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As the Earth warms, alternatives to traditional farming are crucial. Exploring fungi, especially poly extremophilic and extremotolerant species, to be used as plant probiotics, represents a promising option. Extremophilic fungi offer avenues for developing and producing innovative biofertilizers, effective biocontrol agents against plant pathogens, and resilient enzymes active under extreme conditions, all of which are crucial to enhance agricultural efficiency and sustainability through improved soil fertility and decreased reliance on agrochemicals. Yet, extremophilic fungi's potential remains underexplored and, therefore, comprehensive research is needed to understand their roles as tools to foster sustainable agriculture practices amid climate change. Efforts should concentrate on unraveling the complex dynamics of plant-fungi interactions and harnessing extremophilic fungi's ecological functions to influence plant growth and development. Aspects such as plant's epigenome remodeling, fungal extracellular vesicle production, secondary metabolism regulation, and impact on native soil microbiota are among many deserving to be explored in depth. Caution is advised, however, as extremophilic and extremotolerant fungi can act as both mitigators of crop diseases and as opportunistic pathogens, underscoring the necessity for balanced research to optimize benefits while mitigating risks in agricultural settings., (© 2024. The Author(s).)

Thermophilic fungi have been seldom studied despite the fact that they can contribute to understanding ecological mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano "El Chichonal" in Mexico. This strain was capable of surviving in soil with a temperature of 60 °C and a pH of neutral acidity, which preluded a high thermostability and a potential in industrial application. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in 37 Mb of genomic DNA. We performed a comprehensive phylogenomic analysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasiliensis . Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. A. brasiliensis E_15.1 was found to degrade chitin, chitooligosaccharides, xylan, and cellulose. The genes to biosynthesize clavaric acid (a triterpene with antitumor activity) were found, thus probably having antitumor activity. In addition to the genomic analysis, a set of enzymatic assays confirmed the thermostability of extracellular xylanases and cellulases of A. brasiliensis E_15.1. The enzymatic repertoire of A. brasiliensis E_15.1 suggests that A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.

Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L - 1 ), and efficient degradation of pyrene (0.2 g L - 1 ) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges., (© 2024 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd.)

Halophilic fungi thrive in hypersaline habitats and face a range of extreme conditions. These fungal species have gained considerable attention due to their potential applications in harsh industrial processes, such as bioremediation and fermentation under unfavorable conditions of hypersalinity, low water activity, and extreme pH. However, the role of the cell wall in surviving these environmental conditions remains unclear. Here we employ solid-state NMR spectroscopy to compare the cell wall architecture of Aspergillus sydowii across salinity gradients. Analyses of intact cells reveal that A. sydowii cell walls contain a rigid core comprising chitin, β-glucan, and chitosan, shielded by a surface shell composed of galactomannan and galactosaminogalactan. When exposed to hypersaline conditions, A. sydowii enhances chitin biosynthesis and incorporates α-glucan to create thick, stiff, and hydrophobic cell walls. Such structural rearrangements enable the fungus to adapt to both hypersaline and salt-deprived conditions, providing a robust mechanism for withstanding external stress. These molecular principles can aid in the optimization of halophilic strains for biotechnology applications., (© 2023. The Author(s).)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Obligate halophily is extremely rare in fungi. Nevertheless, Aspergillus atacamensis (strain EXF-6660), isolated from a salt water-exposed cave in the Coastal Range hills of the hyperarid Atacama Desert in Chile, is an obligate halophile, with a broad optimum range from 1.5 to 3.4 M of NaCl. When we tested its ability to grow at varied concentrations of both kosmotropic (NaCl, KCl, and sorbitol) and chaotropic (MgCl 2 , LiCl, CaCl 2 , and glycerol) solutes, stereoscopy and laser scanning microscopy revealed the formation of phialides and conidia. A. atacamensis EXF-6660 grew up to saturating levels of NaCl and at 2.0 M concentration of the chaotropic salt MgCl 2 . Our findings confirmed that A. atacamensis is an obligate halophile that can grow at substantially higher MgCl 2 concentrations than 1.26 M, previously considered as the maximum limit supporting prokaryotic life. To assess the fungus' metabolic versatility, we used the phenotype microarray technology Biolog FF MicroPlates. In the presence of 2.0 M NaCl concentration, strain EXF-6660 metabolism was highly versatile. A vast repertoire of organic molecules (~95% of the substrates present in Biolog FF MicroPlates) was metabolized when supplied as sole carbon sources, including numerous polycyclic aromatic hydrocarbons, benzene derivatives, dyes, and several carbohydrates. Finally, the biotechnological potential of A. atacamensis for xenobiotic degradation and biosolid treatment was investigated. Interestingly, it could remove biphenyls, diphenyl ethers, different pharmaceuticals, phenols, and polyaromatic hydrocarbons. Our combined findings show that A. atacamensis EXF-6660 is a highly chaotolerant, kosmotolerant, and xerotolerant fungus, potentially useful for xenobiotic and biosolid treatments., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Moreno-Perlin, Valdés-Muñoz, Jiménez-Gómez, Gunde-Cimerman, Yarzábal Rodríguez, Sánchez-Carbente, Vargas-Fernández, Gutiérrez-Cepeda and Batista-García.)

