Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

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Soil bacterial and fungal communities across a pH gradient in an arable soil.

An expectation in soil ecology is that a microbial communities' fungal:bacterial dominance indicates both its response to environmental change and its impact on ecosystem function. We review a selection of the increasing body of literature on this subject and assess the relevance of its expectations by examining the methods used to determine, the impact of environmental factors on, and the expected ecosystem consequences of fungal:bacterial dominance. Considering methods, we observe that fungal:bacterial dominance is contingent on the actual measure used to estimate it. This has not been carefully considered; fungal:bacterial dominance of growth, biomass, and residue indicate different, and not directly relatable aspects, of the microbial community's influence on soil functioning. Considering relationships to environmental factors, we found that shifts in fungal:bacterial dominance were not always in line with the general expectation, in many instances even being opposite to them. This is likely because the traits expected to differentiate bacteria from fungi are often not distinct. Considering the impact of fungal:bacterial dominance on ecosystem function, we similarly found that expectations were not always upheld and this too could be due to trait overlap between these two groups. We explore many of the potential reasons why expectations related to fungal:bacterial dominance were not met, highlighting areas where future research, especially furthering a basic understanding of the ecology of bacteria and fungi, is needed. (C) 2010 Elsevier Ltd. All rights reserved. (Less)

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

Mycotoxin production by Aspergillus, Fusarium and Penicillium species

The application of physical stress to microorganisms is the most widely used method to induce cell inactivation and promote food stability. To survive, microorganisms have evolved both physiological and genetic mechanisms to tolerate some extreme physical conditions. This is clearly of significance to the food industry in relation to survival of pathogens or spoilage organisms in food. In some microorganisms, the “cold shock response” has been observed in response to abrupt changes to lower temperatures. This results in the production of specific sets of proteins (cold shock proteins), the continued synthesis of proteins involved in transcription and translation, and the repression of heat shock proteins. The addition of weak acid preservatives (for example, sorbates, benzoates) also induces a specific pattern of gene expression (for example, ‘Acid Tolerance Response’), which is likely to be required for optimal adaptation of bacteria to weak acid preservatives and low pH. The primary mode of the antimicrobial action of low pH is to reduce the internal cell pH (pHi) below the normal physiological range tolerated by the cell, leading to growth inhibition. Survival mechanisms involve maintaining pH homeostasis, and this is achieved by a combination of passive and active mechanisms. Microorganisms adapt to osmotic stress by accumulating non-ionic or compatible solutes such as trehalose, glycerol, sucrose, and mannitol. These compatible solutes help balance the osmotic pressure and help preserve protein function inside the cells. By understanding and controlling such mechanisms of adaptation, it may be possible to prevent growth of key microorganisms in food products.

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Adaptation of Microorganisms to Cold Temperatures, Weak Acid Preservatives, Low pH, and Osmotic Stress: A Review

Publisher Summary The response of a fungus to osmotic stress involves the integrated function of many components of cell metabolism. The dehydration stress is countered by an important mechanism that entails accumulation of polyols, primarily glycerol, to achieve an internal environment that is conducive for enzyme function and growth under water stress. The changes in the composition of the cytoplasm are controlled by systems for biosynthesis of polyols and for transport of inorganic ions. The intracellular retention of glycerol is controlled at the level of glycerol efflux and by systems for glycerol uptake. The osmoregulatory processes require energy to drive transport and carbon supply for polyol formation. The capacity for substrate uptake under osmotic stress and the efficiency operating the osmoregulatory processes are important in setting the limits for growth at low water potentials. The fungal response to changes in the external water potential must involve sensing as well as transduction of the received signal. Combined genetic and physiological analysis is required for a deeper understanding of fungus-water relations. Analysis at this level has revealed sequential induction of osmotically controlled genes in enteric bacteria and given exciting insights in signal transduction and regulation of the process.

Physiology of osmotolerance in fungi

Influence of pH on the growth of some toxigenic species of Aspergillus, Penicillium and Fusarium

The normal mycoflora of commodities from Thailand. 2. Beans, rice, small grains and other commodities

The normal mycoflora of commodities from Thailand. 1. Nuts and oilseeds.

Interactions were investigated among five xerophilic fungi, Polypaecilum pisce, Basipetospora halophila, Eurotium rubrum, Aspergillus wentii and A. penicillioides, isolated from Indonesian dried salted fish. A range of water activities (aw) (0.98, 0.95, 0.90 and 0.84) and temperatures (15 degrees, 25 degrees and 30 degrees C) were studied on agar media in Petri dishes, and with dried fish as a substrate at 0.90 and 0.84 aw at 30 degrees C. Generally, the fungi exhibited one of two interaction types: mutual inhibition on contact, or inhibition of one or both species on contact, with the inhibited species continuing to grow at a significantly reduced rate. On glucose-based agar media A. wentii and E. rubrum were most competitive at all aw values and temperatures studied, while on NaCl media P. pisce and B. halophila were usually most competitive. The Petri dish system was a useful model, but did not completely simulate the interactions observed on dried fish. Polypaecilum pisce and B. halophila were able to compete more strongly on fish than on agar media, especially at 0.90 aw. This study provides some evidence that each species examined had a niche in which it was dominant, and that species interactions as well as environmental factors are important in determining the dominant fungal species on dried salted fish.

Kathryn A. Wheeler

Papers

Influence of pH on the growth of some toxigenic species of Aspergillus, Penicillium and Fusarium

The normal mycoflora of commodities from Thailand. 2. Beans, rice, small grains and other commodities

The normal mycoflora of commodities from Thailand. 1. Nuts and oilseeds.

Interactions among xerophilic fungi associated with dried salted fish

Fungi associated with Indonesian dried fish