Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent

Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization. Supplementary InformationThe online version contains supplementary material available at 10.1007/s12088-021-00935-5.     

Valorization of solid olive mill wastes by cultivation of a local strain of edible mushrooms

Olive oil industry generates huge quantities of solid olive mill wastes (SOMW), causing environmental damage. Cultivation of edible mushrooms, such as Pleurotus ostreatus is a valuable approach for SOMW valorization. A local strain mycelium (Tizi-Ouzou, Algeria) of P. ostreatus (LPO) was isolated from castor oil plants. Oyster mushroom spawn, produced on barley grains, was used to inoculate wet SOMW, steamed in a traditional steamer during 45 min. The mycelium growth rate on SOMW was first estimated in Petri dish by measuring the surface colonized by the mycelium. The fruit body yields were estimated on culture bags containing 2 kg each of SOMW inoculated at 7% (w/w). The local strain potential was compared with that of a commercial one. Both strains produced high-quality mushrooms, but with low yields. The supplementation of the SOMW with wheat straw at the rate of 10% and 2% of CaCO₃ had significantly enhanced the productivity of the two strains, multiplying it by 3.2 for LPO and by 2.6 for CPO.     

Metabolic engineering for valorization of macroalgae biomass

Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.     

Olive-derived biomass as a renewable source of value-added products

Olive oil is a characteristic product of Mediterranean countries, and its production is rapidly expanding to many other regions due to the health benefits attributed to the consumption of high-quality olive oil. Taking into account that the oil content is, on average, only 20% by weight of olives, a great amount of biomass, including leaves, pits, and pomace, is produced in the mill along with the main product. Moreover, the pruning of olive trees and the production of the olive pomace also generates a great amount of biomass. Currently, the usual practices for disposal of these different biomasses do not take advantage of the wide range of products that can be produced from them. This work summarizes the most relevant practices considering both the bioprocesses studied for the exploitation of the olive-derived biomass and the potential products obtained. The integration of processes in a single facility, i.e., the concept of a biorefinery based on olive-derived biomass, is also reviewed, including technoeconomic and environmental assessment.     

Biotechnological valorization potential indicator for lignocellulosic materials

This report introduces the biotechnological valorization potential indicator (BVPI) concept, a metric to measure the degree of suitability of lignocellulosic materials to be used as feedstock in a biorefinery framework. This indicator groups the impact of the main factors influencing upgrade-ability, both the biological/chemical nature of the materials, and the economical, technological and geographical factors. The BVPI was applied to the identification of the most relevant opportunities and constraints pertaining to the lignocellulosic by-products from the Portuguese agro-industrial cluster. Several by-products were identified with a high valorization potential, e.g., rice husks, brewery's spent grain, tomato pomace, carob pulp, de-alcoholized grape bagasse, and extracted olive bagasse, that would greatly benefit from the further development of specific biotechnology processes, specifically concerning the upgrade of their hemicellulosic fraction.     

Valorization of date palm (Phoenix dactylifera) fruit processing by-products and wastes using bioprocess technology – Review

The date palm Phoenix dactylifera has played an important role in the day-to-day life of the people for the last 7000 years. Today worldwide production, utilization and industrialization of dates are continuously increasing since date fruits have earned great importance in human nutrition owing to their rich content of essential nutrients. Tons of date palm fruit wastes are discarded daily by the date processing industries leading to environmental problems. Wastes such as date pits represent an average of 10% of the date fruits. Thus, there is an urgent need to find suitable applications for this waste. In spite of several studies on date palm cultivation, their utilization and scope for utilizing date fruit in therapeutic applications, very few reviews are available and they are limited to the chemistry and pharmacology of the date fruits and phytochemical composition, nutritional significance and potential health benefits of date fruit consumption. In this context, in the present review the prospects of valorization of these date fruit processing by-products and wastes’ employing fermentation and enzyme processing technologies towards total utilization of this valuable commodity for the production of biofuels, biopolymers, biosurfactants, organic acids, antibiotics, industrial enzymes and other possible industrial chemicals are discussed.