Amphichorda monjolensis sp. nov., a new fungal species isolated from a Brazilian limestone cave, with an update on acremonium-like species in Bionectriaceae.

Caves are unique environments characterized by spatial limitations, partial or total absence of direct light, and scarcity of organic carbon and nutrients. Caves are shelters for a variety of adapted animals and microorganisms such as fungi, many of which are still unknown. Amphichorda is a fungal genus belonging to the family Bionectriaceae, which includes cave-dwelling and entomopathogenic species with biotechnological applications. In this study, a new fungal species was identified using morphological and multi-locus phylogenetic analyses of the ITS, LSU, and TEF loci, in the Gruta Velha Nova limestone cave located in the Southern Espinhaço Range, Monjolos, Minas Gerais, Brazil. During the exposure of potato dextrose agar plates to the cave environment, an insect from the family Rhaphidophoridae passed by and fed on the culture medium, resulting in three fungal isolates. Phylogenetic analyses showed that these isolates formed a clade distinct from all known species, leading us to introduce a new species, Amphichorda monjolensis, which may be associated with this insect. Here, we also proposed two new combinations for species of acremonium-like fungi in the Bionectriaceae: Bulbithecium globosisporum (synonym: Acremonium globosisporum) and Hapsidospora curva (synonym: Acremonium curvum). The discovery of A. monjolensis highlights the potential of caves as shelters for new species with significant biotechnological importance.

Intestinal microbial diversity of swines fed with different sources of lithium.

A drug that is widely used in the treatment of psychiatric disorder is lithium (Li) salts. The people who make therapeutic use of this drug develop a series of side effects. Through metataxonomic data, this study assessed the impacts of lithium, as Li carbonate or Li-enriched mushrooms, on the microbial composition of the ileum, colon, and feces of piglets. Employing Bray-Curtis metric, no differences were observed among the treatments evaluated. Nevertheless, the alpha diversity indices showed differences in the Simpson, Shannon, and Chao-1 indices in the colon and Chao-1 in the feces in the diets with Li compared with the diets without Li. The taxa with the highest relative abundance varied among the ileum, colon, and feces, with a predominance of the phyla Firmicutes, Bacteroidota, and Proteobacteria in diets with Li. Many groups of microorganisms that are important for the health of the host (e.g., Lactobacillus, Ruminococcaceae, Enterorhabdus, Muribaculaceae, and Coprococcus) had their relative abundance increased in animals that received diets with the recommended dose of lithium. Furthermore, there was an increase in the abundance of Prevotellaceae and Bacteroidales (in the diet with Li-enriched mushroom) and Clostridia, Ruminococcus, Burkholderia, and Bacteroidales (diets with Li carbonate) at the recommended dosages. This is the first study to show the effects of Li carbonate and Li-enriched mushrooms on the intestinal microbiota of piglets. Thus, the effects of lithium on the body may be related to its ability to change the composition of the intestinal microbiota. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03938-3.

Machine learning-based soil quality assessment for enhancing environmental monitoring in iron ore mining-impacted ecosystems.

In November 2015, a catastrophic rupture of the Fundão dam in Mariana (Brazil), resulted in extensive socio-economic and environmental repercussions that persist to this day. In response, several reforestation programs were initiated to remediate the impacted regions. However, accurately assessing soil health in these areas is a complex endeavor. This study employs machine learning techniques to predict soil quality indicators that effectively differentiate between the stages of recovery in these areas. For this, a comprehensive set of soil parameters, encompassing 3 biological, 16 chemical, and 3 physical parameters, were evaluated for samples exposed to mining tailings and those unaffected, totaling 81 and 6 samples, respectively, which were evaluated over 2 years. The most robust model was the decision tree with a restriction of fewer levels to simplify the tree structure. In this model, Cation Exchange Capacity (CEC), Microbial Biomass Carbon (MBC), Base Saturation (BS), and Effective Cation Exchange Capacity (eCEC) emerged as the most pivotal factors influencing model fitting. This model achieved an accuracy score of 92% during training and 93% during testing for determining stages of recovery. The model developed in this study has the potential to revolutionize the monitoring efforts conducted by regulatory agencies in these regions. By reducing the number of parameters that necessitate evaluation, this enhanced efficiency promises to expedite recovery monitoring, simultaneously enhancing cost-effectiveness while upholding the analytical rigor of assessments.

Lentinula edodes lignocellulolases and lipases produced in Macaúba residue and use of the enzymatic extract in the degradation of textile dyes.

