Progress 02/01/03 to 09/30/07
Outputs
We have conducted studies in diverse Oregon soils under different forest types in an attempt to determine the relative contributions of bacteria and fungi to nitrogen cycling. Adjacent sites were chosen where N inputs differed as a result of them being colonized either by the nitrogen fixing actinorhizal tree species, red alder, or by the non nitrogen fixer, Douglas fir. Soils were recovered from two locations where N availability at the sites differed dramatically i.e. high N inputs and N availability at Cascade Head in the Coastal Mountain Range of Oregon,and lower N inputs and N availability at the HJ Andrews experimental forest located in the Cascade moutains of Oregon. Bacterial and fungal antibiotics were added to soil to discriminately prevent either bacteria, or fungi, respectively, from assimilating N into cell proteins. Then, the 15N isotope dilution procedure was used to evaluate the impact of the antibiotics on N cycling processes. The results have been
disseminated in peer reviewed scientific journals, and also at the annual field days at the Experimental forest to other scientists and forest management personnel.
Impacts
When bacterial protein synthesis was blocked, NH4+ consumption decreased in all treatments except for the Douglas fir plots at the low N site in the HJ Andrews suggesting that procaryotes were the major assimilators of N in these acidic forest soils of high N availability, while fungi were the dominant force under low N availability. Antibiotic additions enhanced ammonification implying that microorganisms are a sink for organic N, and that when N assimilation into proteins either by fungi or bacteria is blocked, the organic N is ammonified and released from the cells at a faster rate. Inhibition of fungal protein synthesis stimulated ammonification at both sites, whereas inhibiton of bacterial protein synthesis only enhanced ammonification at the N-rich Cascade Head site. These data are the first of their kind to show unequivocally that both bacteria and fungi can assimilate organic N directly in soil, and that the relative contribution of bacteria to the process is
influenced by the N status of the soil at the site.
Publications
- Williams, M.A., D.D. Myrold, and P.J. Bottomley. 2007. Insights into residue colonization by a soil microbial community under western Oregon field conditions. Soil Biology & Biochemistry 39: 819-822.
- Cliff, J.B., P.J. Bottomley, D. J. Gaspar, and D.D. Myrold. 2007. Nitrogen Mineralization and Assimilation at millimeter scales. Soil Biology and Biochemistry. 39: 823-826
- Boyle, S.A., P.J. Bottomley and D.D. Myrold. 2007. Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and Red alder at two sites in Oregon. Soil Biol. Biochem. 40:443-451.
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Progress 01/01/06 to 12/31/06
Outputs
We have conducted a series of studies in different Oregon soils to examine how soil heterogeneities interact with environmental conditions to influence N cycling processes. Very little is known about how bacterial and fungal populations respond to treatments that impact vegetation and soil conditions, and how soil processes might be influenced by change in the relative contribution of fungi and bacteria to soil biomass. An experiment was conducted in which soil cores were reciprocally transferred between immediately adjacent forests and meadows. After 2y, cores were removed and changes in fungal and bacterial populations determined by microscopy, and changes in community composition determined by PLFA analysis, and by length heterogeneity PCR of the internal transcribed spacer region of fungal ribosomal DNA. At one site both fungal and bacterial community responded to transfer of forest soil to the meadow environment with the shift in fungal community accompanied by a
significant decrease in fungal biomass. At the other site, both fungal and bacterial community structures shifted in response to open versus closed cores, with the shift in fungal community accompanied by a decrease in biomass of closed cores, while bacterial biomass increased in closed cores. Fungal biomass of open cores increased in meadow soil transferred to forest and community structure changed, whereas there was no effect on bacterial commuity structure of transfer. We noted a correlation between fungal biomass decrease, wchange in fungl community structure, and decline in mineralizable C upon transfer from forest to meadow. Similarly, there was an increase in fungal biomass and mineralizable C of meadow soil open cores transferred to forest, and of bacterial biomass and mineralizable C in the equivalent closed cores. These data infer that vegetation and climate influence the relative contributions of fungi and bacteria to soil biomass, which can play a role in mineralization of
organic C pools.
Impacts
Although we have known for many years that fungi and bacteria are the major microbial components of soils, and that their ratio differs in response to soil properties, no manipulative studies have been performed to determine if the ratios can be changed, and what conditions control the ratios. In this study we showed that both climate and vegetation were major players, and that the fungi were more sensitive to manipulation than were the bacteria. We obtained evidence that soil mineralizable C responded to transfer of soil and to change in the fungal biomass implying that perhaps fungi and bacteria access different pools of C, and that changes in community composition promote chnages in the pools of soil C that are being accessed.
