Forms of phosphorus in bacteria and fungi isolated from two Australian soils

To understand the origin of organic and condensed forms of phosphorus (P) in soils, detailed information about P forms in microorganisms is required. We isolated 7 bacteria and 8 fungi from two Australian soils and analyzed the P forms in their pure cultures by extraction with NaOH-EDTA followed by ³¹P solution nuclear magnetic (NMR) spectroscopy. The bacteria belonged to the actinobacteria and the fungi to the ascomycota, as determined by rDNA sequencing. The proportions of broad forms of P were significantly different between the bacterial and fungal isolates (analysis of similarities, p = 0.001). Ortho-, pyro- and polyphosphate were present in higher proportions in fungi, while monoester and diester P were present in higher proportions in bacteria. Spectral deconvolution of the monoester region revealed 15 distinct resonances. The three major ones, which were identified by spiking experiments as glycerol 1-phosphate, glycerol 2-phosphate and adenosine-5′-monophosphate (AMP), comprised 56–74% of P in the monoester region. Ordination by principal component analysis and testing for treatment effects using analysis of similarities showed significant separation of P distribution in the monoester region between bacterial and fungal isolates (p = 0.007). However, neither group of microorganisms had a specific single P form which might be considered characteristic. As such, it may be difficult to distinguish soil P from bacterial or fungal origins, with the possible exception of a predominantly fungal origin of pyro- and polyphosphate. The identification of three major resonances in the monoester region of microorganisms is important, since the same resonances are found in ³¹P NMR spectra of soil extracts.     

Contributions by fungi and bacteria to aggregate stability of cultivated soils

Stability changes during ageing (sterile) or incubation (non-sterile) of both natural field aggregates and remoulded aggregates from five soils were studied for periods up to 30 days. Growth of fungal hyphae, estimated by ergosterol measurement, corresponded to temporary stability increases in both types of aggregates during the first 15 days. Thereafter, fungal hyphae disappeared and were replaced by actinomycetes and bacteria. Increased stability due to entanglement by hyphae was comparable to that due to thixotropy in remoulded aggregates. Bacterial growth accompanied the fall in stability associated with fungal decline, but had little direct effect in stabilizing soil aggregates. Destruction of polysaccharides by periodate oxidation greatly diminished aggregate stability. The role of bacterial polysaccharides in soil aggregate stability is discussed.     

Nature of antagonism of fungi by bacteria isolated from soils

The influence of 457 bacteria isolated from soil on spore germination by Aspergillus flavus was studied by light and scanning microscopy. Bacteria were found to be in physical association with the fungus. The bacteria were tested for antagonism against 11 fungal phytopathogens. A number of the bacterial antagonists displayed a wide spectrum in their activity against the fungi.     

Phosphate solubilizing bacteria and fungi in desert soils: species,limitations and mechanisms

Desert soils are infertile, and the ability to improve them by P-fertilization is limited by the solubility of phosphate. We aimed to understand the function of phosphate solubilizing bacteria and the mechanisms behind phosphate solubilization in desert soils. Vegetated and barren desert soils, mine spoil and a fertile temperate grassland loam were sampled. Bacteria and fungi were isolated and identified, and their phosphate-solubilizing abilities were measured in vitro. The release of plant available PO₄, SO₄, NO₃ and NH₄ from desert soils did not compare with that of a grassland soil. Desert soils had substantially lower solubilization than grassland, 162 and 99–121 µg PO₄-P g^?1 dry soil, respectively. Phosphate-solubilizing bacteria and fungi were inhabiting the soils. Si addition increased phosphate solubilization of fungi by 50%. The isolated microbes were shown, using ³¹P nuclear magnetic resonance (NMR) analysis, to rapidly take-up both intracellular and extracellular phosphate during the phosphate solubilizing process. Desert soil had potentially active microbial populations that are capable to solubilize inorganic phosphorus; S and Si as the limiting factors. Acidification as the main mechanism to solubilize mineral phosphate was not as evident in our desert soils as in former studies dealing more fertile soils.     