Agro-industrial residue and textile effluents have caused environmental damage to soil and water bodies. The production of fungal enzymes using agro-industrial residues and the use of these enzymes in the degradation of textile dyes can be a viable alternative to reduce these environmental damages. Lentinula edodes is a white rot fungus with high nutritional value that produces edible mushrooms and enzymes of commercial interest. Thus, the objectives of this study were to produce, purify, and biochemically characterize the lignocellulolytic enzymes and lipases produced for L. edodes in Macaúba coconut and to evaluate their potential for the degradation of textile dyes. The L. edodes UFV 73 had maximum enzymatic activity at 37 days of incubation. After the purification steps, the laccase, manganese peroxidase (MnP), cellulase, and, xylanase yields were 489.01, 264.2, 105.02, and 9.5%. The optimum temperature of cellulase activity did not change from 4 to 60 °C. The MnP, laccase, and lipase had activity directly proportional to the increase in temperature, while the cellulase and xylanase activity did not change. The optimum pH varied among analyzed enzymes. All the enzymes analyzed are according to Michaelis-Menten kinetics. The lignocellulolytic enzymes were stable up to 8 h of incubation and lipase had a reduction of activity after one hour. The discoloration rate of indigo dye by partially purified enzymatic extract (PPPE) was 40%, which shows its potential for degradation of dyes from textile industries.

Two new Cladosporium species from a quartzite cave in Brazil.

Caves are underground and natural environments mainly found in rocky terrain. Caves have a very specific microclimate, which benefits the occurrence of specific fungi. In recent studies, researchers have observed that caves harbour a great diversity of fungi. However, studies on fungal diversity in Brazilian caves are still incipient. In September 2019, airborne spore and soil samples were collected from the Monte Cristo cave, in the Southern Espinhaço Range, Diamantina, Minas Gerais state, Brazil. Two Cladosporium single-spore isolates, among other genera, were obtained from these samples. This study aimed to characterise these two fungal isolates based on their DNA sequence data and morphology. Phylogenetic analyses of the rDNA-ITS, ACT and TEF1-α loci revealed that the isolates belonged to the Cladosporium cladosporioides species complex. Both isolates did not cluster with any known species and were formally described and named herein as C. diamantinense and C. speluncae. This study presents taxonomic novelties and contributes to the knowledge about the fungal diversity in Brazilian caves.

Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil.

Brazilian coffee production relies on the cultivation of Coffea arabica and Coffea canephora. Climate change has been responsible for the decreasing yield of the crops in the country yet the associated microbial community can mitigate these effects by improving plant growth and defense. Although some studies have tried to describe the microorganisms associated with these Coffea species, a study that compares the microbiome on a wider spatial scale is needed for a better understanding of the terroir of each coffee planting region. Therefore, our aim was to evaluate the microbial communities harbored in soils and fruits of these Coffea species in four Brazilian floristic domains (Amazon, Atlantic Forest Caatinga, and Cerrado). One hundred and eight samples (90 of soil and 90 of fruits) were used in the extraction and sequencing of the fungal and bacterial DNA. We detected more than 1000 and 500 bacterial and fungal genera, respectively. Some soil microbial taxa were more closely related to one coffee species than the other species. Bacillus bataviensis tends to occur more in arid soils from the Caatinga, while the fungus Saitozyma sp. was more related to soils cultivated with C. arabica. Thus, the species and the planting region (floristic domain) of coffee affect the microbial composition associated with this crop. This study is the first to report microbial communities associated with coffee produced in four floristic domains that include sites in eight Brazilian states. Data generated by DNA sequencing provides new insights into microbial roles and their potential for the developing more sustainable coffee management, such as the production of biofertilizers and starter culture for fermentation of coffee cherries.

Bioavailability of Li-enriched mushrooms and protection against oxidative stress in pigs: First study in vivo.

Mycelia and mushrooms are able to bioaccumulate minerals. Lithium is the active principle of drugs used in the treatment of psychiatric diseases. However, a dietary source of Li can reduce the side effects of these drugs. Thus, the objective of this study was to evaluate the bioavailability of Li-enriched mushroom of Pleurotus djamor in pigs and the effects of this element on oxidative stress in the animal tissues. Pigs 28-30 days-old were fed with diets containing or not Li for five days. Levels of serum cortisol were related to the Li dosage from diet. Li-enriched mushrooms were more bioavailable source of Li to the body than Li2CO3. These mushrooms also improved the effects of oxidative enzymes and showed less oxidative damage than Li2CO3. These results demonstrate the potential to use Li-enriched P. djamor as a source of Li that is more bioavailable and present protective effects against oxidative stress.

