Changes in chemical properties and microbial communities' composition of a forest litter-based biofertilizer produced through aerated solid-state culture under different oxygen conditions

Fermented forest litter (FFL) is a bioproduct used as biofertilizer for several decades in Eastern Asia and Latin America. It is locally handcrafted by farmers in anaerobic conditions by fermenting forest litter added with agricultural by-products such as whey, cereal bran, and molasses. The aim of this study was to characterize the FFL process and product through gas and liquid chromatography analyses. It also provides some highlights on the influence of O2 on this solid-state culture. Under anoxic condition, a maximum CO2 production rate (CDPR) of 0.41 mL/h∙g dry matter (dm) was reached after 8 days. The main volatile organic compounds (VOCs) were ethanol and ethyl acetate, with a production rate profile similar to CDPR. After 21 days of culture, no residual sucrose nor lactose was detected. Lactic and acetic acids reached 58.8 mg/g dm and 10.2 mg/g dm, respectively, ensuring the acidification of the matrix to a final pH of 4.72. A metabarcoding analysis revealed that heterolactic acid bacteria (Lentilactobacillus, Leuconostoc), homolactic acid bacteria (Lactococcus), and yeasts (Saccharomyces, Clavispora) were predominant. Predicted genes in the microbiome confirmed the potential link between detected bacteria and acids and VOCs produced. When O2 was fed to the cultures, final pH reached values up to 8.5. No significant amounts of lactic nor acetic acid were found. In addition, a strong shift in microbial communities was observed, with a predominance of Proteobacteria and molds, among which are potential pathogens like Fusarium species. This suggests that particular care must be brought to maintain anoxic conditions throughout the process.

Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil

Thermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.

Uncovering new indicators to predict stability, maturity and biodiversity of compost on an industrial scale

Currently, the metagenomic study of the composting process has gained great importance since it has allowed the identification of the existence of microorganisms that, until now, had not been isolated during the process by traditional techniques. However, it is still complex to determine which bioindicators could reveal the degree of maturity and stability of a particular compost. Thereby, the main objective of this work was to demonstrate the possible correlation between traditional parameters of maturity and stability of compost, with other indicators of biodiversity in products highly heterogeneous from composting processes on an industrial scale. The results demonstrated the enormous influence of the raw materials in characterizing the products obtained. Even so, important relationships were established between the Chao1 and Shannon indexes, and certain parameters related to the maturity, stability and toxicity of the samples, such as nitrification index, humification rate, phenolic content, germination index or oxygen consumption.

Profiling of the viable bacterial and fungal microbiota in fermented feeds using single-molecule real-time sequencing

Fermented concentrated feed has been widely recognized as an ideal feed in the animal industry. In this study, we used a powerful method, coupling propidium monoazide (PMA) pretreatment with single-molecule real-time (SMRT) sequencing technology to compare the bacterial and fungal composition of feeds before and after fermentation with four added lactic acid bacteria (LAB) inoculants (one Lactobacillus casei strain and three L. plantarum strains). Five feed samples consisting of corn, soybean meal, and wheat bran were fermented with LAB additives for 3 d. Following anaerobic fermentation, the pH rapidly decreased, and the mean numbers of LAB increased from 106 to 109 colony-forming units (cfu)/g fresh matter. SMRT sequencing results showed that the abundance and diversity of bacteria and fungi in the feed were significantly higher before fermentation than after fermentation. Fifteen bacterial species and eight fungal genera were significantly altered following fermentation, and L. plantarum was the dominant species (relative abundance 88.94%) in the post-fermentation group. PMA treatment revealed that the bacteria Bacillus cereus, B. circulans, Alkaliphilus oremlandii, Cronobacter sakazakii, Paenibacillus barcinonensis, and P. amylolyticus (relative abundance >1%) were viable in the raw feed. After fermentation, their relative abundances decreased sharply to <0.2%; however, viable L. plantarum was still the dominant species post fermentation. We inferred that our LAB additives grew rapidly and inhibited harmful microorganisms and further improved feed quality. In addition, coupling PMA treatment with the Pacific Biosciences SMRT sequencing technology was a powerful tool for providing accurate live microbiota profiling data in this study.

Enhancement effect of earthworm (Eisenia fetida) on acetochlor biodegradation in soil and possible mechanisms

Acetochlor is a widely used chloroacetanilide herbicide and has posed environmental risks in soil and water due to its toxicity and high leaching capacity. Earthworm represents the dominant invertebrate in soil and can promote the decomposition of organic pollutants. The effect of earthworm on acetochlor degradation in soil was studied by soil column experiment with or without acetochlor and earthworm in sterile and natural soils. The degradation capacities of drilosphere components to acetochlor were investigated by microcosm experiments. Bacterial and fungal acetochlor degraders stimulated by earthworm were identified by high-throughput sequencing. The degradation kinetics of acetochlor suggested that both indigenous microorganisms and earthworm played important roles in acetochlor degradation. Acetochlor degradation was quicker in soil with earthworms than without earthworms, with the degradation rates increased by 62.3 ± 15.2% and 9.7 ± 1.7% in sterile and natural treatments respectively. The result was related to the neutralized pH, higher enzyme activities and enhanced soil microbial community diversity and richness in the presence of earthworms. Earthworm cast was the degradation hotpot in drilosphere and exhibited better anaerobic degradation capacity in microcosm experiments. The acetochlor degradation rate of cast in anaerobic environment was 12.0 ± 0.1% quicker than that in aerobic environment. Residual acetochlor in soil conferred a long-term impairment on fungal community, and this inhibition could be repaired by earthworm. Earthworm stimulated indigenous degraders like Sphingomonas and Microascales and carried suspected intestinal degraders like Mortierella and Escherichia_coli to degradation process. Cometabolism between nutrition cycle species and degraders in casts also contributed to its faster degradation rates. The study also presented some possible anaerobic degradation species like Rhodococcus, Pseudomonas_fulva and Methylobacillus.

Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues

The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure.

DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing

DNA metabarcoding is increasingly being used to characterize the microbiological composition of both the indoor and outdoor environments of dwellings. Our study aimed to evaluate metabarcoding and bioinformatic analysis resulting from calibrated samples and samples collected by an electrostatic dust collector (EDC) in dwellings with no moisture problems. Thus, the fungal communities of 14 dwellings (eastern France, Franche-Comté region) were analyzed by Illumina MiSeq technology after amplification of the ITS2 region. Using the standard samples of 11 species of yeasts and molds allowed us to validate the Operational taxonomic units (OTU) assignment. These calibrated samples also showed a low amplification bias, a low rate of sequencing errors and the semi-quantitative nature of the technique. Only one species from the calibrated samples (Lichtheimia corymbifera) was less amplified probably due to the presence of two mismatches in its3 primer. EDC analysis identified 3594OTU with 75% of reads corresponding to 30 genera. The main genera are those usually found by culture techniques (Penicillium, Aspergillus and Cladosporium), but findings also indicate others less commonly isolated in culture such as Epicoccum, the fourth detected genus in our study. The type of heating systems was correlated with fungal diversity. We found less diversity in the dwellings with wood heating and larger quantities of Epicoccum nigrum verified by qPCR. DNA metabarcoding analysis applied to EDC seems promising. However, we think that it must be used along with qPCR, to obtain a more global view of microbial ecology and relative quantification of species of interest within communities.

The fungal composition of natural biofinishes on oil-treated wood

BACKGROUND

Biofinished wood is considered to be a decorative and protective material for outdoor constructions, showing advantages compared to traditional treated wood in terms of sustainability and self-repair. Natural dark wood staining fungi are essential to biofinish formation on wood. Although all sorts of outdoor situated timber are subjected to fungal staining, the homogenous dark staining called biofinish has only been detected on specific vegetable oil-treated substrates. Revealing the fungal composition of various natural biofinishes on wood is a first step to understand and control biofinish formation for industrial application.

RESULTS

A culture-based survey of fungi in natural biofinishes on oil-treated wood samples showed the common wood stain fungus Aureobasidium and the recently described genus Superstratomyces to be predominant constituents. A culture-independent approach, based on amplification of the internal transcribed spacer regions, cloning and Sanger sequencing, resulted in clone libraries of two types of biofinishes. Aureobasidium was present in both biofinish types, but was only predominant in biofinishes on pine sapwood treated with raw linseed oil. Most cloned sequences of the other biofinish type (pine sapwood treated with olive oil) could not be identified. In addition, a more in-depth overview of the fungal composition of biofinishes was obtained with Illumina amplicon sequencing that targeted the internal transcribed spacer region 1. All investigated samples, that varied in wood species, (oil) treatments and exposure times, contained Aureobasidium and this genus was predominant in the biofinishes on pine sapwood treated with raw linseed oil. Lapidomyces was the predominant genus in most of the other biofinishes and present in all other samples. Surprisingly, Superstratomyces, which was predominantly detected by the cultivation-based approach, could not be found with the Illumina sequencing approach, while Lapidomyces was not detected in the culture-based approach.

CONCLUSIONS

Overall, the culture-based approach and two culture-independent methods that were used in this study revealed that natural biofinishes were composed of multiple fungal genera always containing the common wood staining mould Aureobasidium. Besides Aureobasidium, the use of other fungal genera for the production of biofinished wood has to be considered.

Fungal communities in pressmud composting harbour beneficial and detrimental fungi for human welfare

Pressmud is a substrate derived from sugarcane juice filtrate, and around 26-40  kg of this residue are produced per ton of sugarcane. It is mainly used as fertilizer in crops, and its application in the field is often made without any prior treatment, but, in this research, it was studied for the risk this practice poses for human health. This research was stimulated by previous results indicating the presence of opportunistic pathogens in residues used in various composting systems and the extensive use of fresh pressmud in agriculture. Here, It was assessed the fungal diversity present in both fresh and composting pressmud using 454 pyrosequencing. In addition, heat-tolerant fungi were isolated and surveyed for their enzymatic repertoire of biomass-degrading enzymes (cellulase, xylanase, laccase and polygalacturonase). A wide range of opportunistic pathogens was found among the most abundant taxa in the fresh pressmud, such as Lomentospora prolificans (43.13 %), Trichosporon sp. (10.07 %), Candida tropicalis (7.91 %), and Hormographiella aspergillata (8.19 %). This indicates that fresh pressmud might be a putative source of human pathogenic fungi, presenting a potential threat to human health if applied as fertilizer without any treatment. With regard to the heat-tolerant fungi found in this substrate, all the 110 isolates screened were able to produce at least one of the tested enzymes. The pressmud composting process not only effectively reduces the load of pathogenic fungi, but also creates an interesting environment for fungi able to produce thermostable hydrolytic and oxidative enzymes with biotechnological applications.