Biomass-derived molecules modulate the behavior of Streptomyces coelicolor for antibiotic production

Insights into Streptomyces coelicolor A3(2) growth and pigment formation with high-throughput online monitoring

Streptomyces species are intensively studied for their ability to produce a variety of natural products. However, conditions influencing and leading to product formation are often not completely recognized. Therefore, in this study, high-throughput online monitoring is presented as a powerful tool to gain in-depth understanding of the cultivation of the model organism Streptomyces coelicolor A3(2). Through online measurements of oxygen transfer rate and autofluorescence, valuable information about availability of nutrients and product formation patterns of the pigments actinorhodin and undecylprodigiosin can be obtained and explained. Therefore, it is possible to determine the onset of pigmentation and to study in detail the influencing factors thereof. One factor identified in this study is the filling volume of the cultivation vessel. Slight variations led to varying pigmentation levels. By combining optical and metabolic online monitoring techniques, the correlation of the filling volume with pigmentation could be explained as a result of different growth trajectories caused by varying specific power inputs and their influence on the pellet formation of the filamentous system. Finally, experiments with the addition of supernatant from unpigmented and pigmented cultures could highlight the applicability of the presented approach to study quorum sensing and cell-cell interaction.

SCO6992, a Protein with β-Glucuronidase Activity, Complements a Mutation at the absR Locus and Promotes Antibiotic Biosynthesis in Streptomyces coelicolor

Streptomyces coelicolor is a filamentous soil bacterium producing several kinds of antibiotics. S. coelicolor abs8752 is an abs (antibiotic synthesis deficient)-type mutation at the absR locus; it is characterized by an incapacity to produce any of the four antibiotics synthesized by its parental strain J1501. A chromosomal DNA fragment from S. coelicolor J1501, capable of complementing the abs^- phenotype of the abs8752 mutant, was cloned and analyzed. DNA sequencing revealed that two complete ORFs (SCO6992 and SCO6993) were present in opposite directions in the clone. Introduction of SCO6992 in the mutant strain resulted in a remarkable increase in the production of two pigmented antibiotics, actinorhodin and undecylprodigiosin, in S. coelicolor J1501 and abs8752. However, introduction of SCO6993 did not show any significant difference compared to the control, suggesting that SCO6992 is primarily involved in stimulating the biosynthesis of antibiotics in S. coelicolor. In silico analysis of SCO6992 (359 aa, 39.5 kDa) revealed that sequences homologous to SCO6992 were all annotated as hypothetical proteins. Although a metalloprotease domain with a conserved metal-binding motif was found in SCO6992, the recombinant rSCO6992 did not show any protease activity. Instead, it showed very strong β-glucuronidase activity in an API ZYM assay and toward two artificial substrates, p-nitrophenyl-β-D-glucuronide and AS-BI-β-D-glucuronide. The binding between rSCO6992 and Zn²⁺ was confirmed by circular dichroism spectroscopy. We report for the first time that SCO6992 is a novel protein with β-glucuronidase activity, that has a distinct primary structure and physiological role from those of previously reported β-glucuronidases.

The Evolution and Ecology of Bacterial Warfare

Bacteria have evolved a wide range of mechanisms to harm and kill their competitors, including chemical, mechanical and biological weapons. Here we review the incredible diversity of bacterial weapon systems, which comprise antibiotics, toxic proteins, mechanical weapons that stab and pierce, viruses, and more. The evolution of bacterial weapons is shaped by many factors, including cell density and nutrient abundance, and how strains are arranged in space. Bacteria also employ a diverse range of combat behaviours, including pre-emptive attacks, suicidal attacks, and reciprocation (tit-for-tat). However, why bacteria carry so many weapons, and why they are so often used, remains poorly understood. By comparison with animals, we argue that the way that bacteria live - often in dense and genetically diverse communities - is likely to be key to their aggression as it encourages them to dig in and fight alongside their clonemates. The intensity of bacterial aggression is such that it can strongly affect communities, via complex coevolutionary and eco-evolutionary dynamics, which influence species over space and time. Bacterial warfare is a fascinating topic for ecology and evolution, as well as one of increasing relevance. Understanding how bacteria win wars is important for the goal of manipulating the human microbiome and other important microbial systems.

