Differential Siderophore Utilization and Iron Uptake by Soil and Rhizosphere Bacteria

The differential availabilities of the hydroxamate siderophores ferrioxamine B (FOB) and ferrichrome (FC) and the pseudobactin siderophores St3, 7NSK₂, and WCS 358 as sources of Fe for soil and rhizosphere bacteria were studied. About 20% of the total bacterial CFU from the rhizospheres of four plant species were able to use FOB as the sole Fe source in an Fe-deficient medium, while about 12, 10, 2, and > 1% were able to use FC and pseudobactins 7NSK₂, St3, and WCS 358, respectively. Of the 165 colonies isolated from plates containing pseudobactins, 64 were able to use the pseudobactin on which they were isolated as the sole Fe source in pure culture. Cross-feeding tests showed that almost all of these 64 strains were also able to use at least one of the other siderophores studied (pseudobactin, FOB, or FC). Pseudomonas putida StS2, Pseudomonas maltophilia 7NM1, and Vibrio fluvialis WS1, which were originally isolated on pseudobactins St3, 7NSK₂, and WCS 358, respectively, were selected for their ability to grow with pseudobactin St3 as the sole Fe source. They incorporated ⁵⁵Fe³⁺ mediated by pseudobactin St3 at various rates (71.5, 4, and 23 pmol/min/mg [dry weight] of cells, respectively). Similarly, P. putida St3 was shown to incorporate ⁵⁵Fe³⁺ mediated by FOB and FC. We suggest that the ability of bacteria to utilize a large variety of siderophores confers an ecological advantage.     

Fungi Benefit from Two Decades of Increased Nutrient Availability in Tundra Heath Soil

If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover of complex organic compounds such as vanillin, while warming has had no such effects. Furthermore, the NLFA-to-PLFA ratio for ¹³C-incorporation from acetate increased in warmed plots but not in fertilized ones. Thus, fertilization cannot be used as a proxy for effects on warming in arctic tundra soils. Furthermore, the different functional responses suggest that the biomass increase found in both fertilized and warmed plots was mediated via different mechanisms.     

Effect of Carbon Substrates on Rock Phosphate Solubilization by Bacteria from Composts and Macrofauna

Five of the 207 isolates from different composts, farm waste compost (FWC), rice straw compost (RSC), Gliricidia vermicompost (GVC), and macrofauna, showed rock phosphate (RP) solubilization in buffered medium in plate culture. When tested in RP broth medium, all five strains, Enterobacter cloacae EB 27, Serratia marcescens EB 67, Serratia sp. EB 75, Pseudomonas sp. CDB 35, and Pseudomonas sp. BWB 21, showed gluconic acid production and solubilized RP. Based on cellulose-degrading and P-solubilizing ability, two strains were selected for further studies. In the presence of different carbon sources, both strains showed a drop in pH and solubilized RP. P released was maximum with glucose (1212 and 522 μmol) and minimum with cellobiose (455 and 306 μmol) by S. marcescens EB 67 and Pseudomonas sp. CDB 35, respectively. Glucose dehydrogenase (GDH) activity was 63 and 77% with galactose and 35 and 46% with cellobiose when compared to glucose (100%) by EB 67 and CDB 35, respectively. Both strains solubilized RP in the presence of different crop residues. EB 67 and CDB 35 showed maximum cellulase activity (0.027 units) in the presence of rice straw and a mixture of rice straw and root. P solubilized from RP in the presence of pigeonpea root was 134 and 140 μmol with EB 67 and CDB 35. Significantly, these bacteria isolated from composts and macrofauna solubilized rock phosphate in the presence of various pure carbon substrates and crop residues and their importance in soil/rhizosphere conditions is discussed.     

Utilization of Methylthio-s-Triazine for Growth of Soil Fungi

Aspergillus niger van Tieghem, Aspergillus tamarii Kita, and Aspergillus flavus Link ex Fries utilized the methylthio moiety of 2,4-bis(isopropylamino) -6-methyl-mercapto-s-triazine (prometryne) as a sulfur nutrient source. Other soil fungal isolates not affected by prometryne concentrations to 1 mg/ml culture included: Aspergillus oryzae (Ahlburg) Cohn, Curvularia lunata (Wakker) Boedijn, Trichoderma viride Persoon ex Fries, Alternaria tenuis Nees ex Corda, Penicillium funiculosum Thom, and Paecilomyces varioti Bainier.     