Biotechnologist interest in extremophile microorganisms has increased in recent years. Alkaliphilic and alkali-tolerant fungi that resist alkaline pH are among these. Alkaline environments, both terrestrial and aquatic, can be created by nature or by human activities. Aspergillus nidulans and Saccharomyces cerevisiae are the two eukaryotic organisms whose pH-dependent gene regulation has received the most study. In both biological models, the PacC transcription factor activates the Pal/Rim pathway through two successive proteolytic mechanisms. PacC is a repressor of acid-expressed genes and an activator of alkaline-expressed genes when it is in an active state. It appears, however, that these are not the only mechanisms associated with pH adaptations in alkali-tolerant fungi. These fungi produce enzymes that are resistant to harsh conditions, i.e., alkaline pH, and can be used in technological processes, such as in the textile, paper, detergent, food, pharmaceutical, and leather tanning industries, as well as in bioremediation of pollutants. Consequently, it is essential to understand how these fungi maintain intracellular homeostasis and the signaling pathways that activate the physiological mechanisms of alkali resistance in fungi.

Although various studies have investigated osmoadaptations of halophilic fungi to saline conditions, only few analyzed the fungal mechanisms occurring at saturated NaCl concentrations. Halophilic Aspergillus sydowii is a model organism for the study of molecular adaptations of filamentous fungi to hyperosmolarity. For the first time a multi-omics approach (i.e., transcriptomics and metabolomics) was used to compare A. sydowii at saturated concentration (5.13 M NaCl) to optimal salinity (1 M NaCl). Analysis revealed 1,842 genes differentially expressed of which 704 were overexpressed. Most differentially expressed genes were involved in metabolism and signal transduction. A gene ontology multi-scale network showed that ATP binding constituted the main network node with direct interactions to phosphorelay signal transduction, polysaccharide metabolism, and transferase activity. Free amino acids significantly decreased and amino acid metabolism was reprogrammed at 5.13 M NaCl. mRNA transcriptional analysis revealed upregulation of genes involved in methionine and cysteine biosynthesis at extreme water deprivation by NaCl. No modifications of membrane fatty acid composition occurred. Upregulated genes were involved in high-osmolarity glycerol signal transduction pathways, biosynthesis of β-1,3-glucans, and cross-membrane ion transporters. Downregulated genes were related to the synthesis of chitin, mannose, cell wall proteins, starvation, pheromone synthesis, and cell cycle. Non-coding RNAs represented the 20% of the total transcripts with 7% classified as long non-coding RNAs (lncRNAs). The 42% and 69% of the total lncRNAs and RNAs encoding transcription factors, respectively, were differentially expressed. A network analysis showed that differentially expressed lncRNAs and RNAs coding transcriptional factors were mainly related to the regulation of metabolic processes, protein phosphorylation, protein kinase activity, and plasma membrane composition. Metabolomic analyses revealed more complex and unknown metabolites at saturated NaCl concentration than at optimal salinity. This study is the first attempt to unravel the molecular ecology of an ascomycetous fungus at extreme water deprivation by NaCl (5.13 M). This work also represents a pioneer study to investigate the importance of lncRNAs and transcriptional factors in the transcriptomic response to high NaCl stress in halophilic fungi., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jiménez-Gómez, Valdés-Muñoz, Moreno-Ulloa, Pérez-Llano, Moreno-Perlín, Silva-Jiménez, Barreto-Curiel, Sánchez-Carbente, Folch-Mallol, Gunde-Cimerman, Lago-Lestón and Batista-García.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Key Message: Evolutionary conserved defense mechanisms present in extant bryophytes and angiosperms, as well as moss-specific defenses are part of the immune response of Physcomitrium patens. Bryophytes and tracheophytes are descendants of early land plants that evolved adaptation mechanisms to cope with different kinds of terrestrial stresses, including drought, variations in temperature and UV radiation, as well as defense mechanisms against microorganisms present in the air and soil. Although great advances have been made on pathogen perception and subsequent defense activation in angiosperms, limited information is available in bryophytes. In this study, a transcriptomic approach uncovered the molecular mechanisms underlying the defense response of the bryophyte Physcomitrium patens (previously Physcomitrella patens) against the important plant pathogen Botrytis cinerea. A total of 3.072 differentially expressed genes were significantly affected during B. cinerea infection, including genes encoding proteins with known functions in angiosperm immunity and involved in pathogen perception, signaling, transcription, hormonal signaling, metabolic pathways such as shikimate and phenylpropanoid, and proteins with diverse role in defense against biotic stress. Similarly as in other plants, B. cinerea infection leads to downregulation of genes involved in photosynthesis and cell cycle progression. These results highlight the existence of evolutionary conserved defense responses to pathogens throughout the green plant lineage, suggesting that they were probably present in the common ancestors of land plants. Moreover, several genes acquired by horizontal transfer from prokaryotes and fungi, and a high number of P. patens-specific orphan genes were differentially expressed during B. cinerea infection, suggesting that they are important players in the moss immune response., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.)

Here, we analyzed the effects on Capsicum annuum plants of Trichoderma atroviride P. Karst strains altered in the expression of SWOLLENIN (SWO1), a protein with amorphogenic activity on plant cell wall components. Strains of T. atroviride that overexpressed the Taswo1 gene were constructed as well as deletion mutants. A novel, cheap and accurate method for assessing root colonization was developed. Colonization assays showed that the Taswo1 overexpressing strains invaded the host root better than the WT, resulting in a stronger plant growth-promoting effect. The expression of plant defense marker genes for both the systemic acquired resistance and induced systemic resistance pathways was enhanced in plants inoculated with Taswo1 overexpressing strains, while inoculation with deletion mutant strains resulted in a similar level of expression to that observed upon inoculation with the wild-type strain. Response to pathogen infection was also enhanced in the plants inoculated with the Taswo1 overexpressing strains, and surprisingly, an intermediate level of protection was achieved with the mutant strains. Tolerance to abiotic stresses was also higher in plants inoculated with the Taswo1 overexpressing strains but was similar in plants inoculated with the wild-type or the mutant strains. Compatible osmolyte production in drought conditions was studied. This study may contribute to improving Trichoderma biocontrol and biofertilization abilities.

