Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a

Characterization of arbuscular mycorrhizal fungal species associating with Zea mays

Taxonomic identification of arbuscular mycorrhizal (AM) fungal spores extracted directly from the field is sometimes difficult because spores are often degraded or parasitized by other organisms. Single-spore inoculation of a suitable host plant allows for establishing monosporic cultures of AM fungi. This study aimed to propagate AM fungal spores isolated from maize soil using single spores for morphological characterization. First, trap cultures were established to trigger the sporulation of AM fungal species. Second, trap cultures were established with individual morphotypes by picking up only one spore under a dissecting microscope and transferring it to a small triangle of sterilized filter paper, which was then carefully inoculated below a root from germinated sorghum seeds in each pot and covered with a sterile substrate. All pots were placed in sunbags and maintained in a plant growth room for 120 days. Spores obtained from single spore trap cultures from each treatment, maize after oats (MO), maize after maize (MM), maize after peas (MP), and maize after soybean (MS), were extracted using the sieving method. Healthy spores were selected for morphological analysis. Direct PCR was conducted by crushing spores in RNAlater and applying three sets of primer pairs: ITS1 × ITS4, NS31 × AML2, and SSUmcf and LSUmBr. Nucleotide sequences obtained from Sanger sequencing were aligned on MEGA X. The phylogenetic tree showed that the closest neighbors of the propagated AM fungal species belonged to the genera Claroideoglomus, Funneliformis, Gigaspora, Paraglomus, and Rhizophagus. The morphological characteristics were compared to the descriptive features of described species posted on the INVAM website, and they included Acaulospora cavernata, Diversispora spurca, Funneliformis geosporus, Funneliformis mosseae, Gigaspora clarus, Gigaspora margarita, Glomus macrosporum, Paraglomus occultum, and Rhizophagus intraradices. These findings can provide a great contribution to crop productivity and sustainable management of the agricultural ecosystem. Also, the isolate analyzed could be grouped into efficient promoters of growth and mycorrhization of maize independent of their geographical location.

Effective photocatalytic inactivation of Microcystis aeruginosa by Ag3VO4/BiVO4 heterojunction under visible light

In recent years, photocatalytic technology has been increasingly used for the treatment of algal blooms in water bodies due to its high efficiency and environmental advantages. However, conventional semiconductor materials suffer from high electron-hole recombination rate, low carrier mobility and weak surface adsorption ability, which made their photocatalytic performance limited. Therefore, the photocatalytic performance of the composites can be improved by coupling another semiconductor material to form a heterojunction to accelerate electron transfer. In this study, a novel composite Ag3VO4/BiVO4 (ABV) photocatalyst was successfully prepared by in-situ deposition method for the photocatalytic inactivation of Microcystis aeruginosa (M. aeruginosa) under visible light. The photocatalyst showed excellent photocatalytic activity, and the degradation rate of M. aeruginosa chlorophyll a was up to 99.8% within 4 h under visible light. During the photocatalytic degradation, the morphology of algae cells, the permeability of cell membrane, the organic matter inside and outside the cells, the antioxidant system and the soluble protein were seriously damaged. Moreover, three cycle experiments showed that the prepared ABV photocatalyst had high reusability. Finally, a possible mechanism of M. aeruginosa inactivation was proposed. In general, the synthesized ABV photocatalyst can effectively inactivate cyanobacteria under visible light and provided a new method for M. aeruginosa removal in water.

Transcriptome Analysis Reveals the Algicidal Mechanism of Brevibacillus laterosporus against Microcystis aeruginosa through Multiple Metabolic Pathways

It is widely accepted that eutrophication has played an important role in the formation of harmful cyanobacterial blooms in recent decades, which impacts water quality and ecological environment and causes huge economic losses. Algicidal bacteria have a promising application prospect in controlling cyanobacterial blooms in aquaculture water. Here, the process of the algicidal bacterium Brevibacillus laterosporus strain Bl-zj acting on Microcystis aeruginosa was explored using transcriptome analysis to elucidate the algicidal mechanism. The results of the co-culture of bacterium and alga showed a strong alga-lysing effect of B. laterosporus against M. aeruginosa with an extreme morphology deformation of the algal cells. A total of 2744 differentially expressed genes of B. laterosporus were identified, which were mainly involved in the metabolism of amino acid, carbohydrate, and lipid. In the co-cultured group, the expression of genes mainly enriched in valine, leucine and isoleucine degradation, and fatty acid degradation were significantly increased. However, the expression of the genes related to ribosome were mainly inhibited. Transcriptome analysis showed that B. laterosporus obtained ATP and energy by the degradation of valine, leucine, isoleucine, and fatty acids, and destroyed algal cells by efflux pump transporters, secretion of hydrolytic enzymes, antibiotics, proteases, and other secondary metabolites, resulting in algal death and achieving the algicidal effect.