Effect of Selenium-Enriched Substrate on the Chemical Composition, Mineral Bioavailability, and Yield of Edible Mushrooms.

Mushrooms absorb minerals from substrates in which they are cultivated, so they could be used as vehicles of minerals that are deficient in human or animal diets, such as selenium. Selenium deficiency aggravates cardiovascular diseases, diabetes mellitus, and intestinal cancer. This work presents the latest discoveries related to the production of edible mushrooms in selenium-enriched substrates and discusses their use as an alternative to supply the deficiency of this mineral in human and animal diets. Selenized mushrooms and their derived extracts present bioaccessible and bioavailable forms of selenium, as antioxidant and antitumor activity, as demonstrated in various in vitro and in vivo experiments. Consequently, the consumption of these mushrooms reduces the levels of blood cholesterol and glucose. On the other hand, growing mushrooms in selenium-enriched substrates may alter the yield and their chemical composition, and this lack of standardization is still an obstacle to the scale up of the production process. On the other hand, the use of agro-industrial by-products as substrates can enable the cultivation of enriched edible mushrooms and their commercialization.

Extinction of anciently associated gut bacterial symbionts in a clade of stingless bees.

Animal-microbe symbioses are often stable for millions of years. An example is the clade consisting of social corbiculate bees-honeybees, bumblebees, and stingless bees-in which a shared ancestor acquired specialized gut bacteria that subsequently diversified with hosts. This model may be incomplete, however, as few microbiomes have been characterized for stingless bees, which are diverse and ecologically dominant pollinators in the tropics. We surveyed gut microbiomes of Brazilian stingless bees, focusing on the genus Melipona, for which we sampled multiple species and biomes. Strikingly, Melipona lacks Snodgrassella and Gilliamella, bacterial symbionts ubiquitous in other social corbiculate bees. Instead, Melipona species harbor more environmental bacteria and bee-specific Starmerella yeasts. Loss of Snodgrassella and Gilliamella may stem from ecological shifts in Melipona or the acquisition of new symbionts as functional replacements. Our findings demonstrate the value of broadly sampling microbiome biodiversity and show that even ancient symbioses can be lost.

Summer school: a warm journey through teaching microbiology to undergraduate students.

The Núcleo de Estudos em Microbiologia Agrícola (NEMA) is an academic-scientific group created by graduate students in the Post Graduate in Agricultural Microbiology in the Department of Microbiology at Universidade Federal de Viçosa, Brazil. NEMA's purposes include promoting and sharing research and knowledge on microbiology in different fields of application. Here, we will comment on our experience in organizing the Summer School on Microbiology and teaching microbiology to undergraduate students during the program. NEMA offers this annual event to disseminate and stimulate knowledge about microbiology for undergraduate students in a participatory, collaborative and interactive way.

Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil.

In recent years, several studies have been developed to understand the impact of fermentation on the final quality of coffee and have indicated that postharvest processing could be a determinant of quality. However, a trend has appeared as a scientific counterpoint, indicating that the interactions between soil, fruit, altitude, and slope exposures with respect to the Sun are important to understand the behavior of the microbiome in coffee. Studies on the microbiota of coffee have addressed its role during the fermentation process, however the knowledge of indigenous microorganisms harbored in fruits and soil of coffee trees growing in fields are essential, as they can contribute to fermentation. Therefore, the aim of this work was to evaluate the influence of topographic and edaphic factors on the bacterial and fungal communities present in the soil and in the fruits of Coffea arabica trees. Samples of fruits and soil were collected from different growing areas at different altitudes and soil conditions. The microbial DNA was extracted and sequenced. The results showed the contribution of environmental factors in the structure of bacterial and fungal communities. The richness, evenness and diversity of the mycobiome and bacteriome were higher in the soil than in the fruits, independent of altitude. In addition, coffee trees at higher altitudes tended to have more bacteria shared between the soil and fruits. The co-occurrence/co-exclusion network showed that bacteria-bacteria connections were greater in higher altitudes. On another hand, fungi-fungi and fungi-bacteria connections were higher in low altitudes. This was the first study that evaluates in deep the influence of environmental factors in the microbiota habiting fruits and soil coffee trees, which may affect the coffee beverage quality.

Genome-Scale Characterization of Fungal Phytases and a Comparative Study Between Beta-Propeller Phytases and Histidine Acid Phosphatases.