Influence of Environmental Factors on Antagonism of Fungi by Bacteria in Soil: Nutrient Levels

The addition of 0.25, 0.5, or 1.0% glucose to a soil (K) amended with either 6% kaolinite (K6K) or montmorillonite (K6M) or the adjustment of the C/N ratio of the soils from 23/1 to 10/1 with NH₄NO₃ eliminated the inhibition of Aspergillus niger by Serratia marcescens, regardless of whether the fungus and bacterium were inoculated into the same or separate sites in the soils. The adjustment of the C/N ratio to 15/1 or of the C/P ratio from 1,000/1 to 100/1 with KH₂PO₄ did not eliminate the antagonism. However, with the higher glucose and NH₄NO₃ amendments, S. marcescens died out in the K and K6K (but not in the K6M) soils, apparently due to reductions in pH that resulted from the increased metabolism induced by added nutrients. In soils amended with CaCO₃, S. marcescens did not die out, but the inhibition of A. niger by S. marcescens or Agrobacterium radiobacter was eliminated or reduced by the addition of glucose, but not of NH₄NO₃, and was influenced by the clay mineralogy and pH of the soils. When NH₄NO₃ was added to the soils adjusted with CaCO₃ to pH values above 6.0, growth of A. niger was inhibited, regardless of whether bacteria were present or not, as a result of the volatilization of NH₃. Bacillus cereus and another species of Bacillus did not inhibit A. niger under any of the environmental conditions. There was a direct correlation between the degree of inhibition and the rate of glucose utilization by the various bacteria, indicating that the antagonism of A. niger by some bacteria in soil was the result primarily of a competition for carbon and that this competition was influenced by other environmental factors, such as pH and clay mineralogy.     

Short-Term Response of Soil Bacteria to Carbon Enrichment in Different Soil Microsites

The response of bacteria in bulk soil and earthworm casts to carbon enrichment was studied by an RNA stable-isotope probing/terminal restriction fragment length polymorphism strategy with ¹³C-labeled glucose and acetate. Both the soil microsite status and the carbon enrichment selected rapidly for different active bacterial communities, which resulted in different degradation kinetics. Our study clearly illustrates the biases that are generated by adding C substrates to detect metabolically active bacteria in soil.     

Degradation of Soil Humic Extract by Wood- and Soil-Associated Fungi, Bacteria, and Commercial Enzymes

Abstract An alkaline humic extract (HE) of a black calcareous forest mull was exposed to 36 fungal and 9 eubacterial isolates in liquid standing culture. At 21 d in fungi, and 4 d in bacteria, the groups of wood-degrading basidiomycetes, terricolous basidiomycetes, ectomycorrhizal fungi, soil-borne microfungi, and eubacteria had reduced the absorbance (A ₃₄₀) of HE media by 57, 28, 19, 26 and 5%, respectively. Gel permeation chromatography revealed that the large humic acid molecules were more readily degraded than the smaller fulvic acid molecules and served as a sole source of carbon and energy. The more active HE degraders reduced the overall molecular weight of humic and fulvic acids by 0.25 to 0.47 kDa. They also reduced the chemical reactivity of HE to tetrazotized o-dianisidine, indicating the degradation of hydroxylated aromatic molecules (which are responsible for this reaction). Decreases in absorbance, molecular weight, and reactivity were caused by fungal manganese peroxidase, horseradish peroxidase, β-glucosidase, and abiotic oxidants such as H₂O₂ and Mn(III) acetate. It is concluded that fungi, some of which are propagated in contaminated soils to control xenobiotics, metabolize HE compounds enzymatically. They use enzymes which are also involved in the degradation of soil xenobiotics. Because of reductions in the molecular weight of HE, which is a potential carrier of heavy metal ions and xenobiotics, solubility and motility of humic substances in soil and surface waters are increased. Received: 4 March 1998; Accepted: 1 June 1998     

Effect of Cadmium on Fungi and on Interactions Between Fungi and Bacteria in Soil: Influence of Clay Minerals and pH

Fungi (Rhizopus stolonifer, Trichoderma viride, Fusarium oxysporum f. sp. conglutinans, Cunninghamella echinulata, and several species of Aspergillus and Penicillium) tolerated higher concentrations of cadmium (Cd) when grown in soil than when grown on laboratory media, indicating that soil mitigated the toxic effects of Cd. In soil amended with clay minerals, montmorillonite provided partial or total protection against fungistatic effects of Cd, whereas additions of kaolinite provided little or no protection. Growth rates of Aspergillus niger were inhibited to a greater extent by 100 or 250 μg of Cd per g in soil adjusted to pH 7.2 than in the same soil at its natural pH of 5.1. However, there were no differences in the growth rates of Aspergillus fischeri with 100 or 250 μg of Cd per g in the same soil, whether at pH 5.1 or adjusted to pH 7.2. Growth of A. niger and A. fischeri in a soil contaminated with a low concentration of Cd (i.e., 28 μg/g), obtained from a site near a Japanese smelter, did not differ significantly from growth in a soil collected some distance away and containing 4 μg of Cd per g. Growth of A. niger in sterile soil amended with 100 μg of Cd per g and inoculated with Bacillus cereus or Agrobacterium tumefaciens was reduced to a greater extent than in the same soil containing 100 μg of Cd per g but no bacteria. The inhibitory effects of Agrobacterium radiobacter to A. niger were slightly reduced in the presence of 100 μg of Cd per g, whereas the inhibitory effects of Serratia marcescens were enhanced.     

