Rhae A. Drijber

Changes in soil microbial community structure with tillage under long-term wheat-fallow management

Fatty acid methyl esters (FAMEs) were used to ‘fingerprint’ soil microbial communities that evolved during 25 years of wheat-fallow cropping following native mixed prairie sod at Sidney, Nebraska, USA. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs) were compared for their ability to discriminate between plots remaining in sod and those cropped to wheat or left fallow under no-till, sub-till or plow management. Cropped plots were higher in microbial biomass than their fallowed counterparts, and did not diAer significantly with tillage for the 0‐15 cm depth. Under fallow, microbial biomass was greatest in no-till and least in plow. Both cluster and discriminant analysis of PL- and EL-FAMEs clearly separated the remaining native sod plots from the existing wheat-fallow plots. This separation was particularly pronounced for the EL-FAMEs and was largely driven by high amounts in sod of a single FAME, C16:1(cis11), which has been cited as a biomarker for arbuscular mycorrhizal (AM) fungi. Within wheat-fallow, C16:1(cis11) declined significantly from no-till to plow, which supports the origin of C16:1(cis11) from extraradical mycelium and spores of AM fungi known to be sensitive to soil disturbance. Although discriminant analysis of PL- and EL-FAMEs diAerentiated wheat and fallow systems by tillage, discrimination among tillage treatments was expressed most strongly during fallow. FAME profiles from fallow plow were most dissimilar from cropped soils which suggests a relationship between tillage management and the long-term resiliency of the microbial community developed under the wheat crop. 7 2000 Elsevier Science Ltd. All rights reserved.

Survey of extreme solvent tolerance in gram-positive cocci: membrane fatty acid changes in Staphylococcus haemolyticus grown in toluene.

ABSTRACT We exploited the unique ecological niche of oil fly larval guts to isolate a strain of Staphylococcus haemolyticus which may be the most solvent-tolerant gram-positive bacterium yet described. This organism is able to tolerate 100% toluene, benzene, and p-xylene on plate overlays and saturating levels of these solvents in monophasic liquid cultures. A comparison of membrane fatty acids by gas chromatography after growth in liquid media with and without toluene showed that in cells continuously exposed to solvent the proportion of anteiso fatty acids increased from 25.8 to 33.7% while the proportion of 20:0 straight-chain fatty acids decreased from 19.3 to 10.1%. No changes in the membrane phospholipid composition were noted. Thus, S. haemolyticus alters its membrane fluidity via fatty acid composition to become more fluid when it is exposed to solvent. This response is opposite that commonly found in gram-negative bacteria, which change their fatty acids so that the cytoplasmic membrane is less fluid. Extreme solvent tolerance in S. haemolyticus is not accompanied by abnormal resistance to anionic or cationic detergents. Finally, six strains of Staphylococcus aureus and five strains of Staphylococcus epidermidis, which were not obtained by solvent selection, also exhibited exceptional solvent tolerance.

A long-term nitrogen fertilizer gradient has little effect on soil organic matter in a high-intensity maize production system

Global maize production alters an enormous soil organic C (SOC) stock, ultimately affecting greenhouse gas concentrations and the capacity of agroecosystems to buffer climate variability. Inorganic N fertilizer is perhaps the most important factor affecting SOC within maize-based systems due to its effects on crop residue production and SOC mineralization. Using a continuous maize cropping system with a 13 year N fertilizer gradient (0-269 kg N ha(-1) yr(-1)) that created a large range in crop residue inputs (3.60-9.94 Mg dry matter ha(-1) yr(-1)), we provide the first agronomic assessment of long-term N fertilizer effects on SOC with direct reference to N rates that are empirically determined to be insufficient, optimum, and excessive. Across the N fertilizer gradient, SOC in physico-chemically protected pools was not affected by N fertilizer rate or residue inputs. However, unprotected particulate organic matter (POM) fractions increased with residue inputs. Although N fertilizer was negatively linearly correlated with POM C/N ratios, the slope of this relationship decreased from the least decomposed POM pools (coarse POM) to the most decomposed POM pools (fine intra-aggregate POM). Moreover, C/N ratios of protected pools did not vary across N rates, suggesting little effect of N fertilizer on soil organic matter (SOM) after decomposition of POM. Comparing a N rate within 4% of agronomic optimum (208 kg N ha(-1) yr(-1)) and an excessive N rate (269 kg N ha(-1) yr(-1)), there were no differences between SOC amount, SOM C/N ratios, or microbial biomass and composition. These data suggest that excessive N fertilizer had little effect on SOM and they complement agronomic assessments of environmental N losses, that demonstrate N2 O and NO3 emissions exponentially increase when agronomic optimum N is surpassed.

Arbuscular mycorrhizal fungi differ in their ability to regulate the expression of phosphate transporters in maize (Zea mays L.)

