Linking Microbial-Scale Findings to Farm-Scale Outcomes in a Dryland Cropping System

Soil biological response to management is best evaluated in field-scale experiments within the context of the soil environment and crop; however, cost-effective methods are lacking to relate these data which span multiple spatial scales. We hypothesized that zones of apparent electrical conductivity (EC_a) could be used to integrate soil properties (sampling-site scale), microbial-scale measures of vesicular-arbuscular mycorrhizal (VAM) fungi, and field-scale wheat yields from yield maps. An on-farm dryland experiment (250 ha) was established wherein two (32-ha) fields were assigned to each phase of a winter wheat (Triticum aestivum L.) – corn (Zea mays L.) – proso millet (Panicum miliaceum L.) – fallow rotation. Each field was mapped and classified into four zones (ranges) of EC_a. Soil samples were collected from geo-referenced sites within EC_a zones and analyzed for multiple soil properties associated with productivity (0–7.5 and/or 0–30 cm). Additionally, VAM fungi were assessed using C16:1(cis)11 fatty acid methyl ester biomarker (C16_vam), glomalin immunoassay, and wet-aggregate stability (WAS) techniques (1–2mm aggregates from 0- to 7.5-cm soil samples). Concentrations of C16_vam and WAS increased among cropping treatments as: fallow < wheat < corn < millet. Glomalin across crops and replicates, C16_vam and WAS in fallow (crop effect removed), soil properties associated with productivity, and wheat yields were negatively correlated with EC_a and different among EC_a zones (P 0.05). Zones of EC_a provide a point of reference for relating data collected at different scales. Monitoring cropping system parameters and profitability, over time, may allow linkage of microbial-scale processes to farm-scale economic and ecological outcomes.     

Diversity and vertical distribution of indigenous arbuscular mycorrhizal fungi under two soybean rotational systems

To evaluate the importance of arbuscular mycorrhizal fungi (AMF) to crop production, it is imperative to move beyond the plow layer to include the full soil profile impacted by plant roots. To illustrate this, we investigated the vertical distribution of AMF biomass and community structure within the top 100 cm of soil in soybean (Glycine max (L.) Merr., cv: Enrei) rotational systems cropped to wheat (Triticuma estivum L. cv: Bandowase) or left fallow using fatty acid methyl ester (FAME) biomarkers and molecular analysis, respectively. AMF biomass, as measured by concentration of C16:1cis11, declined during fallow and with increasing soil depth. Greater than 50 % of the stored AMF biomass was found at depths below 35 cm. Phylogenetic analysis revealed 16 AMF phylotypes, including nine Glomus, two Gigaspora, two Scutellospora, and one each of Diversispora, Paraglomus, and an unknown glomeromycete, at different sampling depths in this study. Cluster analysis based on the number and abundance of each AMF phylotype formed two distinct clusters separating wheat from fallow rotations. There was no distinct relationship with soil depth beyond clustering AMF communities above and below 20 cm under wheat. Redundancy analysis (RDA) and hierarchical cluster analysis demonstrated that AMF communities by soil depth within each rotation were not significantly different. However, AMF communities were clearly influenced by crop rotation, where the distribution of specific AMF phylotypes responded to the presence of the wheat crop.     

Sorghum growth,root responses,and soil‐solution aluminum and manganese on pH‐stratified sandy soil§

A stratified subsurface layer of acidic soil can develop in minimally disturbed soil such as no‐till receiving injection of N fertilizer (e.g., anhydrous ammonia). The objective of this study was to evaluate the effectiveness of subsurface band treatments in alleviating soluble Al³⁺ and Mn²⁺ toxicities on sorghum growth. Soil columns 40 cm in length were packed with soil (Valentine fine sand mixed mesic Typic Ustipsamment and Thurman loamy sand mixed Mesic Udorhentic Haplustoll) with treatments applied at the 10–18 cm depth to mimic soil pH stratification. The treatments at this depth were: (1) entire layer at soil pH of 3.7; (2) band of soil 6 cm wide at pH of 5.8 with the rest of the soil at pH 3.7; (3) band of soil 6 cm wide at pH of 6.3 with the rest of the soil at pH 3.7; and (4) entire layer at soil pH of 5.8. The soil above and below the 10–18 cm depth was at pH 5.8. Sorghum (Sorghum bicolor L. Moench) was grown in the soil columns under a controlled environment for 6 weeks. High concentration of Al in soil solution was found in soil at soil pH 3.7 which was overcome by either banding to pH 5.8, 6.3, or having the soil layer at pH 5.8. Treatment with pH of 5.8 throughout the soil 10–18 cm depth produced significantly greater top growth, although all other pH or liming strategies performed better than the soil pH 3.7 treatment. The banded treatments at pH 5.8 and 6.3 allowed roots to grow below the 10–18 cm layer of soil, but root growth was still significantly less than in the soil where the entire soil treatment layer was at pH 5.8. The increase in biomass yield with soil pH of 5.8 in the entire treatment layer was higher compared to band treatment at pH 5.8; however, the lime requirement would be 3.4 times more with liming the entire layer compared to banding a portion of the soil to pH 5.8 and would thus be translated into a higher liming cost.     

A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

Although arbuscular mycorrhizal fungi (AMF) are crucial for ecosystem functioning, characterizing AMF community structure in soil is challenging. In this study, nested polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined with cloning of fungal 18S ribosomal gene fragments for the rapid comparison of AMF community structure in soil. Reference AMF isolates, representing four major genera of AMF, were used to develop the method. Sequential amplification of 18S rDNA fragments by nested PCR using primer pairs AM1-NS31 and Glo1-NS31GC followed by DGGE analysis yielded a high-resolution band profile. In parallel, 18S rDNA fragment clone libraries were constructed and clones screened by DGGE. Sequence identity was inferred by matching the electrophoretic mobility of the sample fingerprint bands to that of bands from individual clones. The effectiveness of this approach was tested on soil samples from different ecosystems, yielding reproducible, complex DGGE band patterns specific to each site. The coupling of PCR–DGGE with clone library analysis provides a robust, reliable, and precise means to characterize AMF community structure in soils.     

Soil attributes in a furrow-irrigated bed planting system in northwest Mexico

In the Yaqui valley, northwest Mexico, wheat (Triticum aestivum L.) is grown as a winter crop followed by maize (Zea mays L.) as a summer crop both planted on beds. Straw of both crops is usually burned to facilitate seedbed preparation for the succeeding crop. Soil physical and biological attributes were determined from 1996 to 2000 from a study initiated in 1992 at the CIANO (Centro de Investigaciones Agrícolas del Noroeste) experiment station. The objective was to compare five treatments: (1) conventional tilled bed (CTB)-straw incorporated, and permanent bed (PB) with (2) straw removed, (3) straw partly removed, (4) straw retained, and (5) straw burned — on soil strength, soil structure, and soil microbial biomass carbon (SMB). Seven N treatments were applied to wheat, but for the purpose of this study we chose a subset of three N treatments (0, 150 and 300 kg N ha⁻¹) for measurements. Maize received a uniform application of 150 kg N ha⁻¹ each year. Soil strength decreased as the amount of crop residues applied for each tillage-straw treatment increased. Permanent beds-straw burned treatment had the highest soil strength and CTB-straw incorporated the lowest. The largest soil aggregate fractionation, evaluated with a fractal dimension parameter (D), corresponded to PB-straw burned treatment and the lowest to PB-straw retained treatment. SMB was greater at 0–7 cm than at 7–15 cm depth. As the amount of crop residues increased in each tillage PB-straw treatment, the SMB generally increased. The largest amount of SMB occurred most often on either CTB-straw incorporated or PB-straw retained and the lowest in PB-straw burned treatment. The practice of retaining crop residues as stubble should be adopted in the Yaqui valley since changes resulting from burning crop residues showed the tendency to decrease productivity and soil quality as shown by increased soil strength and soil fractionation, and reduced SMB.     

Redistribution of crop residues during row cultivation creates a biologically enhanced environment for soil microorganisms

Formation of ridges during row cultivation creates microsites that could enhance spatial heterogeneity of soil properties, such as organic C, and thereby influence soil microbial communities. A study was conducted during 2003 near Shelton, NE, on a corn (Zea mays L.) field mapped using apparent electrical conductivity (ECa). New ridges were built each year with a row cultivator when corn reached the V3–V4 growth stage. Cultivation increased labile C fractions and soil microbial biomass in the row position for all ECa classes. Canonical discrimination analysis showed no clear differences in relative abundance of specific microbial groups among ECa classes or between row and furrow position, except for enhanced mycorrhizal biomass in the row. Microbial biomass responded strongly to changes in C redistribution, but was not accompanied by a significant change in the abundance of specific microbial groups. Labile C fractions (coarse and fine particulate organic matter) and crop residues in diverse stages of decomposition are associated with diverse microbial groups. Thus, row cultivation for weed control creates a biologically enhanced root zone that may improve early season performance of corn.     

Microbial biomass,functional capacity,and community structure after 12 years of soil warming

We examined the effect of chronic soil warming on microbial biomass, functional capacity, and community structure in soil samples collected from the Soil Warming Study located at the Harvard Forest Long-term Ecological Research (LTER) site. Twelve years of chronic soil warming at 5 °C above the ambient temperature resulted in a significant reduction in microbial biomass and the utilization of a suite of C substrates which included amino acids, carbohydrates, and carboxylic acids. Heating significantly reduced the abundance of fungal biomarkers. There was also a shift in the mineral soil microbial community towards gram positive bacteria and actinomycetes.     

Labile soil organic matter as a potential nitrogen source in golf greens

The loss of fertilizer N from golf greens can be high depending upon management (irrigation schedule, N source, rate and timing of fertilizer application) as well as soil conditions. Although soil organic matter (SOM) is acknowledged as a major source of N and other nutrients, its potential as an N source seems to be neglected in the management of golf greens. The susceptibility of SOM to degradation is one indication of how active a role SOM plays as a nutrient source. An extraction method developed by Olk et al. [Geoderma 65 (1995) 195] distinguishes humic acid fractions by their binding to dominant stabilizing soil cations and separates them into calcium-bound (CaHA) and non calcium-bound or mobile (MHA) fractions. Mobile humic acid is a relatively young, N-rich HA fraction that does not appear to form stable complexes with Ca. The MHA could therefore play a greater role in nutrient availability than CaHA. We determined C and N distributions within SOM extracted from these two HA fractions in 11 golf greens ranging in age from 4 to 28 yr. Because SOM in golf greens is recently formed, and MHA is an N-rich fraction representing an early stage of SOM evolution, we hypothesized that the MHA fraction would account for a larger proportion of soil organic N than CaHA. The amounts of both HA-C and HA-N increased significantly with green age. MHA accounted for a larger proportion (20-27%) of total soil C than CaHA-C (8-14%). MHA was also enriched in N compared to CaHA with consistently smaller C-to-N ratios. Thus, the greater abundance of MHA and its higher N concentration accounted for a larger proportion of soil organic N (24-45%). The equivalence of MHA-N ranged between 250 kg N ha⁻¹ for a 4 yr-old green and 775 kg N ha⁻¹ for a 21 yr-old green. Thus, soils of established greens contain significant quantities of labile SOM rich in N that could through mineralization supply part of the fertilizer N requirement of turf grass. A greater understanding of the dynamics of this resource is needed if we are to manage golf greens for optimal use without negative consequences to the environment.     

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.