Publications

The objective of the Fossil Creek Riparian Vegetation, Water Quality and Visitor Use Monitoring Plan (NAU 2010) is to determine the effectiveness of the Middle Fossil Creek Riparian Habitat Protection and Restoration Project. This final report discusses the results of riparian vegetation and water quality monitoring conducted twice each year starting in 2010 (baseline monitoring) and for the following three and one-half years (2011, 2012, 2013, spring 2014). It also outlines the results of the recent spring 2014 monitoring effort.

The impacts of climate extremes on terrestrial ecosystems are poorly understood but important for predicting carbon cycle feedbacks to climate change. Coupled climate–carbon cycle models typically assume that vegetation recovery from extreme drought is immediate and complete, which conflicts with the understanding of basic plant physiology. We examined the recovery of stem growth in trees after severe drought at 1338 forest sites across the globe, comprising 49,339 site-years, and compared the results with simulated recovery in climate-vegetation models. We found pervasive and substantial “legacy effects” of reduced growth and incomplete recovery for 1 to 4 years after severe drought. Legacy effects were most prevalent in dry ecosystems, among Pinaceae, and among species with low hydraulic safety margins. In contrast, limited or no legacy effects after drought were simulated by current climate-vegetation models. Our results highlight hysteresis in ecosystem-level carbon cycling and delayed recovery from climate extremes.

The concentration detection threshold (CDT) is the concentration of particles in solution beyond which a (serial dilution) assay detects particle presence. By our account, CDTs typically are not estimated but are fixed at some value. Setting a CDT to zero (<span id="IEq1" class="InlineEquation"><span id="MathJax-Element-1-Frame" class="MathJax" style="box-sizing: inherit; display: inline-table; font-style: normal; font-weight: normal; line-height: normal; font-size: 12.75px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;" tabindex="0" data-mathml="&lt;math xmlns=&quot;http://www.w3.org/1998/Math/MathML&quot;&gt;&lt;mi&gt;d&lt;/mi&gt;&lt;mo&gt;=&lt;/mo&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/math&gt;"><span id="MathJax-Span-1" class="math"><span id="MathJax-Span-2" class="mrow"><span id="MathJax-Span-3" class="mi">d</span><span id="MathJax-Span-4" class="mo">=</span><span id="MathJax-Span-5" class="mn">0</span></span></span><span class="MJX_Assistive_MathML">d=0</span></span></span>) implies perfect detection, a common assumption, and setting <span id="IEq2" class="InlineEquation"><span id="MathJax-Element-2-Frame" class="MathJax" style="box-sizing: inherit; display: inline-table; font-style: normal; font-weight: normal; line-height: normal; font-size: 12.75px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;" tabindex="0" data-mathml="&lt;math xmlns=&quot;http://www.w3.org/1998/Math/MathML&quot;&gt;&lt;mi&gt;d&lt;/mi&gt;&lt;mo&gt;&amp;gt;&lt;/mo&gt;&lt;mn&gt;0&lt;/mn&gt;&lt;/math&gt;"><span id="MathJax-Span-6" class="math"><span id="MathJax-Span-7" class="mrow"><span id="MathJax-Span-8" class="mi">d</span><span id="MathJax-Span-9" class="mo">&gt;</span><span id="MathJax-Span-10" class="mn">0</span></span></span><span class="MJX_Assistive_MathML">d&gt;0</span></span></span> gives results that are “denominated” in units of <span id="IEq3" class="InlineEquation"><span id="MathJax-Element-3-Frame" class="MathJax" style="box-sizing: inherit; display: inline-table; font-style: normal; font-weight: normal; line-height: normal; font-size: 12.75px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;" tabindex="0" data-mathml="&lt;math xmlns=&quot;http://www.w3.org/1998/Math/MathML&quot;&gt;&lt;mi&gt;d&lt;/mi&gt;&lt;/math&gt;"><span id="MathJax-Span-11" class="math"><span id="MathJax-Span-12" class="mrow"><span id="MathJax-Span-13" class="mi">d</span></span></span><span class="MJX_Assistive_MathML">d</span></span></span>, i.e., are relative to the choice of <span id="IEq4" class="InlineEquation"><span id="MathJax-Element-4-Frame" class="MathJax" style="box-sizing: inherit; display: inline-table; font-style: normal; font-weight: normal; line-height: normal; font-size: 12.75px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px; margin: 0px; position: relative;" tabindex="0" data-mathml="&lt;math xmlns=&quot;http://www.w3.org/1998/Math/MathML&quot;&gt;&lt;mi&gt;d&lt;/mi&gt;&lt;/math&gt;"><span id="MathJax-Span-14" class="math"><span id="MathJax-Span-15" class="mrow"><span id="MathJax-Span-16" class="mi">d</span></span></span><span class="MJX_Assistive_MathML">d</span></span></span>. Using multiple, different serial dilution assays, each with its own CDT, we choose a “reference assay,” to which we assign a fixed CDT value, to obtain relative estimates of the remaining assays’ CDTs and the underlying particle concentration. We present the CDTs as a novel way to account for or to compare different serial dilution assays, “sensitivities”. We apply our methodology to data from four assays of the presence of bacterial (<em class="EmphasisTypeItalic ">B. abortus</em>) antibodies in the serum of elk in the Greater Yellowstone Ecosystem, where transmission of brucellosis—the disease ensuing from infection—to commercial livestock is managed by the Wyoming Game and Fish Department to avoid the primary symptom of abnormal fetal abortion. Results agree qualitatively with the more traditional notion of sensitivity as the true positive rate.

