Publications

Amidst a network of tunnels and pores, soil organisms recycle carbon and nutrients. They mix plant litter and detritus, causing changes in soil structure that can ultimately influence the amount of water and oxygen available for plant roots. They are also eaten by aboveground predators, providing direct connections between below-and aboveground food webs. Root herbivory is very difficult to quantify, but likely just as important as leaf herbivory.

Increased carbon storage in ecosystems due to elevated CO₂ may help stabilize atmospheric CO₂ concentrations and slow global warming. Many field studies have found that elevated CO₂ leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO₂ doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting ≈52% of the additional carbon that had accumulated at elevated CO₂ in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO₂ had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO₂. The isotopic composition of microbial fatty acids confirmed that elevated CO₂ increased microbial utilization of soil organic matter. These results show how elevated CO₂, by altering soil microbial communities, can cause a potential carbon sink to become a carbon source.

At the time of this study Fossil Creek was being considered as a site for the restoration of a native fish assemblage, however there was concern amongst fisheries managers about the stream being food limited due to calcium carbonate (travertine) deposition. To evaluate the effects of travertine deposition on the aquatic food base we used leaf litterbags to compare decomposition rates and nutrient diffusing artificial substrates to compare algal accrual rates and nutrient limitation between two distinct reaches in Fossil creek: a travertine dam forming reach and a reach without travertine dam formation (riffle-pool reach). Decomposition was significantly faster in the travertine dam forming reach than in the riffle-pool reach. Macroinvertebrates in the leaf packs were more diverse in the travertine reach but more abundant in the riffle-pool reach. Algae accrued more quickly in the travertine reach than in the riffle-pool reach and only responded to nutrient enrichment in the travertine reach. This study was conducted prior to a hydroelectric dam decommissioning project in Fossil Creek where full flows were reintroduced back into the stream after a century of diversion. Our results suggest concurrent increases in algal productivity, decomposition, and macroinvertebrate diversity in the next decade as travertine dams rebuild, providing a richer food base for fish and other aquatic organisms.

Restoration of native fish to freshwater habitats often requires nonnative fish removal via chemicals such as antimycin A. Despite widespread use, there are limited field studies quantifying the effects of antimycin A on aquatic macroinvertebrates. We studied the immediate and short-term effects of antimycin A on macroinvertebrates during a fish renovation project in Fossil Creek, Arizona. We employed before–after control–impact (BACI) designs to measure the effects of antimycin A (at extraordinarily high levels of >54 and >100 μg/L) on macroinvertebrate drift, density, and species composition. We used the Hilsenhoff biotic index, a measure of invertebrate pollution tolerance, to study changes in species composition. At the highest dose (>100 μg/L), drift was five times the pretreatment drift level and invertebrate standing stocks in pools and riffles decreased immediately. Densities rebounded in riffles within 5 months but remained depressed in pools. At the lower concentration (>54 μg/L), macroinvertebrate mortality, measured as increased drift, was 24 times the pretreatment level. At this lower concentration, however, macroinvertebrate densities in the benthos were not reduced. Under both concentrations, species composition shifted toward more tolerant species. Although antimycin A effects were mostly short term, several species were locally extirpated. We found no explanation for the loss of some species over others. These results indicate that there is a high end concentration at which antimycin A can have deleterious effects on aquatic invertebrates. We caution managers contemplating the use of antimycin A in fish restoration to consider the risks to macroinvertebrates. We suggest the use of pretreatment surveys and bioassays at anticipated treatment levels to predict the effects upon macroinvertebrates, especially sensitive species. Where there are sensitive species, steps should be taken to mitigate effects.

Understanding river food webs requires distinguishing energy derived from primary production in the river itself (autochthonous) from that produced externally (allochthonous), yet there are no universally applicable and reliable techniques for doing so. We compared the natural abundance stable isotope ratios of hydrogen (δD) of allochthonous and autochthonous energy sources in four different aquatic ecosystems. We found that autochthonous organic matter is uniformly far more depleted in deuterium (lower δD values) than allochthonous: an average difference of ∼100‰. We also found that organisms at higher trophic levels, including both aquatic invertebrates and fish, have δD values intermediate between aquatic algae and terrestrial plants. The consistent differences between leaves and algae in δD among these four watersheds, along with the intermediate values in higher trophic levels, indicate that natural abundance hydrogen isotope signatures are a powerful tool for partitioning energy flow in aquatic ecosystems.