Anthracnose caused by the hemibiotroph fungus Colletotrichum gloeosporioides is a devastating plant disease with an extensive impact on plant productivity. The process of colonization and disease progression of C. gloeosporioides has been studied in a number of angiosperm crops. To better understand the evolution of the plant response to pathogens, the study of this complex interaction has been extended to bryophytes. The model moss Physcomitrium patens Hedw. B&S (former Physcomitrella patens ) is sensitive to known bacterial and fungal phytopathogens, including C. gloeosporioides , which cause infection and cell death. P. patens responses to these microorganisms resemble that of the angiosperms. However, the molecular events during the interaction of P. patens and C. gloeosporioides have not been explored. In this work, we present a comprehensive approach using microscopy, phenomics and RNA-seq analysis to explore the defense response of P. patens to C. gloeosporioides . Microscopy analysis showed that appressoria are already formed at 24 h after inoculation (hai) and tissue colonization and cell death occur at 24 hai and is massive at 48 hai. Consequently, the phenomics analysis showed progressing browning of moss tissues and impaired photosynthesis from 24 to 48 hai. The transcriptomic analysis revealed that more than 1200 P. patens genes were differentially expressed in response to Colletotrichum infection. The analysis of differentially expressed gene function showed that the C. gloeosporioides infection led to a transcription reprogramming in P. patens that upregulated the genes related to pathogen recognition, secondary metabolism, cell wall reinforcement and regulation of gene expression. In accordance with the observed phenomics results, some photosynthesis and chloroplast-related genes were repressed, indicating that, under attack, P. patens changes its transcription from primary metabolism to defend itself from the pathogen.

Marchantia polymorpha L. responds to environmental changes using a myriad set of physiological responses, some unique to the lineage related to the lack of a vascular- and root-system. This study investigates the physiological response of M. polymorpha to high doses of anthracene analysing the antioxidant enzymes and their relationship with the photosynthetic processes, as well as their transcriptomic response. We found an anthracene dose-dependent response reducing plant biomass and associated to an alteration of the ultrastructure of a 23.6% of chloroplasts. Despite a reduction in total thallus-chlorophyll of 31.6% of Chl a and 38.4% of Chl b , this was not accompanied by a significant change in the net photosynthesis rate and maximum quantum efficiency ( Fv/Fm ). However, we found an increase in the activity of main ROS-detoxifying enzymes of 34.09% of peroxidase and 692% of ascorbate peroxidase, supported at transcriptional level with the upregulation of ROS-related detoxifying responses. Finally, we found that M. polymorpha tolerated anthracene-stress under the lowest concentration used and can suffer physiological alterations under higher concentrations tested related to the accumulation of anthracene within plant tissues. Our results show that M. polymorpha under PAH stress condition activated two complementary physiological responses including the activation of antioxidant mechanisms and the accumulation of the pollutant within plant tissues to mitigate the damage to the photosynthetic apparatus.

Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent xenobiotic compounds, with high toxicity effects. Mycoremediation with halophilic Aspergillus sydowii was used for their removal from a hypersaline medium (1 M NaCl). A. sydowii metabolized PAHs as sole carbon sources, resulting in the removal of up to 90% for both PAHs [benzo [a] pyrene (BaP) and phenanthrene (Phe)] after 10 days. Elimination of Phe and BaP was almost exclusively due to biotransformation and not adsorption by dead mycelium and did not correlate with the activity of lignin modifying enzymes (LME). Transcriptomes of A. sydowii grown on PAHs, or on glucose as control, both at hypersaline conditions, revealed 170 upregulated and 76 downregulated genes. Upregulated genes were related to starvation, cell wall remodelling, degradation and metabolism of xenobiotics, DNA/RNA metabolism, energy generation, signalling and general stress responses. Changes of LME expression levels were not detected, while the chloroperoxidase gene, possibly related to detoxification processes in fungi, was strongly upregulated. We propose that two parallel metabolic pathways (mitochondrial and cytosolic) are involved in degradation and detoxification of PAHs in A. sydowii resulting in intracellular oxidation of PAHs. To the best of our knowledge, this is the most comprehensive transcriptomic analysis on fungal degradation of PAHs., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Aspergillus sydowii is a moderate halophile fungus extensively studied for its biotechnological potential and halophile responses, which has also been reported as a coral reef pathogen. In a recent publication, the transcriptomic analysis of this fungus, when growing on wheat straw, showed that genes related to cell wall modification and cation transporters were upregulated under hypersaline conditions but not under 0.5 M NaCl, the optimal salinity for growth in this strain. This led us to study osmolyte accumulation as a mechanism to withstand moderate salinity. In this work, we show that A. sydowii accumulates trehalose, arabitol, mannitol, and glycerol with different temporal dynamics, which depend on whether the fungus is exposed to hypo- or hyperosmotic stress. The transcripts coding for enzymes responsible for polyalcohol synthesis were regulated in a stress-dependent manner. Interestingly, A. sydowii contains three homologs (Hog1, Hog2 and MpkC) of the Hog1 MAPK, the master regulator of hyperosmotic stress response in S. cerevisiae and other fungi. We show a differential regulation of these MAPKs under different salinity conditions, including sustained basal Hog1/Hog2 phosphorylation levels in the absence of NaCl or in the presence of 2.0 M NaCl, in contrast to what is observed in S. cerevisiae . These findings indicate that halophilic fungi such as A. sydowii utilize different osmoadaptation mechanisms to hypersaline conditions.

