approaches have been proposed considering process optimization, cost-effective methods and larger-scale experiments in the search for practical and realistic applications. In this work, the latest research in the rubber biodegradation field is shown and discussed, aiming to analyze the combination of detoxification, devulcanization and polymer-cleavage mechanisms to achieve better degradation yields. The modified superficial structure of rubber materials after biological treatments might be an interesting way to reuse old rubber for re-vulcanization or to find new materials.

Solimonas fluminis has an active latex-clearing protein

The utilization of rubber (poly (cis-1,4-isoprene)) by rubber-degrading bacteria depends on the synthesis of rubber oxygenases that cleave the polymer extracellularly to low molecular weight products that can be taken up and used as a carbon source. All so far described Gram-negative rubber-degrading species use two related ≈ 70 kDa rubber oxygenases (RoxA and RoxB) for the primary attack of rubber while all described Gram-positive rubber-degrading strains use RoxA/RoxB-unrelated latex-clearing proteins (Lcps, ≈ 40 kDa) as rubber oxygenase(s). In this study, we identified an lcp orthologue in a Gram-negative species (Solimonas fluminis). We cloned and heterologously expressed the lcp gene of S. fluminis HR-BB, purified the corresponding Lcp protein (Lcp_HR-BB) from recombinant Escherichia coli, and biochemically characterised the Lcp_HR-BB activity. Lcp_HR-BB cleaved polyisoprene to a mixture of C₂₀ and higher oligoisoprenoids at a specific activity of 1.5 U/mg. Furthermore, spectroscopic investigation identified Lcp_HR-BB as a b-haem-containing protein with an oxidised, fivefold coordinated (open) haem centre. To the best of our knowledge, this is the first report that Gram-negative bacteria can have an active rubber oxygenase of the Lcp type.

Rubber oxygenases

Natural rubber (NR), poly(cis-1,4-isoprene), is used in an industrial scale for more than 100 years. Most of the NR-derived materials are released to the environment as waste or by abrasion of small particles from our tires. Furthermore, compounds with isoprene units in their molecular structures are part of many biomolecules such as terpenoids and carotenoids. Therefore, it is not surprising that NR-degrading bacteria are widespread in nature. NR has one carbon-carbon double bond per isoprene unit and this functional group is the primary target of NR-cleaving enzymes, so-called rubber oxygenases. Rubber oxygenases are secreted by rubber-degrading bacteria to initiate the break-down of the polymer and to use the generated cleavage products as a carbon source. Three main types of rubber oxygenases have been described so far. One is rubber oxygenase RoxA that was first isolated from Xanthomonas sp. 35Y but was later also identified in other Gram-negative rubber-degrading species. The second type of rubber oxygenase is the latex clearing protein (Lcp) that has been regularly found in Gram-positive rubber degraders. Recently, a third type of rubber oxygenase (RoxB) with distant relationship to RoxAs was identified in Gram-negative bacteria. All rubber oxygenases described so far are haem-containing enzymes and oxidatively cleave polyisoprene to low molecular weight oligoisoprenoids with terminal CHO and CO-CH3 functions between a variable number of intact isoprene units, depending on the type of rubber oxygenase. This contribution summarises the properties of RoxAs, RoxBs and Lcps.

Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment

BACKGROUND

Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments.

RESULTS

The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria.

CONCLUSION

This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.

Biodegradation of High Concentrations of Aliphatic Hydrocarbons in Soil from a Petroleum Refinery: Implications for Applicability of New Actinobacterial Strains

At present, there is great demand for new resistant and metabolically active strains of biodegrading bacteria capable of degrading high concentrations of petroleum pollutants. In this study, we undertook a series of pot-based biodegradation experiments on soil from a petroleum refinery lagoon heavily polluted with aliphatic hydrocarbons (81.6 ± 2.5 g·kg−1 dry weight) and metals. Periodical bioaugmentation with either a mixture of isolated degraders identified as Bacillus sp. and Ochrobactrum sp. or biostimulation with nutrient medium, singly or in combination, did not produce any significant decrease in hydrocarbons, even after 455 days. Inoculation with Gordonia rubripertincta CWB2 and Rhodococcus erythropolis S43 in iron-limited media, however, resulted in a significant decrease in hydrocarbons 45 days after bioaugmentation. These actinobacterial strains, therefore, show significant potential for bioremediation of such highly polluted soils.

Rhizobacter gummiphilus NS21 has two rubber oxygenases (RoxA and RoxB) acting synergistically in rubber utilisation

Biodegradation of poly(cis-1,4-isoprene) (rubber) by Gram-negative bacteria has been investigated on the enzymatic level only in Steroidobacter cummioxidans 35Y (previously Xanthomonas sp. 35Y). This species produces two kinds of rubber oxygenases, RoxA_35Y and RoxB_35Y, one of which (RoxB_35Y) cleaves polyisoprene to a mixture of C₂₀- and higher oligoisoprenoids while the other (RoxA_35Y) cleaves polyisoprene and RoxB_35Y-derived oligoisoprenoids to the C₁₅-oligoisoprenoid 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). ODTD can be taken up by S. cummioxidans and used as a carbon source. Gram-positive rubber-degrading bacteria employ another type of rubber oxygenase, latex clearing protein (Lcp), for the initial oxidative attack of the polyisoprene molecule. In this contribution, we examined which type of rubber oxygenase is present in the only other well-documented Gram-negative rubber-degrading species, Rhizobacter gummiphilus NS21. No homologue for an Lcp protein but homologues for a putative RoxA and a RoxB protein (the latter identical to a previously postulated LatA-denominated rubber cleaving enzyme) were identified in the genome of strain NS21. The roxA_NS21 and roxB_NS21 genes were separately expressed in a ∆roxA_35Y/∆roxB_35Y background of S. cummioxidans 35Y and restored the ability of the mutant to produce oligoisoprenoids. The RoxA_NS21 and RoxB_NS21 proteins were each purified and biochemically characterised. The results-in combination with in silico analysis of databases-indicate that Gram-negative rubber-degrading bacteria generally utilise two synergistically acting rubber oxygenases (RoxA/RoxB) for efficient cleavage of polyisoprene to ODTD.