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Conventionally, the commercial supply of chitin and chitosan relies on shellfish wastes as the extraction sources. However, the fungal sources constitute a valuable option, especially for biomedical and pharmaceutical applications, due to the batch-to-batch unsteady properties of chitin and chitosan from conventional ones. Fungal production of these glycans is not affected by seasonality enables accurate process control and, consequently, more uniform properties of the obtained product. Moreover, liquid and solid production media often are derived from wastes, thus enabling the application of circular economy criteria and improving the process economics. The present review deals with fungal chitosan production processes focusing on waste-oriented and integrated production processes. In doing so, contrary to other reviews that used a genus-specific approach for organizing the available information, the present one bases the discussion on the bioprocess typology. Finally, the main process parameters affecting chitosan production and their interactions are critically discussed.

Orange peel waste (OPW), the primary byproduct of the juice extraction process, is annually generated in massive amounts (21 Mton), and its aqueous extraction in biorefining operations yields a liquid fraction, referred to as orange peel extract (OPE). Although OPE contains significant amounts of easily assimilable carbohydrates, such as fructose, glucose, and sucrose, no investigations have been conducted yet to assess its possible use in biodiesel production by oleaginous yeasts. Consequently, the objective of the present study was to assess whether OPE might act as the basis of a liquid medium for microbial lipid production. A screening conducted with 18 strains of oleaginous yeasts in shaken flask on the OPE-based medium showed that Rhodosporidium toruloides NRRL 1091 and Cryptococcus laurentii UCD 68-201 gave the best results in terms of lipid production (5.8 and 4.5 g L−1, respectively) and accumulation (77 and 47% on a dry matter basis, respectively). The subsequent scale transfer of the process to a 3-L STR operated in batch mode halved the time required to reach the lipid peak with the ensuing increase in volumetric productivities in R. toruloides NRRL 1091 (3646 mg L−1 day−1) and C. laurentii UCD 68-201 (2970.7 mg L−1 day−1). The biodiesel yields from the lipids of the former and the latter strain were 36.9 and 31.9%, respectively. Based on multivariate analysis of fatty acid methyl ester compositions, the lipids from the former and the latter strain were highly resembling those of Jatropha and palm oils, two commonly used feedstocks for biodiesel manufacturing.

Bioaugmentation, defined as the strategic incorporation of specifically selected microbial biomass into contaminated environments, can significantly enhance the biodegradation of pollutants and is extensively employed in soil bioremediation efforts. A multistep screening process was applied to develop an autochthonous microbial consortium, including (i) hydrocarbonoclastic strain isolation from soil chronically contaminated with petroleum hydrocarbons, (ii) bacterial selection according to genomic and functional traits, and (iii) consortium validation in the native contaminated soil through microcosm experiments. The selection of strains with the ability to degrade alkanes and aromatic hydrocarbons on synthetic media was further supported by genomic analysis, delivering a consortium with complementary degradative properties. The outcomes of the microcosm experiments corroborated the efficacy of the selected indigenous consortium, demonstrating that the combination of Acinetobacter guillouiae, A. radioresistens, and Pseudomonas zarinae as an inoculum in the bioaugmentation strategy was successful in achieving the removal of up to 26% and 76% of linear and polycyclic aromatic hydrocarbons, respectively, thereby effectively addressing areas where natural attenuation was insufficient.

The valorisation of lignocellulosic residues into bio-based feedstocks is a key strategy for advancing circular bioeconomy models. In this study, chestnut wood residues, including virgin wood (VW) and detannized wood (DT) from the tannin industry, were evaluated as substrates for polyhydroxyalkanoate (PHA) production using Cupriavidus necator. Biomass was subjected to thermo-acid hydrolysis followed by ion-exchange detoxification, yielding hydrolysates rich in organic acids (levulinic, acetic, and formic acids) and residual inhibitory compounds. Both substrates supported microbial growth and PHA accumulation, although clear differences in performance were observed. The maximum biomass concentration reached 1.26 ± 0.01 g L−1 in VW hydrolysate and 0.40 ± 0.03 g L−1 in DT hydrolysate. PHA production was higher in VW hydrolysate, reaching 68.51 mg L−1 with 5.44% (w/w) accumulation, while DT hydrolysate yielded 0.21 mg L−1 with 6.01% (w/w). The reduced biomass formation in DT hydrolysate was associated with the greater persistence of inhibitory compounds generated during thermo-acid treatment. Although the obtained PHA yields are lower than those reported for optimized lignocellulosic systems, this study demonstrates for the first time the feasibility of producing PHA from chestnut wood residues, including industrial detannized byproducts, without nutrient supplementation. These findings highlight the potential of tannin-industry waste streams as alternative feedstocks for biopolymer production, while indicating that optimization of hydrolysis conditions, detoxification efficiency, and fermentation strategy is required to improve process performance.