Growth measurements of saprotrophic fungi and bacteria reveal differences between canopy and forest floor soils

Canopy-held organic matter develops into a distinct soil system separate from the forest floor in wet temperate coniferous forests, creating a natural microcosm. We distinguished between fungal and bacterial components of the decomposer community in one site with Maple (Acer macrophyllum) and one site with Alder (Alnus rubra) by using direct measurements of growth; acetate incorporation into ergosterol, and leucine incorporation for fungi and bacteria, respectively. The higher organic matter content of the canopy soils correlated with higher fungal growth. The relative importance of fungi, indicated by fungal:bacterial growth ratio, was higher in the canopy soil of the Maple site, while there was no difference in the Alder site. The high C:N ratio of the Maple canopy soil likely contributed to this difference. These results demonstrate a divergence between canopy and forest floor that should be explored to gain insights in decomposer ecology using the natural microcosms that the canopy soils provide.     

Utilization of rock phosphate in alkaline soils by plants inoculated with mycorrhizal fungi and phosphate-solubilizing bacteria

Interactions between vesicular-arbuscular (VA) mycorrhizal fungi and phosphate-solubilizing bacteria were studied in a low-phosphate alkaline soil amended with 0, 0.1% and 0.5% rock phosphate. Endogone (E3 and yellow vacuolate spore types) and two bacteria able to solubilize rock phosphate in vitro and produce plant growth regulating substances were used as inocula. Lavender (Lavandula spica var. vera L.) plants with mycorrhiza plus bacteria (either E3 plus bacteria or “yellow vacuolate” plus bacteria treatments) took up more total P than plants with either Endogone or bacteria separately at each concentration of rock phosphate. Plants not inoculated with bacteria or Endogone derived no benefit from the rock phosphate.     

Mineralization of nitrogen in fertilizer-acidified lime-amended soils

Summary The application of NH _inf4 ^su+ -based fertilizers to soils slowly lowers soil pH, which in turn decreases nitrification rates. Under these conditions nitrification and N mineralization may be reduced. We therefore investigated the impact of liming fertilizer-acidified soils on nitrification and N mineralization. Soil samples were collected in the spring of 1987 from a field experiment, initiated in 1980, investigating N, tillage, and residue management under continuous corn (Zea mays L.). The pH values (CaCl₂) in the surface soil originally ranged from 6.0 to 6.5. After 6 years the N fertilizer and tillage treatments had reduced the soil pH to values that ranged between 3.7 and 6.2. Incubation treatments included two liming rates (unlimed or SMP-determined lime requirement), two ¹⁵N-labeled fertilizer rates (0 or 20 g N m^-2), and three replicates. Field-moist soil was mixed with lime and packed by original depth into columns. Labeled-¹⁵N ammonium sulfate in solution was surface-applied and columns were leached with 1.5 pore volumes of deionized water every 7 days over a 70-day period. Nitrification occurred in all pH treatments, suggesting that a ferilizer-acidified soil must contain a low-pH tolerant nitrifier population. Liming increased soil pH values (CaCl₂) from 3.7 to 6.2, and increased by 10% (1.5 g N m^-2) the amount of soil-derived NO₃ ^--N that moved through the columns. This increase was the result of enhanced movement of soil-derived NO₃ ^--N through the columns during the first 14 days of incubation. After the initial 14-day period, the limed and unlimed treatments had similar amounts of soil N leaching through the soil columns. Lime increased the nitrification rates and stimulated the early movement of fertilizer-derived NO₃ ^--N through the soil.     

Mineralization and nitrification in three Malaysian forest soils

Examination of three forest soils from Malaysia using the soil incubation technique suggests that nitrification was not inhibited in these oligotrophic soils. Nitrification rates were between 40 and 750 ngN produced g^?1 dry weight soil day^?1 of incubation. Addition of phenolic metabolites (tannic acid) and leaf filtrates from hill and lowland forest litter did not significantly inhibit nitrification. Addition of sucrose (1% w/w carbon source) decreased nitrification but not ammonification.     

Mineralization of sulphur in sulphoquinovose by forest soils

Surface soils from four watersheds located in the Coweeta Basin near Franklin, North Carolina were assayed for their capacity to mineralize sulphur in 6-sulphoquinovose. All soils rapidly converted S in this component of the plant sulpholipid to inorganic sulphate, a soluble (salt extractable) ester sulphate and an insoluble ester sulphate. Sulphur in this latter fraction was released by acidhydrolysis of soil residues at 121°C. Although maximum concentrations of S in each fraction varied with duration of incubation, rates of conversion of S into all fractions were highest during the first hour. Mineralization rates based upon sulphate release and total S released from sulphoquinovose are reported.     

