Character of interactions of saprophytic soil microflora via gaseous metabolites

The character of interaction between saprophytic soil bacteria via gaseous metabolites was studied. It was established that, at the metabolic level, a diverse character of interspecies interrelationships between bacteria exist, directly influencing their reproduction and preservation in soil. Volatile compounds produced by bacteria are able to act as both intra- and interspecies regulators of microbial communities. The soil microbiocenosis composition may be therefore regulated by volatile products of metabolism of saprophytic soil bacteria. Methanol released by bacteria into the environment plays an important role in this process.     

Influence of volatile metabolites of saprophytic soil microflora on the propagation of pathogenic bacteria

The influence of volatile metabolites of saprophytic soil microflora on the propagation of Listeria monocytogenes and Yersinia pseudotuberculosis is shown. Different character of interspecific relationships between bacteria, influencing their propagation, can be observed on the metabolic level. Volatile compounds produced by microorganisms are capable to act as both intra- and interspecific regulators of microbial communities. In this connection the propagation of pathogenic bacteria inhabiting soil may be stimulated or inhibited by the metabolic products of soil microorganisms. Methanol released by saprophytic bacteria into the environment play an important role in this process.     

Plant species richness,identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility

The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness per se. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by Anthoxantum odoratum. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity per se and plant species composition than are abundances of saprophytic microbes.     

The microbiology of soils under successive wheat crops in relation to take-all disease

Abstract Thirty-eight wheat fields in southern England were sampled in an attempt to correlate the amount of take-all disease with 35 microbiological and chemical measurements of soil. There was little correlation between field take-all and pot tests to determine soil infectivity. Myxogastrids were important components of the soil population, being up to half of the amoebal population, and most soils contained dictyostelids, reticulate amoebae and myxobacteria. Amoebae, ciliates, bacteria and saprophytic fungi were recorded for all soils. pH was a major determinant of soil populations, being clearly correlated with fungal abundance and with numbers of ciliates, dictyostelids and bacteria. Principal component analysis separated dictyostelids from the other soil amoebae and again showed the importance of pH in determining soil microbial populations. Take-all was negatively correlated with soil fertility and positively related to nematodes and myxobacteria, but this was probably an effect of take-all, and represented saprophytic growth on dead roots rather than being a cause. Reticulate amoebae and dictyostelids were both correlated with low levels of take-all. This study emphasises the large number of interrelated populations of soil microorganisms which could have an effect on the severity of take-all infections.     

Correlation of abundance of arbuscular mycorrhizal fungi, bacteria and saprophytic microfungi with soil carbon, nitrogen and phsophorus

A significant positive correlation between the concentration of CFU of soil saprophytic microfungi and total soil carbon content, organic matter (oxidizable carbon) and available phosphorus was observed in field collected soil samples. Concentration of CFU of culturable bacteria correlated negatively with soil organic matter. Specific length of hyphae of arbuscular mycorrhizal fungi in the soil correlated only with soil respiration rate. The results indicate that arbuscular mycorrhizal fungi are associated with soil microsites rich in some easily mineralizable fraction of soil, organic matter rather than with total or oxidizable organic carbon.     

Hyphal growth and mycorrhiza formation by the arbuscular mycorrhizal fungus Glomus claroideum BEG 23 is stimulated by humic substances

Effects of humic substances (humic acid or fulvic soil extract) or saprophytic microorganisms (Paecilomyces lilacinus and an unidentified actinomycete) on growth of mycelium and mycorrhiza formation by Glomus claroideum BEG23 were studied in a hydroponic system. Humic substances stimulated root colonization and production of extraradical mycelium by the mycorrhizal fungus. Both humic and fulvic acids tended to decrease populations of culturable bacteria and fungi in the cultivation system, indicating a moderately antibiotic activity. The addition of saprophytic microorganisms able to use humic substances to the cultivation system further stimulated the development of the mycorrhizal fungus. However, stimulation of G. claroideum was also observed when the saprophytic microorganisms were heat-killed, suggesting that their effect was not linked to a specific action on humic substances. The results indicate that humic substances may represent a stimulatory component of the soil environment with respect to arbuscular mycorrhizal fungi.     

Influence of organic soil amendments on Verticillium dahliae and on the microbial composition of the strawberry rhizosphere

A technique was developed for assessing the saprophytic activity of Verticillium dahliae, using a strawberry root extract medium. The germination of conidia and microsclerotia, and mycelial growth in soil, was inhibited by the addition of chitin, laminarin, wheat straw and oven-dried green clover as soil amendments. A significant decrease in the number of viable propagules of the pathogen counted from soil, and in disease severity, was obtained with chitin and laminarin. More bacteria and actinomycetes were recorded from the rhizosphere of plants grown in chitin-amended soil than from those in natural soil.     