Decomposing leaf litter in streams provides habitat and nutrition for aquatic insects. Despite large differences in the nutritional qualities of litter among different plant species, their effects on aquatic insects are often difficult to detect. We evaluated how leaf litter of two dominant riparian species (Populus fremontii and P. angustifolia) influenced carbon and nitrogen assimilation by aquatic insect communities, quantifying assimilation rates using stable isotope tracers (13C, 15N). We tested the hypothesis that element fluxes from litter of different plant species better define aquatic insect community structure than insect relative abundances, which often fail. We found that (1) functional communities (defined by fluxes of carbon and nitrogen from leaf litter to insects) were different between leaf litter species, whereas more traditional insect communities (defined by relativized taxa abundances) were not different between leaf litter species, (2) insects assimilated N, but not C, at a higher rate from P. angustifolia litter compared to P. fremontii, even though P. angustifolia decomposes more slowly, and (3) the C:N ratio of material assimilated by aquatic insects was lower for P. angustifolia compared to P. fremontii, indicating higher nutritional quality, despite similar initial litter C:N ratios. These findings provide new evidence for the effects of terrestrial plant species on aquatic ecosystems via their direct influence on the transfer of elements up the food web. We demonstrate how isotopically labeled leaf litter can be used to assess the functioning of insect communities, uncovering patterns undetected by traditional approaches and improving our understanding of the association between food web structure and element cycling

Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the ¹⁵N:¹⁴N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among soil N isotopes, mean annual temperature (MAT), mean annual precipitation (MAP), and the concentrations of organic carbon and clay in soil. In both hot ecosystems and dry ecosystems, soil organic matter was more enriched in ¹⁵N than in corresponding cold ecosystems or wet ecosystems. Below a MAT of 9.8°C, soil δ¹⁵N was invariant with MAT. At the global scale, soil organic C concentrations also declined with increasing MAT and decreasing MAP. After standardizing for variation among mineral soils in soil C and clay concentrations, soil δ¹⁵N showed no consistent trends across global climate and latitudinal gradients. Our analyses could place new constraints on interpretations of patterns of ecosystem N cycling and global budgets of gaseous N loss.

In the tundra, mosses play an important functional role regulating belowground and ecosystem processes, but there is still considerable uncertainty about how tundra moss communities will respond to climate change. We examined the effects of 5 years of <em class="EmphasisTypeItalic ">in situ</em> air and soil warming on net primary productivity (NPP), carbon (C) and nitrogen (N) isotope signatures (δ¹³C and δ¹⁵N), and C:N in dominant Alaskan tundra mosses. Air warming increased mean air temperatures by up to 0.5°C and resulted in an 80–90% reduction in NPP in the feather moss <em class="EmphasisTypeItalic ">Pleurozium</em> and the peat moss <em class="EmphasisTypeItalic ">Sphagnum</em>. Soil warming increased permafrost thaw depth by 12–18%, upper soil water content by 23–27%, and resulted in a threefold increase in <em class="EmphasisTypeItalic ">Sphagnum</em> NPP. δ¹³C was positively correlated with moss NPP, and increased by 0.5–1‰ in all mosses under soil warming. C:N was reduced in <em class="EmphasisTypeItalic ">Sphagnum</em> and <em class="EmphasisTypeItalic ">Pleurozium</em>, due to increases in tissue %N in the soil warming treatment, suggesting that moss N availability could increase as temperatures increases. Higher N availability in warmer conditions, however, may be offset by unfavorable moisture conditions for moss growth. Similar to responses in tundra vascular plant communities, our results forecast interspecific differences in productivity among tundra mosses. Specifically, air warming may reduce productivity in <em class="EmphasisTypeItalic ">Sphagnum</em> and <em class="EmphasisTypeItalic ">Pleurozium</em>, but soil warming could offset this response in <em class="EmphasisTypeItalic ">Sphagnum</em>. Such responses may lead to changes in tundra moss community structure and function as temperatures increase that have the potential to alter tundra C and N cycling in a future climate.

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical–chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, <em>Chitinophaga</em>, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.