Polyaromatic phenanthrene (Phe) and benzo[a]pyrene (BaP) are highly toxic, mutagenic, and carcinogenic contaminants widely dispersed in nature, including saline environments. Polyextremotolerant Rhodotorula mucilaginosa EXF-1630, isolated from Arctic sea ice, was grown on a huge concentration range -10 to 500 ppm- of Phe and BaP as sole carbon sources at hypersaline conditions (1 M NaCl). Selected polycyclic aromatic hydrocarbons (PAHs) supported growth as well as glucose, even at high PAH concentrations. Initially, up to 40% of Phe and BaP were adsorbed, followed by biodegradation, resulting in 80% removal in 10 days. While extracellular laccase, peroxidase, and un-specific peroxygenase activities were not detected, NADPH-cytochrome c reductase activity peaked at 4 days. The successful removal of PAHs and the absence of toxic metabolites were confirmed by toxicological tests on moss Physcomitrium patens, bacterium Aliivibrio fischeri, human erythrocytes, and pulmonary epithelial cells (A549). Metabolic profiles were determined at the midpoint of the biodegradation exponential phase, with added Phe and BaP (100 ppm) and 1 M NaCl. Different hydroxylated products were found in the culture medium, while the conjugative metabolite 1-phenanthryl-β-D-glucopyranose was detected in the medium and in the cells. Transcriptome analysis resulted in 870 upregulated and 2,288 downregulated transcripts on PAHs, in comparison to glucose. Genomic mining of 61 available yeast genomes showed a widespread distribution of 31 xenobiotic degradation pathways in different yeast lineages. Two distributions with similar metabolic capacities included black yeasts and mainly members of the Sporidiobolaceae family (including EXF-1630), respectively. This is the first work describing a metabolic profile and transcriptomic analysis of PAH degradation by yeast., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 10 21 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes-many of which disappeared from the face of the Earth thousands and even millions of years ago-could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost., Supplementary Information: The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users., Competing Interests: Conflict of interestOn behalf of all authors, the corresponding author states that there is no conflict of interest., (© Society for Environmental Sustainability 2021.)

Botrytis cinerea is a necrotrophic pathogen that causes grey mold in many plant species, including crops and model plants of angiosperms. B. cinerea also infects and colonizes the bryophyte Physcomitrium patens (previously Physcomitrella patens ), which perceives the pathogen and activates defense mechanisms. However, these defenses are not sufficient to stop fungal invasion, leading finally to plant decay. To gain more insights into B. cinerea infection and virulence strategies displayed during moss colonization, we performed genome wide transcriptional profiling of B. cinerea during different infection stages. We show that, in total, 1015 B. cinerea genes were differentially expressed in moss tissues. Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that infection of P. patens tissues by B. cinerea depends on reactive oxygen species generation and detoxification, transporter activities, plant cell wall degradation and modification, toxin production and probable plant defense evasion by effector proteins. Moreover, a comparison with available RNAseq data during angiosperm infection, including Arabidopsis thaliana, Solanum lycopersicum and Lactuca sativa , suggests that B. cinerea has virulence and infection functions used in all hosts, while others are more specific to P. patens or angiosperms.

Lignin obtained from renewable biomass is a potential feedstock for the synthesis of various value-added chemicals through efficient biocatalytic routes. The ligninolytic enzymes-assisted depolymerization of lignin to vanillin constitutes the most commercially attractive and promising approach in green chemistry as vanillin constitutes the second most prevalent flavoring agent. Thus, in the present work, immobilized laccase and versatile peroxidase, and further, a co-immobilized laccase and versatile peroxidase system on magnetic silica microspheres (MSMS) were developed to generate a robust biocatalytic system that mediates the depolymerization of lignin obtained from Casuarina equisetifolia biomass. The depolymerization of lignin by free and immobilized laccase showed a vanillin yield of 24.8% and 23%, respectively, at pH 4.0 in 6 h at 30°C against a vanillin yield of 20% and 21.7% with the free and immobilized versatile peroxidase, respectively, at pH 5.0°C and 50°C. Comparatively, the system with the co-immobilized laccase and versatile peroxidase exhibited a 1-fold and 1.2-fold higher vanillin yield than the free and immobilized laccase system, respectively. On comparing with the versatile peroxidase system, the co-immobilized biocatalytic system displayed 1.3-fold and 1.2-fold increased vanillin yield than the free and immobilized versatile peroxidase system, respectively, at a pH of 6.0 in 6 h at 30°C with an enzyme concentration of 1 U/ml. The reusability studies of the co-immobilized biocatalytic system exhibited that both the enzymes retained up to 40% of its activity till sixth cycle. Implications : The waste biomass of Casuarina equisetifolia is widely available around the coastal regions of India which does not have any agricultural or industrial applications. The present work exploits the lignocellulosic content of the Casuarina biomass to extract the lignin, which provides a renewable alternative for the production of the commercially high-valued compound, vanillin. This work also integrates a co-immobilized biocatalytic process comprising of laccase and versatile peroxidase leading to an environmentally benign enzymatic process for the depolymerization of lignin to vanillin.

Water activity (a w ) is critical for microbial growth, as it is severely restricted at a w < 0.90. Saturating NaCl concentrations (~5.0 M) induce extreme water deprivation (a w ≅ 0.75) and cellular stress responses. Halophilic fungi have cellular adaptations that enable osmotic balance and ionic/oxidative stress prevention to grow at high salinity. Here we studied the morphology, osmolyte synthesis, and oxidative stress defenses of the halophile Aspergillus sydowii EXF-12860 at 1.0 M and 5.13 M NaCl. Colony growth, pigmentation, exudate, and spore production were inhibited at NaCl-saturated media. Additionally, hyphae showed unpolarized growth, lower diameter, and increased septation, multicellularity and branching compared to optimal NaCl concentration. Trehalose, mannitol, arabitol, erythritol, and glycerol were produced in the presence of both 1.0 M and 5.13 M NaCl. Exposing A. sydowii cells to 5.13 M NaCl resulted in oxidative stress evidenced by an increase in antioxidant enzymes and lipid peroxidation biomarkers. Also, genes involved in cellular antioxidant defense systems were upregulated. This is the most comprehensive study that investigates the micromorphology and the adaptative cellular response of different non-enzymatic and enzymatic oxidative stress biomarkers in halophilic filamentous fungi.

Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus , Thermomonas , Thiomonas , Acinetobacter , Sulfurovum , and Bacillus , highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus , Thiomonas , Thermonas , and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis . The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.

Nitric oxide (NO) has been recognized as a major player in the regulation of plant physiology and development. NO regulates cell cycle progression and cell elongation in flowering plants and green algae, although the information about NO function in non-vascular plants is scarce. Here, we analyze the effect of exogenous NO on Physcomitrella patens protonema growth. We find that increasing concentrations of the NO donor sodium nitroprusside (SNP) inhibit protonema relative growth rate and cell length. To further comprehend the effect of NO on moss development, we analyze the effect of SNP 5 and 10 µM on protoplast regeneration and, furthermore, protonema formation compared with untreated plants (control). Isolated protoplasts were left to regenerate for 24 h before starting the SNP treatments that lasted five days. The results show that SNP restrains the protoplast regeneration process and the formation of new protonema cells. When SNP treatments started five days after protoplast isolation, a decrease in cell number per protonema filament was observed, indicating an inhibition of cell cycle progression. Our results show that in non-vascular plants, NO negatively regulates plant regeneration, cell cycle and cell elongation.

Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.

Since Aromatic hydrocarbons are recalcitrant and toxic, strategies to remove them are needed. The aim of this work was to isolate fungi capable of using aromatic hydrocarbons as carbon sources. Two isolates from an oil polluted site in Mexico were identified through morphological and molecular markers as a novel Rhodotorula sp. and an Exophiala sp. Both strains were able to grow in a wide range of pH media, from 4 to 12, showing their optimal growth at alkaline pH's and are both halotolerant. The Exophiala strain switched from hyphae to yeast morphotype in high salinity conditions. To the best of our knowledge, this is the first report of salt triggering dimorphism. The Rhodotorula strain, which is likely a new undescribed species, was capable of removing singled ringed aromatic compounds such as benzene, xylene, and toluene, but could not remove benzo[ a ] pyrene nor phenanthrene. Nevertheless, these hydrocarbons did not impair its growth. The Exophiala strain showed a different removal capacity. It could remove the polyaromatic hydrocarbons but performed poorly at removing toluene and xylene. Nevertheless, it still could grow well in the presence of the aromatic compounds. These strains could have a potential for aromatic compounds removal.

An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids. Growth was severely restricted at salinities below 15% NaCl and cell lysis is avoided at a minimal 10% NaCl. Maximal concentrations of magnesium chloride and sodium or magnesium perchlorates that supported SGH1 growth were 0.5 and 0.15M, respectively. Haloterrigena sp. strain SGH1 accumulates bacterioruberin (BR), a C 50 xanthophyll, as the major carotenoid. Total carotenoids in strain SGH1 amounted to nearly 400 μg BR per gram of dry biomass. Nearly 80% of total carotenoids accumulated as geometric isomers of BR: all- trans -BR (50%), 5- cis -BR (15%), 9- cis -BR (10%), 13- cis -BR (4%); other carotenoids were dehydrated derivatives of BR. Carotenogenesis in SGH1 was a reversible and salt-dependent process; transferring BR-rich cells grown in 25% (w/v) NaCl to 15% (w/v) NaCl medium resulted in depigmentation, and BR content was recovered after transference and growth of unpigmented cells to high salinity medium. Methanol extracts and purified BR isomers showed an 8-9-fold higher antioxidant activity than Trolox or β-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells., (Copyright © 2020 Flores, Hoyos, Venegas, Galetovic´, Zúñiga, Fábrega, Paredes, Salazar-Ardiles, Vilo, Ascaso, Wierzchos, Souza-Egipsy, Araya, Batista-García and Gómez-Silva.)

In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.

(1) Background: Mechanisms of cellular and molecular adaptation of fungi to salinity have been commonly drawn from halotolerant strains and few studies in basidiomycete fungi. These studies have been conducted in settings where cells are subjected to stress, either hypo- or hyperosmotic, which can be a confounding factor in describing physiological mechanisms related to salinity. (2) Methods: We have studied transcriptomic changes in Aspergillus sydowii , a halophilic species, when growing in three different salinity conditions (No NaCl, 0.5 M, and 2.0 M NaCl). (3) Results: In this fungus, major physiological modifications occur under high salinity (2.0 M NaCl) and not when cultured under optimal conditions (0.5 M NaCl), suggesting that most of the mechanisms described for halophilic growth are a consequence of saline stress response and not an adaptation to saline conditions. Cell wall modifications occur exclusively at extreme salinity, with an increase in cell wall thickness and lamellar structure, which seem to involve a decrease in chitin content and an augmented content of alfa and beta-glucans. Additionally, three hydrophobin genes were differentially expressed under hypo- or hyperosmotic stress but not when the fungus grows optimally. Regarding compatible solutes, glycerol is the main compound accumulated in salt stress conditions, whereas trehalose is accumulated in the absence of salt. (4) Conclusions: Physiological responses to salinity vary greatly between optimal and high salt concentrations and are not a simple graded effect as the salt concentration increases. Our results highlight the influence of stress in reshaping the response of extremophiles to environmental challenges., Competing Interests: The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Heavy metal pollution has become an environmental and health problem worldwide. With the aim of finding novel strategies for metal bioremediation, endophytic fungi from the heavy metal hyperaccumulator plant Vachellia farnesiana were isolated and characterized. The plants were growing in mine tailings, rich in Zn, Pb, and Cu. Morphological and phylogenetic analyses indicated that the fungal strains belonged to Neocosmospora and Aspergillus genera. The Neocosmospora isolate belongs to the Fusarium solani species complex (FSSC) that groups phytopathogen species. However, in this case the plants from which it was isolated did not show any signs of disease. Both fungal strains were able to remove significant amounts of heavy metals from liquid cultures, either in a mixture of the three metals or each metal in a single culture. In response to lead exposure, the Neocosmospora sp. strain secreted specific novel phenolic compounds other than anthraquinones or naphtoquinones, which have been described in similar situations. The Aspergillus sp. dropped the pH in the medium. High-performance liquid chromatography determinations indicated that this strain secreted mainly glutamic acid in response to lead, a novel mechanism, which has not been reported elsewhere. Malic and succinic acids were also produced in response to lead exposure. Possibly, glutamic and succinic acids (synthesized in the Krebs cycle) can be used to cope with metal toxicity due to the plant providing photosynthates to the fungus. These fungi showed the potential to be used for bioremediation or restoration of metal-polluted environments., Competing Interests: The authors declare no conflict of interest.