Recent developments in pretreatment technologies on lignocellulosic biomass: Effect of key parameters, technological improvements, and challenges

Lignocellulosic biomass is an inexpensive renewable source that can be used to produce biofuels and bioproducts. The recalcitrance nature of biomass hampers polysaccharide accessibility for enzymes and microbes. Several pretreatment methods have been developed for the conversion of lignocellulosic biomass into value-added products. However, these pretreatment methods also produce a wide range of secondary compounds, which are inhibitory to enzymes and microorganisms. The selection of an effective and efficient pretreatment method discussed in the review and its process optimization can significantly reduce the production of inhibitory compounds and may lead to enhanced production of fermentable sugars and biochemicals. Moreover, evolutionary and genetic engineering approaches are being used for the improvement of microbial tolerance towards inhibitors. Advancements in pretreatment and detoxification technologies may help to increase the productivity of lignocellulose-based biorefinery. In this review, we discuss the recent advancements in lignocellulosic biomass pretreatment technologies and strategies for the removal of inhibitors.

Bioengineering of anaerobic digestion for volatile fatty acids, hydrogen or methane production: A critical review

Anaerobic digestion (AD) is a well-established technology used for producing biogas or biomethane alongside the slurry used as biofertilizer. However, using a variety of wastes and residuals as substrate and mixed cultures in the bioreactor makes AD as one of the most complicated biochemical processes employing hydrolytic, acidogenic, hydrogen-producing, acetate-forming bacteria as well as acetoclastic and hydrogenoclastic methanogens. Hydrogen and volatile fatty acids (VFAs) including acetic, propionic, isobutyric, butyric, isovaleric, valeric and caproic acid and other carboxylic acids such as succinic and lactic acids are formed as intermediate products. As these acids are important precursors for various industries as mixed or purified chemicals, the AD process can be bioengineered to produce VFAs alongside hydrogen and therefore biogas plants can become biorefineries. The current review paper provides the theory and means to produce and accumulate VFAs and hydrogen, inhibit their conversion to methane and to extract them as the final products. The effects of pretreatment, pH, temperature, hydraulic retention time (HRT), organic loading rate (OLR), chemical methane inhibitions, and heat shocking of the inoculum on VFAs accumulation, hydrogen production, VFAs composition, and the microbial community were discussed. Furthermore, this paper highlights the possible techniques for recovery of VFAs from the fermentation media in order to minimize product inhibition as well as to supply the carboxylates for downstream procedures.

Bioconversion of barley straw lignin into biodiesel using Rhodococcus sp. YHY01

Rhodococcus sp. YHY01 was studied to utilize various lignin derived aromatic compounds. It was able to utilize p-coumaric acid, cresol, and 2,6 dimethoxyphenol and resulted in biomass production i.e. 0.38 g dcw/L, 0.25 g dcw/L and 0.1 g dcw/L, and lipid accumulation i.e. 49%, 40%, 30%, respectively. The half maximal inhibitory concentration (IC₅₀) value for p-coumaric acid (13.4 mM), cresol (7.9 mM), and 2,6 dimethoxyphenol (3.4 mM) was analyzed. Dimethyl sulfoxide (DMSO) solubilized barley straw lignin fraction was used as a carbon source for Rhodococcus sp. YHY01 and resulted in 0.130 g dcw/L with 39% w/w lipid accumulation. Major fatty acids were palmitic acid (C16:0) 51.87%, palmitoleic acid (C16:l) 14.90%, and oleic acid (C18:1) 13.76%, respectively. Properties of biodiesel produced from barley straw lignin were as iodine value (IV) 27.25, cetane number (CN) 65.57, cold filter plugging point (CFPP) 14.36, viscosity (υ) 3.81, and density (ρ) 0.86.

Biotechnological potential of microbial consortia and future perspectives

Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.

Microbial biodiesel production from oil palm biomass hydrolysate using marine Rhodococcus sp. YHY01

The effect of various biomass derived inhibitors (i.e. furfural, hydroxymethylfurfural (HMF), vanillin, 4-hydroxy benzaldehyde (4-HB) and acetate) was investigated for fatty acid accumulation in Rhodococcus sp. YHY 01. Rhodococcus sp. YHY01 was able to utilize acetate, vanillin, and 4-HB for biomass production and fatty acid accumulation. The IC₅₀ value for furfural (3.1mM), HMF (3.2mM), vanillin (2.0mM), 4-HB (2.7mM) and acetate (3.7mM) was calculated. HMF and vanillin affect fatty acid composition and increase saturated fatty acid content. Rhodococcus sp. YHY 01 cultured with empty fruit bunch hydrolysate (EFBH) as the main carbon source resulted in enhanced biomass (20%) and fatty acid productivity (37%), in compression to glucose as a carbon source. Overall, this study showed the beneficial effects of inhibitory molecules on growth and fatty acid production, and support the idea of biomass hydrolysate utilization for biodiesel production by avoiding complex efforts to remove inhibitory compounds.