The efficiency with which microbes use substrate (Carbon Use Efficiency or CUE) to make new microbial biomass is an important variable in soil and ecosystem C cycling models. It is generally assumed that CUE of microbial activity in soils is low, however measured values vary widely. It is hypothesized that high values of CUE observed in especially short-term incubations reflect the build-up of storage compounds in response to a sudden increase in substrate availability and are therefore not representative of CUE of microbial activity in unamended soil. To test this hypothesis, we measured the 13CO2 release from six position-specific 13C-labeled glucose isotopomers in ponderosa pine and pinon-juniper soil. We compared this position-specific CO2 production pattern with patterns expected for 1) balanced microbial growth (synthesis of all compounds needed to build new microbial cells) at a low, medium, or high CUE, and 2) synthesis of storage compounds (glycogen, tri-palmitoyl-glycerol, and polyhydroxybutyrate). Results of this study show that synthesis of storage compounds is not responsible for the observed high CUE. Instead, it is the position-specific CO2 production expected for balanced growth and high CUE that best matches the observed CO2 production pattern in these two soils. Comparison with published studies suggests that the amount of glucose added in this study is too low and the duration of the experiment too short to affect microbial metabolism. We conclude that the hypothesis of high CUE in undisturbed soil microbial communities remains viable and worthy of further testing.

Molybdenum (Mo) is critical for the function of enzymes related to nitrogen cycling. Concentrations of Mo are very low in sandy, acidic soils, and biologically available Mo is only a small fraction of the total pool. While several methods have been proposed to measure plant-available Mo, there has not been a recent comprehensive analytical study that compares soil extraction methods as predictors of plant Mo uptake. A suite of five assays [total acid microwave digestion, ethylenediamenetetraaacetic acid (EDTA) extraction, Environmental Protection Agency (EPA) protocol 3050B, ammonium oxalate extraction, and pressurized hot water] was employed, followed by the determination of soil Mo concentrations via inductively coupled mass spectroscopy. The concentrations of soil Mo determined from these assays and their relationships as predictors of plant Mo concentration were compared. The assays yielded different concentrations of Mo: total digest &gt; EPA &gt; ammonium oxalate ≥ EDTA &gt; pressurized hot water. Legume foliar Mo concentrations were most strongly correlated with ammonium oxalate–extractable Mo from soils, but an oak species showed no relationship with any soil Mo fraction and foliar Mo. Bulk fine roots in the 10- to 30-cm soil horizon were significantly correlated with the ammonium oxalate Mo fraction. There were significant correlations between ammonium oxalate Mo and the oxides of iron (Fe), manganese (Mn), and aluminum (Al). Results suggest that the ammonium oxalate extraction for soil Mo is the best predictor of plant-available Mo for species with high Mo requirements such as legumes and that plant-available Mo tracks strongly with other metal oxides in sandy, acidic soils.

Evapotranspiration (ET) comprises a major portion of the water budget in forests, yet few studies have measured or estimated ET in semi-arid, high-elevation ponderosa pine forests of the south-western USA or have investigated the capacity of models to predict ET in disturbed forests. We measured actual ET with the eddy covariance (eddy) method over 4 years in three ponderosa pine forests near Flagstaff, Arizona, that differ in disturbance history (undisturbed control, wildfire burned, and restoration thinning) and compared these measurements (415–510 mm year⁻¹ on average) with actual ET estimated from five meteorological models [Penman–Monteith (P-M), P-M with dynamic control of stomatal resistance (P-M-d), Priestley–Taylor (P-T), McNaughton–Black (M-B), and Shuttleworth–Wallace (S-W)] and from the Moderate Resolution Imaging Spectroradiometer (MODIS) ET product. The meteorological models with constant stomatal resistance (P-M, M-B, and S-W) provided the most accurate estimates of annual eddy ET (average percent differences ranged between 11 and −14%), but their accuracy varied across sites. The P-M-d consistently underpredicted ET at all sites. The more simplistic P-T model performed well at the control site (18% overprediction) but strongly overpredicted annual eddy ET at the restoration sites (92%) and underpredicted at the fire site (−26%). The MODIS ET underpredicted annual eddy ET at all sites by at least 51% primarily because of underestimation of leaf area index. Overall, we conclude that with accurate parameterization, micrometeorological models can predict ET within 30% in forests of the south-western USA and that remote sensing-based ET estimates need to be improved through use of higher resolution products.

Soil carbon in permafrost ecosystems has the potential to become a major positive feedback to climate change if permafrost thaw increases heterotrophic decomposition. However, warming can also stimulate autotrophic production leading to increased ecosystem carbon storage—a negative climate change feedback. Few studies partitioning ecosystem respiration examine decadal warming effects or compare responses among ecosystems. Here, we first examined how 11 years of warming during different seasons affected autotrophic and heterotrophic respiration in a bryophyte-dominated peatland in Abisko, Sweden. We used natural abundance radiocarbon to partition ecosystem respiration into autotrophic respiration, associated with production, and heterotrophic decomposition. Summertime warming decreased the age of carbon respired by the ecosystem due to increased proportional contributions from autotrophic and young soil respiration and decreased proportional contributions from old soil. Summertime warming's large effect was due to not only warmer air temperatures during the growing season, but also to warmer deep soils year-round. Second, we compared ecosystem respiration responses between two contrasting ecosystems, the Abisko peatland and a tussock-dominated tundra in Healy, Alaska. Each ecosystem had two different timescales of warming (&lt;5 years and over a decade). Despite the Abisko peatland having greater ecosystem respiration and larger contributions from heterotrophic respiration than the Healy tundra, both systems responded consistently to short- and long-term warming with increased respiration, increased autotrophic contributions to ecosystem respiration, and increased ratios of autotrophic to heterotrophic respiration. We did not detect an increase in old soil carbon losses with warming at either site. If increased autotrophic respiration is balanced by increased primary production, as is the case in the Healy tundra, warming will not cause these ecosystems to become growing season carbon sources. Warming instead causes a persistent shift from heterotrophic to more autotrophic control of the growing season carbon cycle in these carbon-rich permafrost ecosystems.