A preliminary study of the growth of fungi and bacteria from temperate and antarctic soils in relation to temperature

The growth of fungi isolated from a lowland temperate site (Roudsea Wood National Nature Reserve), an upland temperate moorland (Moor House National Nature Reserve) and an oceanic Antarctic island (Signy, S. Orkneys) was compared at 1, 14 and 25°C. This showed that low temperatures caused greatest retardation of growth in fungi from the warmest site (Roudsea) and least from the coldest site (Signy Island). At Moor House, fungi which were isolated most frequently in winter were able to grow better at 1°C than summer forms. The fungal flora of Signy Island was restricted and consists of cold tolerant cosmopolitan species which have been selected by or become adapted to the prevailing low temperatures. Of fungi isolated from any two of the sites, Mortierella alpina and Mucor hiemalis showed temperature adaptation correlated with prevailing site temperature, while Trichoderma viride, Penicillium thomii, and P. frequentans showed no adaptation.     

Mineralization of methionine sulphur in soils and forest floor layers

A1-horizon soils and 01, 02 forest floor layers from a mixed mature hardwood forest rapidly converted methionine-S to readily-available (salt-extractable) and less readily-available (acid- and base-extractable) inorganic sulphate (SO^?2₄). It is suggested that this latter conversion represents the incorporation into organic matter of a portion of the (SO^?2₄) released by mineralization. On a dry weight basis, the 02 layer of the forest floor was the most active with respect to both conversions. Moreover, capacities for mineralization and (SO^?2₄) incorporation decreased with increasing sample depth within the mineral horizon. Both conversions were dependent upon temperature and duration of incubation and were absent from samples which had been autoclaved. Sodium azide and the broad-spectrum antibiotic, tetracycline also inhibited each conversion to varying extents depending upon the type of sample incubated with methionine.     

Mineralization of hydroxylated isoproturon metabolites produced by fungi

When exposed to the herbicide isoproturon, some soil fungi in pure culture metabolize the substance to hydroxylated metabolites. Hydroxylated metabolites of isoproturon have also been detected in soil studies. In an agricultural soil not previously exposed to isoproturon we found that the hydroxylated isoproturon metabolite N-(4-(2-hydroxy-1-methylethyl)phenyl)-N′,N′-dimethylurea mineralized faster than both isoproturon and its N-demethylated metabolite N-(4-isopropylphenyl)-N′-methylurea (MDIPU), thus indicating that mineralization of isoproturon is stimulated by fungal hydroxylation in this soil. In soils previously treated with isoproturon, in contrast, isoproturon and both its hydroxylated and demethylated metabolites mineralized at almost the same rate with up to 52% of the ¹⁴C-ring-carbon being degraded to ¹⁴CO₂ within 63 days. Thus hydroxylated metabolites of isoproturon do not seem to be more persistent than isoproturon, and hence may degrade before they can leach from topsoil and contaminate the aquatic environment. While an isoproturon-mineralizing bacterium Sphingomonas sp. SRS2 and a MDIPU-mineralizing mixed bacterial culture were able to deplete the medium of hydroxylated metabolites, little or no mineralization took place. This indicates that other bacteria must be present in the soil that are able to benefit from isoproturon being made available to mineralization by fungal hydroxylation.     

Mineralization of nitrogen compounds in soils of south-taiga ecosystems

The productivity of the nitrogen mineralization in the A0 (0–2 cm), A1 (2–3 cm), and A2 (3–13 cm) horizons of a soddy-podzolic soil was measured in a wood-sorrel-whortleberry birch forest (7Birch3Asp, 80 years, the second stand quality class, tree canopy density 0.7, Yaroslavl oblast) using the sample incubation method; the measurements were performed from May till October in eight replicates for each horizon. In 2007, 5.85 ± 0.73 g N/m² were mineralized in the soil. In the litter, 2.01 ± 0.23 g N/m² were mineralized, whereas 0.35 ± 0.03 and 3.49 ± 0.72 g N/m² were mineralized in the A1 and A2 horizons, respectively. In 2008, 3.34 ± 0.25 g N/m² were mineralized in the A0 and A1 horizons, of which 2.44 ± 0.23 g N/m² were in the former. Ammonification prevailed in all the horizons. The contribution of nitrification was assessed as 1.6 and 0.3% of the process’s productivity in 2007 and 2008, respectively. The C_org and N_org pools decreased in the litter by 407 g C/m² and 13.7g N/m² (or 33%) from May to October. Of this carbon amount, 67% is spent for humification and the organic mass preservation and 33% was transformed to carbonic acid. The nitrogen expenses for the synthesis of humus acids are equal to 70 and 30%; it is spent equally for the mineralization of the element and its immobilization by microorganisms. In the A0 and A1 horizons, the seasonal trends of the ammonification correlated with the carbon dioxide emission from these horizons in the year of 2008 with r = 0.75 atp = 0.09 and r = 0.82 atp = 0.04 for both horizons, respectively.     