Previous studies have found that some phosphate (Pi) starvation inducible transporter genes are downregulated and arbuscular mycorrhizal (AM) inducible Pi transporter genes are upregulated in maize roots associated with the fungus Glomus intraradices. However, little is known about the functional diversity of different AM fungal species in influencing the expression of Pi transporters in maize roots. Here, we studied the expression of two Pi transporter genes ZEAma:Pht1;3 (Pi starvation inducible) and ZEAma:Pht1;6 (AM inducible) in maize root colonized by different AM fungal inoculants. Non-mycorrhizal maize, maize colonized by Glomus deserticola (CA113), Glomus intraradices (IA506), Glomus mosseae (CA201), Gigaspora gigantea (MN922A) and the co-inoculation of all four species were established. The expression patterns of the two genes were quantified using real-time, reverse transcription polymerase chain reaction. The expression level of ZEAma:Pht1;6 was 26–135 times higher in AM plants than in non-mycorrhizal maize roots, whereas the expression level of ZEAma:Pht1;3 was five to 44 times lower in AM plants than in non-mycorrhizal plants. Expression of the two genes differed with inoculation treatment, and increasing the diversity of AM fungi in maize roots led to greater expression of ZEAma:Pht1;6 as well as Pi uptake in shoots. The expression of ZEAma:Pht1;6 was significantly positively correlated with AM colonization rate, concentration of AM biomarkers in maize roots, Pi uptake and dry weight of shoot, but negatively correlated with the expression of ZEAma:Pht1;3. Addition of Pi fertilizer at a low concentration significantly increased the expression of ZEAma:Pht1;6 but had no effect on the expression of ZEAma:Pht1;3.

Rapid spectrophotometric determination of 2,4,6-trinitrotoluene in a Pseudomonas enzyme assay

Although TNT (2,4,6-trinitrotoluene) and its degradation products can be quantified by HPLC, this method is not suitable for simultaneous analyses of the numerous samples typically encountered in enzyme studies. To solve this problem, we developed a simple and rapid spectrophotometric assay for TNT and tested the procedure using partially purified nitroreductase(s) from a Pseudomonas aeruginosa isolate, which transformed TNT in the culture medium. In highly alkaline solution, TNT (pK(a)=11.99) exhibits significant absorbance at 447 nm, while major metabolites, 2-amino-4, 6-dinitrotoluene (2ADNT), 4-amino-2,6-dinitrotoluene (4ADNT), and 2,6-diamino-4-nitrotoluene (2,6DANT) display no absorbance at this wavelength. Assay mixtures of TNT, Tris-HCl buffer, a reductant, and the enzyme(s) were analyzed by measuring absorbance 4 min after adjusting the pH to 12.2. TNT transformation to colorless metabolites was linear with respect to protein and substrate concentrations. Using the assay, we determined that TNT nitroreductase(s) from the isolate required an electron donor and preferred NADH to NADPH. TNT transformation increased when NAD was recycled to NADH using glucose-6-phosphate (GP) and glucose-6-phosphate dehydrogenase (GPDH). Enzymatic transformation of TNT was completely inhibited by Cu(2+) (5 mM) and was partially inhibited by other divalent metallic cations. Because the assay is sensitive to ammonium sulfate, dithiothreitol, ascorbic acid, and sodium phosphate, extracts should be assayed in the absence of these components.

Soil Microbial Community Response to Corn Stover Harvesting Under Rain-Fed, No-Till Conditions at Multiple US Locations

Harvesting of corn stover (plant residues) for cellulosic ethanol production must be balanced with the requirement for returning plant residues to agricultural fields to maintain soil structure, fertility, crop protection, and other ecosystem services. High rates of corn stover removal can be associated with decreased soil organic matter (SOM) quantity and quality and increased highly erodible soil aggregate fractions. Limited data are available on the impact of stover harvesting on soil microbial communities which are critical because of their fundamental relationships with C and N cycles, soil fertility, crop protection, and stresses that might be imposed by climate change. Using fatty acid and DNA analyses, we evaluated relative changes in soil fungal and bacterial densities and fungal-to-bacterial (F:B) ratios in response to corn stover removal under no-till, rain-fed management. These studies were performed at four different US locations with contrasting soil-climatic conditions. At one location, residue removal significantly decreased F:B ratios. At this location, cover cropping significantly increased F:B ratios at the highest level of residue removal and thus may be an important practice to minimize changes in soil microbial communities where corn stover is harvested. We also found that in these no-till systems, the 0- to 5-cm depth interval is most likely to experience changes, and detectable effects of stover removal on soil microbial community structure will depend on the duration of stover removal, sampling time, soil type, and annual weather patterns. No-till practices may have limited the rate of change in soil properties associated with stover removal compared to more extensive changes reported at a limited number of tilled sites. Documenting changes in soil microbial communities with stover removal under differing soil-climatic and management conditions will guide threshold levels of stover removal and identify practices (e.g., no-till, cover cropping) that may mitigate undesirable changes in soil properties.

