Kermit Cromack

Calcium oxalate accumulation and soil weathering in mats of the hypogeous fungus Hysterangium crassum

Abstract Fungal mats of Hysterangium crassum (Tul. and Tul.) Fischer occupied a mean of 9.6% of the upper 10 cm of soil developed under a 40–65 yr old stand of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in Oregon. This hypogeous basidiomycete exudes large amounts of oxalic acid, some of which precipitates with Ca in microscopic crystals of calcium oxalate, resulting in a mean CaC2O4 content of 82g m−2 for the entire soil. Soil oxalate concentration was significantly greater within fungal mats (P

Community Composition and Functioning of Denitrifying Bacteria from Adjacent Meadow and Forest Soils

ABSTRACT We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in α-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.

Cellulose and lignin degradation in forest soils: Response to moisture, temperature, and acidity.

The concentration of lignin in plant tissue is a major factor controlling organic matter degradation rates in forest ecosystems. Microbial biomass and lignin and cellulose decomposition were measured for six weeks in forest soil microcosms in order to determine the influence of pH, moisture, and temperature on organic matter decomposition. Microbial biomass was determined by chloroform fumigation; lignin and cellulose decomposition were measured radiometrically. The experiment was designed as a Latin square with soils of pH of 4.5, 5.5, and 6.5 adjusted to 20, 40, or 60% moisture content, and incubated at temperatures of 4, 12, or 24°C. Microbial biomass and lignin and cellulose decomposition were not significantly affected by soil acidity. Microbial biomass was greater at higher soil moisture contents. Lignin and cellulose decomposition significantly increased at higher soil temperatures and moisture contents. Soil moisture was more important in affecting microbial biomass than either soil temperature or soil pH.

Ammonia-Oxidizing Bacteria along Meadow-to-Forest Transects in the Oregon Cascade Mountains

ABSTRACT Although nitrification has been well studied in coniferous forests of Western North America, communities of NH3-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization and nitrification potential rates changed significantly between vegetation zones. Nonetheless, terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR-amplified NH3 monooxygenase subunit A gene (amoA) showed the same DNA fragments (TaqI [283 bp], CfoI [66 bp], and AluI [392 bp]) to dominate ≥45 of 47 soil samples recovered from both sites. Two fragments (491-bp AluI [AluI491] and CfoI135) were found more frequently in meadow and transition zone soil samples than in forest samples at both sites. At the Lookout site the combination AluI491-CfoI135 was found primarily in meadow samples expressing the highest N mineralization rates. Four unique amoA sequences were identified among 15 isolates recovered into pure culture from various transect locations. Six isolates possessed the most common T-RFLP amoA fingerprint of the soil samples (TaqI283-AluI392-CfoI66), and their amoA sequences shared 99.8% similarity with a cultured species, Nitrosospira sp. strain Ka4 (cluster 4). The other three amoA sequences were most similar to sequences of Nitrosospira sp. strain Nsp1 and Nitrosospira briensis (cluster 3). 16S ribosomal DNA sequence analysis confirmed the affiliation of these isolates with Nitrosospira clusters 3 and 4. Two amoA clone sequences matched T-RFLP fingerprints found in soil, but they were not found among the isolates.

Coupled Nitrogen and Calcium Cycles in Forests of the Oregon Coast Range

Nitrogen (N) is a critical limiting nutrient that regulates plant productivity and the cycling of other essential elements in forests. We measured foliar and soil nutrients in 22 young Douglas-fir stands in the Oregon Coast Range to examine patterns of nutrient availability across a gradient of N-poor to N-rich soils. N in surface mineral soil ranged from 0.15 to 1.05% N, and was positively related to a doubling of foliar N across sites. Foliar N in half of the sites exceeded 1.4% N, which is considered above the threshold of N-limitation in coastal Oregon Douglas-fir. Available nitrate increased five-fold across this gradient, whereas exchangeable magnesium (Mg) and calcium (Ca) in soils declined, suggesting that nitrate leaching influences base cation availability more than soil parent material across our sites. Natural abundance strontium isotopes (87Sr/86Sr) of a single site indicated that 97% of available base cations can originate from atmospheric inputs of marine aerosols, with negligible contributions from weathering. Low annual inputs of Ca relative to Douglas-fir growth requirements may explain why foliar Ca concentrations are highly sensitive to variations in soil Ca across our sites. Natural abundance calcium isotopes (δ44Ca) in exchangeable and acid leachable pools of surface soil measured at a single site showed 1 per mil depletion relative to deep soil, suggesting strong Ca recycling to meet tree demands. Overall, the biogeochemical response of these Douglas-fir forests to gradients in soil N is similar to changes associated with chronic N deposition in more polluted temperate regions, and raises the possibility that Ca may be deficient on excessively N-rich sites. We conclude that wide gradients in soil N can drive non-linear changes in base-cation biogeochemistry, particularly as forests cross a threshold from N-limitation to N-saturation. The most acute changes may occur in forests where base cations are derived principally from atmospheric inputs.