Publications
- Bottomley, P.J., Yarwood, R.R., Kageyama, S.A., Waterstripe, K.E., Williams, M.A., Cromack, K., D.D. Myrold. 2006. Responses of soil bacterial and fungal populations to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Plant Soil 289: 35-45.
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Progress 01/01/05 to 12/31/05
Outputs
Our on-going studies have examined how soil heterogeneities interact with environmental conditions to promote the activity of particular members of a soil community and influence carbon and nitrogen flow through the soil. Throughout a cropping season (Sep to Jun), we investigated the colonization of clover and ryegrass straw residues by a microbial community. After mixing of the straw into the soil in September(0 to 18-cm depth), the straw residue and firmly associated soil particles (detritusphere) were periodically sampled (Oct, Nov, Apr, and Jun) for phospholipid fatty acids (PLFA). By Oct, we detected strong evidence of microbial colonization (i15:0, a15:0, i16:0, 16:1w7+, 17cy, 18:0) in the clover but not the ryegrass detritusphere. By Nov, microorganisms had also colonized the ryegrass detritusphere, and the microbial communities associated with each residue-type were very similar in structure. In contrast, the structures of the microbial communities were
different between the two detrituspheres in Apr and Jun. The type of PLFA found associated with the clover and straw detritusphere, however, were generally the same, except for the Oct sampling. Numerous bacterial PLFA were detected on the straw, but fungal colonization was difficult to discern in the early months of the study because of the high amounts of 18:2w6,9 associated with the unincorporated straw residues. Thereafter, the concentrations of 18:2w6,9 decreased to its lowest level (Nov), and then increased during April and June, providing evidence that fungal colonization had taken place. Isotopic changes in the 13C signatures of the PLFA suggest that microorganisms on clover were primarily growing on C derived from straw residue, whereas microbes on the ryegrass were utilizing C derived from both soil and straw residues. The accrual of PLFA and their associated 13C signatures provided novel data on the colonization and dynamics by microorganisms in the detritusphere. Further
work is needed to examine the N dynamics associated with the straw and root residues, and the fate of the residue C transformed during the different times of the year.
Impacts
The agricultural industry of Oregon generates large amounts of crop residues. There is considerable debate on the best management strategies needed to enahnce residue C stabilization in soil without compromising crop yield due to N immobilization and disease enhancement. Furthermore, much less is known about the impact of root residues on soil organic matter breakdown and C storage. The objective of our work is to use sophisticated isotope techniques to examine the fate of both straw and root residues in soil and their impact on soil C stabilization.
Publications
- Williams, M.A., D.D. Myrold and P.J. Bottomley. 2005. In Press. Carbon flow from 13C labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions. Soil Biol. Biochem.
- Williams, M., D.D. Myrold and P.J. Bottomley. 2005. In Press. Distribution and fate of 13C labeled root and straw residues from ryegrass and crimson clover in soil under western Oregon field conditions. Biol Fertil. Soils.
- McMahon, S.K., Bottomley, P.J., and Myrold, D.D. 2005. Dynamics of microbial communities during decomposition of 13C labeled ryegrass fractions in soil. Sci. Soc. Amer. J. 69: 1238-1247
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Progress 01/01/04 to 12/31/04
Outputs
Our on-going studies have examined if soil heterogeneities interact with different temporal conditions to promote the activity of particular members of the soil community and influence nutrient cycling. Ryegrass and crimson clover plants were labeled with 13CO2 under field conditions throughout the growing season (Feb through June). Both 13C-labeled straw, and soil containing 13C labeled root residues and root-derived C were mixed reciprocally with unlabeled residue or soil and incubated in the field. Plots were sampled five times between September and June to determine the fate of the different sources of residue C. GC-IRMS was used to follow incorporation of 13C into the PLFA fraction of microbial biomass because it provided insights into which groups of soil microbes had grown in response to particular residues at specific times of the year. The data showed that while the percent contribution of ryegrass root-derived C to soil microbial biomass remained relatively
constant throughout the incubation, the contribution of clover root C declined. The contributions of both ryegrass and clover straw C to soil biomass increased steadily throughout the incubation. The contribution of soil C to biomass increased initially, yet its percentage contribution to biomass declined from about 70% to about 40% by the end of the incubation. The distribution of 13C from root residue C into microbial PLFAs differed from straw C. Furthermore, a shift in the 13C content of PLFAs was observed on all sampling dates, indicating that different components of the soil community benefited from residue C at different times of the year.