Old soil carbon (C) respired to the atmosphere as a result of permafrost thaw has the potential to become a large positive feedback to climate change. As permafrost thaws, quantifying old soil contributions to ecosystem respiration (<i>R</i>_eco) and understanding how these contributions change with warming is necessary to estimate the size of this positive feedback. We used naturally occurring C isotopes (δ¹³C and Δ¹⁴C) to partition <i>R</i>_eco into plant, young soil and old soil sources in a subarctic air and soil warming experiment over three years. We found that old soil contributions to <i>R</i>_eco increased with soil temperature and <i>R</i>_eco flux. However, the increase in the soil warming treatment was smaller than expected because experimentally warming the soils increased plant contributions to <i>R</i>_eco by 30%. On the basis of these data, an increase in mean annual temperature from −5 to 0<span class="mb"><span class="mb"> </span></span>°C will increase old soil C losses from moist acidic tundra by 35–55<span class="mb"><span class="mb"> </span></span>g C<span class="mb"><span class="mb"> </span></span>m⁻² during the growing season. The largest losses will probably occur where the plant response to warming is minimal.

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in 18O and 13C composition after exposure to [18O]water or [13C]glucose. The addition of glucose increased the assimilation of 18O into DNA from [18O]water. However, the increase in 18O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.

Quantification of aboveground biomass (AGB) in Alaska's boreal forest is essential to the accurate evaluation of terrestrial carbon stocks and dynamics in northern high-latitude ecosystems. Our goal was to map AGB at 30 m resolution for the boreal forest in the Yukon River Basin of Alaska using Landsat data and ground measurements. We acquired Landsat images to generate a 3-year (2008-2010) composite of top-of-atmosphere reflectance for six bands as well as the brightness temperature (BT). We constructed a multiple regression model using field-observed AGB and Landsat-derived reflectance, BT, and vegetation indices. A basin-wide boreal forest AGB map at 30 m resolution was generated by applying the regression model to the Landsat composite. The fivefold cross-validation with field measurements had a mean absolute error (MAE) of 25.7 Mg ha⁻¹ (relative MAE 47.5%) and a mean bias error (MBE) of 4.3 Mg ha⁻¹ (relative MBE 7.9%). The boreal forest AGB product was compared with lidar-based vegetation height data; the comparison indicated that there was a significant correlation between the two data sets.

Structural and physiological changes that occur as trees grow taller are associated with increased hydraulic constraints on leaf gas exchange, yet it is unclear if leaf-level constraints influence whole-tree growth as trees approach their maximum size. We examined variation in leaf physiology, leaf area to sapwood area ratio (<em class="EmphasisTypeItalic ">L</em>/<em class="EmphasisTypeItalic ">S</em>), and annual aboveground growth across a range of tree heights in<em class="EmphasisTypeItalic "> Eucalyptus regnans</em>. Leaf photosynthetic capacity did not differ among upper crown leaves of individuals 61.1–92.4 m tall. Maximum daily and integrated diurnal stomatal conductance (<em class="EmphasisTypeItalic ">g</em>_s) averaged 36 and 34 % higher, respectively, in upper crown leaves of ~60-m-tall, 80-year-old trees than in ~90-m-tall, 300-year-old trees, with larger differences observed on days with a high vapor pressure deficit (VPD). Greater stomatal regulation in taller trees resulted in similar minimum daily leaf water potentials (<em class="EmphasisTypeItalic ">Ψ</em>_L) in shorter and taller trees over a broad range of VPDs. The long-term stomatal limitation on photosynthesis, as inferred from leaf <em class="EmphasisTypeItalic ">δ</em>¹³C composition, was also greater in taller trees. The <em class="EmphasisTypeItalic ">δ</em>¹³C of wood indicated that the bulk of photosynthesis used to fuel wood production in the main trunk and branches occurred in the upper crown. <em class="EmphasisTypeItalic ">L</em>/<em class="EmphasisTypeItalic ">S</em> increased with tree height, especially after accounting for size-independent variation in crown structure across 27 trees up to 99.8 m tall. Despite greater stomatal limitation of leaf photosynthesis in taller trees, total <em class="EmphasisTypeItalic ">L</em> explained 95 % of the variation in annual aboveground biomass growth among 15 trees measured for annual biomass growth increment in 2006. Our results support a theoretical model proposing that, in the face of increasing hydraulic constraints with height, whole-tree growth is maximized by a resource trade-off that increases <em class="EmphasisTypeItalic ">L</em> to maximize light capture rather than by reducing <em class="EmphasisTypeItalic ">L</em>/<em class="EmphasisTypeItalic ">S</em> to sustain <em class="EmphasisTypeItalic ">g</em>_s.

We present an approach to estimate the feedback from large-scale thawing of permafrost soils using a simplified, data-constrained model that combines three elements: soil carbon (C) maps and profiles to identify the distribution and type of C in permafrost soils; incubation experiments to quantify the rates of C lost after thaw; and models of soil thermal dynamics in response to climate warming. We call the approach the Permafrost Carbon Network Incubation–Panarctic Thermal scaling approach (PInc-PanTher). The approach assumes that C stocks do not decompose at all when frozen, but once thawed follow set decomposition trajectories as a function of soil temperature. The trajectories are determined according to a three-pool decomposition model fitted to incubation data using parameters specific to soil horizon types. We calculate litterfall C inputs required to maintain steady-state C balance for the current climate, and hold those inputs constant. Soil temperatures are taken from the soil thermal modules of ecosystem model simulations forced by a common set of future climate change anomalies under two warming scenarios over the period 2010 to 2100. Under a medium warming scenario (RCP4.5), the approach projects permafrost soil C losses of 12.2–33.4 Pg C; under a high warming scenario (RCP8.5), the approach projects C losses of 27.9–112.6 Pg C. Projected C losses are roughly linearly proportional to global temperature changes across the two scenarios. These results indicate a global sensitivity of frozen soil C to climate change (<em>γ</em> sensitivity) of −14 to −19 Pg C °C⁻¹ on a 100 year time scale. For CH₄ emissions, our approach assumes a fixed saturated area and that increases in CH₄ emissions are related to increased heterotrophic respiration in anoxic soil, yielding CH₄ emission increases of 7% and 35% for the RCP4.5 and RCP8.5 scenarios, respectively, which add an additional greenhouse gas forcing of approximately 10–18%. The simplified approach presented here neglects many important processes that may amplify or mitigate C release from permafrost soils, but serves as a data-constrained estimate on the forced, large-scale permafrost C response to warming.

Stomata simultaneously regulate plant carbon gain and water loss, and patterns of stomatal conductance (<em class="EmphasisTypeItalic ">g</em>_s) provide insight into water use strategies. In arid systems, <em class="EmphasisTypeItalic ">g</em>_s varies seasonally based on factors such as water availability and temperature. Moreover, the presence and species identity of neighboring plants likely affects <em class="EmphasisTypeItalic ">g</em>_s of the focal plant by altering available soil water and microclimate conditions. We investigated stomatal behavior in <em class="EmphasisTypeItalic ">Larrea tridentata</em>, a drought-tolerant, evergreen shrub occurring throughout the arid southwestern United States. We measured <em class="EmphasisTypeItalic ">g</em>_s in <em class="EmphasisTypeItalic ">Larrea</em> over multiple seasons in the presence of neighbors representing different woody species. The data were analyzed in the context of a commonly used phenomenological model that relates <em class="EmphasisTypeItalic ">g</em>_s to vapor pressure deficit (<em class="EmphasisTypeItalic ">D</em>) to understand spatial and temporal differences in stomatal behavior. We found that <em class="EmphasisTypeItalic ">g</em>_s in <em class="EmphasisTypeItalic ">Larrea</em> was affected by neighborhood association, and these effects varied seasonally. The greatest effect of neighborhood association on <em class="EmphasisTypeItalic ">g</em>_s occurred during the winter period, where <em class="EmphasisTypeItalic ">Larrea</em> growing alone (without neighbors) had higher <em class="EmphasisTypeItalic ">g</em>_s compared to <em class="EmphasisTypeItalic ">Larrea</em> growing with neighbors. <em class="EmphasisTypeItalic ">Larrea</em>’s stomatal sensitivity to <em class="EmphasisTypeItalic ">D</em> and reference conductance (i.e., <em class="EmphasisTypeItalic ">g</em>_s at <em class="EmphasisTypeItalic ">D</em> = 1 kPa) also differed significantly among different neighbor associations. Random effects indicated reference <em class="EmphasisTypeItalic ">g</em>_s varied over short time scales (daily), while stomatal sensitivity showed little daily or seasonal variation, but was notably affected by neighbor associations such that neighboring species, especially trees, reduced <em class="EmphasisTypeItalic ">Larrea</em>’s sensitivity to <em class="EmphasisTypeItalic ">D</em>. Overall, seasonal dynamics and neighborhood conditions appear critical to understanding temporal and spatial variation in <em class="EmphasisTypeItalic ">Larrea</em>’s physiological behavior.