Patterns of basidiomycete nutrient accumulation in conifer and deciduous forest litter

Abstract Nutrient data were obtained for basidiomycete sporocarps, rhizomorphs and forest floor leaf litter samples collected from a white pine (Pinus strobus L.) watershed and from a mixed hardwood watershed at Coweeta Hydrologic Laboratory, N.C. Basidiocarps taken from the surface litter of both watersheds were fleshy representatives of Agaricaceae, Cantharellaceae or Clavariaceae. Forest floor basidiocarp samples (cap + stalk) from both watersheds had significantly greater concentrations of Cu, K, Na, P and Zn than the leaf litter from which they were removed. Bulked rhizomorph samples from both watersheds contained significantly more Ca, K, Na and Sr than forest floor leaf litter. Polyporaceae growing on hardwood branches concentrated Al, Mo, P and Zn.

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.

Long-term effects of prescribed underburning on litter decomposition and nutrient release in ponderosa pine stands in central Oregon

The effects of low-intensity prescribed underburning on the rates of litter decomposition and N and P release in ponderosa pine (Pinus ponderosa Dougl. ex. Laws) stands were studied by a litter-bag technique for 18 months in sites burned 0.3, 5, or 12 years earlier. Litter decomposition rates (k) were low, between 0.15 and 0.28 year−1, and were significantly (P < 0.1) reduced by prescribed fire on the sites burned 0.3 and 12 years earlier. However, the reduction in decomposition rates was small, from 0.22 to 0.19 year−1 on the sites burned 12 years earlier, and from 0.172 to 0.167 year−1 on the sites burned 0.3 year earlier. Nitrogen tended to be immobilized in the decomposing litter, while P was rapidly released, suggesting that these ecosystems are limited by N but not by P. Nitrogen showed a distinctive seasonal pattern of net immobilization during winter and a net release during summer. Prescribed burning significantly increased the release of N and P from the litter on the sites burned 5 years earlier, a pattern that may indicate changes in microbial activity in the forest floor. However, there were no significant differences in nutrient dynamics on the remaining sites.

Interactions between soil animals and ectomycorrhizal fungal mats

Estimates of microbial biomass were made for ectomycorrhizal fungal mats colonizing mineral soil in a 50–75-year-old Douglas-fir stand in western Oregon. The ectomycorrhizal fungal mats are from the basidiomycete, Hysterangium setchellii. Numbers and biomass of soil animals including microarthropods and nematodes were estimated for both fungal mat and non-mat areas. The mats generally showed a significantly greater microbial biomass and also greater numbers of soil microarthropods. Protozoans were also sampled and exhibited greater abundance in fungal mats for amoebae and ciliates, but not flagellates. We hypothesize that these mats represent a larger and more active microbial biomass, available as a soil-animal food resource. Fungal mats had greater concentrations of soil C and soil N, and soil respiration and enzyme activity rates were significantly greater in mat than non-mat soil.

Responses of Nitrification and Ammonia-Oxidizing Bacteria to Reciprocal Transfers of Soil between Adjacent Coniferous Forest and Meadow Vegetation in the Cascade Mountains of Oregon

Despite the critical position of nitrification in N cycling in coniferous forest soils of western North America, little information exists on the composition of ammonia-oxidizing bacteria (AOB) in these soils, or their response to treatments that promote or reduce nitrification. To this end, an experiment was conducted in which a set of soil cores was reciprocally transplanted between adjacent forest (low nitrification potential) and meadow (high nitrification potential) environments, at two high-elevation (~1500 m) sites in the H.J. Andrews Experimental Forest located in the Cascade Mountains of Oregon. Half of the cores were placed in screened PVC pipe (closed) to prevent new root colonization, large litter debris inputs, and animal disturbance; the other cores were placed in open mesh bags. A duplicate set of open and closed soil cores was not transferred between sites and was incubated in place. Over the 2-year experiment, net nitrification increased in both open and closed cores transferred from forest to meadow, and to a lesser extent in cores remaining in the forest. In three of four forest soil treatments, net nitrification increases were accompanied by increases in nitrification potential rates (NPR) and 10- to 100-fold increases in AOB populations. In open cores remaining in the forests, however, increases in net nitrification were not accompanied by significant increases in either NPR or AOB populations. Although some meadow soil treatments reduced both net nitrification and nitrification potential rates, significant changes were not detected in most probable number (MPN)-based estimates of AOB population densities. Terminal restriction fragment profiles (T-RFs) of a PCR-amplified 491-bp fragment of the ammonia monooxygenase subunit A gene (amoA) changed significantly in response to some soil treatments, and treatment effects differed among locations and between years. A T-RF previously shown to be a specific biomarker of Nitrosospira cluster 4 (Alu390) was widespread and dominant in the majority of soil samples. Despite some treatments causing substantial increases in AOB population densities and nitrification potential rates, nitrosomonads remained undetectable, and the nitrosospirad AOB community composition did not change radically following treatment.