Impacts
Determining the factors that influence the dynamics of mineralization and immobilization of C and N in the same soil volume, could provide important insight into the balance between organic matter meeting some fraction of a crop's nutrient requirements and its accumulation. Furthermore, it will give insights into the conditions that are needed to maintain a healthy balance between mineralization of crop residues as sources of plant nutrients, and sequestration of C and N to maintain and enhance soil organic matter levels.
Publications
- Williams, M.A., P.J. Bottomley and D.D. Myrold. 2004. Environmental and plant controls on C flow to the soil microbial community. Abstr. Annu. Mtg. SSSA, Seattle, WA
- Bottomley, P.J., and D.D. Myrold. 2004. Is there a link between microbial community composition and microbial processes in soils. Abstr. Annu. Mtg. SSSA, Seattle, WA
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Progress 01/01/03 to 12/31/03
Outputs
We have initiated our studies to examine how soil factors influence the ability of N cycling processes to occur simultaneously in soil volumes. Two different studies are underway. In the first study, we are examining the relationship between the level of extractable soil NH4+ and concentration of soil solution NH4+ on the efficacy whereby two different soil ammonia oxidizing bacteria can carry out ammonia oxidation. We have determined from our studies that Nitrosospira oxidizes ammonia more effectively than Nitrosomonas in unamended soils because it has the ability to sequester NH4+ from soil solution at much lower concentrations that Nitrosomonas does. In the case of Nitrosospira, the Ks for NH4+ is less than 0.5mM, whereas in the case of Nitrosomonas the Ks is in the range of 2-4mM. Supplementing soil with fertilizer type levels of 80ppm NH4+ stimulate the rate of ammonia oxidation by Nitrosomonas to far exceed that of Nitrosospira. In another study we examined the
ability of secondary ion mass spectrometry (SIMS) to measure 15N assimilation by soil microbes at microbially meaningful scales. Using a model soil system consisting of a mixture of fine sand and clay minerals, we have been able to detect 15N assimilation in microbes in the soil fabric by SIMS across a scale of millimeters. We have developed mathematically procedures to discriminate between the SIMS signature derived from Aluminum and CN and quantified the 15N content of organic material along the gradient. We have confirmed the 15N content in these samples by conventional isotope ratio mass spectrometry. Now we are in a position to ask interesting questions regarding the interaction between mineralization and immobilization of N at microbially meaningful scales.
Impacts
Determining how mineralization and immobilization of mineral N occurs in the same soil volume, and the factors that influence this phenomenon could provide important insight into the role of indigenous soil N in meeting some fraction of a crop's N requirements. Furthermore, it will give insights into the conditions that are needed to maintain a healthy balance between mineralization of crop residues as sources of plant nutrients, and sequestration of C and N to maintain and enhance soil organic matter levels.
Publications
- Cliff, J.B., D.J. Gaspar, P.J. Bottomley, and D.D. Myrold. 2003. Peak fitting to resolve CN- isotope ratios in biological and environmental samples using TOF-SIMS. Proceedings of the Secondary Ion Mass Spectrometry SIMS XIV.
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Progress 01/01/02 to 12/31/02
Outputs
We have continued our studies to examine the relationships between soil physical properties and N cycling processes in Oregon soils. We are particularly focused upon the process of nitrification because of a lack of knowledge about the nature of nitrifying bacteria in soils, and the factors that influence the rate of nitrification in Oregon agroecosystems. Our approach has been two-fold. We are interested in obtaining isolates of ammonia oxidizing bacteria from Oregon soils to determine what physiological characteristics make them specifically adept at nitrifying under the acidic, high organic matter conditions routinely found in these soils. Using molecular biological techniques we have shown that Nitrosospira cluster 4 is widely distributed in our soils. We have recovered several isolates from cluster 4 of which very few isolates are available throughout the world. Currently, we are determining properties of these bacteria. Our second approach has been to focus upon
understanding how spatial heterogeneities develop in soil and how they influence the coupling and decoupling of N cycling processes. We have developed a model that examines the role of impedance of ammonium diffusivity through soils of different texture and water content in permitting different N cycling processes to occur in close proximity. We are using state-of-the-art instrumentation, namely time-of-flight secondary ion mass spectrometry, to examine relative assimilation of 15N labeled ammonium and nitrate by individual microorganisms and colonies of microorganisms at spatial scales less than 1mm. We are using soils of varying texture and water content, in combination with substrates of different C:N to evaluate their relative influences on spatial heterogeneity of N cycling processes.