Compost extract enhances desorption of α-naphthol and naphthalene from pristine and contaminated soils

Abstract Enhancing desorption of hydrophobic organic compounds (HOCs) may be necessary to achieve bioremediation of soils. We measured desorption of added α-naphthol and naphthalene in compost extract (200 mg C in 10 mmol l −1 CaCl 2 ) and in 10 mmol l −1 CaCl 2 alone from (i) soils varying in age, diagenesis, and quantity and quality of organic matter, and (ii) wettable and non-wettable soil samples from a 20-y-old oil spill. Compost extract increased desorption of α-naphthol and naphthalene from all soils compared to desorption in CaCl 2 alone, despite the wide range of values among the soils for linear partition coefficients ( K d varied 40-fold for α-naphthol and 50-fold for naphthalene) and partition coefficients normalized for organic C content ( K oc varied 3-fold for α-naphthol and 2.5-fold for naphthalene). The proportional enhancement of desorption tended to be higher for α-naphthol than for naphthalene. No consistent relationship, however, was detected between the character of the soil organic matter, as measured by CPMAS- 13 C NMR, and the magnitude of enhanced desorption. Furthermore, enhanced desorption could not be attributed to surfactant-like activity of the compost extract as measured by a Du Nouy tensiometer. Sorption of the compost extract on soil, however, was substantial ( f oc = 0.047, K d = 0.42) and may have contributed to enhanced desorption of HOCs. Our results reinforce previous reports that dissolved organic C can enhance desorption of HOCs from soils. Our study identified sorption of compost extract C and displacement of sorbed HOCs as a possible mechanism of desorption enhancement meriting further investigation. Furthermore, the enhanced desorption of HOCs in the presence of co-sorbed organic contaminants needs to be addressed.

Soil organic carbon: The value to soil properties

Maintaining or improving soil properties is becoming increasingly important to sustain modern agriculture under increasing demands to preserve biodiversity and environmental quality. Enhancing the inherent capacity of a soil to buffer changes against anthropogenic stresses and extreme climatic events such as droughts, intense rainstorms, heat waves, and floods is also a priority. Managing soil organic carbon (SOC) through optimized management practices is one strategy to enhance soil ecosystem services. Increasing organic C storage in the soil not only sequesters atmospheric C but often enhances soil physical, chemical, and biological processes and properties. Soil organic C has been widely discussed in terms of C sequestration, but its benefits on soil processes and properties have received less attention in recent years. Thus, this article discusses (1) the value of SOC to soil properties and (2) potential for increasing SOC through management. SOIL CARBON DYNAMICS The balance between C inputs and outputs is important to SOC change. Inputs include aboveground and belowground crop residues, animal manure, compost, and others, whereas outputs are losses through water and wind erosion, gas fluxes associated with microbial and plant respiration, and deep leaching. How fast residues decompose following the well-known exponential decay function depends…

Impact of a 5-year winter cover crop rotational system on the molecular diversity of arbuscular mycorrhizal fungi colonizing roots of subsequent soybean

The impact of winter cover crops, specifically wheat (Triticum aestivum L.), red clover (Trifolium pratense L.), and rapeseed (Brassica napus L.) or winter fallow, on community composition of arbuscular mycorrhizal fungi (AMF) in subsequent soybean roots was investigated in a 5-year field trial on andosolic soils in Japan. Soybean roots were sampled at full-flowering and analyzed for AMF communities using a partial LSU rDNA region. Phylogenetic analysis detected 22 AMF phylotypes, including eight Glomus, three Gigaspora, two Scutellospora, three Acaulospora, two Rhizophagus, and one of Funneliformis, Diversispora, Paraglomus, and an unknown glomeromycete in the roots. The 5-year rotation of different winter cover crops or winter fallow did not impact the molecular diversity of AMF communities colonizing the roots of subsequent soybean. In all of the rotations, Glomus and Gigaspora phylotypes were common to soybean roots over the 5-year period. Redundancy analysis (RDA) demonstrated that AMF communities in the roots of subsequent soybean were not significantly different among winter cover crop rotations or fallow. However, AMF communities in soybean roots were clearly influenced by rotation year suggesting that climate or other environmental factors were more important than winter cover cropping system management.

Accelerated Transformation and Binding of 2,4,6-Trinitrotoluene in Rhizosphere Soil

Enhanced microbial activity and xenobiotic transformations take place in the rhizosphere. Degradation and binding of 2,4,6-trinitrotoluene (TNT) were determined in two rhizosphere soils (RS) and compared to respective unplanted control soils (CS). The rhizosphere soils were obtained after growing corn for 70 d in soils containing 2.8% (Soil A) or 5.9% (Soil B) organic matter. Aerobically agitated soil slurries (3:1, solution/soil) were prepared from RS and CS and amended with 75 mg TNT L−1 (14C-labeled). TNT degraded more rapidly and formed more un-extractable bound residue in RS than in CS. In Soil A, total extractable TNT decreased from 225 to 1.0 mg kg−1 in RS, whereas 11 mg kg−1 remained in CS after 15 d. Unextractable bound 14C residues accounted for 40% of the added 14C-TNT in RS and 28% in CS. The smaller differences in Soil B were attributed partially to the higher organic matter content. The predominant TNT degradation products were monoaminodinitrotoluenes (ADNT), which accumulated and disappear...