Community genetics studies frequently focus on individual communities associated with individual plant genotypes, but little is known about the genetically based relationships among taxonomically and spatially disparate communities. We integrate studies of a wide range of communities living on the same plant genotypes to understand how the ecological and evolutionary dynamics of one community may be constrained or modulated by its underlying genetic connections to another community. We use pre-existing data sets collected from Populus angustifolia (narrowleaf cottonwood) growing in a common garden to test the hypothesis that the composition of pairs of distinct communities (e.g. endophytes, pathogens, lichens, arthropods, soil microbes) covary across tree genotypes, such that individual plant genotypes that support a unique composition of one community are more likely to support a unique composition of another community. We then evaluate the hypotheses that physical proximity, taxonomic similarity, time between sampling (time attenuation), and interacting foundation species within communities explain the strength of correlations. Three main results emerged. First, Mantel tests between communities revealed moderate to strong (q = 0.25–0.85) community–genetic correlations in almost half of the comparisons; correlations among phyllosphere endophyte, pathogen and arthropod communities were the most robust. Secondly, physical proximity determined the strength of community–genetic correlations, supporting a physical proximity hypothesis. Thirdly, consistent with the interacting foundation species hypothesis, the most abundant species drove many of the stronger correlations. Other hypotheses were not supported. Synthesis. The field of community genetics demonstrates that the structure of communities varies among plant genotypes; our results add to this field by showing that disparate communities covary among plant genotypes. Eco-evolutionary dynamics between plants and their associated organisms may therefore be mediated by the shared connections of different communities to plant genotype, indicating that the organization of biodiversity in this system is genetically based and non-neutral.

Biodiversity at many scales (functional group, species, genetic) can result in emergent ecological patterns. Here we explore the influence of tree genotypic variation and diversity on in-stream ecosystem processes and aquatic communities. We test whether genetically diverse inputs of leaf litter interact with a keystone organism, anadromous salmon, to influence in-stream ecosystem function. We used reach-level manipulation of salmon carcasses and leaf litter bags to examine how nutrient inputs interact with genetic variation in leaf litter decomposition. Genotypic variation in black cottonwood (<i>Populus balsamifera</i> ssp. <i>trichocarpa</i>) significantly influenced leaf litter chemistry, litter mass loss, and fungal biomass, but these variables were only weakly influenced by salmon carcass presence or a genotype × salmon (G × E) interaction. Mixtures of genotypes tended to demonstrate antagonistic effects (slower than expected decomposition) in the absence of salmon, but synergistic effects (faster than expected decomposition) when salmon were present. Our findings suggest that the influence of plant genotypic variation in linking aquatic and terrestrial ecosystems may be altered and in some cases intensified in the presence of a keystone vertebrate species.

Although the temperature sensitivity (Q₁₀) of soil organic matter (SOM) decomposition has been widely studied, the estimate substantially depends on the methods used with specific assumptions. Here we compared several commonly used methods (i.e., one-pool (1P) model, two-discrete-pool (2P) model, three-discrete-pool (3P) model, and time-for-substrate (T4S) Q₁₀ method) plus a new and more process-oriented approach for estimating Q₁₀ of SOM decomposition from laboratory incubation data to evaluate the influences of the different methods and assumptions on Q₁₀ estimation. The process-oriented approach is a three-transfer-pool (3PX) model that resembles the decomposition sub-model commonly used in Earth system models. The temperature sensitivity and other parameters in the models were estimated from the cumulative CO₂emission using the Bayesian Markov Chain Monte Carlo (MCMC) technique. The estimated Q₁₀s generally increased with the soil recalcitrance, but decreased with the incubation temperature increase. Our results indicated that the 1P model did not adequately simulate the dynamics of SOM decomposition and thus was not adequate for the Q₁₀ estimation. All the multi-pool models fitted the soil incubation data well. The Akaike information criterion (<em>AIC</em>) analysis suggested that the 2P model is the most parsimonious. As the incubation progressed, Q₁₀ estimated by the 3PX model was smaller than those by the 2P and 3P models because the continuous C transfers from the slow and passive pools to the active pool were included in the 3PX model. Although the T4S method could estimate the Q₁₀ of labile carbon appropriately, our analyses showed that it overestimated that of recalcitrant SOM. The similar structure of 3PX model with the decomposition sub-model of Earth system models provides a possible approach, via the data assimilation techniques, to incorporate results from numerous incubation experiments into Earth system models.

Bacterial vaginosis (BV) is a common vaginal bacterial imbalance associated with risk for HIV and poor gynecologic and obstetric outcomes. Male circumcision reduces BV-associated bacteria on the penis and decreases BV in female partners, but the link between penile microbiota and female partner BV is not well understood. We tested the hypothesis that having a female partner with BV increases BV-associated bacteria in uncircumcised men. We characterized penile microbiota composition and density (i.e., the quantity of bacteria per swab) by broad-coverage 16S rRNA gene-based sequencing and quantitative PCR (qPCR) in 165 uncircumcised men from Rakai, Uganda. Associations between penile community state types (CSTs) and female partner’s Nugent score were assessed. We found seven distinct penile CSTs of increasing density (CST1 to 7). CST1 to 3 and CST4 to 7 were the two major CST groups. CST4 to 7 had higher prevalence and abundance of BV-associated bacteria, such as <em>Mobiluncus</em> and <em>Dialister</em>, than CST1 to 3. Men with CST4 to 7 were significantly more likely to have a female partner with a high Nugent score (<em>P</em> = 0.03). Men with two or more extramarital partners were significantly more likely to have CST4 to 7 than men with only marital partners (CST4 to 7 prevalence ratio, 1.84; 95% confidence interval [CI], 1.16 to 2.92). Female partner Nugent BV is significantly associated with penile microbiota. Our data support the exchange of BV-associated bacteria through intercourse, which may explain BV recurrence and persistence.