Violet-Pigmented Pseudomonads With Antifungal Activity From the Rhizosphere of Beans

Bean rhizosphere bacteria antagonistic to four root-infecting fungi and an antibiotic produced by these bacteria were studied. The bacteria were violet-pigmented gram-negative rods, probably belonging to the genus Pseudomonas. The antibiotic, which was localized largely in the bacterial cell mass, was easily extracted with acetone. It was selectively active against a wide variety of plant-pathogenic and saprophytic fungi tested in vitro but was relatively inactive against bacteria. The compound, partially purified by chromatography, was soluble in all organic solvents tried, but nearly insoluble in water. It demonstrated no characteristic ultraviolet- or visible-absorption spectrum and was chemically unidentified. The antagonistic bacteria or crude antibiotic applied to buried buckwheat segments suppressed the colonization of this substrate by Rhizoctonia spp. The data suggested that the bacteria or the antibiotic may play a role in the suppression of root-infecting fungi in soil.     

Linking Microbial Community Structure and Function to Seasonal Differences in Soil Moisture and Temperature in a Chihuahuan Desert Grassland

Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.     

Influence of gaseous metabolites of soil bacteria on the multiplication of Listeria monocytogenes and Yersinia pseudotuberculosis

The influence of gaseous metabolites of saprophytic soil bacteria on the growth and multiplication of L. monocytogenes and Y. pseudotuberculosis was studied. The study revealed that all cultures under study exhibited selectively both inhibiting and stimulating action on the multiplication of test cultures. Bacteria of the genera Pseudomonas and Acinetobacter showed the highest inhibiting activitywith respect to the test cultures. Volatile metabolites of bacteria of the genus Aeromonas showed the highest stimulating activity. Methanol, according to the data of chromatographic analysis, supposedly played the main role in this process and was contained in the volatile substances of Aeromonas bacteria in greater amounts than in the volatile substances of Pseudomonas bacteria.     

Dynamic of the volume and structure of the soil bacterial complex in the presence of azobenzene

Azobenzene exerted no significant effect on the dynamics and the species composition of the saprophytic soil bacterial complex, which remained almost the same as in the control and was characterized by the predominance of Curtobacterium sp., Arthrobacter globiformis, and Bacillus megaterium in all stages of succession. Some heterotrophic bacteria were found to be able to accumulate azobenzene. Bac. cereus and Bac. polymyxa degraded azobenzene during their cultivation in nutrient media.     

Various methodological approaches in controlled screening of antibiotic producers among the group of Coryneform bacteria]

A methodical system for directed screening of cultures producing broad-spectrum antibiotics among soil saprophytic coryneform bacteria was developed. To isolate such cultures, it was recommended to use the glucose-yeast medium supplemented with malt extract (No. 18/3) and soybean-glucose medium with sodium sulfate and cobalt chloride (No. 20/3). The preliminary alkaline treatment of the soil substrates and the use of acidic soil samples were found to favour isolation of the Mycobacterium type cultures. It was recommended to use gram-negative tests microbes with relatively low antibiotic resistance for screening cultures producing broad spectrum antibiotics. Various agarized and liquid fermentation media were compared in regard to detection of antibiotic activity in the soil coryneform bacteria. The corn medium supplemented with protein-vitamin concentrate, glucose, lactose and starch (No. 116) proved to be the most efficient.     

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β‐1,4‐glucosidase and cellobiohydrolase), chitin (i.e., β‐1,4‐N‐acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram‐negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.     

Occurrence and activity of phosphate-solubilizing fungi from coconut plantation soils

Summary The occurrence of phosphate-solubilizing fungi in coconut plantation soil types was investigated. The laterite, alluvial and clayey soils harboured more of the P-solubilizing fungi than the sandy soils. The isolated P-solubilizing fungi solubilized 26 to 74 per cent of the tricalcium phosphate in 5 to 15 days. The competitive saprophytic ability of the active P-solubilizing fungi in soil varied between the isolates. Eight fungi with high P-solubilizing capacity and high competitive saprophytic ability were recognised. They have better capacity to survive in soil and express their role in P-solubilization.Contribution No. 291 of the Central Plantation Crops Research Institute, Kasaragod, India     

The effect of soil compaction on the saprophytic growth of Rhizoctonia solani

The increase in bare patch of cereals associated with minimum tillage practices prompted an investigation of the relationship between soil compaction and saprophytic growth of Rhizoctonia solani. In soils wetter than 10 kPa there was a greater density of hyphae in compacted than in non-compacted soil. In relatively dry soil, however, there was wider exploration by hyphae in non-compacted than in compacted soil. The implications of these findings for disease management are discussed.     

The Dynamics of the Size and Structure of the Soil Bacterial Complex in the Presence of Azobenzene

Azobenzene exerted no significant effect on the dynamics and the species composition of the saprophytic soil bacterial complex, which remained almost the same as in the control and was characterized by the predominance of Curtobacteriumsp., Arthrobacter globiformis, and Bacillus megateriumin all stages of succession. Some heterotrophic bacteria were found to be able to accumulate azobenzene. Bacillus cereusand Bac. polymyxadegraded azobenzene during their cultivation in nutrient media.     

