Fossil Creek, Paul S. Hamilton

Can we restore a river after a century of disturbance? Research in the Marks Lab has addressed the following questions:

Related Publications

Adams KJ, Harrop B, James MA, and Marks JC. 2015. Riparian Vegetation and Water Quality Monitoring: Middle Fossil Creek Riparian Habitat Protection and Restoration Project Final Report: Monitoring Data and Analysis, 2010-2014 (Task 4) Revised Final. Prepared for Coconino National Forest, Grant No. 09-162WPF, Arizona Water Protection Fund, July 17, 2015.

Avery, LA, Ward, DL, and Marks, JC. 2011. Exercise Conditioning Decreases Downstream Movement of Pond-Reared Razorback Suckers Released Into a Stream Environment. Western North American Naturalist 71(1):78-85.

Fuller, B.M., Sklar, L.S., Compson, Z., Adams, K.J., Marks, J.C. and Wilcox, A.C. 2010. Ecogeomorphic feedbacks in regrowth of travertine step-pool morphology after dam decomissioning, Fossil Creek, Arizona. Geomorphology.

Compson, Z., Mier, M.Z. and Marks, J.C. 2009. Effects of travertine and flow on leaf retention in Fossil Creek, Ariona. Hydrobiologia 630: 187-197.

Marks, JC, Haden, GA, O’Neill, Pace, C. 2009. Effects of Flow Restoration and Exotic Species Removal on Recovery of Native Fish:  Lessons from a Dam Decommissioning. Restoration Ecology, doi: 10:1111/j.1526-100x.2009.00574.x

Meulbauer, JD, LeRoy, CJ, Lovett, JM, Flaccus, KK, Vlieg, JK, Marks, JC. 2009. Short-term responses of decomposers to flow restoration in Fossil Creek, Arizona, USA. Hydrobiologia 618: 35-45. DOI 10.1007/s10750-008-9545-3.

Dinger and Marks, JC. 2007. Effects of high levels of antimycin A on aquatic invertebrates in a warmwater Arizona Stream. North American Journal of Fisheries Management. 27: 1243-1256.

Carter CD and Marks JC. 2007. Influences of travertine dam formation on leaf litter decomposition and algal accrual. Hydrobiologia 575: 329-341.

Doucette RR, Marks JC, Blinn DW, Caron M, and Hungate BA. 2007. Measuring terrestrial subsidies to aquatic food webs using stable isotopes of hydrogen. Ecology 88(6):1587-1592.

Marks, JC. 2007. Down Go the Dams. Scientific American 296(3): 66-71.

LeRoy CJ, Marks JC. 2006. Three southwestern streams show differences in leaf litter processing capacities and associated macroinvertebrate communities. Freshwater Biology 51: 605-617.

Marks JC, Parnell R,Carter C, Dinger EC, Haden GA. 2006. Invited Special Feature: Interactions between geomorphology and ecosystem processes in travertine streams–implications for dam decommissioning in Fossil Creek, Arizona. Geomorphology, 77: 299-307.

Flaccus K, Vleig J, Marks JC, and LeRoy CJ. 2004. Restoring Fossil Creek. The Science Teacher, Summer Issue, 36-40.

Researcher climbing a large redwood tree.

Ecoss studies the interactions of plants with their physical and biotic environments at a fundamental level common to all organisms: gas exchange, energy balance, and water relations. We explore how plants make a living in diverse environments ranging from deserts to rainforests. A longstanding interest is the biophysical and ecological determinants of height and size growth in the world’s giant trees, including the towering redwoods of California and massive eucalypts of Australia. Here we’ve learned that the inescapable influence of gravity increases water stress as trees grow taller. And we’ve dispelled the dogma of decadence in old trees by showing that largest and oldest trees are the most productive individuals in their stands. With an eye to a warmer, drier future we’re examining how soil and atmospheric drying conspire to stress the hydraulic system of plants. Here we’re using new technology that enables high temporal resolution measurements of xylem tension that may reveal the threshold conditions that lead to hydraulic dysfunction. Recently we’ve taken a fresh look at plant water relations by investigating the role of “metabolic water”, water generated during respiratory metabolism. We’ve developed a new technique for labeling metabolic water with “heavy” oxygen that lets us see where that water is produced. We suspect metabolic water contributes to tissue-level phenomena including xylem embolism repair, turgor maintenance, and seed germination. Stay tuned!