Interactions between bacteria and ectomycorrhizal fungi

Interactions between eight ectomycorrhizal fungi and eight bacteria were tested on five laboratory media and in the rhizoplane of Pinus radiata. Depression of growth of the fungi by the bacteria in laboratory media was dependent on the medium and bore little relation to effects in the rhizoplane. In the rhizoplane, different bacteria could depress, have no effect or even stimulate growth of mycorrhizal fungi. Competition and antagonism are suggested as mechanisms for depression of the fungi. Some bacteria gave protection against the depressive effects of other bacteria. Considerable differences occurred between ectomycorrhizal fungi in their colonization of the rhizoplane in the absence of bacteria and also in their presence. The common mycorrhizal fungi Rhizopogon luteolus and Thelephora terrestris generally colonized roots well but the strain of Pisolithus tinctorius studied colonized poorly. Direct microscopy showed the percentage cover of the root by microorganisms was usually only 10–20%.It is proposed that interactions of ectomycorrhizal fungi with soil organisms are important in determining the successful introduction and persistence of inoculated ectomycorrhizal fungi. Fungi should be selected for compatibility with a wide range of soil microflora as well as efficiency in plant stimulation.     

Conversion of forest to agricultural land affects the relative contribution of bacteria and fungi to nitrification in humid subtropical soils

Land-use and management practices can affect soil nitrification. However, nitrifying microorganisms responsible for specific nitrification process under different land-use soils remains unknown. Thus, we investigated the relative contribution of bacteria and fungi to specific soil nitrification in different land-use soils (coniferous forest, upland fields planted with corn and rice paddy) in humid subtropical region in China. ¹⁵N dilution technique in combination with selective biomass inhibitors and C₂H₂ inhibition method were used to estimate the relative contribution of bacteria and fungi to heterotrophic nitrification and autotrophic nitrification in the different land-use soils in humid subtropical region. The results showed that autotrophic nitrification was the predominant nitrification process in the two agricultural soils (upland and paddy), while the nitrate production was mainly from heterotrophic nitrification in the acid forest soil. In the upland soils, streptomycin reduced autotrophic nitrification by 94%, whereas cycloheximide had no effect on autotrophic nitrification, indicating that autotrophic nitrification was mainly driven by bacteria. However, the opposite was true in another agricultural soil (paddy), indicating that fungi contributed to the oxidation of NH₄⁺ to NO₃^?. In the acid forest soil, cycloheximide, but not streptomycin, inhibited heterotrophic nitrification, demonstrating that fungi controlled the heterotrophic nitrification. The conversion of forest to agricultural soils resulted in a shift from fungi-dominated heterotrophic nitrification to bacteria- or fungi-dominated autotrophic nitrification. Our results suggest that land-use and management practices, such as the application of N fertilizer and lime, the long-term waterflooding during rice growth, straw return after harvest, and cultivation could markedly influence the relative contribution of bacteria and fungi to specific soil nitrification processes.     

Mineral transformations by fungi in culture and in soils

• 1 Although micro-organisms are regarded as the principal agents of mineral cycling in soils, the role of bacteria has generally been emphasized, while that of fungi has been neglected.
• 2 Fungi are able to transform the majority of elements in vitro but whether they play an important role in soil is as yet unknown.
• 3 There is sufficient circumstantial evidence from soil studies to suggest that fungi may under certain conditions nitrify and oxidize reduced forms of sulphur. Their role in denitrification and sulphate reduction process is more speculative. While they appear incapable of nitrogen fixation, fungi undoubtedly play a major role in the mineralization of organic N,P, and S in soils, in the solubilization of insoluble phosphates, and participate in oxidation of manganese. Perhaps one of their most important roles is in the dissolution of silica and rocks thus releasing ions into the soil solution during weathering.
• 4 The ability of fungi to oxidize elements in vitro does not compare with that of the chemoautotrophic bacteria. On the other hand in vitro activity tells us little about the activity of an organism in the soil.
• 5 At present our appreciation of the part played by fungi in mineral cycling in soils is limited by the techniques available, but there is little doubt that they have a major role to play in the cycling of elements other than carbon.

