Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans

Reception

Soil bioaugmentation involves the inoculation of pollutant-degrading bacteria to accelerate pollutant degradation. Often the inoculum shows a dramatic decrease in Colony Forming Units (CFU) upon soil inoculation but this behavior is not well-understood. In this study, the physiology and transcriptomic response of a GFP tagged variant of <i>Novosphingobium</i> sp. LH128 was examined after inoculation into phenanthrene spiked soil. Four hours after inoculation, strain LH128-GFP showed about 99% reduction in CFU while microscopic counts of GFP-expressing cells were identical to the expected initial cell density, indicating that the reduction in CFU number is explained by cells entering into a Viable But Non-Culturable (VBNC)-like state and not by cell death. Transcriptome analysis showed a remarkably higher expression of phenanthrene degradation genes 4 h after inoculation, compared to the inoculum suspension concomitant with an increased expression of genes involved in stress response. This indicates that the cells were active in phenanthrene degradation while experiencing stress. Between 4 h and 10 days, CFU numbers increased to numbers comparable to the inoculated cell density. Our results suggest that strain LH128-GFP enters a VBNC-like state upon inoculation into soil but is metabolically active and that VBNC cells should be taken into account in evaluating bioaugmentation approaches

The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation

Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail <i>Folsomia candida</i> an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in <i>Acidobacteria</i>, while <i>Actinobacteria</i> and <i>Gammaroteobacteria</i> communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan <i>F. candida</i> was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of <i>F. candida</i> is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology

The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation

Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail <i>Folsomia candida</i> an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in <i>Acidobacteria</i>, while <i>Actinobacteria</i> and <i>Gammaroteobacteria</i> communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan <i>F. candida</i> was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of <i>F. candida</i> is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology

The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation

Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail <i>Folsomia candida</i> an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in <i>Acidobacteria</i>, while <i>Actinobacteria</i> and <i>Gammaroteobacteria</i> communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan <i>F. candida</i> was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of <i>F. candida</i> is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology

Impacts of Shallow Geothermal Energy Production on Redox Processes and Microbial Communities

Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5–80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10^–10 M s^–1), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100–160 kJ mol^–1) than mesophilic sulfate reduction (30–60 kJ mol^–1), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive

Impacts of Shallow Geothermal Energy Production on Redox Processes and Microbial Communities

Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5–80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10^–10 M s^–1), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100–160 kJ mol^–1) than mesophilic sulfate reduction (30–60 kJ mol^–1), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive