Elaine R. Ingham

Comparison of direct vs fumigation incubation microbial biomass estimates from ectomycorrhizal mat and non-mat soils

Abstract Direct estimates of microbial biomass were compared to chloroform fumigation incubation estimates of microbial biomass using samples collected from mesic forest stands. Paired soil samples were collected from ectomycorrhizal mats, which contain visible amounts of fungal material, and from non-mat areas immediately adjacent to the mats but which contain no visible fungal material. As much as 30–50% of the dry wt of soil collected from ectomycorrhizal mats can be comprised of strictly fungal biomass. Direct estimates of microbial biomass from both mat and non-mat soils were 10–300 times higher than biomass estimates obtained using the fumigation incubation method. Fumigation incubation estimates of microbial biomass showed little seasonal variation, while direct estimates revealed that microbial biomass peaked during both the spring and fall when rainfall and temperatures were optimal and were lowest during the dry summer. We compared our values to ones reported for shortgrass prairies and in Jenkinsons original fumigation incubation paper. Fumigation incubation estimates indicated that microbial biomass carbon was the same in both prairie and forest soils, about 0.5 mg C g −1 soil. Direct estimates showed that microbial biomass was actually greater, by factors of 10–300, in these forest soils. Some forest soils, for which fumigation incubation indicated very low microbial biomass, contained visible amounts of fungal hyphae. Our conclusion is that fumigation incubation does not necessarily measure microbial biomass, and that the error can be extremely high when soils contain high quantities of fungal biomass.

Population responses of target and non-target forest soil organisms to selected biocides☆

Abstract Oxytetracycline-penicillin (combined), captan, fumigillan and dimethoate-carbofuran (combined) were applied to forest soils to test their effects on soil populations of active and total bacteria, active and total fungi, protozoa, nematodes and microarthropods. All biocides significantly reduced the populations of target organisms, except dimethoate-carbofuran, which failed to reduce the number of microarthropods. All biocides also affected populations of non-target organisms. Oxytetracycline-penicillin reduced lengths of active hyphae. Captan reduced nematode and bacterial numbers. Fumagillin reduced active hyphal lengths and the number of nematodes and total bacteria. Dimethoate-carbofuran reduced active hyphal lengths and the number of active bacteria.

Microbial characteristics of ectomycorrhizal mat communities in Oregon and California

SummarySpecialized ectomycorrhizal fungi form dense mats in forest soils that have different enzyme levels, higher respiration rates, more biomass, different soil fauna, and different soil chemistry compared with adjacent soils not obviously colonized by these mats. In this study, mats formed by two genera of fungi collected in three locations were compared with a wide range of measurements. Per cent moisture, pH, chloroform fumigation-flush C, anaerobic N mineralization, exchangeable ammonium, and respiration, N2 fixation, and denitrification rates were compared between soils or litter colonized by ectomycorrhizal mat-forming fungi and adjacent non-mat material. Significant differences were observed between the two genera of mat-forming fungi and also between mats formed primarily in mineral soil and those formed in litter. These differences suggest that different mat-forming fungi perform different functions in forest soils and that these fungi function differently in mineral soil compared with litter.

Chemistry and microbial activity of forest and pasture riparian-zone soils along three Pacific Northwest streams

Throughout the United States, agricultural practices are responsible for large quantities of nutrients entering lakes and streams. Previous studies have shown that forested riparian areas can filter nutrients from surface runoff and groundwater that may potentially contaminate lakes and streams. This study examined seasonal differences in soil chemistry and soil microorganisms in paired mixed-forest riparian and pasture systems, the aim being to gain understanding of the sequestering of N and P. The forest soils retained higher levels of organic C and N, mineralizable N, extractable P, and fungal biomass, and had higher respiration rates than pasture soils. These findings suggest that forested riparian zones have a greater capacity than pasture soils to sequester C and retain nutrients. In past studies, fungal biomass has been shown to be less than bacterial biomass in grassland soils, but in this study, fungal biomass was greater than bacterial biomass throughout the year in both forest and pasture soils.

Effect of cover crops and tillage system on symphylan (Symphlya: Scutigerella immaculata, Newport) and Pergamasus quisquiliarum Canestrini (Acari: Mesostigmata) populations, and other soil organisms in agricultural soils

Abstract The garden symphylan ( Scutigerella immaculata : Newport) is a common myriapod soil pest of vegetable crops in the Pacific Northwest and other regions of the US. Symphylans consume germinating seeds, plant roots, and above-ground plant parts in contact with the soil. Factors regulating symphylan populations in agricultural soil systems are poorly understood, particularly the effects of farming practices such as cover cropping and reduced-tillage. Cover crops were planted in the fall of 1994 through 1996 and either incorporated into the soil in the spring with tillage or killed with glyphosate and the residue left on the soil surface. Fewer symphylans were recovered with Berlese funnels from soil under cereal cover crops than soil in mustard cover crops, regardless of tillage system. Fewer symphylans were recovered from soil under the spring oat cover crop than soil under the barley cover crop. Eliminating spring tillage may have increased symphylan populations but the effect of reduced tillage on symphylan populations was less important than cover cropping. Predaceous mites were more abundant in soil under large amounts of cover crop residue but these predators were not correlated with lower populations of symphylans. Spring tillage dramatically reduced populations of Pergamasus quisquiliarum , a known predator of symphylans. Cover crops increased both the ratio of predaceous mites to symphylans and the total population of potential prey, thereby, reducing the capacity of predaceous mites to regulate symphylan populations.

Dynamics of soil fungal and bacterial biomass in a temperate climate alley cropping system

Soil bacterial and fungal dynamics were measured in an alley cropping system using direct microscopy techniques. The alley cropping system involved hedgerows of alder trees (Alnus rubra) and sweet corn (Zea mays) grown in the alleys. Trees were periodically coppiced and prunings were incorporated into the soil as green manure. Active fungal and bacterial biomass were greatest in tree rows and declined with distance from the trees. Active fungal biomass was greatest at the first year July sampling, ranging from 44 mg g dry soil ˇ1 in the tree row to 22 mg g dry soil ˇ1 in the middle of the alley. Bacterial biomass in all sampling locations peaked during May before coppicing of trees and cultivation of the alley. Bacterial and fungal biomass in the middle of the alley were similar to sweet corn monocropping plots throughout the growing season. The results suggested that the relatively low pruning biomass that can be produced and incorporated into the soil of temperate climate alley cropping systems compared to tropical alley cropping systems has little effect on microbial biomass. However, additional green manure in the form of leaf fall, additional below ground substrate from tree roots, and favorable conditions in untilled tree rows contribute to higher soil fungal and bacterial counts in and near the tree rows. # 1999 Elsevier Science B.V. All rights reserved.

Responses of soil foodweb organisms in the first year following clearcutting and application of chloropicrin to control laminated root rot

Abstract Alteration in soil foodweb organism populations (numbers, biomass and activity) were monitored following clearcutting of a mature 70-year old Douglas-fir forest and compared with an uncut mature Douglas-fir stand. Changes in soil foodweb organisms were assessed following application of chloropicrin to stumps in the clearcut to reduce infection by Phellinus weirii, which causes laminated root rot. The effect of chloropicrin was measured using two different spatial scales: (1) around treated stumps, and (2) within 0.2 ha areas where all stumps within the area were treated with chloropicrin. A 10-fold decrease in total fungal biomass, between 2- and 3-fold reductions in total bacterial biomass, a 2-fold reduction in nematode numbers and a nearly 10-fold reduction in the ratio of total fungal to total bacterial biomass were observed between 9 months to a year following clearcutting. Active fungal biomass in the 20% chloropicrin treatment was reduced 1 year (October) after application. Reduction in amoebae numbers were observed between April and June in the 100% chloropicrin treatments, while no effects of chloropicrin on total fungal biomass, total bacterial biomass, flagellate, ciliate or nematode numbers were observed. The ratio of total fungal to total bacterial biomass was reduced as compared to the control in the 100% chloropicrin-treated infected areas in April following chloropicrin treatment. Chloropicrin decreased soil foodweb organisms in only one out of 45 random soil samples from 0.2 ha areas. In samples collected from around stumps, three points out of 180 had significant decreases in all organism numbers as compared to non-chloropicrin treated stumps. Chloropicrin-sensitive tomato and alfalfa seedlings, planted at 2 m from stumps to monitor the release of chloropicrin from stumps, indicated there was no significant release of chloropicrin in the first year following clearcutting and chloropicrin application.