     

Mycelial bacteria of saline soils

The actinomycetal complexes of saline soils comprise the representatives of the Streptomyces and Micromonospora genera, the number of which are hundreds and thousands of CFU/g soil. Complexes of mycelial bacteria in saline soils are poorer in terms of number (by 1–3 orders of magnitude) and taxonomic composition than the complexes of the zonal soil types. A specific feature of the actinomycetal complexes of saline soils is the predominance of halophilic, alkaliphilic, and haloalkaliphilic streptomycetes that well grow at pH 8–9 and concentrations of NaCl close to 5%. Actinomycetes in saline soils grow actively, and the length of their mycelium reaches 140 m in 1 gram of soil. The haloalkaliphilic streptomycetes grow fast and inhibit the formation of spores at pH 9 and high concentrations of salts (Na₂SO₄ and MgCl₂, 5%) as compared to their behavior on a neutral medium with a salt concentration of 0.02%. They are characterized by the maximal radial growth rate of colonies on an alkaline medium with 5% NaCl.     

Diversity and biogeography of arbuscular mycorrhizal fungi in agricultural soils

It has widely been acknowledged that the diversity of arbuscular mycorrhizal fungi (AMF) is greatly affected by climate, land use intensity, and soil parameters. The objective of this study was to investigate AMF diversity in multiple agricultural soils (154 sites; 92 grasslands and 62 croplands) distributed over all agricultural regions in Switzerland and differing in a number of soil parameters (e.g., land use type and intensity, and altitude). We highlighted the main factors responsible for major AMF community shifts and documented specific distribution patterns for each AMF species. AMF spores were morphologically identified and counted for each species. In total, 17,924 spores were classified and 106 AMF species were identified. In general, AMF species richness (SR) was higher in grasslands than in croplands. In croplands, SR increased with altitude but this trend was not observed in grasslands. Some species occurred at virtually all sites, while others were rarely detected, and for others, species-specific distribution patterns were revealed. Some species were affected by land use type or intensity, or related factors like soil organic matter, soil microbial biomass and respiration or nutrient availability. Other species were more affected by soil pH and related parameters like base saturation and carbonate contents, by soil texture, or by altitude, or by a combination of two to several of all these parameters. We conclude that a high number of AMF species may serve as indicator species for specific habitats and land use. These species might deliver certain ecosystem services at their habitats and deserve further investigation about their functional diversity.     

Traceability of ammonia-oxidizing bacteria in compost-treated soils

Composts are increasingly used as environmentally safe biofertilizers in sustainable agriculture all over the world. Although it is well known that composts may contribute to soil vitality and sustainability, and in the enhancement of various soil microbiological processes, little is known about their direct or indirect effects on a microbial-community or population level. Ammonia oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and plays an important role in the global nitrogen cycle. Here, we studied the diversity and community composition of ammonia oxidizers in a long-term crop rotation field experiment (>10 years) where four major types of compost (from organic waste, cattle manure, green waste and sewage sludge) had been applied annually. The methods used ranged from PCR-DGGE (denaturing gradient gel electrophoresis) and cloning of 16S rDNA fragments to quantitative real-time PCR. Cluster analysis of DGGE profiles differentiated between the microbial communities of composts, compost-treated soils and mineral-fertilized soils. The community composition of the composts was not reflected in the community composition of the compost-treated soils. Sequencing of screened clones revealed a characteristic AOB community structure for the representative soil sample and the four composts. All AOB-like sequences grouped within the Nitrosospira cluster 3 and 4 and within the Nitrosomonas cluster 6 and 7. The average AOB abundance in compost-treated soils was two times higher than in mineral-fertilized soils (4.3×10⁷ and 1.9×10⁷, respectively). Our data suggest that composts do not leave direct microbial imprints in soils after long-term amendment, but an indirect effect on the AOB community was evident.