This work intended to prospect new phytase-producing organisms. In silico genomic analyses allowed the selection of twelve potential phytase-producing fungi. Based on gene sequence, it was possible to identify four well-defined groups of phytate-degrading enzymes: esterase-like, ß-propeller phytases (ßPP), phosphoglycerate mutase-like, and phytases of the histidine acid phosphatases (HAP) family. Analysis of the predicted genes encoding phytases belonging to the HAP family and ßPP phytases and in silico characterization of these enzymes indicated divergence among the catalytic activities. Predicted fungal ßPP phytases exhibited higher molecular mass (around 77 kDa) probably due to the epidermal growth factor-like domain. Twelve sequences of phytases contained signal peptides, of which seven were classified as HAP and five as ßPP phytases, while ten sequences were predicted as phytases secreted by non-classical pathways. These fungi were grown in liquid or semi-solid medium, and the fungal enzymatic extracts were evaluated for their ability to hydrolyze sodium phytate at 50 °C and pH ranging from 2.0 to 9.0. Seven fungi were identified as phytase producers based on phosphate release under enzyme assay conditions. Results obtained from in silico analyses combining experimental enzymatic activities suggest that some selected fungi could secrete ßPP phytases and HAP phytases.

Diversity of mycorrhizal Tulasnella associated with epiphytic and rupicolous orchids from the Brazilian Atlantic Forest, including four new species.

The genus Tulasnella often forms mycorrhizas with orchids and has worldwide distribution. Species of this genus are associated with a wide range of orchids, including endangered hosts. Initially, species identification relied mostly on morphological features and few cultures were preserved for later phylogenetic comparisons. In this study, a total of 50 Tulasnella isolates were collected from their natural sites in Minas Gerais, Brazil, cultured, and subjected to a phylogenetic analysis based on alignments of sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal DNA. Our results, based on phylogeny, integrated with nucleotide divergence and morphology, revealed the diversity of isolated Tulasnella species, which included four new species, namely, Tulasnella brigadeiroensis, Tulasnella hadrolaeliae, Tulasnella orchidis and Tulasnella zygopetali. The conservation of these species is important due to their association with endangered orchid hosts and endemic features in the Brazilian Atlantic Forest.

Agroecological coffee management increases arbuscular mycorrhizal fungi diversity.

Agroecology aims to maintain ecosystem services by minimizing the impact of agriculture and promoting the use of biological potential. Arbuscular mycorrhizal fungi (AMF) are elements which are key to improving crop productivity and soil quality. It is pertinent to understand how agricultural management in the tropics affects the AMF spatio-temporal community composition, especially in crops of global importance, such as coffee (Coffea arabica L.). Soil and root samples were collected from three localities under three management systems (agroecological, conventional and forest fragment), during the phenological stages of coffee (flowering, grain filling, harvesting). Spores were extracted for morphological identification and molecular community analysis by PCR-DGGE. Dendrograms were prepared and the bands were sequenced and analyzed by bioinformatics. No differences were observed in the richness of morphospecies between management systems, localities and period, but little is known about tropical species. Molecular analysis showed that the agroecological management system was similar to natural forest and with a higher diversity indices than conventional management. Locality and period of sample affect AMF community composition. It is necessary to associate classical taxonomic evaluations with molecular biological techniques because different approaches can lead to different outcomes. This study contributes to the understanding of the impact of agriculture management systems on AMF and provides evidence that agroecology is a management system applicable to sustainable coffee production.

Multi-enzyme complex of white rot fungi in saccharification of lignocellulosic material

ABSTRACT The multi-enzyme complex (crude extract) of white rot fungi Pleurotus ostreatus, Pleurotus eryngii, Trametes versicolor, Pycnosporus sanguineus and Phanerochaete chrysosporium were characterized, evaluated in the hydrolysis of pretreated pulps of sorghum straw and compared efficiency with commercial enzyme. Most fungi complexes had better hydrolysis rates compared with purified commercial enzyme.

Food Value and Safety Status of Raw (Unfermented) and Fermented Higher Basidiomycetes, Lenzites quercina (L) P. Karsten.