Modelling the effects of loss of soil biodiversity on ecosystem function

There are concerns about whether accelerating worldwide loss of biodiversity will adversely affect ecosystem functioning and services such as forage production. Theoretically, the loss of some species or functional groups might be compensated for by changes in abundance of other species or functional groups such that ecosystem processes are unaffected. A simulation model was constructed for carbon and nitrogen transfers among plants and functional groups of microbes and soil fauna. The model was based on extensive information from shortgrass prairie, and employed stabilizing features such as prey refuges and predator switching in the trophic equations. Model parameters were derived either from the literature or were estimated to achieve a good fit between model predictions and data. The model correctly represented (i) the major effects of elevated atmospheric CO₂ and plant species on root and shoot biomass, residue pools, microbial biomass and soil inorganic nitrogen, and (ii) the effects on plant growth of manipulating the composition of the microbial and faunal community. The model was evaluated by comparing predictions to data not used in model development. The 15 functional groups of microbes and soil fauna were deleted one at a time and the model was run to steady state. Only six of the 15 deletions led to as much as a 15% change in abundance of a remaining group, and only two deletions (bacteria and saprophytic fungi) led to extinctions of other groups. Functional groups with greater effect on abundance of other groups were those with greater biomass or greater number of consumers, regardless of trophic position. Of the six deletions affecting the abundance of other groups, only three (bacteria, saprophytic fungi, and root‐feeding nematodes) caused as much as 10% changes in indices of ecosystem function (nitrogen mineralization and primary production). While the soil fauna as a whole were important for maintenance of plant production, no single faunal group had a significant effect. These results suggest that ecosystems could sustain the loss of some functional groups with little decline in ecosystem services, because of compensatory changes in the abundance of surviving groups. However, this prediction probably depends on the nature of stabilizing mechanisms in the system, and these mechanisms are not fully understood.     

Bdellovibrio bacteriovorus Parasitizing Rhizobium in Western Australia

S ummary . Bdellovibrio bacteriovorus strains which parasitize Rhizobium meliloti, R. trifolii, Agrobacterium tumefaciens and A. radiobacter have been found in Western Australian soils. Rhizobium lupini was not lysed by any strain. Some Bdellovibrio cells pass through 0·22 μm membrane filters, whilst the 0·45 μm filters allow several saprophytic soil bacteria to pass. The strength of the medium is shown to be of great importance for the detection or counting of Bdellovibrio cells. The Bdellovibrio strains are capable of destroying large numbers of rhizobia in the laboratory.     

Identification of genes essential for prey-independent growth of Bdellovibrio bacteriovorus HD100

Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that attacks and invades Gram-negative bacteria. The predator requires living bacteria to survive as growth and replication take place inside the bacterial prey. It is possible to isolate mutants that grow and replicate outside prey bacteria. Such mutants are designated host or prey independent, and their nutritional requirements vary. Some mutants are saprophytic and require prey extracts for extracellular growth, whereas other mutants grow axenically, which denotes the formation of colonies on complete medium in the absence of any prey components. The initial events leading to prey-independent growth are still under debate, and several genes may be involved. We selected new mutants by three different methods: spontaneous mutation, transposon mutagenesis, and targeted gene knockout. By all approaches we isolated mutants of the hit (host interaction) locus. As the relevance of this locus for the development of prey independence has been questioned, we performed whole-genome sequencing of five prey-independent mutants. Three mutants were saprophytic, and two mutants could grow axenically. Whole-genome analysis revealed that the mutation of a small open reading frame of the hit locus is sufficient for the conversion from predatory to saprophytic growth. Complementation experiments were performed by introduction of a plasmid carrying the wild-type hit gene into saprophytic mutants, and predatory growth could be restored. Whole-genome sequencing of two axenic mutants demonstrated that in addition to the hit mutation the colony formation on complete medium was shown to be influenced by the mutations of two genes involved in RNA processing. Complementation experiments with a wild-type gene encoding an RNA helicase, RhlB, abolished the ability to form colonies on complete medium, indicating that stability of RNA influences axenic growth.     

Transfer of transformation and conjugation plasmids from Escherichia coli to Bacillus subtilis and Azospirillum brasilense]

The conjugative transfer of RP4 plasmid from Escherichia coli to Azospirillum brasilense was detected after introduction and subsequent incubation of these microorganisms in soil. The plasmid transfer via transformation from Escherichia coli to Bacillus subtilis was observed in case both bacteria were growing together in sand containing sucrose solution. The possible reason for low frequency interspecies plasmid transformation under conditions close to natural habitats is poor survival of "domesticated" rather than wild type Bacillus subtilis strains and lack of competence state in this case.