Ecological and Biophysical Determinants of Tree Height and Size Growth

Extremes have long fascinated biologists. Studying the fastest, the deepest, the smallest, the hottest, and the largest organisms offers insights to the constraints on life imposed by the laws of physics and chemistry. How tall can a tree grow? Does growth slow as trees age and grow taller and larger? How does gravity influence water stress as trees grow taller? Our research on California’s redwoods – the world’s tallest trees –  and Australia’s giant eucalyptus, which may once have been even taller, has demonstrated that height growth is a dynamic interaction of a tree’s need to outcompete neighbors for light and the increasing influence of gravity on water within the tree as height increases. The tops of taller trees are more water stressed than those of shorter trees, even in wet soils. This water stress can cause irreversible damage to the water conducting system, and to avoid this, trees regulate water loss through the microscopic pores (stomata) on the leaf surface. This necessarily reduces photosynthesis and may explain the slowing of height growth as trees grow ever taller. Yet, although height growth slows as trees grow taller, we now know that the tallest and largest trees are actually growing extremely fast. In fact, we’ve convincingly dispelled the dogma of decadence – that large old trees are unproductive- by documenting that the biggest redwoods and eucalyptus are producing more new wood each year than any other tree in the stands where they occur.

Publications

Sillett SC, Van Pelt R, Kramer RD, Carroll AL, Koch GW. (2015) Biomass and growth potential of Eucalyptus regnans up to 100m tall.  Forest Ecology and Management 348:78-91.

Ambrose AA, Sillett SC, Koch GW, Van Pelt R, Antoine ME,  Dawson TE. (2010) Effects of height on treetop transpiration and stomatal conductance in coast redwood (Sequoia sempervirens). Tree Physiology, 30:1260-1272.

Inspired by Nature: Engineering a Synthetic Tree

There are no biological water pumps, at least none has been discovered. Yet plants raise water to heights over 100 meters. What’s the source of energy for this impressive lifting feat? In fact, the energy is the heat that drives evaporation from leaves into the drier outside air. This results in capillary forces in the liquid water at the microscale sites of evaporation inside leaves, and because of water’s strong cohesive property, these forces pull on the continuous column of water throughout the plant, drawing it up from the roots. What if we could construct a synthetic version of this as an “energy free” means of moving water? We’re working with engineers and materials scientists to do just this, and it’s not easy! Plants have a 350 million year head start, but of course evolution proceeds by trial and error, whereas we use a more directed approach to reverse engineer nature. We’re applying biophysical insights gleaned from nature to physical systems comprised of microcapillary tubing, porous ceramics, and a new nanomaterial, graphene oxide.

Metabolic Water: Not Just for Rodents Anymore?

All organisms that “breath” oxygen, be they microbes, plants, or animals, produce water as a byproduct of respiratory metabolism. This “metabolic water” is a vital source for some animals, notably desert rodents, some of which meet the majority of their water needs by metabolic production. We are now exploring the significance of metabolic water for soil microorganisms and plants, groups for which this water source has not been studied. We hypothesize that for soil bacteria, especially during dry periods, metabolic water production may prove to be essential for maintenance of water balance. And for plants, while the huge flux of water associated with transpiration would seem to make metabolic water production of trivial importance, we suspect that in certain life stage, plant tissues, and environmental conditions, this internal source of water may make a critical contribution to water balance. For our metabolic work with microbes and plants, we have developed new methodological approaches using stable isotopes that greatly increase our ability to detect and quantify the importance of metabolic water.

Research outlined above is being conducted by George Koch and others.

Fossil Creek, Arizona in the fall. Copyright Steve Rich

Aquatic ecosystems in the southwestern US are among the most threatened in the country: rates of species loss are high, with few remaining refuges for natives, and water extraction for human use and diversion for power generation impose major demands on the defining feature of aquatic ecosystems: water. Work at Ecoss assesses how changes to aquatic ecosystems affect their functioning, from a community and ecosystems perspective. Our work has involved two major ecosystems in the southwest: the Colorado River, where the Glen Canyon Dam has completely altered the river and its foodweb, and Fossil Creek, where removal of a hydropower dam and extirpation of exotic species has caused a native foodweb to flourish. Our work also investigates the impacts of riparian plants and river functioning, focusing on how the types of plants affect microbial processes, nutrient cycling, and the performance of insect communities so essential for higher trophic levels and energy exchange between the terrestrial and aquatic environments.