The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by <em>Staphylococcus aureus</em>. However, what determines our resident nasal microbiota—the host or the environment—and can interactions among nasal bacteria determine <em>S. aureus</em> colonization? Our study of 46 monozygotic and 43 dizygotic twin pairs revealed that nasal microbiota is an environmentally derived trait, but the host’s sex and genetics significantly influence nasal bacterial density. Although specific taxa, including lactic acid bacteria, can determine <em>S. aureus</em> colonization, their negative interactions depend on thresholds of absolute abundance. These findings demonstrate that nasal microbiota is not fixed by host genetics and opens the possibility that nasal microbiota may be manipulated to prevent or eliminate <em>S. aureus</em> colonization.

Nitrogen use efficiency (NUE) is a crucial index for developing sustainable bioenergy cropping systems. The objective of this study was to examine switchgrass (<em class="EmphasisTypeItalic ">Panicum virgatum</em> L.) NUE by using a low-cost organic amendment under different harvest frequencies. Aerobically digested biosolids were applied at 0, 153, 306, and 459 kg N ha⁻¹ in a small plot study, and lime-stabilized biosolids were applied at 0, 77, and 154 kg N ha⁻¹ in a field-scale study in Virginia, USA. Switchgrass was harvested once or twice per season. Switchgrass N concentration and N removal were measured to estimate switchgrass NUE, annual N recovery (ANR), and partial factor productivity (PFP). Across N rates, biosolid application increased biomass N concentration and removal by 29 % and 84 % and decreased NUE, ANR, and PFP in the plot study, but effects were inconsistent in the field study. Low NUE, ANR, and PFP obtained with a single, end-of-season harvest were likely functions of low feedstock N concentrations. Switchgrass harvested in summer had highest N concentrations. Cutting twice per season removed more N than cutting once; the resulting increase in NUE reflects differences in feedstock N concentrations rather than differences in yield. Our results suggest that biosolids can be applied as an alternative N source to support plant growth, and cutting once per season is preferable in sustainable biofuel production systems.

Sustainable development of a bioenergy industry will require low-cost, high-yielding biomass feedstock of desirable quality. Switchgrass (<em>Panicum virgatum</em> L.) is one of the primary feedstock candidates in North America, but the potential to grow this biomass crop using fertility from biosolids has not been fully explored. The objective of this study was to examine the effects of harvest frequency and biosolids application on switchgrass in Virginia, USA. ‘Cave-in-Rock’ switchgrass from well-established plots was cut once (November) or twice (July and November) per year between 2010 and 2012. Class A biosolids were applied once at rates of 0, 153, 306, and 459 kg N ha⁻¹ in May 2010. Biomass yield, neutral and acid detergent fiber, cellulose, hemicellulose, lignin, and ash were determined. Theoretical ethanol potential (TEP, l ethanol Mg⁻¹ biomass) and yield (TEY, l ethanol ha⁻¹) were calculated based on cellulose and hemicellulose concentrations. Cutting twice per season produced greater biomass yields than one cutting (11.7 vs. 9.8 Mg ha⁻¹) in 2011, but no differences were observed in other years. Cutting once produced feedstock with greater TEP (478 vs. 438 l Mg⁻¹), but no differences in TEY between cutting frequencies. Biosolids applied at 153, 306, and 459 kg N ha⁻¹ increased biomass yields by 25%, 37%, and 46%, and TEY by 25%, 34%, and 42%, respectively. Biosolids had inconsistent effects on feedstock quality and TEP. A single, end-of-season harvest likely will be preferred based on apparent advantages in feedstock quality. Biosolids can serve as an effective alternative to N fertilizer in switchgrass-to-energy systems.

Concerns about rising greenhouse gas (GHG) concentrations have spurred the promotion of no-tillage practices as a means to stimulate carbon storage and reduce CO₂ emissions in agro-ecosystems. Recent research has ignited debate about the effect of earthworms on the GHG balance of soil. It is unclear how earthworms interact with soil management practices, making long-term predictions on their effect in agro-ecosystems problematic. Here we show, in a unique two-year experiment, that earthworm presence increases the combined cumulative emissions of CO₂ and N₂O from a simulated no-tillage (NT) system to the same level as a simulated conventional tillage (CT) system. We found no evidence for increased soil C storage in the presence of earthworms. Because NT agriculture stimulates earthworm presence, our results identify a possible biological pathway for the limited potential of no-tillage soils with respect to GHG mitigation.