Ectomycorrhizae establishment on Douglas-fir seedlings following chloropicrin treatment to control laminated-root rot disease: Assessment 4 and 5 years after outplanting

Abstract Laminated-root rot, caused by Phellinus weirii (Murr.) Gilb., is a serious disease affecting Douglas-fir and other commercially important species of conifers in northwestern North America. Recent work has shown that this fungus is successfully reduced or eliminated by the fumigant chloropicrin. However, the effect of this biocide on nontarget organisms, including ectomycorrhizae, is uncertain. Following an initial assessment of organisms 2 years after application of the fumigant, a reassessment of the establishment of ectomycorrhizae on Douglas-fir seedlings was undertaken 4.5 and 5.5 years following chloropicrin application. Our findings show that in areas around stumps treated with 20% and 100% of the labeled dosage and in areas around non-treated stumps, chloropicrin did not adversely affect the formation of ectomycorrhizae on young Douglas-fir seedlings by naturally occurring fungi. No significant effect on the abundance or type of mycorrhizae were detected. On this site, chloropicrin did not affect these mycorrhizal associations, at least for 5 years following application.

Effects of Klebsiella planticola SDF20 on soil biota and wheat growth in sandy soil

Abstract The potential for ecological effects to occur after the release of genetically engineered microorganisms is a global concern and the release of biotechnology products must be assessed on a case-by-case basis. In this research, a genetically engineered strain of Klebsiella planticola (SDF20) bacteria was added to microcosms containing sandy soil and wheat plants to assess the potential for effects on soil biota and plant growth. One half of the soil treatments in this study contained wheat plants to compare some effects on growing rhizosphere communities in the experimental system. When SDF20 was added to soil with plants, the numbers of bacterial and fungal feeding nematodes increased significantly, coinciding with death of the plants. In contrast, when the parental strain, SDF15 was added to soil with plants, only the number of bacterial feeding nematodes increased, but the plants did not die. The introduction of either SDF15 or SDF20 strains to soil without plants did not alter the nematode community. No effects were observed on the activity of native bacterial and fungal communities by either SDF15 or SDF20. This study is evidence that SDF20 can persist under conditions found in some soil ecosystems and for long enough periods of time to stimulate change in soil biota that could affect nutrient cycling processes. Further investigation is needed to determine the extent these observations may occur in situ but this study using soil microcosms was the first step in assessing potential for the release of genetically engineered microorganisms to result in ecological effects.

Assessing interactions between the soil foodweb and a strain of Pseudomonas putida genetically engineered to degrade 2,4-D

Abstract The addition of nonindigenous microorganisms to soil can alter the structure of the soil foodweb and, consequently, the manner in which nutrients cycle through soil. Alterations in the cycling of nutrients through soil may, in turn, affect the growth, reproduction, and competitive ability of the vegetative community. To assess the effectsof introduced organisms on soil foodwbs, a xeric soil was amended with 500 μg g−1 of the herbicide 2,4-D and inoculated with either the genetically engineered organisms (GEM) Pseudomonas putida PP0301(pRO103) or P. putida PP0301 (the wild-type strain), as well as controls where no 2,4-D was added. Plasmid pRO103 contains constitutively expressed genes that encode for the mineralization of phenoxyacetate and the partial degradation of 2,4-D. Soil for this study was collected from the same site as the soil used in previous studies, but was not amended with glucose. Degradation of 2,4-D was not detected during the course of this study, although isolates of P. putida PPO301(pRO103) obtained from soil amended with 2,4-D at the end of of the study were able to catabolize phenoxyacetate in pure culture, suggesting that they retained the constitutive pathway for the partial degradation of 2,4-D. In all treatments amended with 2,4-D (with or without added PP0301(pRO103) or PP0301), active fungal biomass, active bacterial biomass, plate count estimates of bacteria, numbers of nitrifying bacteria, and numbers of flagellates and amoebae decreased. In soil without 2,4-D treatment and inoculated with the GEM, PP0301(pRO103) , active fungal biomass and total fungal biomass was reduced relative to that inoculated with PP0301. Increases in protozoan biomass were clearly evident in unamended soil inoculated with either PP0301(pRO103) or PP0301. The GEM had no continuing effects on the structure and function of the soil foodweb relative to the wild-type strain, in contrast to previous studies where 2,4-D was degraded and the fungal community was affected throughout the experiment.