Forest management, climatic change, and atmospheric N deposition can affect soil biogeochemistry, but their combined effects are not well understood. We examined the effects of water and N amendments and forest thinning and burning on soil N pools and fluxes in ponderosa pine forests near Flagstaff, Arizona (USA). Using a ¹⁵N-depleted fertilizer, we also documented the distribution of added N into soil N pools. Because thinning and burning can increase soil water content and N availability, we hypothesized that these changes would alleviate water and N limitation of soil processes, causing smaller responses to added N and water in the restored stand. We found little support for this hypothesis. Responses of fine root biomass, potential net N mineralization, and the soil microbial N to water and N amendments were mostly unaffected by stand management. Most of the soil processes we examined were limited by N and water, and the increased N and soil water availability caused by forest restoration was insufficient to alleviate these limitations. For example, N addition caused a larger increase in potential net nitrification in the restored stand, and at a given level of soil N availability, N addition had a larger effect on soil microbial N in the restored stand. Possibly, forest restoration increased the availability of some other limiting resource, amplifying responses to added N and water. Tracer N recoveries in roots and in the forest floor were lower in the restored stand. Natural abundance δ¹⁵N of labile soil N pools were higher in the restored stand, consistent with a more open N cycle. We conclude that thinning and burning open up the N cycle, at least in the short term, and that these changes are amplified by enhanced precipitation and N additions. Our results suggest that thinning and burning in ponderosa pine forests will not increase their resistance to changes in soil N dynamics resulting from increased atmospheric N deposition or increased precipitation due to climatic change. Restoration plans should consider the potential impact on long-term forest productivity of greater N losses from a more open N cycle, especially during the period immediately after thinning and burning.

Hurricane disturbances have profound impacts on ecosystem structure and function, yet their effects on ecosystem CO₂ exchange have not been reported. In September 2004, our research site on a fire-regenerated scrub-oak ecosystem in central Florida was struck by Hurricane Frances with sustained winds of 113 km h⁻¹ and wind gusts as high as 152 km h⁻¹. We quantified the hurricane damage on this ecosystem resulting from defoliation: we measured net ecosystem CO₂ exchange, the damage and recovery of leaf area, and determined whether growth in elevated carbon dioxide concentration in the atmosphere (<em>C</em>_a) altered this disturbance. The hurricane decreased leaf area index (LAI) by 21%, which was equal to 60% of seasonal variation in canopy growth during the previous 3 years, but stem damage was negligible. The reduction in LAI led to a 22% decline in gross primary production (GPP) and a 25% decline in ecosystem respiration (<em>R</em>_e). The compensatory declines in GPP and <em>R</em>_e resulted in no significant change in net ecosystem production (NEP). Refoliation began within a month after the hurricane, although this period was out of phase with the regular foliation period, and recovered 20% of the defoliation loss within 2.5 months. Full recovery of LAI, ecosystem CO₂ assimilation, and ecosystem respiration did not occur until the next growing season. Plants exposed to elevated <em>C</em>_a did not sustain greater damage, nor did they recover faster than plants grown under ambient <em>C</em>_a. Thus, our results indicate that hurricanes capable of causing significant defoliation with negligible damage to stems have negligible effects on NEP under current or future CO₂-enriched environment.