Deeper Snow Enhances Winter Respiration from Both Plant-associated and Bulk Soil Carbon Pools in Birch Hummock Tundra

It has only recently become apparent that biological activity during winter in seasonally snow-covered ecosystems may exert a significant influence on biogeochemical cycling and ecosystem function. One-seventh of the global soil carbon pool is stored in the bulk soil component of arctic ecosystems. Consistent climate change predictions of substantial increases in winter air temperatures and snow depths for the Arctic indicate that this region may become a significant net annual source of CO₂ to the atmosphere if its bulk soil carbon is decomposed. We used snow fences to investigate the influence of a moderate increase in snow depth from approximately 0.3 m (ambient) to approximately 1 m on winter carbon dioxide fluxes from mesic birch hummock tundra in northern Canada. We differentiated fluxes derived from the bulk soil and plant-associated carbon pools using an experimental ‘weeding’ manipulation. Increased snow depth enhanced the wintertime carbon flux from both pools, strongly suggesting that respiration from each was sensitive to warmer soil temperatures. Furthermore, deepened snow resulted in cooler and relatively stable soil temperatures during the spring-thaw period, as well as delayed and fewer freeze–thaw cycles. The snow fence treatment increased mean total winter efflux from 27 to 43 g CO₂-C m⁻². Because total 2004 growing season net ecosystem exchange for this site is estimated at 29–37 g CO₂-C m⁻², our results strongly suggest that a moderate increase in snow depth can enhance winter respiration sufficiently to switch the ecosystem annual net carbon exchange from a sink to source, resulting in net CO₂ release to the atmosphere.     

Alteration of Soil Carbon Pools and Communities of Mycorrhizal Fungi in Chaparral Exposed to Elevated Carbon Dioxide

We examined the effects of atmospheric carbon dioxide (CO₂) enrichment on belowground carbon (C) pools and arbuscular mycorrhizal (AM) fungi in a chaparral community in southern California. Chambers enclosing intact mesocosms dominated by Adenostoma fasciculatum were exposed for 3.5 years to CO₂ levels ranging from 250 to 750 ppm. Pools of total C in bulk soil and in water-stable aggregates (WSA) increased 1.5- and threefold, respectively, between the 250- and 650-ppm treatments. In addition, the abundance of live AM hyphae and spores rose markedly over the same range of CO₂, and the community composition shifted toward dominance by the AM genera Scutellospora and Acaulospora. Net ecosystem exchange of C with the atmosphere declined with CO₂ treatment. It appears that under CO₂ enrichment, extra C was added to the soil via AM fungi. Moreover, AM fungi were predominant in WSA and may shunt C into these aggregates versus bulk soil. Alternatively, C may be retained longer within WSA than within bulk soil. We note that differences between the soil fractions may act as a potential feedback on C cycling between the soil and atmosphere.     

Antioxidant Activity in Fungi Degrading Lignocellulose Substrates

Considerable differences in lignin degradation by fungi of two ecological groups have been revealed. Xylotrophs cause a twofold decrease in the molecular weight of lignin. The degrading activity of saprotrophs is insignificant. Xylotrophs demethoxylate and oxidize lignin more rapidly than saprotrophs, showing a higher level of antioxidant activity. As follows from the comparison of the degrading and antioxidative effects, measurement of the antioxidant activity can be used in screening of fungi for the ability to degrade lignocellulose substrates.     

