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382 records · Page 22

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets—from soil and seawater microbiomes—to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon’s abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.

59 BASIC BIOLOGICAL SCIENCES↗

Arctic Shrub Expansion, Plant Functional Trait Variation, and Effects on Belowground Carbon Cycling (Final Technical Report)

Terrestrial ecosystems are undergoing dramatic changes in response to climate warming, and these changes are expected to feedback to the atmosphere, potentially altering the trajectory of future climate change. Feedbacks from Arctic ecosystems are a major concern because the Arctic is projected to warm significantly in the 21 st century and because >50% of global belowground organic carbon is stored in permafrost and overlying soils. Warming-driven release of this carbon could drastically increase atmospheric greenhouse gas concentrations and accelerate climate warming. Plant communities are also responding to warming, as evidenced by the widely documented increase in woody-shrub growth and “greening” across much of the Arctic tundra biome. This vegetation shift may offset or amplify warming by altering carbon cycling. The direction and magnitude of shrub effects remain highly uncertain, however, due to limited understanding of the consequences of shrub expansion for belowground carbon cycling and simplification of these relationships in models. The major shrubs expanding in the Arctic (Betula, Salix, and Alnus) vary widely with respect to aboveground and belowground traits (e.g., tissue production and chemistry, rooting depth, microbial symbionts), and may also exhibit substantial intraspecific variation in these traits in response to environmental conditions. Such variation is likely to have profound implications for soil carbon cycling. The overarching goal of this project was to improve process-based understanding of the influence of shrub expansion on carbon cycling to enable improved representation of carbon dynamics in ecosystem and Earth system models. We investigated how plant functional traits vary among shrub genera, respond to environmental conditions, and affect belowground carbon and nutrient cycling by quantifying relationships among functional traits and biogeochemical cycling along edaphic gradients nested within a climate gradient in the Alaskan tundra. We found consistent differences in leaf and root traits among shrub genera and between shrubs and a widespread sedge species, indicating diverse nutrient acquisition strategies and belowground impacts among different arctic shrubs. We also found striking differences in trait values among individuals within the same species or genera within sites. Soil parameters were more important than climate parameters for predicting size and leaf trait variation, and root trait responses were less dependent on climate overall. For all but one root trait, including parameters representing aboveground traits improved the predictive ability of models. These results demonstrate that tundra shrub traits vary considerably at local scales and soil factors drive this variation, especially belowground. Furthermore, leveraging information about aboveground traits and soil conditions can improve predictions of how belowground traits will respond to climate change. Despite these differences, soil carbon and nitrogen pools in the active layer did not vary among plots dominated by different shrub or sedge genera. Instead, pool sizes generally decreased from warmer to colder sites, consistent with a productivity gradient. Patterns of isotopic N composition indicate that shrubs tighten nitrogen cycling via nitrogen resorption or immobilization of shrub litter. Overall, these results suggest that further identifying the specific shrub genera in the tundra landscape will ultimately provide better predictions of belowground dynamics across the changing arctic. We also performed simulation experiments with the Terrestrial Ecosystem Model (TEM) incorporated in the Predictive Ecosystem Analyzer (PEcAn) framework, treats model parameters as probability distributions, estimates parameters based on a synthesis of available field data, and then quantifies both model sensitivity and uncertainty to a given parameter or suite of parameters. We performed simulations across different types of tundra, including shrub tundra. One key finding was that both model sensitivity and uncertainty to a given parameter could vary within the same type of tundra, but in a different geographical location, such as over the climate gradient of shrub tundra described above. We organized a special session at the annual meeting of the Ecological Society of America in August 2019 to disseminate our results, refine recommendations for model improvement, and initiate collaborations to implement these recommendations in existing models of tundra carbon dynamics at ecosystem to Earth system scales. Our results support DOE near-term priorities by providing mechanistic insights into the role of vegetation change in the terrestrial carbon cycle in a region that is inadequately represented in Earth system models. Current models reduce the complexity of Arctic vegetation to a small number of plant functional types (PFTs). This approach implicitly assumes that each PFT represents the average ecological function of its constituent species, thus ignoring the effects of trait variation on biogeochemical cycling and potentially leading to large uncertainty in the sign and magnitude of ecosystem feedbacks to climate. By quantifying variation of plant functional traits across broad gradients of climatic and edaphic conditions and elucidating the linkages of such variation with carbon and nutrient cycling, our results illustrate the need and create a foundation for further developing trait-based modeling approaches that allow the traits of PFTs to vary as a function of environmental conditions. These approaches should improve the capacity of simulation models to offer insights into ecosystem carbon dynamics associated with novel plant communities in a rapidly changing Arctic.

54 ENVIRONMENTAL SCIENCES↗

Effect of fluctuating redox conditions on trace metal release from wetland soils from South Carolina and stream sediments from Tennessee

Natural aquatic systems undergo fluctuating redox conditions due to microbial activity, varying water saturation levels, and nutrients dynamics. With fluctuating oxic and anoxic conditions, trace metals can be mobilized or sequestered in response to changes in iron and sulfur speciation and the concentrations and lability of organic carbon. We conducted a systematic laboratory-based microcosm study to examine the effect of redox fluctuations on trace metal mobility in samples collected from two different natural aquatic systems: riparian wetlands and a stream. We incubated water-saturated soils under three cycles of anoxic-oxic conditions (τanoxic:τoxic = 3) spanning 24 days and monitored the change in dissolved and bioavailable metal (copper (Cu), nickel (Ni), zinc (Zn), cobalt (Co), iron (Fe), and manganese (Mn)) concentrations. The dataset includes the results of the variation in metal concentrations due to redox fluctuations in wetland soils and stream sediments. Additionally, the variation in the bioavailable concentration of metals obtained using passive samplers based on diffuse gradient in thin-films technique is included in the dataset. We have also reported the change in the pH values and dissolved oxygen concentrations in the microcosms during the entire study of 24 days. The dataset also contains the dissolved organic carbon and sulfate concentrations, and the data on fractions of metals bound to reducible and oxidizable phases. For materials from both the wetlands and the stream, anoxic conditions favored Co and Zn release, which corresponded with the reductive dissolution of iron oxides. In contrast, dissolved Cu concentrations increased under oxic conditions for both sites and correlated positively with the release of sulfate. In wetland soils, dissolution of Fe (hydr)oxides increased Ni solubility; however, in stream sediments, Ni release occurred when sulfides or organic matter were oxidized. For stream sediments, each subsequent redox cycle increased the bioavailability of trace metals. Upon redox fluctuations in wetland soils, the bioavailability of Zn and Cu increased, whereas bioavailable Ni and Co decreased. This study illustrates that different trace metals display distinct bioavailability patterns during oxic-anoxic fluctuations in natural environments. The biogeochemical cycling of carbon and nitrogen in systems with redox fluctuations may be influenced by these patterns in trace metal availability in addition to the availability of electron donors and acceptors.

54 ENVIRONMENTAL SCIENCES↗

Data from TropiRoot 1.0 database: tropical root characteristics across environments

TropiRoot 1.0 is a new tropical root database with root characteristics across environment gradients. It has data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 includes root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology and root chemistry. This initiative represents an approximately 30% increase in the currently available data for tropical roots in the Fine Root Ecology Database (FRED). TropiRoot 1.0, contains root characteristics from 25 different countries where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data was available, including soil data, these data was either extracted and included in the database or their availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match the ones reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions, and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models.

54 ENVIRONMENTAL SCIENCES↗