Impacts
Nitrogen management continues to be a challenge to our cropping systems in western Oregon where excessive rainfall and mild winters are conducive to excess N mineralization and leaching. N management becomes even more complex as agroecosystems incorporate more organic N containing residues, and as soil organic matter sequestration and soil structural properties change with improved conservation practises. Our research will lead to the development of improved N cycling models that will help us to better understand how soil and climatic factors influence the fate of organic N added to soils. Improving the management of N in agricultural soils has both economic and environmental benefits, especially in landscapes and under climatic conditions where nitrate run-off is severe.
Publications
- Cliff, J.B., D. Gaspar, D.D. Myrold, and P.J. Bottomley. 2002. Exploration of inorganic C and N assimilation by soil microbes with Time-of-flight Secondary Ion Mass Spectrometry. Appl. Environ. Microbiol. 68: 4067-4073.
- Cliff, J.B., P.J. Bottomley, R. Haggerty, and D.D. Myrold. 2002. Modeling the effect of mass transfer limitations on 15N isotope dilution experiments in soil aggregates. Soil Sci. Soc. Am. J. Vol. 66: 1868-1877.
- Duddleston, K. N., D. J. Arp, and P. J. Bottomley. 2002. Biodegradation of monohalogenated alkanes by soil ammonia-oxidizing bacteria. Appl. Microbiol. Biotechnol. 59: 535-539.
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Progress 01/01/01 to 12/31/01
Outputs
Several studies have been conducted to examine the impact of soil physical properties upon N cycling phenomena in Oregon soils. We have examined the interaction between ammonium levels and ammonia oxidiation by two different ammonia-oxidizing bacteria (Nitrosomonas europaea and Nitrosospira sp. AV) in soils of different textures. Data indicate that the rate of nitrite production by N. europaea was soil dependent, independent of the level of extractable ammonium, until ammonium levels >25 ppm. These data indicate that diffusional constraints differ in the soils and influence the responsiveness of this type of ammonia oxidizing bacterium. In contrast, the rate of ammonia oxidation by Nitrosospira AV was the same regardless of soil and level of extractable ammonium and did not respond to further additions of ammonium. These data indicate that the nitrifying activity of Nitrosospira AV was saturated at very low extractable NH4+ levels and activity was largely independent
of texture. Isotope pool dilution studies were conducted to examine the differences between N cycling processes in rhizosphere and nonrhizosphere soil associated with rye grass (Lolium multiforme L.) Our data clearly showed that the rate of gross mineralization of N was higher in root-associated soil than in bulk soil, and highest in soil associated with clipped plants. Further studies are required to better understand what underlies the interaction between the plant root and soil microbial community to enhance N mineralization, and what benefit accrues to the plant. It is particularly important to ascertain what promotes enhanced mineralization of N in rhizospheres of plants that are periodically clipped because this could have applied significance in grazing and hay mangement systems.
Impacts
Agriculture continues to face pressures to reach economically sustainable prodcution levels with minimal damage to the environment. Nitrogen management continues to be a challenge to our cropping systems in the west because of N losses from wet soils. We will pursue our studies of ammonia oxidiation by bacteria in Oregon soils to get a better understanding of the interaction between soil and bacterial properties that influence the rates of ammonia oxidation in Oregon soils. In addition, the stimulation of N mineralization in rye grass rhizospheres raises questions about the contribution of this available N to plant growth, and especially its availability to plants that are undergoing regrowth after harvest. The management of N applications during regrowth of forage and hay crops continues to be a difficult topic that might be improved by an unforeseen benefit of soil microorganisms.
Publications
- Taylor, A.E., (2001). Comparative behavior of two nitrifying bacteria in soil. MS thesis, Oregon State University, Corvallis, 25pp.
- Whalen, J.K., P.J. Bottomley, and D.D. Myrold. (2001). Short term N transformations in bulk and root-associated soils under ryegrass. Soil Biol.& Biochem. 33: 1937-1945.
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