Leaf Litter Effects on Stream Ecosystems

Our work on leaf litter effects on stream ecosystems includes organic matter processing, leaf retention and litter decomposition of cottonwood cross types, influence of leaf litter cross type and genotype on aquatic insect emergence, influence of exotic crayfish on aquatic insect emergence, riparian leaf litter influences on carbon and nitrogen transfer to aquatic insects, microbial function, as well as fungal and bacterial abundance. For more information, click here.

Stream Restoration

Our work on stream restoration has focused on Fossil Creek, a spring-fed perennial stream that was dammed for nearly a century for hydropower production. The hydropower facility diverted the majority of Fossil Creek’s flow out of the creek bed. The restoration had three major components: First, in 2004 a fish barrier was constructed upstream of the confluence with the Verde River. Second, non-native fish were removed from a large section of the river using antimycin A, a chemical that targets fish. And lastly, in June 2005, full flows were restored to the creek and the two associated hydropower plants were decommissioned.

Our research has focused on aquatic insects, native fish population dynamics pre- and post-restoration, invasive crayfish, leaf retention, geomorphology, stream metabolism and restoration, and native/non-native interactions. For more information, click here.

This research is being conducted by Jane Marks.

The identities of organisms profoundly influence ecosystems, and microbial diversity is vast. The obvious disconnect between this diversity and its treatment in C cycling models is perhaps the best manifestation of the common complaint that so much physiology, taxonomy, ecology, and diversity is ignored when microbial communities are described with boxes and arrows. A recent report from the American Society for Microbiology captured this complaint by depicting on the cover the hackneyed “black box” of microbial ecology, although the report emphasized the promise of new approaches by showing the box open and illuminated from within. In this project, we are exploring relationships between the diversity of soil microorganisms and the processing of soil carbon and its conversion from organic C to carbon dioxide (CO₂). Our approach is designed to connect multiple element biogeochemistry and microbial community ecology, by linking isotopes to genomics, taking advantage of developments in stable isotope probing and isopycnic separation, microarrays and sequencing technology, and NanoSIMS.

Details

Tackling this problem is important to understanding soil C persistence, because the sensitivity of soil C to external forcings has the potential to mitigate or exacerbate global climate change. Warming can cause soil C release, and these losses have implications for the distribution and retention of nitrogen, which in turn can feed back to the C cycle through changes in plant productivity. Increased atmospheric carbon dioxide (CO₂) increases photosynthesis but not necessarily soil C, and in some cases can even cause soil C loss. Soil C content changes with long-term differences in precipitation, and soil CO₂ production exhibits strong short-term changes in response to wet-dry cycles. Multiple global environmental changes drive changes in soil C, but patterns in the diversity of organism driving these changes are poorly understood. Which organisms catalyze soil C losses? Are the same organisms involved when the forcings altering soil C are different? Are the activities of the organisms related to their phylogenies? What are their growth rates, and relative reliance on more labile C sources, such as those derived from rhizoexudates by living plants, or from plant litter? How do their activities interact with other resources, like nutrients? These are broad questions that to date have been nearly impossible to answer on a scale appropriate for the diversity of soils, because of the difficulty of coupling biogeochemistry with genomics. Understanding which microorganisms catalyze soil C losses is especially difficult, because the chemical forms of native soil organic C are diverse, heterogeneous, and not well characterized, making it impractical to identify the organisms that utilize them using classical stable isotope probing. We have developed advanced SIP methods that use isotope tracers to quantify the growth (18O, 2H) and carbon (13C) and nitrogen (15N) sources of specific microorganisms that are actively degrading soil organic C. We will also use secondary ion mass spectrometry coupled with microarrays to allow high-level taxonomic resolution.

Related publications

Mau RL, Liu CM, Aziz M, Schwartz E, Dijkstra P, Marks JC, Price LB, Keim P, Hungate BA, 2015. Linking soil bacterial biodiversity and soil carbon stability. ISME 9, 1477-1480.