Membrane composition and successful bioaugmentation. Studies of the interactions of model thylakoid and plasma cyanobacterial and bacterial membranes with fungal membrane-lytic enzyme Lecitase ultra

Cyanobacterial/bacterial consortia are frequently inoculated to soils to increase the soil fertility and to accelerate the biodegradation of organic pollutants. Moreover, such consortia can also be successfully applied in landfills especially for the biodegradation of plastic wastes. However, the bioaugmentation techniques turn out frequently inefficient due to the competition of the indigenous microorganisms attacking directly these inoculated or secreting to their surroundings cell wall and membrane-lytic enzymes. It can be hypothesized that the resistance of the microbial membrane to the enzymatic degradation is correlated with its lipid composition. To verify this hypothesis glycolipid and phospholipid Langmuir monolayers were applied as models of thylakoid and plasma cyanobacterial and bacterial membranes. Hybrid fungal enzyme Lecitase ultra joining the activity of lipase and phospholipase A1 was applied as the model of fungal membrane-lytic enzyme. It turned out that anionic thylakoid lipids sulfoquinovosyldiacylglycerol and phosphatidylglycerols were the main targets of Lecitase ultra in the model multicomponent thylakoid membranes. The resistance of the model plasma bacterial membranes to enzymatic degradation depended significantly to their composition. The resistance increased generally when the unsaturated lipids were exchanged to their saturated counterparts. However, most resistant turned out the membranes composed of unsaturated phosphatidylamine and saturated anionic phospholipids.

Transcriptional Analysis of Microcystis aeruginosa Co-Cultured with Algicidal Bacteria Brevibacillus laterosporus

Harmful algal blooms caused huge ecological damage and economic losses around the world. Controlling algal blooms by algicidal bacteria is expected to be an effective biological control method. The current study investigated the molecular mechanism of harmful cyanobacteria disrupted by algicidal bacteria. Microcystis aeruginosa was co-cultured with Brevibacillus laterosporus Bl-zj, and RNA-seq based transcriptomic analysis was performed compared to M. aeruginosa, which was cultivated separately. A total of 1706 differentially expressed genes were identified, which were mainly involved in carbohydrate metabolism, energy metabolism and amino acid metabolism. In the co-cultured group, the expression of genes mainly enriched in photosynthesis and oxidative phosphorylation were significantly inhibited. However, the expression of the genes related to fatty acid synthesis increased. In addition, the expression of the antioxidant enzymes, such as 2-Cys peroxiredoxin, was increased. These results suggested that B. laterosporus could block the electron transport by attacking the PSI system and complex I of M. aeruginosa, affecting the energy acquisition and causing oxidative damage. This further led to the lipid peroxidation of the microalgal cell membrane, resulting in algal death. The transcriptional analysis of algicidal bacteria in the interaction process can be combined to explain the algicidal mechanism in the future.

Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species

Trametes species are efficient wood decomposers that are widespread throughout the world. Mitogenomes have been widely used to understand the phylogeny and evolution of fungi. Up to now, two mitogenomes from the Trametes genus have been revealed. In the present study, the complete mitogenomes of two novel Trametes species, Trametes versicolor and T. coccinea, were assembled and compared with other Polyporales mitogenomes. Both species contained circular DNA molecules, with sizes of 67,318 bp and 99,976 bp, respectively. Comparative mitogenomic analysis indicated that the gene number, length and base composition varied between the four Trametes mitogenomes we tested. In addition, all of the core protein coding genes in Trametes species were identified and subjected to purifying selection. The mitogenome of T. coccinea contained the largest number of introns among the four Trametes species tested, and introns were considered the main factors contributing to size variations of Polyporales. Several novel introns were detected in the Trametes species we assembled, and introns identified in Polyporales were found to undergo frequent loss/gain events. Large-scale gene rearrangements were detected between closely related Trametes species, including gene inversions, insertions, and migrations. A well-supported phylogenetic tree for 77 Basidiomycetes was obtained based on the combined mitochondrial gene set using 2 phylogenetic inference methods. The results showed that mitochondrial genes are effective molecular markers for understanding the phylogeny of Basidiomycetes. This study is the first to report the mitogenome rearrangement and intron dynamics of Trametes species, which shed light on the evolution of Trametes and other related species.

Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor

Fungal mycelia can eliminate almost all cocultured cyanobacterial cells within a short time. However, molecular mechanisms of algicidal fungi are poorly understood. In this study, a time‐course transcriptomic analysis of algicidal fungus Bjerkandera adusta T1 was applied to investigate gene expression and regulation. A total of 132, 300, 422, and 823 differentially expressed genes (DEGs) were identified at 6, 12, 24, and 48 hr, respectively. Most DEGs exhibited high endopeptidase activity, cellulose catabolic process, and transmembrane transporter activity by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Many decomposition genes encoding endopeptidases were induced a little later in B. adusta T1 when compared with previously investigated algicidal fungus Trametes versicolor F21a. Besides, the accumulated expression of Polysaccharide lyases8 (PL8) gene with peptidoglycan and alginate decomposition abilities was greatly delayed in B. adusta T1 relative to T. versicolor F21a. It was implied that endopeptidases and enzymes of PL8 might be responsible for the strong algicidal ability of B. adusta T1 as well as T. versicolor F21a.

Quantitative proteomic analysis provides insights into the algicidal mechanism of Halobacillus sp. P1 against the marine diatom Skeletonema costatum

Algicidal behavior is a common interaction between marine microalgae and bacteria, especially in the dissipation phase of algal blooms. The marine bacterium Halobacillus sp. P1 was previously isolated and exhibits high algicidal activity against the diatom Skeletonema costatum. However, little is known about the mechanism underlying this algicidal process. Here, a tandem mass tag (TMT)-based proteomic approach was coupled with physiological analysis to investigate the cellular responses of S. costatum when treated with P1 culture supernatant. Among the 4582 proteins identified, 82 and 437 proteins were differentially expressed after treatment for 12 and 24 h, respectively. The proteomic results were in accordance with the results of verification by parallel reaction monitoring (PRM) assays. Proteins involved in reactive oxygen species scavenging, protein degradation and transport were upregulated, while proteins participating in nitrogen metabolism, protein translation, photosynthetic pigment biosynthesis and cell cycle regulation were significantly downregulated (p-value ≤0.05), corresponding to the increasing malondialdehyde content and the decreasing nitrogen, protein and chlorophyll a contents. A nutrient competitive relationship might exist between the bacterium P1 and S. costatum, and the inhibition of nitrogen metabolism by the P1 culture supernatant might be the key lethal factor that results in the dysfunction of S. costatum metabolism. Our study sheds light on the algicidal mechanism of P1 at the molecular level and provides new insights into algae-bacteria interactions.

Mycoremediation: Expunging environmental pollutants

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Mycoremediation of polycyclic aromatic hydrocarbons, challenges, and strategies to overcome.

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Role of the fungi in eradicating heavy metal contamination from the polluted sites.

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Mycoremediation of agricultural wastes including pesticides, herbicides, and cyanotoxins.

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Pharmaceutical wastes and strategies for its remediation using white-rot and ligninolytic fungus.

The ever-increasing population, rapid rate of urbanization, and industrialization are exacerbating the pollution-related problems. Soil and water pollution affect human health and the ecosystem. Thus, it is crucial to develop strategies to combat this ever-growing problem. Mycoremediation, employing fungi or its derivatives for remediation of environmental pollutants, is a comparatively cost-effective, eco-friendly, and effective method. It has advantages over other conventional and bioremediation methods. In this review, we have elucidated the harmful effects of common pollutants on public health and the environment. The role of several fungi in degrading these pollutants such as heavy metals, agricultural, pharmaceutical wastes, including polycyclic aromatic hydrocarbons, is enumerated. Future strategies to improve the rate and efficiency of mycoremediation are suggested. The manuscript describes the strategies which can be used as a future framework to address the global problem of pollution.