Extreme ecosystems are a possible source of new interesting microorganisms, in this study the isolation of psychrophilic and psychrotolerant plant growth promoting microorganisms was pursued in a cold habitat, with the aim of finding novel microbes that can protect crops from cold. Eight yeast and four bacterial strains were isolated from rhizospheric soil collected from the Xinantécatl volcano in Mexico, and characterized for plant growth promoting properties. Most of the yeasts produced indole acetic acid and hydrolytic enzymes (cellulases, xilanases and chitinases), but none of them produced siderophores, in contrast to their bacterial counterparts. Inorganic phosphate solubilization was detected for all the bacterial strains and for two yeast strains. Yeast and bacterial strains may inhibit growth of various pathogenic fungi, propounding a role in biological control. Microorganisms were identified up to genera level, by applying ribotyping techniques and phylogenetic analysis. Bacterial strains belonged to the genus Pseudomonas, whereas yeast strains consisted of Rhodotorula sp. (4), Mrakia sp. (3) and Naganishia sp. (1). New species belonging to the aforementioned genera seem to have been isolated from both bacteria and yeasts. Germination promoting activity on Solanum lycopersicum seeds was detected for all strains compared to a control, whereas tomato plantlets, grown at 15 °C in the presence of some of the strains, performed better than the non-inoculated plantlets. This study offers the possibility of using these strains as an additive to improve culture conditions of S. lycopersicum in a more environmentally compatible way. This is the first study to propose psychrophilic/psychrotolerant yeasts, as plant growth promoting microbes., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites.

Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria , Bacteroidetes , Balneolaeota , and Actinobacteria ; in contrast, Archaea from the phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis , as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata -like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.

Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 10 7 viruses per milliliter and 10 9 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives., (Copyright © 2019 Dávila-Ramos, Castelán-Sánchez, Martínez-Ávila, Sánchez-Carbente, Peralta, Hernández-Mendoza, Dobson, Gonzalez, Pastor and Batista-García.)

Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Cellulases have a broad range of different industrial applications, ranging from food and beverages to pulp and paper and the biofuels area. Here a metagenomics based strategy was used to identify the cellulolytic enzyme CelRH5 from the rhizosphere. CelRH5 is a novel monospecific endo-β-1,4-glucanase belonging to the glycosyl hydrolase family 5 (GH5). Structural based modeling analysis indicated that CelRH5 is related to endo-β-1,4-glucanases derived from thermophilic microorganisms such as Thermotoga maritima , Fervidobacterium nodosum , and Ruminiclostridium thermocellum sharing 30-40% amino acid sequence identity. The molecular weight of the enzyme was determined as 40.5 kDa. Biochemical analyses revealed that the enzyme displayed good activity with soluble forms of cellulose as a substrate such as ostazin brilliant red hydroxyethyl cellulose (OBR-HEC), carboxymethylcellulose (CMC), hydroxyethyl cellulose (HEC), and insoluble azurine cross-linked hydroxyethylcellulose (AZCL-HEC). The enzyme shows highest enzymatic activity at pH 6.5 with high pH tolerance, remaining stable in the pH range 4.5-8.5. Highest activity was observed at 40°C, but CelRH5 is psychrotolerant being active and stable at temperatures below 30°C. The presence of the final products of cellulose hydrolysis (glucose and cellobiose) or metal ions such as Na + , K + , Li + , and Mg 2+ , as well as ethylenediaminetetraacetic acid (EDTA), urea, dithiothreitol (DTT), dimethyl sulfoxide (DMSO), 2-mercaptoethanol (2-ME) or glycerol, did not have a marked effect on CelRH5 activity. However, the enzyme is quite sensitive to the presence of 10 mM ions Zn 2+ , Ni 2+ , Co 2+ , Fe 3+ and reagents such as 1 M guanidine HCl, 0.1% sodium dodecyl sulfate (SDS) and 20% ethanol. Given that it is psychrotolerant and retains activity in the presence of final cellulose degradation products, metal ions and various reagents, which are common in many technological processes; CelRH5 may be potential suitability for a variety of different biotechnological applications.