Grants supporting this work

• Department of Energy, Systems Biology Enabled Research on the Role of Microbial Communities in Carbon Cycling: Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change, $1,430,493, 9/13-8/16

Research topics covered by funding source

• Ecosystem Sciences and Metagenomics: The Role of Microorganisms in Soil Carbon Losses
• Future of the Soil Carbon Sink: the Priming Effect
• Taxonomic, genomic, and functional diversity of soil carbon dynamics

Permafrost and ice core

Soil microorganisms are biogeochemical forces of global significance. They affect nutrient availability to plants, the amount of carbon stored in soils, and the evolution of the atmosphere over geologic time. The research we conduct in Ecoss examines many aspects of soil microbial ecology.

Metabolic Flux Analysis of Soil Microbial Communities

Microbial processing of soil organic compounds is a key ecosystem process that largely determines the soil carbon cycle. Yet, we know little about the biochemical pathways involved, and how these pathways respond to environmental change. At Ecoss, we examine changes in the fundamental processes of soil microbial metabolism that are important for the soil carbon cycle:  carbon use efficiency, energy production, and biosynthesis. We use stable isotope labeling of specific C-atoms in microbial substrates to study how microbial metabolism changes with temperature, and with different amounts of available carbon and nitrogen. The approach we have developed can be directly applied to other microbial communities, for example communities in marine and freshwater ecosystems and sediments, gastrointestinal communities, communities in environments such as hot springs, and in waste-water treatment plants. Results from this study will improve the representation of soil carbon dynamics in ecosystem models that are used to understand the role of soil processes in the global carbon cycle under current and future climates.

Related publications

Dijkstra P, Salpas E, Fairbanks D, Miller EB, Hagerty SB, van Groenigen KJ, Hungate BA, Marks JC, Koch GW, Schwartz E, 2015. High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis. Soil Biology & Biochemistry 89, 35-43.

Hagerty SB, van Groenigen KJ, Allison SD, Hungate BA, Schwartz E, Koch GB, Kolka RK, Dijkstra P, 2014. Accelerated microbial turnover but constant growth efficiency with warming in soil. Nature Climate Change 4, 903-906.

Linking Biogeochemistry and Microbial Community Chemistry

The identities of organisms profoundly influence ecosystems, and microbial diversity is vast. The obvious disconnect between this diversity and its treatment in C cycling models is perhaps the best manifestation of the common complaint that so much physiology, taxonomy, ecology, and diversity is ignored when microbial communities are described with boxes and arrows. A recent report from the American Society for Microbiology captured this complaint by depicting on the cover the hackneyed “black box” of microbial ecology, although the report emphasized the promise of new approaches by showing the box open and illuminated from within. At Ecoss, we are exploring relationships between the diversity of soil microorganisms and the processing of soil carbon and its conversion from organic C to carbon dioxide (CO₂). Our approach is designed to connect multiple element biogeochemistry and microbial community ecology, by linking isotopes to genomics, taking advantage of developments in stable isotope probing and isopycnic separation, microarrays and sequencing technology, and NanoSIMS. More details here.

Soil Microbial Legacies of Invasive Species

Invasive plants like cheatgrass have huge and costly effects on ecosystems. Restoring native plants to areas invaded by cheatgrass is challenging, and one explanation for poor seedling establishment is the absence of beneficial soil microbes. Ecoss is testing the idea that restoring microbial communities promotes ecosystem recovery and the re-establishment of native plants. More details here.

Research outlined above is being conducted by Paul Dijkstra, Bruce Hungate and others.

Detail of Yellow Fremont Cottonwood Leaves in Autumn Stream

Describing the role of leaves in aquatic ecosystems based on functional communities, rather than structural communities (e.g. presence/absence), provides a useful way of describing the community and how different leaf types function as food resources. This approach also allows one to determine how C and N function and flow through aquatic food webs.

Research conducted by the Marks Lab has found that different riparian leaf species function as substrate for specific microbes. Using Q-PCR methodology, we have found the microbes are keying in on the specific functions provided by each leaf species.

The research conducted by the Marks Lab challenges the notion that decomposition alone determines the leaf quality, suggesting instead that different leaf types benefit aquatic insects in different ways: some insects use slow-decomposing leaf litter for habitat and its temporal longevity, while others use fast-decomposing litter with more immediate nutrient release. This leaf litter paradigm is exemplified by the finding that up to 25% of the leaf litter from Fremont cottonwood is unavailable to microbes compared to that of narrowleaf cottonwood; the narrowleaf litter continues to hold C and N and provide resources to microbes for a much longer period of time. Further, the leaves of these two species leach at different rates and provide both immediate and longer-term food resources for aquatic insect communities.

