Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure

LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems

The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.

Agro waste as a potential carbon feedstock for poly-3-hydroxy alkanoates production: Commercialization potential and technical hurdles

The enormous production and widespread applications of non -biodegradable plastics lead to their accumulation and toxicity to animals and humans. The issue can be addressed by the development of eco-friendly strategies for the production of biopolymers by utilization of waste residues like agro residues. This will address two societal issues - waste management and the development of an eco-friendly biopolymer, poly-3-hydroxy alkanoates (PHAs). Strategies adopted for utilization of agro-residues, challenges and future perspectives are discussed in detail in this comprehensive review. The possibility of PHA properties improvements can be increased by preparation of blends.

Biotreatment Potential and Microbial Communities in Aerobic Bioreactor Systems Treating Agro-Industrial Wastewaters

The thriving agro-industry sector accounts for an essential part of the global gross domestic product, as the need for food and feed production is rising. However, the industrial processing of agricultural products requires the use of water at all stages, which consequently leads to the production of vast amounts of effluents with diverse characteristics, which contain a significantly elevated organic content. This fact reinforces the need for action to control and minimize the environmental impact of the produced wastewater, and activated sludge systems constitute a highly reliable solution for its treatment. The current review offers novel insights on the efficiency of aerobic biosystems in the treatment of agro-industrial wastewaters and their ecology, with an additional focus on the biotechnological potential of the activated sludge of such wastewater treatment plants.

Thauera aminoaromatica MZ1T Identified as a Polyhydroxyalkanoate-Producing Bacterium within a Mixed Microbial Consortium

Polyhydroxyalkanoates (PHAs) form a highly promising class of bioplastics for the transition from fossil fuel-based plastics to bio-renewable and biodegradable plastics. Mixed microbial consortia (MMC) are known to be able to produce PHAs from organic waste streams. Knowledge of key-microbes and their characteristics in PHA-producing consortia is necessary for further process optimization and direction towards synthesis of specific types of PHAs. In this study, a PHA-producing mixed microbial consortium (MMC) from an industrial pilot plant was characterized and further enriched on acetate in a laboratory-scale selector with a working volume of 5 L, and 16S-rDNA microbiological population analysis of both the industrial pilot plant and the 5 L selector revealed that the most dominant species within the population is Thauera aminoaromatica MZ1T, a Gram-negative beta-proteobacterium belonging to the order of the Rhodocyclales. The relative abundance of this Thauera species increased from 24 to 40% after two months of enrichment in the selector-system, indicating a competitive advantage, possibly due to the storage of a reserve material such as PHA. First experiments with T. aminoaromatica MZ1T showed multiple intracellular granules when grown in pure culture on a growth medium with a C:N ratio of 10:1 and acetate as a carbon source. Nuclear magnetic resonance (NMR) analyses upon extraction of PHA from the pure culture confirmed polyhydroxybutyrate production by T. aminoaromatica MZ1T.

Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense)

Naranjilla ("little orange"), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).

Overall process of using a valerate-dominant sludge hydrolysate to produce high-quality polyhydroxyalkanoates (PHA) in a mixed culture

The overall process of polyhydroxyalkanoates (PHA) production in a mixed culture fed by thermophilic fermented valerate-dominant sludge hydrolysate with high-level soluble organics (proteins and carbohydrates) and nutrients (nitrogen and phosphorus) was investigated in this study. The valerate-dominant hydrolysate was fed to enrich a PHA culture with an increasing concentration, and the enriched culture displayed a strong PHA-producing capacity under feast-famine conditions. Valerate in the feedstock was preferentially utilized over acetate and butyrate, and its uptake correlated with the production of 3-hydroxyvalerate (3HV) and 3-hydroxy-2-methylvalerate (3H2MV). The maximum PHA content (42.31%) was highest to date in a mixed culture with complex feedstock, and the PHA consisted of 3-hydroxybutyrate (3HB), 3HV, 3H2MV at 68.4, 23.7, 7.9 mmol C%. PHA production was inhibited when the nutrients exceeded a certain limit. Microbial analysis revealed that valerate-dominant feedstock caused Delftia (53%) to become the prevailing group over other PHA-producing bacteria. For long-term operation, 75% of the biomass at the end of feast phase was collected for PHA recovery, and the entire process exhibited a potential to produce 5 g PHA from 1 kg sludge. These findings indicate that the complex valerate-dominant sludge hydrolysate can be used to stably produce PHA containing high 3HV and 3H2MV.