Tracking gene expression, metabolic profiles, and biochemical analysis in the halotolerant basidiomycetous yeast Rhodotorula mucilaginosa EXF-1630 during benzo[a]pyrene and phenanthrene biodegradation under hypersaline conditions

Martínez-Ávila, Liliana; Peidro-Guzmán, Heidy; Pérez-Llano, Yordanis; Moreno-Perlín, Tonatiuh; Sánchez-Reyes, Ayixón; Aranda, Elisabet; Paz, Gabriela Ángeles de; Fernández-Silva, Arline; Folch-Mallol, Jorge Luis; Cabana, Hubert; Gunde‐Cimerman, Nina; Batista-García, Ramón Alberto

doi:10.1016/j.envpol.2020.116358

Cited by 22 publications

(14 citation statements)

References 76 publications

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“…What is noted is that in the electron transfer carriers ( Table 1 ), three up-regulated proteins, biogenesis protein CcsA (A0A172WRB4, 1.55 folds) and Cbb3-type cytochrome c oxidase subunit II (A0A0H3YVF2, 1.57 folds), I (A0A023WTI7, 1.55 folds), are identified as cytochrome C and cytochrome C oxidase, respectively. Similarly, in the process of PHE and benzo[a]pyrene biodegradation by Rhodotorula mucilaginosa EXF-1630, high NADPH-cytochrome c reductase activity was observed ( Martínez-Ávila et al, 2021 ). Cytochrome C is an electron transmitter in biological respiration, which transfers electrons to molecular oxygen, accompanying ATP producing.…”

Section: Resultsmentioning

confidence: 99%

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

et al. 2021

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The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.

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Section: Resultsmentioning

confidence: 99%

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

et al. 2021

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“…Rhizophydium species belonging to Rhysophydiales are parasites of invertebrates, chytrids, and algae, assuming a possible role in the control of aquatic populations, and are also common in soil, primarily as saprobes, with a possible role in nutrient recycling ( Powell, 1993 ; Nieves-Rivera, 2003 ; Ibelings et al, 2004 ; van der Wal et al, 2013 ; Burow et al, 2019 ). Ochroconis is a fungal genus reported in caves ( Novakova, 2009 ; Martin-Sanchez et al, 2012b ; Martinez-Avila et al, 2021 ), guano, and bats ( Cunha et al, 2020 ). A few novel species were described in cave habitats, such as Ochroconis anellii , Ochroconis lascauxensis , and Ochroconis anomala ( de Hoog and von Arx, 1973 ; Martin-Sanchez et al, 2012a ).…”

Section: Resultsmentioning

confidence: 99%

Heat Shock Response of the Active Microbiome From Perennial Cave Ice

Mondini¹,

Anwar²,

Ellegaard-Jensen³

et al. 2022

Front. Microbiol.

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Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4°C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.

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“…These results suggested that fungal degradation led to metabolites that were less toxic than the precursor compounds. It is considered that along with the enhancement of the lipophilic character of compounds, their ecotoxicity increases, which strongly inhibits cellular respiration and disturbs bioluminescence [ 17 , 36 ]. Considering the structure of the intermediates, we identified earlier.…”

Section: Resultsmentioning

confidence: 99%

Ecotoxicological Estimation of 4-Cumylphenol, 4-t-Octylphenol, Nonylphenol, and Volatile Leachate Phenol Degradation by the Microscopic Fungus Umbelopsis isabellina Using a Battery of Biotests

Janicki

Długoński

Felczak

et al. 2022

IJERPH

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The phenolic xenobiotics nonylphenol (NP), 4-tert-octylphenol (4-t-OP), and 4-cumylphenol (4-CP) have the potential to seriously disrupt the endocrine system. Volatile phenols (VPs), especially those present in landfill leachate, also adversely affect the health of numerous organisms. Microbial degradation of xenobiotics can result in the formation of intermediates with higher toxicity than the precursor substrates. Therefore, the main aim of this study was to assess the changes in environmental ecotoxicity during the biotransformation of nonylphenol, 4-tert-octylphenol, 4-cumylphenol and volatile phenols by Umbelopsis isabellina using a battery of biotests. The application of bioindicators belonging to different taxonomic groups and diverse trophic levels (producers, consumers, and reducers) indicated a significant reduction in toxicity during the cultivation of fungus cultures both for nonylphenol, 4-tert-octylphenol, 4-cumylphenol and volatile phenols. The rate of toxicity decline was correlated with the degree of xenobiotic biotransformation. Removal of 4-cumylphenol and 4-tert-octylphenol also led to a decrease in the anti-androgenic potential. Moreover, this is the first report demonstrating the anti-androgenic properties of 4-cumylphenol. The results showed that U. isabellina is an attractive tool for the bioremediation and detoxification of contaminated environments.

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Tracking gene expression, metabolic profiles, and biochemical analysis in the halotolerant basidiomycetous yeast Rhodotorula mucilaginosa EXF-1630 during benzo[a]pyrene and phenanthrene biodegradation under hypersaline conditions

Cited by 22 publications

References 76 publications

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

Heat Shock Response of the Active Microbiome From Perennial Cave Ice

Ecotoxicological Estimation of 4-Cumylphenol, 4-t-Octylphenol, Nonylphenol, and Volatile Leachate Phenol Degradation by the Microscopic Fungus Umbelopsis isabellina Using a Battery of Biotests

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