Bioremediation is an environmental sustainable and cost-effective technology for the cleanup of hydrocarbon-polluted soils and coasts. In spite of that longer times are usually required compared with ...physicochemical strategies, complete degradation of the pollutant can be achieved, and no further confinement of polluted matrix is needed. Microbial aerobic degradation is achieved by the incorporation of molecular oxygen into the inert hydrocarbon molecule and funneling intermediates into central catabolic pathways. Several families of alkane monooxygenases and ring hydroxylating dioxygenases are distributed mainly among
Proteobacteria
,
Actinobacteria
,
Firmicutes
and
Fungi
strains. Catabolic routes, regulatory networks, and tolerance/resistance mechanisms have been characterized in model hydrocarbon-degrading bacteria to understand and optimize their metabolic capabilities, providing the basis to enhance microbial fitness in order to improve hydrocarbon removal. However, microbial communities taken as a whole play a key role in hydrocarbon pollution events. Microbial community dynamics during biodegradation is crucial for understanding how they respond and adapt to pollution and remediation. Several strategies have been applied worldwide for the recovery of sites contaminated with persistent organic pollutants, such as polycyclic aromatic hydrocarbons and petroleum derivatives. Common strategies include controlling environmental variables (e.g., oxygen availability, hydrocarbon solubility, nutrient balance) and managing hydrocarbon-degrading microorganisms, in order to overcome the rate-limiting factors that slow down hydrocarbon biodegradation.
Coordinated regulation of the ubiquitin-proteasome system (UPS) is crucial for the cell to adjust its protein degradation capacity to changing proteolytic requirements. We have shown previously that ...mammalian cells upregulate proteasome gene expression in response to proteasome inhibition. Here, we report the identification of the transcription factor TCF11 (long isoform of Nrf1) as a key regulator for 26S proteasome formation in human cells to compensate for reduced proteolytic activity. Under noninducing conditions, TCF11 resides in the endoplasmic reticulum (ER) membrane. There, TCF11 is targeted to ER-associated protein degradation requiring the E3 ubiquitin ligase HRD1 and the AAA ATPase p97. Proteasome inhibitors trigger the accumulation of oxidant-damaged proteins and promote the nuclear translocation of TCF11 from the ER, permitting activation of proteasome gene expression by binding to antioxidant response elements in their promoter regions. Thus, we uncovered the transcriptional control loop regulating human proteasome-dependent protein degradation to counteract proteotoxic stress caused by proteasome inhibition.
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► TCF11 (long isoform of Nrf1) regulates proteasome gene transcription in human cells ► TCF11 interacts with ARE sequences in proteasome subunit promoters ► TCF11 levels are regulated by ERAD requiring HRD1 and p97 ► ER transit of TCF11 is important for its translocation into the nucleus
Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to ...hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.
Petroleum-based plastics constitute a major environmental problem due to their low biodegradability and accumulation in various environments. Therefore, searching for novel biodegradable plastics is ...of increasing interest. Microbial polyesters known as polyhydroxyalkanoates (PHAs) are biodegradable plastics. Life cycle assessment indicates that PHB is more beneficial than petroleum-based plastics. In this report, bacterial production of PHAs and their industrial applications are reviewed and the synthesis of PHAs in Burkholderia xenovorans LB400 is described. PHAs are synthesized by a large number of microorganisms during unbalanced nutritional conditions. These polymers are accumulated as carbon and energy reserve in discrete granules in the bacterial cytoplasm. 3-hydroxybutyrate and 3-hydroxyvalerate are two main PHA units among 150 monomers that have been reported. B. xenovorans LB400 is a model bacterium for the degradation of polychlorobiphenyls and a wide range of aromatic compounds. A bioinformatic analysis of LB400 genome indicated the presence of pha genes encoding enzymes of pathways for PHA synthesis. This study showed that B. xenovorans LB400 synthesize PHAs under nutrient limitation. Staining with Sudan Black B indicated the production of PHAs by B. xenovorans LB400 colonies. The PHAs produced were characterized by GC–MS. Diverse substrates for the production of PHAs in strain LB400 were analyzed.
Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: ...salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g.,
from Tatio Geyser), acidophiles (e.g.,
from Atacama Desert and Central Chile copper ores), halophiles (e.g.,
sp. Asc-3 from Altiplano,
sp. HKF-8 from Patagonia), alkaliphiles (
sp. SH31 from Altiplano), xerotolerant bacteria (
from Atacama Desert), UV- and Gamma-resistant bacteria (
from Atacama Desert) and psychrophiles (e.g.,
ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were ...studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized.
DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively.
This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.
Summary
The relevance of the β‐proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this ...review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring‐cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring‐cleavage, catechol ortho ring‐cleavage, homogentisate ring‐cleavage and phenylacetyl‐CoA ring‐cleavage pathways found in at least 60% of genomes analysed. In general, a genus‐specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus‐specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
Antioxidants can be encapsulated to enhance their solubility or bioavailability or to protect them from external factors. Electrospinning has proven to be an excellent option for applications in ...nanotechnology, as electrospun nanofibers can provide the necessary environment for antioxidant encapsulation. Forty-nine papers related to antioxidants loaded onto electrospun nanofibers were categorized and reviewed to identify applications and new trends. Medical and food fields were commonly proposed for the newly obtained composites. Among the polymers used as a matrix for the electrospinning process, synthetic poly (lactic acid) and polycaprolactone were the most widely used. In addition, natural compounds and extracts were identified as antioxidants that help to inhibit free radical and oxidative damage in tissues and foods. The most recurrent active compounds used were tannic acid (polyphenol), quercetin (flavonoid), curcumin (polyphenol), and vitamin B
(pyridoxine). The incorporation of active compounds in nanofibers often improves their bioavailability, giving them increased stability, changing the mechanical properties of polymers, enhancing nanofiber biocompatibility, and offering novel properties for the required field. Although most of the polymers used were synthetic, natural polymers such as silk fibroin, chitosan, cellulose, pullulan, polyhydroxybutyrate, and zein have proven to be proper matrices for this purpose.
Microbial metabolism is responsible for the removal of persistent organic pollutants including PCBs from the environment. Anaerobic dehalogenation of highly chlorinated congeners in aquatic sediments ...is an important process, and recent evidence has indicated that Dehalococcoides and related organisms are predominantly responsible for this process. Such anaerobic dehalogenation generates lower chlorinated congeners which are easily degraded aerobically by enzymes of the biphenyl upper pathway (bph). Initial biphenyl 2,3-dioxygenases are generally considered the key enzymes of this pathway which determine substrate range and extent of PCB degradation. These enzymes have been subject to different protein evolution strategies, and subsequent enzymes have been considered as crucial for metabolism. Significant advances have been made regarding the mechanistic understanding of these enzymes, which has also included elucidation of the function of BphK glutathione transferase. So far, the genomes of two important PCB-metabolizing organisms, namely Burkholderia xenovorans strain LB400 and Rhodococcus sp. strain RHA1, have been sequenced, with the rational to better understand their overall physiology and evolution. Genomic and proteomic analysis also allowed a better evaluation of PCB toxicity. Like all bph gene clusters which have been characterized in detail, particularly in strains LB400 and RHA1, these genes were localized on mobile genetic elements endowing single strains and microbial communities with a high flexibility and adaptability. However, studies show that our knowledge on enzymes and genes involved in PCB metabolism is still rather fragmentary and that the diversity of bacterial strategies is highly underestimated. Overall, metabolism of biphenyl and PCBs should not be regarded as a simple linear pathway, but as a complex interplay between different catabolic gene modules.
Stressors to microbial life include expected physical and chemical concerns such as: temperature, pressure, redox state, pH, ionic strength, osmolarity, UV light exposure and shear forces. The ...diverse genetic diversity of the remarkable number of microbial species on the planet usually means that a species somewhere has evolved the ability to use such compounds as a carbon and/or energy source. Organisms as diverse as bacteria, yeast, and mammals share a requirement for the regulation of cellular content of essential metals to ensure correct function of several metal-binding proteins, like copper, iron, nickel, and zinc. To prevent the consequences of metal overload, living organisms have evolved molecular mechanisms that regulate uptake, intracellular traffic, storage, and efflux, reduction/oxidation to change species, chemical modification, sequestration, repair of damage (typically from ROS) 11,12,13,14.
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