Drought is a normal, recurrent feature of climate. In order to understand the potential effect of increasing atmospheric CO₂ concentration (<em class="EmphasisTypeItalic ">C</em> _a) on ecosystems, it is essential to determine the combined effects of drought and elevated <em class="EmphasisTypeItalic ">C</em> _a (EC) under field conditions. A severe drought occurred in Central Florida in 1998 when precipitation was 88 % less than the average between 1984 and 2002. We determined daytime net ecosystem CO₂ exchange (NEE) before, during, and after the drought in the Florida scrub-oak ecosystem exposed to doubled <em class="EmphasisTypeItalic ">C</em> _a in open-top chamber since May 1996. We measured diurnal leaf net photosynthetic rate (<em class="EmphasisTypeItalic ">P</em> _N) of <em class="EmphasisTypeItalic ">Quercus myrtifolia</em> Willd, the dominant species, during and after the drought. Drought caused a midday depression in NEE and <em class="EmphasisTypeItalic ">P</em> _N at ambient CO₂ concentration (AC) and EC. EC mitigated the midday depression in NEE by about 60 % compared to AC and the effect of EC on leaf <em class="EmphasisTypeItalic ">P</em> _N was similar to its effect on NEE. Growth in EC lowered the sensitivity of NEE to air vapor pressure deficit under drought. Thus EC would help the scrub-oak ecosystem to survive the consequences of the effects of rising atmospheric CO₂ on climate change, including increased frequency of drought, while simultaneously sequestering more anthropogenic carbon.

The article focuses on the decommissioning of dams across the United States. Many dams were built after World War II to provide sources of hydraulic power. Now that these power suppliers make up little of the nation's power resources, policy makers, conservationists, and environmentalists are opting to decommission the dams. Even though the natural ecology is expected to flourish from the decommissioning of dams, scientists are worried that there may be some negative effects.

Elevated CO₂ can increase fine root biomass but responses of fine roots to exposure to increased CO₂ over many years are infrequently reported. We investigated the effect of elevated CO₂ on root biomass and N and P pools of a scrub-oak ecosystem on Merritt Island in Florida, USA, after 7 years of CO₂ treatment. Roots were removed from 1-m deep soil cores in 10-cm increments, sorted into different categories (&lt;0.25 mm, 0.25–1 mm, 1–2 mm, 2 mm to 1 cm, &gt;1 cm, dead roots, and organic matter), weighed, and analyzed for N, P and C concentrations. With the exception of surface roots &lt;0.25 mm diameter, there was no effect of elevated CO₂ on root biomass. There was little effect on C, N, or P concentration or content with the exception of dead roots, and &lt;0.25 mm and 1–2 mm diameter live roots at the surface. Thus, fine root mass and element content appear to be relatively insensitive to elevated CO₂. In the top 10 cm of soil, biomass of roots with a diameter of &lt;0.25 mm was depressed by elevated CO₂. Elevated CO₂ tended to decrease the mass and N content of dead roots compared to ambient CO₂. A decreased N concentration of roots &lt;0.25 mm and 1–2 mm in diameter under elevated CO₂may indicate reduced N supply in the elevated CO₂ treatment. Our study indicated that elevated CO₂ does not increase fine root biomass or the pool of C in fine roots. In fact, elevated CO₂ tends to reduce biomass and C content of the most responsive root fraction (&lt;0.25 mm roots), a finding that may have more general implications for understanding C input into the soil at higher atmospheric CO₂ concentrations.

We report the first simultaneous measurements of <em>δ</em>¹⁵N and <em>δ</em>¹³C of DNA extracted from surface soils. The isotopic composition of DNA differed significantly among nine different soils. The <em>δ</em>¹³C and <em>δ</em>¹⁵N of DNA was correlated with <em>δ</em>¹³C and <em>δ</em>¹⁵N of soil, respectively, suggesting that the isotopic composition of DNA is strongly influenced by the isotopic composition of soil organic matter. However, in all samples DNA was enriched in ¹³C relative to soil, indicating microorganisms fractionated C during assimilation or preferentially used ¹³C enriched substrates. Enrichment of DNA in ¹⁵N relative to soil was not consistently observed, but there were significant differences between <em>δ</em>¹⁵N of DNA and <em>δ</em>¹⁵N of soil for three different sites, suggesting microorganisms are fractionating N or preferentially using N substrates at different rates across these contrasting ecosystems. There was a strong linear correlation between <em>δ</em>¹⁵N of DNA and <em>δ</em>¹⁵N of the microbial biomass, which indicated DNA was depleted in ¹⁵N relative to the microbial biomass by approximately 3.4‰. Our results show that accurate and precise isotopic measurements of C and N in DNA extracted from the soil are feasible, and that these analyses may provide powerful tools for elucidating C and N cycling processes through soil microorganisms.