Polycyclic aromatic hydrocarbons (PAH) and pharmaceutical compounds (PhC) are xenobiotics present in many saline wastewaters. Although fungi are known for their ability to remove xenobiotics, the potential of halophilic fungi to degrade highly persistent pollutants was not yet investigated. The use of two halophilic fungi, Aspergillus sydowii and Aspergillus destruens, for the elimination of PAH and PhC at saline conditions was studied. In saline synthetic medium both fungi used benzo-α-pyrene and phenanthrene as sole carbon source and removed over 90% of both PAH, A. sydowii due to biodegradation and A. destruens to bioadsorption. They removed 100% of a mixture of fifteen PAH in saline biorefinery wastewater. Test using Cucumis sativus demonstrated that wastewater treated with the two fungi lowered considerably the phytotoxicity. This study is the first demonstration that ascomycetous halophilic fungi, in contrast to other fungi (and in particular basidiomycetes) can be used for mycotreatments under salinity conditions., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Legumes establish symbiotic relationships with different microorganisms, which could function as plant growth promotion microorganisms (PGPM). The finding of new PGPM strains is important to increase plant production avoiding or diminishing the use of industrial fertilizers. Thus, in this work we evaluated the plant growth promotion traits of ten strains isolated from Mimosa pudica root nodules. According to the 16S rDNA sequence, the microorganisms were identified as Enterobacter sp. and Serratia sp. To the best of our knowledge this is the first report describing and endophytic interaction between Mimosa pudica and Enterobacter sp. These strains have some plant growth promoting traits such as phosphate solubilization, auxin production and cellulase and chitinase activity. Strains identified as Serratia sp. inhibited the growth of the phytopathogenic fungi Fusarium sp., and Alternaria solani and the oomycete Phytophthora capsici. According to their biochemical characteristics, three strains were selected to test their plant growth promoting activity in a medium with an insoluble phosphate source. These bacteria show low specificity for their hosts as endophytes, since they were able to colonize two very different legumes: Phaseolus vulgaris and M. pudica. Seedlings of P. vulgaris were inoculated and grown for fifteen days. Enterobacter sp. NOD1 and NOD10, promoted growth as reflected by an increase in shoot height as well as an increase in the size and emergence of the first two trifolia. We could localize NOD5 as an endophyte in roots in P. vulgaris by transforming the strain with a Green Fluorescent Protein carrying plasmid. Experiments of co-inoculation with different Rhizobium etli strains allowed us to discard that NOD5 can fix nitrogen in the nodules formed by a R. etli Fix - strain. The isolates described in this work show biotechnological potential for plant growth promoting activity and production of indoleacetic acid and siderophores., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Lignocellulose represents the most abundant source of carbon in the Earth. Thus, fraction technology of the biomass turns up as an emerging technology for the development of biorefineries. Saccharification and fermentation processes require the formulation of enzymatic cocktails or the development of microorganisms (naturally or genetically modified) with the appropriate toolbox to produce a cost-effective fermentation technology. Therefore, the search for microorganisms capable of developing effective cellulose hydrolysis represents one of the main challenges in this era. Schizophyllum commune is an edible agarical with a great capability to secrete a myriad of hydrolytic enzymes such as xylanases and endoglucanases that are expressed in a high range of substrates. In addition, a large number of protein-coding genes for glycoside hydrolases, oxidoreductases like laccases (Lacs; EC 1.10.3.2), as well as some sequences encoding for lytic polysaccharide monooxygenases (LPMOs) and expansins-like proteins demonstrate the potential of this fungus to be applied in different biotechnological process. In this review, we focus on the enzymatic toolbox of S. commune at the genetic, transcriptomic, and proteomic level, as well as the requirements to be employed for fermentable sugars production in biorefineries. At the end the trend of its use in patent registration is also reviewed., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

The heterologous expression and characterization of a Hormone-Sensitive Lipases (HSL) esterase (BaEstB) from the Basidiomycete fungus Bjerkandera adusta is reported for the first time. According to structural analysis, amino acid similarities and conservation of particular motifs, it was established that this enzyme belongs to the (HSL) family. The cDNA sequence consisted of 969 nucleotides, while the gene comprised 1133, including three introns of 57, 50, and 57 nucleotides. Through three-dimensional modeling and phylogenetic analysis, we conclude that BaEstB is an ortholog of the previously described RmEstB-HSL from the phylogenetically distant fungus Rhizomucor miehei. The purified BaEstB was characterized in terms of its specificity for the hydrolysis of different acyl substrates confirming its low lipolytic activity and a noticeable esterase activity. The biochemical characterization of BaEstB, the DLS analysis and the kinetic parameters determination revealed this enzyme as a true esterase, preferentially found in a dimeric state, displaying activity under alkaline conditions and relative low temperature (pH = 10, 20°C). Our data suggest that BaEstB is more active on substrates with short acyl chains and bulky aromatic moieties. Phylogenetic data allow us to suggest that a number of fungal hypothetical proteins could belong to the HSL family., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