Food value and safety of a wild macrofungus, Lenzites quercina were investigated. The proximate and mineral composition of raw and fermented L. quercina were assessed using standard methods. Brine shrimp lethality bioassay was adopted for assessment of the toxicological property of the extracts obtained from raw and fermented L. quercina. The result of proximate composition revealed higher protein content (26.15%) in fermented L. quercina, while the value of carbohydrate (38.3%), crude fibre (27.6%), and ash contents (6.5%) were higher (P<0.05) in raw L. quercina when compared to fermented L. quercina. The macro and micro elements in the raw and fermented L. quercina were in decreasing order of Ca> K> Zn> Fe> Na> Mg> Pb> Cu with values ranging from 4.04 mg/g to 721.6 mg/g. The amino acids in raw and fermented L. quercina ranged from 0.05 mg/g to 23.78 mg/g, while the fatty acids ranged from 0.11% to 38.5%. The mortality rate of the Artemia salina against the extracts was from 8.0% to 38.0% with lethal dose at 50% of population within 49.11 and 250.50 µg/mL. The results from this study revealed that L. quercina possesses essential amino acids, fatty acids, and substantial micro elements, which may be useful in the formulation of functional foods and nutraceuticals.

Multi-enzyme complex of white rot fungi in saccharification of lignocellulosic material.

The multi-enzyme complex (crude extract) of white rot fungi Pleurotus ostreatus, Pleurotus eryngii, Trametes versicolor, Pycnosporus sanguineus and Phanerochaete chrysosporium were characterized, evaluated in the hydrolysis of pretreated pulps of sorghum straw and compared efficiency with commercial enzyme. Most fungi complexes had better hydrolysis rates compared with purified commercial enzyme.

Enzymatic extract containing lignin peroxidase immobilized on carbon nanotubes: Potential biocatalyst in dye decolourization.

The majority of the textile dyes are harmful to the environment and potentially carcinogenic. Among strategies for their exclusion, the treatment of dye contaminated wastewater with fungal extract, containing lignin peroxidase (LiP), may be useful. Two fungi isolates, Pleurotus ostreatus (PLO9) and Ganoderma lucidum (GRM117), produced the enzymatic extract by fermentation in the lignocellulosic residue, Jatropha curcas seed cake. The extracts from PLO9 and GRM117 were immobilized on carbon nanotubes and showed an increase of 18 and 27-fold of LiP specific activity compared to the free enzyme. Also, LiP from both fungi extracts showed higher Vmax and lower Km values. Only the immobilized extracts could be efficiently reused in the dye decolourization, contrary, the carbon nanotubes became saturated and they should be discarded over time. This device may offer a final biocatalyst with higher catalytic efficiency and capability to be reused in the dye decolourization process.

Minimum cocktail of cellulolytic multi-enzyme complexes obtained from white rot fungi via solid-state fermentation.

The objective of this work was to optimize the total cellulase activity of the crude extract cocktails from five white rot fungi produced by solid-state fermentation, by means of the central composite design. The white rot fungi Pleurotus ostreatus PLO 06, Pleurotus eryngii PLE 04, Trametes versicolor TRAM 01, Pycnosporus sanguineus PYC 02 and Phanerochaete chrysosporium PC were tested. For optimization process aiming at the maximum value of total cellulase activity (FPAse), the multi-enzyme cellulase complexes (crude extracts) of each fungus were mixed simultaneously in different proportions. There was increase in FPAse activity for the cocktails formed by the extracts of the five fungi together, compared to the extracts of each fungus alone. The model presented the minimum cocktail of enzymes for maximum total cellulase activity, with 100.00 µL PYC; 100.00 µL PC; 100.00 µL PLO06; 100.00 µL PLE04 and 200 µL TRAM01. The maximum value found was of 304.86 U/L. The result of the cocktails was very relevant, showing that there is an enzymatic complementation in the extracts that should be further studied. Concentrated extract cocktails should also be evaluated for biomass saccharification.

Degradation of Green Polyethylene by Pleurotus ostreatus.

We studied the biodegradation of green polyethylene (GP) by Pleurotus ostreatus. The GP was developed from renewable raw materials to help to reduce the emissions of greenhouse gases. However, little information regarding the biodegradation of GP discarded in the environment is available. P. ostreatus is a lignocellulolytic fungus that has been used in bioremediation processes for agroindustrial residues, pollutants, and recalcitrant compounds. Recently, we showed the potential of this fungus to degrade oxo-biodegradable polyethylene. GP plastic bags were exposed to sunlight for up to 120 days to induce the initial photodegradation of the polymers. After this period, no cracks, pits, or new functional groups in the structure of GP were observed. Fragments of these bags were used as the substrate for the growth of P. ostreatus. After 30 d of incubation, physical and chemical alterations in the structure of GP were observed. We conclude that the exposure of GP to sunlight and its subsequent incubation in the presence of P. ostreatus can decrease the half-life of GP and facilitate the mineralization of these polymers.