Microbial succession in white button mushroom production systems from compost and casing to a marketable packed product

The aim of the study was to investigate microbial succession in the mushroom supply chain from compost, casing to fruit body formation and mushroom growth to the point of harvested, packing and point of sale. The microbial population dynamics of compost, casing and mushrooms were determined using a plate count technique, denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S and 18S rDNA. Plating revealed greater abundance of bacteria, fungi and yeasts in mushroom compost compared to casing and fresh mushroom samples. The viable count method also showed that bacteria and yeasts increased significantly after harvest and during cold storage. Sequencing revealed a more diverse culturable bacterial population in casing and on the mushrooms than in the compost. Phylogenetic analysis revealed a general trend of grouping of species from the same sources. In contrast, a higher microbial diversity was recorded in compost when using the DGGE method, which reflects cultural and non- culturable microorganisms. For compost and casing bacteria studied using DGGE, several species formed separate lineages, demonstrating highly diverse communities in these samples. Fungi were shown to be less abundant and less diverse compared to bacteria and yeasts. The study provides baseline knowledge of microbial populations and -succession trends in mushroom production systems using viable and non- viable methods. The information provided in this study may be useful for microbial ecology studies and to identify and develop biocontrol systems for pathogen control during production or to enhance pinning stimulation by knowing when to apply Pseudomonas spp. to ensure increased yield. Finally an insight is provided into microbial survival during cold storage and marketing of mushrooms. Potential antagonistic populations known to prevent spoilage, quality deterioration and extend shelf life are listed in this paper.This research was funded by the South African Mushroom Farmers Association (SAMFA), National Research Foundation (NRF) and the Technology and Human Resources for Industry Programme (THRIP) (a partnership programme funded by the Department of Trade and Industry and managed by the NRF).http://link.springer.com/journal/132132017-03-31hb2016Plant Production and Soil SciencePlant Scienc

The effect of soil carbon on symboitic nitrogen fixation and symbiotic Rhizobium populations in soil with Trifolium repens as host plant

Soil organic carbon (SOC) is the main attribute of high-quality soil. The amount of nitrogen fixed by Rhizobium symbiotically with Trifolium repens (white clover) is ultimately determined by the quality of the soil environment. The effect of SOC on the total number of symbiotic and saprophytic rhizobia was determined. Subsequently, the amount of nitrogen (N) fixed was assessed by using the N difference technique. Most Rhizobium was detected between a SOC content of 2.03% to 3.80% in both inoculated and non-inoculated soils. Inoculation increased the number of rhizobia in soil. Most N was fixed in the soil with the lowest SOC content. Although the amount of N fixed increased as the level of SOC decreased, the efficiency of N fixation decreased proportionally to SOC. Subsequently, more N was rhizodeposited. It was concluded that symbiotic rhizobia introduced by the inoculant were more efficient than free-living rhizobia in soils with higher carbon content, which highlights the importance of inoculation in improving the sustainable production of T. repens pastures.http://tandfonline.com/loi/tarf20nf201

The quantification of biological nitrogen fixation by Trifolium repens as affected by soil organic matter

Management of the soil environment must receive special attention. Future research will not only be on increasing soil quality, but also on rectifying problems caused by our abusive past practices. Soil organic C is the main factor that influences soil quality, which will in turn determine sustainability and profitability.http://www.elsenburg.co

Bacterial profiling of casing materials for white button mushrooms (Agaricus bisporus) using denaturing gradient gel electrophoresis

Commercial producers of white button mushrooms utilise a casing material to cover the spawn run compost, which stimulates the mushrooms’ reproductive stage. Certain bacteria in this casing are responsible for this stimulation, which is known as pinning. Bacterial species richness and diversity within peat and peat-based casing mixtures made from industrial waste materials (i.e. those containing coir, wattle bark, bagasse and filter cake) were examined using denaturing gradient gel electrophoresis (DGGE) at three phases of mushroom growth: (1) casing, (2) pinning and (3) harvesting. Results from the DGGE established that higher bacterial species richness occurred at pinning and harvesting than at casing. Increases in bacterial population density at pinning were greater in the peat-based mixtures, which contained industrial waste materials, than in peat alone. Peat mixtures containing these alternative materials are therefore favourable substrates for bacterial growth. The DGGE profiles for pasteurised casing materials reflected their ability to rapidly reestablish the original bacterial community. The bacteria found to be dominant in casing materials during pinning were closely related to Pseudomonas, Flavobacterium, alpha-Proteobacterium, beta-Proteobacterium, gamma-Proteobacterium, delta-Proteobacterium and uncultured species

Nodulation potential of four Trifolium repens cultivars under field conditions

Four Trifolium repens (white clover) cultivars were evaluated under field conditions to determine the potential of these cultivars to sucessfully develop Rhizobium-associated root nodules. Nodulation of T. repens is often poor, because of suboptimal environmental conditions or absence of host-specific rhizobia. The cultivars Huia, Haifa, Ladino and Regal were selected, as these are popular cultivars available in South Africa. Thousand seed mass (TSM) of each cultivar was measured to determine viability of seed and the possible interaction between TSM and nodulation. Mean TSM values of the cultivars differed significantly, with Huia having the highest TSM followed by Haifa, Ladino and Regal. Biomass production was also measured as an indicator of nitrogen fixation efficiency. The cultivar Huia, with the highest TSM values, resulted in the highest biomass production. Nodulation indices were determined from the size, number and colour of the nodules. All plants, regardless of cultivar, formed nodules within 8 weeks. It was concluded that TSM had no effect on nodulation. Planting date with associated temperature effects and the intrinsic cultivar effect also had no influence on nodulation. It was therefore concluded that nodulation potential of the four cultivars tested was similar under environmental conditions that prevailed during the study.http://www.tandfonline.com/loi/tarf20nf201

Evaluation of microbial diversity of different soil layers at a contaminated diesel site

In this study, we evaluated the hydrocarbon removal efficiency and microbial diversity of different soil layers. The soil layers with high counts of recoverable hydrocarbon degrading bacteria had the highest hydrocarbon removal rate compared with soil layers with low counts of hydrocarbon degrading bacteria. Removal efficiency was 48% in the topsoil, compared with 31% and 11% at depths of 1.5 and 1m, respectively. In the 1 and 1.5m soil layers, there was no significant difference between total petroleum hydrocarbon (TPH) removal in nutrient amended treatments and controls. The respiration rate reflected the difference in the number of bacteria in each soil layer and the availability of nutrients. High O2 consumption corresponded positively with high TPH removal. Analysis of the microbial diversity in the different soil layers using functional diversity (community-level physiological profile, via Biolog) and genetic diversity using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA revealed differences in, respectively, substrate utilisation patterns and DGGE profiles of 16S rDNA fragments. Microbial diversity as revealed by DNA fragments was lower in the highly contaminated soil layer (1.5m) than in the topsoil and at 1m