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.

Proteomic enzyme analysis of the marine fungus Paradendryphiella salina reveals alginate lyase as a minimal adaptation strategy for brown algae degradation

We set out to investigate the genetic adaptations of the marine fungus Paradendryphiella salina CBS112865 for degradation of brown macroalgae. We performed whole genome and transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina grown on three species of brown algae and under carbon limitation. Genome comparison with closely related terrestrial fungi revealed that P. salina had a similar but reduced CAZyme profile relative to the terrestrial fungi except for the presence of three putative alginate lyases from Polysaccharide Lyase (PL) family 7 and a putative PL8 with similarity to ascomycete chondroitin AC lyases. Phylogenetic and homology analyses place the PL7 sequences amongst mannuronic acid specific PL7 proteins from marine bacteria. Recombinant expression, purification and characterization of one of the PL7 genes confirmed the specificity. Proteomic analysis of the P. salina secretome when growing on brown algae, revealed the PL7 and PL8 enzymes abundantly secreted together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the basic CAZyme repertoire of saprobic and plant pathogenic ascomycetes, with the addition of PL7 alginate lyases, provide P. salina with sufficient enzymatic capabilities to degrade several types of brown algae polysaccharides.

Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz)

Drought stress is one of the potent abiotic stress limiting cassava (Manihot esculenta) yield globally, but studies addressing both physiological and proteomic responses that how cassava crops can adjust their growth and metabolism under drought conditions are lacking. Combining leaf physiological and proteomic characteristics strongly allied with drought tolerance should results in enhanced drought tolerance in cassava crop. Therefore, the aims of this study were to explore the plant physiological and proteomic mechanisms involved in drought adaptation in cassava. Xinxuan 048 (XX048) was exposed to well-watered control (CK, relative soil water content (RSWC) as 80 ± 5%), mild drought stress (LD, RSWC as 65 ± 5%), moderate drought stress (MD, RSWC as 50 ± 5%) and severe drought stress (SD, RSWC as 35 ± 5%) from 30 days after planting. Under drought stress conditions, cassava plant showed a substantial decline in plant height, stem diameter, leaf number, leaf water content, the ratio of free water content to bound water content of leaf (FW/BW), net photosynthetic rate (Pn), intercellular CO₂ concentration (Ci), stomatal conductance (Gs) and transpiration rate (Tr) compared with well watered plants. However, compared with control, leaf water content, SPAD value, cell membrane permeability, malondialdehyde (MDA), soluble sugar, protein proline content SOD and CAT activity were at peak under drought stress. The proteomic analysis revealed that among 3 339 identified proteins, drought stress increased and decreased abundance of 262 and 296 proteins, respectively, compared with control condition. These proteins were involved in carbohydrate energy metabolism, protein homeostasis, transcription, cell structure, cell membrane transport, signal transduction, stress and defense responses. These data not only provides a comprehensive dataset on overall proteomic changes in cassava leaves under drought stress, but also highlights the mechanisms by which euphorbiaceae plants can adapt to drought conditions.

The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis

The molecular mechanism underlying the elimination of algal cells by fungal mycelia has not been fully understood. Here, we applied transcriptomic analysis to investigate the gene expression and regulation at time courses of Trametes versicolor F21a during the algicidal process. The obtained results showed that a total of 193, 332, 545, and 742 differentially expressed genes were identified at 0, 6, 12, and 30 h during the algicidal process, respectively. The gene ontology terms were enriched into glucan 1,4-α-glucosidase activity, hydrolase activity, lipase activity, and endopeptidase activity. The KEGG pathways were enriched in degradation and metabolism pathways including Glycolysis/Gluconeogenesis, Pyruvate metabolism, the Biosynthesis of amino acids, etc. The total expression levels of all Carbohydrate-Active enZYmes (CAZyme) genes for the saccharide metabolism were increased by two folds relative to the control. AA5, GH18, GH5, GH79, GH128, and PL8 were the top six significantly up-regulated modules among 43 detected CAZyme modules. Four available homologous decomposition enzymes of other species could partially inhibit the growth of algal cells. The facts suggest that the algicidal mode of T. versicolor F21a might be associated with decomposition enzymes and several metabolic pathways. The obtained results provide a new candidate way to control algal bloom by application of decomposition enzymes in the future.