A number of fungal strains belonging to the ascomycota, basidiomycota and zygomycota genera were subjected to an in vitro screening regime to assess their ligninolytic activity potential, with a view to their potential use in mycoremediation-based strategies to remove phenolic compounds and polycyclic aromatic hydrocarbons (PAHs) from industrial wastewaters. All six basidiomycetes completely decolorized remazol brilliant blue R (RBBR), while also testing positive in both the guaiacol and gallic acid tests indicating good levels of lignolytic activity. All the fungi were capable of tolerating phenanthrene, benzo-α- pyrene, phenol and p-chlorophenol in agar medium at levels of 10 ppm. Six of the fungal strains, Pseudogymnoascus sp., Aspergillus caesiellus, Trametes hirsuta IBB 450, Phanerochate chrysosporium ATCC 787, Pleurotus ostreatus MTCC 1804 and Cadophora sp. produced both laccase and Mn peroxidase activity in the ranges of 200-560 U/L and 6-152 U/L, respectively, in liquid media under nitrogen limiting conditions. The levels of adsorption of the phenolic and PAHs were negligible with 99% biodegradation being observed in the case of benzo-α-pyrene, phenol and p-chlorophenol. The aforementioned six fungal strains were also found to be able to effectively treat highly alkaline industrial wastewater (pH 12.4). When this wastewater was supplemented with 0.1 mM glucose, all of the tested fungi, apart from A. caesiellus, displayed the capacity to remove both the phenolic and PAH compounds. Based on their biodegradative capacity we found T. hirsuta IBB 450 and Pseudogymnoascus sp., to have the greatest potential for further use in mycoremediation based strategies to treat wastestreams containing phenolics and PAHs., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Activated sludge is produced during the treatment of sewage and industrial wastewaters. Its diverse chemical composition allows growth of a large collection of microbial phylotypes with very different physiologic and metabolic profiles. Thus, activated sludge is considered as an excellent environment to discover novel enzymes through functional metagenomics, especially activities related with degradation of environmental pollutants. Metagenomic DNA was isolated and purified from an activated sludge sample. Metagenomic libraries were subsequently constructed in Escherichia coli. Using tributyrin hydrolysis, a screening by functional analysis was conducted and a clone that showed esterase activity was isolated. Blastx analysis of the sequence of the cloned DNA revealed, among others, an ORF that encodes a putative thioesterase with 47-64% identity to GenBank CDS reported genes, similar to those in the hotdog fold thioesterase superfamily. On the basis of its amino acid similarity and its homology-modelled structure we deduced that this gene encodes an enzyme (ThYest&#95;ar) that belongs to family TE13, with a preference for aryl-CoA substrates and a novel catalytic residue constellation. Plasmid retransformation in E. coli confirmed the clone's phenotype, and functional complementation of a paaI E. coli mutant showed preference for phenylacetate over chlorobenzene as a carbon source. This work suggests a role for TE13 family thioesterases in swimming and degradation approaches for phenyl acetic acid. Proteins 2017; 85:1222-1237. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)

Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.

Fungal laccases are enzymes that have been studied because of their ability to decolorize and detoxify effluents; they are also used in paper bleaching, synthesis of polymers, bioremediation, etc. In this work we were able to express a laccase from Trametes (Pycnoporus) sanguineus in the filamentous fungus Trichoderma atroviride. For this purpose, a transformation vector was designed to integrate the gene of interest in an intergenic locus near the blu17 terminator region. Although monosporic selection was still necessary, stable integration at the desired locus was achieved. The native signal peptide from T. sanguineus laccase was successful to secrete the recombinant protein into the culture medium. The purified, heterologously expressed laccase maintained similar properties to those observed in the native enzyme (Km and kcat and kcat/km values for ABTS, thermostability, substrate range, pH optimum, etc). To determine the bioremediation potential of this modified strain, the laccase-overexpressing Trichoderma strain was used to remove xenobiotic compounds. Phenolic compounds present in industrial wastewater and bisphenol A (an endocrine disruptor) from the culture medium were more efficiently removed by this modified strain than with the wild type. In addition, the heterologously expressed laccase was able to decolorize different dyes as well as remove benzo[α]pyrene and phenanthrene in vitro, showing its potential for xenobiotic compound degradation.

A novel expansin protein (ScExlx1) was found, cloned and expressed from the Basidiomycete fungus Schizophylum commune. This protein showed the canonical features of plant expansins. ScExlx1 showed the ability to form "bubbles" in cotton fibers, reduce the size of avicel particles and enhance reducing sugar liberation from cotton fibers pretreated with the protein and then treated with cellulases. ScExlx1 was able to bind cellulose, birchwood xylan and chitin and this property was not affected by different sodium chloride concentrations. A novel property of ScExlx1 is its capacity to enhance reducing sugars (N-acetyl glucosamine) liberation from pretreated chitin and further added with chitinase, which has not been reported for any expansin or expansin-like protein. To the best of our knowledge, this is the first report of a bona fide fungal expansin found in a basidiomycete and we could express the bioactive protein in Pichia pastoris.

We isolated a putative citrate transporter of the tripartite tricarboxylate transporter (TTT) class from a metagenomic library of activated sludge from a sewage treatment plant. The transporter, dubbed TctA&#95;ar, shares ∼50% sequence identity with TctA of Comamonas testosteroni (TctA&#95;ct) and other β-Proteobacteria, and contains two 20-amino acid repeat signature sequences, considered a hallmark of this particular transporter class. The structures for both TctA&#95;ar and TctA&#95;ct were modeled with I-TASSER and two possible structures for this transporter family were proposed. Docking assays with citrate resulted in the corresponding sets of proposed critical residues for function. These models suggest functions for the 20-amino acid repeats in the context of the two different architectures. This constitutes the first attempt at structure modeling of the TTT family, to the best of our knowledge, and could aid functional understanding of this little-studied family., (© 2014 Wiley Periodicals, Inc.)

A moderate halophile and thermotolerant fungal strain was isolated from a sugarcane bagasse fermentation in the presence of 2 M NaCl that was set in the laboratory. This strain was identified by polyphasic criteria as Aspergillus caesiellus. The fungus showed an optimal growth rate in media containing 1 M NaCl at 28°C and could grow in media added with up to 2 M NaCl. This strain was able to grow at 37 and 42°C, with or without NaCl. A. caesiellus H1 produced cellulases, xylanases, manganese peroxidase (MnP) and esterases. No laccase activity was detected in the conditions we tested. The cellulase activity was thermostable, halostable, and no differential expression of cellulases was observed in media with different salt concentrations. However, differential band patterns for cellulase and xylanase activities were detected in zymograms when the fungus was grown in different lignocellulosic substrates such as wheat straw, maize stover, agave fibres, sugarcane bagasse and sawdust. Optimal temperature and pH were similar to other cellulases previously described. These results support the potential of this fungus to degrade lignocellulosic materials and its possible use in biotechnological applications.