Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil

Insight into the adaptation mechanisms of high hydrostatic pressure in physiology and metabolism of hadal fungi from the deepest ocean sediment

High hydrostatic pressure (HHP) influences the life processes of organisms living at depth in the oceans. While filamentous fungi are one of the essential members of deep-sea microorganisms, few works have explored their piezotolerance to HHP. Here, we obtained three homogeneous Aspergillus sydowii from terrestrial, shallow, and hadal areas, respectively, to compare their pressure resistance. A set of all-around evaluation methods including determination of growth rate, metabolic activity, and microscopic staining observation was established and indicated that A. sydowii DM1 from the hadal area displayed significant piezotolerance. Global analysis of transcriptome data under elevated HHP revealed that A. sydowii DM1 proactively modulated cell membrane permeability, hyphae morphology, and septal quantities for seeking a better livelihood under mild pressure. Besides, differentially expressed genes were mainly enriched in the biosynthesis of amino acids, carbohydrate metabolism, cell process, etc., implying how the filamentous fungi respond to elevated pressure at the molecular level. We speculated that A. sydowii DM1 could acclimatize itself to HHP by adopting several strategies, including environmental response pathway HOG-MAPK, stress proteins, and cellular metabolisms.IMPORTANCEFungi play an ecological and biological function in marine environments, while the physiology of filamentous fungi under high hydrostatic pressure (HHP) is an unknown territory due to current technologies. As filamentous fungi are found in various niches, Aspergillus sp. from deep-sea inspire us to the physiological trait of eukaryotes under HHP, which can be considered as a prospective research model. Here, the evaluation methods we constructed would be universal for most filamentous fungi to assess their pressure resistance, and we found that Aspergillus sydowii DM1 from the hadal area owned better piezotolerance and the active metabolisms under HHP indicated the existence of undiscovered metabolic strategies for hadal fungi. Since pressure-related research of marine fungi has been unexpectedly neglected, our study provided an enlightening strategy for them under HHP; we believed that understanding their adaptation and ecological function in original niches will be accelerated in the perceivable future.

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

Poultices as biofilms of titanium dioxide nanoparticles/carboxymethyl cellulose/Phytagel for cleaning of infected cotton paper by Aspergillus sydowii and Nevskia terrae

In this study, TiO2 nanoparticle (TiO2NP)-coated film was produced to protect manuscripts against microorganisms using ecofriendly benign materials. As a result, a simple method was created that uses poultice biofilm made of carboxymethyl cellulose (CMC) and Phytagel plant cell (PGP) loaded with TiO2NPs to preserve manuscripts against microbes in an environmentally responsible way. Three volumes (1, 2, 4 mL) of TiO2NPs were put into a biofilm combination to produce the poultices known as CMC/PGP/TiO2-1, CMC/PGP/TiO2-2, and CMC/PGP/TiO2-3. The synthesized TiO2NPs were nearly spherical in shape, small in size (98 nm), and stable (zeta potential value - 33 mV). The results showed that the unique deposition of TiO2NPs on the biofilm surface gave the produced films loaded with TiO2NPs a rough structure. The highest values of mechanical characteristics were determined to be in CMC/PGP/TiO2-1 with values of 25.4 g, 6.6 MPa, and 11.4%, for tensile strength, elongation at break, and tear strength, respectively. Based on molecular identification, the fungus Aspergillus sydowii and the bacterium Nevskia terrae, with accession numbers MG991624 and AB806800, respectively, were isolated and identified from an antiquated manuscript formed from cellulosic fibers. Before the experiments, the produced cotton paper samples were aged, and then, one group was infected for 6 months by A. sydowii and the second group with N. terrae. Following the preparation of a CMC/PGP biofilm loaded with various volumes of TiO2NPs, poultices were applied to infected cotton paper in order to clean it. The infected cotton paper was placed inside the sandwich-like poultices that were created. The poultice CMC/PGP/TiO2-2 demonstrated potential for preventing the growth of A. sydowii and N. terrae-infected cotton paper, when the fibers were saved, cleaned, and coated with CMC/PGP/TiO2-2 after absorbing the fungus and the bacterium and exhibiting exceptional antimicrobial activities. Finally, the novel biofilms have demonstrated their capacity to lessen microbial contamination of cotton paper. In order to generalize the usage of these poultices, it is also advised that they be produced on a large scale and tested on a variety of organic materials in the future.

Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation

A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.