This study investigated the feasibility of using both the solid and the liquid fractions of waste from the anaerobic digestion process—the digestate—as a possible liquid growth medium for fungal production of chitosan. An enriched liquid phase (ELP), combining both fractions, and derived from mild acid hydrolysis treatment at 120 °C with 6% H2SO4 (w/v) for 70 min, was screened for its ability to support biomass and chitosan production by 17 fungal strains. The best results were obtained with Absidia blakesleeana NRRL 2696 and Rhizopus oryzae NRRL 1510 cultures, which yielded chitosan volumetric productions of 444 and 324 mg L−1, respectively. The chitosan preparations of the former and the latter strain, characterized by infrared spectroscopy, elemental analysis, viscosimetry and thermogravimetric analysis, showed deacetylation degrees of 79% and 84.2%, respectively, and average viscosimetric molecular weights of around 20 and 5.4 kDa, respectively. Moreover, both fungal chitosan samples exerted significant antibacterial activity towards Gram-negative (i.e., Pseudomonas syringae and Escherichia coli) and Gram-positive (i.e., Bacillus subtilis) species.

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.

The genus Aspergillus encompasses several species with relevant lignocellulose-degrading capacity, and a novel species, denominated A. olivimuriae, was recently discovered after its isolation from table olive brine. The acquisition of insight into this species and the assessment of its potential relied on a bioinformatics approach, based on the CAZy database, associated with enzymatic activity profiles in solid-state cultures on four different types of waste, including residual thistle biomass (RTB), spent coffee grounds (SCG), digestate solid fraction and barley straw. The CAZy analysis of A. olivimuriae genome showed that the number of predicted genes for each family was close to that of other Aspergillus species, except for cellobiose dehydrogenase, acetyl xylan esterase and polygalacturonases. In A. olivimuriae solid-state cultures, hemicellulose degradation outperformed that of cellulose, and lignin removal did not occur, regardless of the growth substrate. This is in line with its CAZy content and the extent of hemicellulolytic, and ligninolytic activities detected in its solid-state cultures. RTB and barley straw were the substrates enabling the best glycosyl hydrolase production levels. The exception was SCG, the hemicellulose composition of which, mainly made of glucomannans and galactomanans, led to the highest β-mannanase and β-mannosidase production levels (3.72 ± 0.20 and 0.90 ± 0.04 IU g−1 substrate, respectively).

Antimicrobial peptides (AMPs) are short peptides active against a wide range of pathogens and, therefore, they are considered a useful alternative to conventional antibiotics. We have identified a new AMP in a transcriptome derived from the Antarctic fish Trematomus bernacchii. This peptide, named Trematocine, has been investigated for its expression both at the basal level and after in vivo immunization with an endemic Antarctic bacterium (Psychrobacter sp. TAD1). Results agree with the expected behavior of a fish innate immune component, therefore we decided to synthesize the putative mature sequence of Trematocine to determine the structure, the interaction with biological membranes, and the biological activity. We showed that Trematocine folds into a α-helical structure in the presence of both zwitterionic and anionic charged vesicles. We demonstrated that Trematocine has a highly specific interaction with anionic charged vesicles and that it can kill Gram-negative bacteria, possibly via a carpet like mechanism. Moreover, Trematocine showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values against selected Gram-positive and Gram-negative bacteria similar to other AMPs isolated from Antarctic fishes. The peptide is a possible candidate for a new drug as it does not show any haemolytic or cytotoxic activity against mammalian cells at the concentration needed to kill the tested bacteria.

A novel bacterium, strain BM90, previously isolated from Tyrrhenian Sea, was metabolically characterized testing its ability to use 95 different carbon sources by the Biolog system. The bacterium showed a broad capacity to use fatty-, organic- and amino-acids; on the contrary, its ability to use carbohydrates was extremely scarce. Strain BM90 was identified and affiliated to Delftia tsuruhatensis by molecular techniques based on 16S rRNA gene sequencing. D. tsuruhatensis BM90, cultivated in shaken cultures, was able to grow on various phenolic compounds and to remove them from its cultural broth. The phenols used, chosen for their presence in industrial or agro-industrial effluents, were grouped on the base of their chemical characteristics. These included benzoic acid derivatives, cinnamic acid derivatives, phenolic aldehyde derivatives, acetic acid derivatives and other phenolic compounds such as catechol and p -hydroxyphenylpropionic acid. When all the compounds (24) were gathered in the same medium (total concentration: 500 mg/l), BM90 caused the complete depletion of 18 phenols and the partial removal of two others. Only four phenolic compounds were not removed. Flow cytometry studies were carried out to understand the physiological state of BM90 cells in presence of the above phenols in various conditions. At the concentrations tested, a certain toxic effect was exerted only by the four compounds that were not metabolized by the bacterium.

The slightly thermophilic bacterium Tepidimonas taiwanensis strain VT154-175 has been isolated from a hot spring in the area of Viterbo, Italy. The whole draft genome of 2.9 Mb obtained by paired-end next-generation sequencing and divided into 60 scaffolds is presented.