Comparison of the Influence of Carbon Substrates on the Fibrolytic Activities of Anaerobic Rumen Fungi

Cellulolytic and xylanolytic activities among genera of anaerobic fungi when grown on glucose, xylan and the cellulosic substrates, filter paper and Avicel were compared. All the fungi had basal extracellular fibrolytic activities that could be enhanced by growth on xylan or the cellulosic substrates. However,Piromyces communisstrain 22 andNeocallimastix patriciarumstrain 27 had substantially greater levels of fibrolytic activity thanOrpinomyces joyoniistrain 19-2 orNeocallimastix frontalisstrain RE1. Zymogram analysis suggested both structural and regulatory differences amongst the enzyme systems of the fungi. Numerous and varied enzyme bands were evidenced for all the fungi, with substantial substrate influences seen in the xylanase activities. Most commonly the smaller molecular weight bands, found exclusively extracellularly, appeared under the greatest regulatory control. Endoglucanase activities ofP. communisandO. joyoniidemonstrated similar regulatory control, while those of the twoNeocallimastixstrains did not appear to exert such control. These results suggest that while the enzymatic activities are functionally similar, there are likely significant variations in the enzyme systems of the anaerobic fungi.     

丛枝菌根真菌对羊草生物量和氮磷吸收及土壤碳的影响

采用大田试验的方法在内蒙古锡林格勒草原进行牧草接种试验,通过灭菌和未灭菌两种土壤研究接种丛枝菌根真菌Glomus mosseae和Glomus claroidium对内蒙古典型草原优势种羊草生长的影响.结果显示,接种丛枝菌根真菌对羊草的地上部干重未产生显著影响,但向未灭菌土壤中接种能显著增加羊草根系量,同时接种G.mosseae显著增加了地上部的N、P含量及吸收量,有效地改善了植株N、P营养,提高了牧草品质;2种菌对根系的营养吸收影响不同,接种G.mosseae在灭菌土壤和未灭菌土壤中均能显著增加根系的N、P吸收量,而接种G.claroidium仅在土壤未灭菌状态下增加根系N、P吸收量;接种对土壤中的菌丝密度未产生显著影响,但接种后土壤中微生物量碳有增加的趋势,短期内难以观察到接种对土壤有机碳的影响.研究表明,丛枝菌根真菌能够提高牧草对N、P吸收,促进牧草的生长,改善牧草品质,增强牧草根际微生物量碳.     

Deterministic Three-Half-Order Kinetic Model for Microbial Degradation of Added Carbon Substrates in Soil

The kinetics of mineralization of carbonaceous substrates has been explained by a deterministic model which is applicable to either growth or nongrowth conditions in soil. The mixed-order nature of the model does not require a priori decisions about reaction order, discontinuity period of lag or stationary phase, or correction for endogenous mineralization rates. The integrated equation is simpler than the integrated form of the Monod equation because of the following: (i) only two, rather than four, interdependent constants have to be determined by nonlinear regression analysis, (ii) substrate or product formation can be expressed explicitly as a function of time, (iii) biomass concentration does not have to be known, and (iv) the required initial estimate for the nonlinear regression analysis can be easily obtained from a linearized form rather than from an interval estimate of a differential equation. ¹⁴CO₂ evolution data from soil have been fitted to the model equation. All data except those from irradiated soil gave better fits by residual sum of squares (RSS) by assuming growth in soil was linear (RSS = 0.71) as opposed to exponential (RSS = 2.87). The underlying reasons for growth (exponential versus linear), no growth, and relative degradation rates of substrates are consistent with the basic mechanisms from which the model is derived.     

Trichloroethylene Degradation by Toluene-Oxidizing Bacteria Grown on Non-aromatic Substrates

The potential of trichloroethylene (TCE) to induce and non-aromatic growth substrates to support TCE degradation in five strains (Pseudomonas mendocina KR1, Ralstonia pickettii PKO1, Pseudomonas putida F1, Burkholderia cepacia G4, B. cepacia PR1) of toluene-oxidizing bacteria was examined. LB broth and acetate did not support TCE degradation in any of the wild-type strains. In contrast, fructose supported the highest specific levels of TCE oxidation observed in each of the strains tested, except B. cepacia G4. We discuss the potential mechanisms and implications of this observation. In particular, cells of P. mendocina KR1 degraded significant amounts of TCE during cell growth on non-aromatic substrates. Apparently, TCE degradation was not completely constrained by any given factor in this microorganism, as was observed with P. putida F1 (TCE was an extremely poor substrate) or B. cepacia G4 (lack of oxygenase induction by TCE). Our results indicate that multiple physiological traits are required to enable useful TCE degradation by toluene-oxidizing bacteria in the absence of aromatic cosubstrates. These traits include oxygenase induction, effective TCE turnover, and some level of resistance to TCE mediated toxicity.     

Utilization of Dichloromethane by Suspended and Fixed-Film Bacteria

Dichloromethane (methylene chloride) was biodegraded by and supported growth of suspended and fixed-film bacteria enriched from sewage.