Secondary Metabolites, Biological Activities, and Industrial and Biotechnological Importance of Aspergillus sydowii

Marine-derived fungi are renowned as a source of astonishingly significant and synthetically appealing metabolites that are proven as new lead chemicals for chemical, pharmaceutical, and agricultural fields. Aspergillus sydowii is a saprotrophic, ubiquitous, and halophilic fungus that is commonly found in different marine ecosystems. This fungus can cause aspergillosis in sea fan corals leading to sea fan mortality with subsequent changes in coral community structure. Interestingly, A. sydowi is a prolific source of distinct and structurally varied metabolites such as alkaloids, xanthones, terpenes, anthraquinones, sterols, diphenyl ethers, pyrones, cyclopentenones, and polyketides with a range of bioactivities. A. sydowii has capacity to produce various enzymes with marked industrial and biotechnological potential, including α-amylases, lipases, xylanases, cellulases, keratinases, and tannases. Also, this fungus has the capacity for bioremediation as well as the biocatalysis of various chemical reactions. The current work aimed at focusing on the bright side of this fungus. In this review, published studies on isolated metabolites from A. sydowii, including their structures, biological functions, and biosynthesis, as well as the biotechnological and industrial significance of this fungus, were highlighted. More than 245 compounds were described in the current review with 134 references published within the period from 1975 to June 2023.

Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments

Introduction

Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.

Methods

Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.

Results and Discussion

The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.

The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface

Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.

Whole-genome sequencing and comparative genomic analysis of potential biotechnological strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei

Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Herein, we performed whole-genome sequencing and assembly of the Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with strains of T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The sequencing coverage value of all genomes evaluated in this study was higher than that of previously reported genomes for the same species of Trichoderma. The resulting assembly revealed total lengths of 40 Mb (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711). A genome-wide phylogenetic analysis provided details on the relationships of the newly sequenced species with other Trichoderma species. Structural variants revealed genomic rearrangements among Th3844, Th0179, Ta0020, and Tr0711 relative to the T. reesei QM6a reference genome and showed the functional effects of such variants. In conclusion, the findings presented herein allow the visualization of genetic diversity in the evaluated strains and offer opportunities to explore such fungal genomes in future biotechnological and industrial applications.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments

Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.

Esfenvalerate biodegradation by marine fungi is affected by seawater and emulsifier formulation

Pesticides already were detected in the oceans, and their fates require evaluation in these environmental conditions. Therefore, marine-derived fungi were assessed for Esfenvalerate biodegradation, approaching the effects of seawater and use of commercial emulsifiable formulation. Residual pesticide and four metabolites were quantified. Furthermore, kinetics were determined for the three tested strains (Microsphaeropsis sp. CBMAI 1675, Acremonium sp. CBMAI 1676, and Westerdykella sp. CBMAI 1679). These facultative marine fungi biodegraded up to 87 ± 2% of 100 mg L^-1 Esfenvalerate in liquid media. However, Esfenvalerate biodegradation was faster in low salinity conditions than in artificial seawater. Moreover, rates of consumption were higher for Esfenvalerate in the pure form than for the commercial emulsifiable formulation. These results suggest that half-life of Esfenvalerate formulated with inert ingredients in seawater can have a double prolongation effect that can contribute to health and environmental issues.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Proteomic response of Pseudomonas aeruginosa IIPIS-8 during rapid and efficient degradation of naphthalene

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the ecosystem and are of significant concern due to their toxicity and mutagenicity. Bioremediation of PAHs is a popular and benign approach that ameliorates the environment. This study investigated the biodegradation and proteome response of Pseudomonas aeruginosa IIPIS-8 for two-ringed PAH: naphthalene (NAP) to understand proteome alteration during its bioremediation. Rapid biodegradation was observed up to 98 ± 1.26% and 84 ± 1.03%, respectively, for initial concentrations of 100 mg L^-1 and 500 mg L^-1 of NAP. Degradation followed first-order kinetics with rate constants of 0.12 h^-1 and 0.06 h^-1 and half-life (t_1/2) of 5.7 h and 11.3 h, respectively. Additionally, the occurrence of key ring cleavage and linear chain intermediates, 2,3,4,5,6, -pentamethyl acetophenone, 1-octanol 2-butyl, and hexadecanoic acid supported complete NAP degradation. Proteomics study of IIPIS-8 throws light on the impact of protein expression, in which 415 proteins were quantified in sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) analysis, of which 97 were found to be significantly up-regulated and 75 were significantly down-regulated by ≥ 2-fold change (p values ≤ 0.05), during the NAP degradation. The study also listed the up-regulation of several enzymes, including oxido-reductases, hydrolases, and catalases, potentially involved in NAP degradation. Overall, differential protein expression, through proteomics study, demonstrated IIPIS-8's capability to efficiently assimilate NAP in their metabolic pathways even in a high concentration of NAP.