Uninvited Guests: a Chronology of Petri Dish Contaminations

Petri dish contaminations are commonplace and personally witnessed by every microbiologist. The vast majority of such contaminations result in nothing more than annoyance following which the Petri dishes are discarded. However, a handful of incidents of contaminations have led to momentous outcomes, the most renowned of which being that perceived by Alexander Fleming on the basis of the immense number of lives saved by penicillin. Petri dish contaminations as reported upon in the literature fall broadly into two categories; those in which the contaminant caused antagonism toward the species being cultured, and those in which the contaminant was established to be a species novum. Accounts of both of these categories of contaminations are set out here.

Biocontrol yeasts: mechanisms and applications

Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.

Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System

Interactions among members of microbial consortia drive the complex dynamics in soil, gut, and biotechnology microbiomes. Proteomic analysis of defined co-cultures of well-characterized species provides valuable information about microbial interactions. We used a label-free approach to quantify the responses to co-culture of two model bacterial species relevant to soil and rhizosphere ecology, Bacillus atrophaeus and Pseudomonas putida. Experiments determined the ratio of species in co-culture that would result in the greatest number of high-confidence protein identifications for both species. The 281 and 256 proteins with significant shifts in abundance for B. atrophaeus and P. putida, respectively, indicated responses to co-culture in overall metabolism, cell motility, and response to antagonistic compounds. Proteins associated with a virulent phenotype during surface-associated growth were significantly more abundant for P. putida in co-culture. Co-culture on agar plates triggered a filamentous phenotype in P. putida and avoidance of P. putida by B. atrophaeus colonies, corroborating antagonistic interactions between these species. Additional experiments showing increased relative abundance of P. putida under conditions of iron or zinc limitation and increased relative abundance of B. atrophaeus under magnesium limitation were consistent with patterns of changes in abundance of metal-binding proteins during co-culture. These results provide details on the nature of interactions between two species with antagonistic capabilities. Significant challenges remaining for the development of proteomics as a tool in microbial ecology include accurate quantification of low-abundance peptides, especially from rare species present at low relative abundance in a consortium.

Segregation of Tetragenococcus halophilus and Zygosaccharomyces rouxii using W1/O/W2 double emulsion for use in mixed culture fermentation

Antagonism in mixed culture fermentation can result in undesirable metabolic activity and negatively affect the fermentation process. Water-oil-water (W₁/O/W₂) double emulsions (DE) could be utilized in fermentation for segregating multiple species and controlling their release and activity. Zygosaccharomyces rouxii and Tetragenococcus halophilus, two predominant microbial species in soy sauce fermentation, were incorporated in the internal W₁ and external W₂ phase of a W₁/O/W₂, respectively. The suitability of DE for controlling T. halophilus and Z. rouxii in soy sauce fermentation was studied in relation to emulsion stability and microbial release profile. The effects of varying concentrations of Z. rouxii cells (5 and 7logCFU/mL) and glucose (0%, 6%, 12%, 30% w/v) in the W₂ phase were investigated. DE stability was determined by monitoring encapsulation stability (%), oil globule size, and microstructure with fluorescence and optical microscopy. Furthermore, the effect of DE on the interaction between T. halophilus and Z. rouxii was studied in Tryptic Soy Broth containing 10% w/v NaCl and 12% w/v glucose and physicochemical changes (glucose, ethanol, lactic acid, and acetic acid) were monitored. DE destabilization resulted in cell release which was proportional to the glucose concentration in W₂. Encapsulated Z. rouxii presented higher survival during storage (~3 log). The application of DE affected microbial cells growth and physiology, which led to the elimination of antagonism. These results demonstrate the potential use of DE as a delivery system of mixed starter cultures in food fermentation, where multiple species are required to act sequentially in a controlled manner.

Construction of PAH-degrading mixed microbial consortia by induced selection in soil

Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source. In addition, we used two engineered PAH-degrading fungal strains producing heterologous ligninolytic enzymes. After a previous selection using microbial antagonism tests, the selection was performed in microcosm systems and monitored using PCR-DGGE, CO₂ evolution and PAH quantitation. The resulting consortia (i.e., C1 and C2) were able to degrade up to 92% of Phe, 64% of Pyr and 65% of BaP out of 1000 mg kg^-1 of a mixture of Phe, Pyr and BaP (1:1:1) after a two-week incubation. The results indicate that constructed microbial consortia have high potential for soil bioremediation by bioaugmentation and biostimulation and may be effective for the treatment of sites polluted with PAHs due to their elevated tolerance to aromatic compounds, their capacity to utilize them as energy source.

Role of allelochemicals in plant growth promoting rhizobacteria for biocontrol of phytopathogens

Soil borne fungal diseases pose serious constraints on agro-productivity. Biological control is non-hazardous strategy to control plant pathogens and improve crop productivity. PGPR (plant growth promoting rhizobacteria) have long been used as plant disease control agents. PGPR produced a wide range of secondary compounds that may act as signals--that is, allelochemicals that include metabolites, siderophores, antibiotics, volatile metabolites, enzymes and others. Their mode of action and molecular mechanisms provide a great awareness for their application for crop disease management. The present review highlights the role of PGPR strains, specifically referring to allelochemicals produced and molecular mechanisms. Further research to fine tune combinations of allelochemicals, plant-microbe-pathogen interaction will ultimately lead to better disease control.