This work is being conducted by Jane Marks.

Related Publications

Wymore AS, Compson ZG, McDowell WH, Potter JD, Hungate BA, Whitham TG, Marks JC. 2015. Leaf-litter leachate is distinct in optical properties and bioavailability to stream heterotrophs. Freshwater Science 34 (3), 857-866.

Compson Z, Hungate B, Koch G, Hart S, Maestas J, Adams K, Whitham T, Marks J, 2015. Closely Related Tree Species Differentially Influence the Transfer of Carbon and Nitrogen from Leaf Litter Up the Aquatic Food Web. Ecosystems, 18, 186-201.

LeRoy, Carri J., Wymore, Adam S., Davis, Rebecca, Marks, Jane C, 2014. Indirect influences of a major drought on leaf litter quality and decomposition in a southwestern stream. Fundamental and Applied Limnology / Archiv fur Hydrobiologie, Volume 184, Number 1.

Pastor, A., Compson, Z.G., Dijkstra, P., Riera, J.L., Marti, E. Sabater, F. Hungate, B.A., and Marks, J.C. 2014. Stream carbon and nitrogen supplements during leaf litter decomposition: contrasting patterns for two foundation species. Oecologia 176: 1111-1121.

Compson, Z.G., Adams, K.J., Edwards, J.A., Maestas, J.A., Whitham, T.G., and Marks, J.C. 2013. Leaf litter quality affects aquatic insect emergence: contrasting patterns from two foundation trees. Oecologia 173: 507-519.

Lamit, Louis J., Busby, P.E. Lau, M.K., Compson, Z.G. Wojtowicz, T., Keith, A.R., Zinkgraf, M.S., Schweitzer, J.A., Shuster, S.M., Gehring, C.A., and Whitham, T.G. (2015) Tree genotype mediates covariance among communities from microbes to lichens and arthropods. Journal of Ecology 103: 840–850.

Wojtowicz, T., Compson, Z.G., Lamit, L.J., Whitham, T. G., and Gehring, C.A. 2014. Plant genetic identity of foundation tree species and their hybrids affects a litter‑dwelling generalist predator. Oecologia 176:799–810.

Cheatgrass

Invasive plants like cheatgrass have huge and costly effects on ecosystems. Restoring native plants to areas invaded by cheatgrass is challenging, and one explanation for poor seedling establishment is the absence of beneficial soil microbes. Ecoss is testing the idea that restoring microbial communities promotes ecosystem recovery and the re-establishment of native plants.

Details

Invasive plants can establish and take over plant communities, causing a long-term absence of host plants. We postulate that this long-term absence causes the abundance of beneficial rhizosphere microbes to decline. These microbes include mycorrhizal fungi, but also many bacterial species. We propose that when these microbes are reintroduced in the cheatgrass-invaded areas, seedling establishment will be improved. Specifically, this project will

– characterize the microbial community composition and function associated with roots of sagebrush (Artemisia tridentata), squirreltail (Elymus elymoides), and cheatgrass (Bromus tectorum) in pristine and cheatgrass-invaded sagebrush habitat across a wide geographical region (DOD locations).
– test whether restoring the rhizosphere community and functions of sagebrush and squirreltail seedlings in cheatgrass-invaded areas improves its establishment, growth, and survival.

This research is being conducted by Paul Dijkstra.

Related publications

Weber CF, Zak DR, Hungate BA, Jackson RB, Vilgalys R, Evans RD, Schadt CW, Megonigal JP, and Kuske CR, 2011. Responses of soil cellulolytic fungal communities to elevated atmospheric CO2 are complex and variable across five ecosystems. Environmental Microbiology 13:2778-2793

Dunbar J, Eichorst SA, Gallegos-Graves LV, Silva S, Xie G, Evans RD, Hungate BA, Jackson RB, Megonigal JP, Schadt CW, Vilgalys R, Zak DR, Kuske CR, 2012. Common bacterial responses in six ecosystems exposed to ten years of elevated atmospheric carbon dioxide. Environmental Microbiology 14:1145-1158 doi:10.1111/j.1462-2920.2011.02695.x

Grants supporting this work

Department of Defense, SERDP: Role of the soil microbial community in sagebrush (Artemisia tridentata) and squirreltail (Elymus elymoides) seedling establishment in cheatgrass-invaded habitats. $1,491,000, 1/13