Conservation agriculture (CA) has been promoted as a method of sustainable intensification and climate change mitigation and is being widely practiced and implemented globally. However, no-till (NT), a fundamental component of CA, has been shown to reduce yields in many cases. In order to maintain yields following adoption of CA, it has been recently suggested that fertilizer application should be an integral component of CA. To determine the contribution of nitrogen (N) fertilizer in minimizing yield declines following NT implementation, we assessed 2759 paired comparisons of NT and conventional tillage (CT) systems from 325 studies reported in the peer-reviewed literature between 1980 and 2013. Overall, we found that NT yields decreased −10.7% (−14.8% to −6.5%) and −3.7% (−5.3% to −2.2%) relative to CT in tropical/subtropical and temperate regions, respectively. Among management and environmental variables that included: the rate of N fertilization; the duration of the NT/CT comparison; residue, rotation, and irrigation practices; the crop type; and the site aridity, N rate was the most important explanatory variable for NT yield declines in tropical/subtropical regions. In temperate regions, N fertilization rates were relatively less important. NT yield declines were most consistently observed at low rates of N fertilization during the first 2 years of NT adoption in tropical/subtropical regions. Applications of N fertilizer at rates of up to 85 ± 12 kg N ha⁻¹ yr⁻¹ significantly reduced NT yield declines in these scenarios. While this result should not be viewed as a rate recommendation, it does suggest that farmers applying rates of N fertilizer that are low for their specific system will, on average, see higher NT yields if they increase application rates. In addition, when crop rotation was not practiced or residues were removed from the field, NT yield declines were magnified by low rates of N fertilization in tropical/subtropical regions. These results, based on a global data set and across a broad range of crops, highlight the importance of N fertilization in counteracting yield declines in NT systems, particularly in tropical/subtropical regions.

Forests are a significant part of the global carbon cycle and are increasingly viewed as tools for mitigating climate change. Natural disturbances, such as fire, can reduce carbon storage. However, many forests and dependent species evolved with frequent fire as an integral ecosystem process. We used a landscape forest simulation model to evaluate the effects of endangered species habitat management on carbon sequestration. We compared unmanaged forests (control) to forests managed with prescribed burning and prescribed burning combined with thinning. Management treatments followed guidelines of the recovery plan for the endangered red-cockaded woodpecker (RCW), which requires low-density longleaf pine (Pinus palustris) forest. The unmanaged treatment provided the greatest carbon storage, but at the cost of lost RCW habitat. Thinning and burning treatments expanded RCW habitat by increasing the dominance of longleaf pine and reducing forest density, but stored 22% less total ecosystem carbon compared to the control. Our results demonstrate that continued carbon sequestration and the provision of RCW habitat are not incompatible goals, although there is a tradeoff between habitat extent and total ecosystem carbon across the landscape. Management for RCW habitat might also increase ecosystem resilience, as longleaf pine is tolerant of fire and drought, and resistant to pests. Restoring fire-adapted forests requires a reduction in carbon. However, the size of the reduction, the effects on sequestration rates, and the co-benefits from other ecosystem services should be evaluated in the context of the specific forest community targeted for restoration

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this ‘priming’ effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

Many northern forests are limited by nitrogen (N) availability, slight changes in which can have profound effects on ecosystem function and the activity of ectomycorrhizal (EcM) fungi. Increasing N and phosphorus (P) availability, an analog to accelerated soil organic matter decomposition in a warming climate, could decrease plant dependency on EcM fungi and increase plant productivity as a result of greater carbon use efficiency. However, the impact of altered N and P availability on the growth and activity of EcM fungi in boreal forests remains poorly understood despite recognition of their importance to host plant nutrition and soil carbon sequestration. To address such uncertainty we examined above and belowground ecosystem properties in a boreal black spruce forest following five years of factorial N and P additions. By combining detailed soil, fungal, and plant <em>δ</em>¹⁵N measurements with <em>in situ</em> metrics of fungal biomass, growth, and activity, we found both expected and unexpected patterns. Soil nitrate isotope values became ¹⁵N enriched in response to both N and P additions; fungal biomass was repressed by N yet both biomass and growth were stimulated by P; and, black spruce dependency on EcM derived N increased slightly when N and P were added alone yet significantly declined when added in combination. These findings contradict predictions that N fertilization would increase plant P demands and P fertilization would further exacerbate plant N demands. As a result, the prediction that EcM fungi predictably respond to plant N limitation was not supported. These findings highlight P as an under appreciated mediator of the activity of denitrifying bacteria, EcM fungi, and the dynamics of N cycles in boreal forests. Further, use of <em>δ</em>¹⁵N values from bulk soils, plants, and fungi to understand how EcM systems respond to changing nutrient availabilities will often require additional ecological information.

Water drives the functioning of Earth’s arid and semiarid lands. Drylands can obtain water from sources other than precipitation, yet little is known about how non-rainfall water inputs influence dryland communities and their activity. In particular, water vapor adsorption – movement of atmospheric water vapor into soil when soil air is drier than the overlying air – likely occurs often in drylands, yet its effects on ecosystem processes are not known. By adding ¹⁸O-enriched water vapor to the atmosphere of a closed system, we documented the conversion of water vapor to soil liquid water across a temperature range typical of arid ecosystems. This phenomenon rapidly increased soil moisture and stimulated microbial carbon (C) cycling, and the flux of water vapor to soil had a stronger impact than temperature on microbial activity. In a semiarid grassland, we also observed that non-rainfall water inputs stimulated microbial activity and C cycling. Together these data suggest that, during rain-free periods, atmospheric moisture in drylands may significantly contribute to variation in soil water content, thereby influencing ecosystem processes. The simple physical process of adsorption of water vapor to soil particles, forming liquid water, represents an overlooked but potentially important contributor to C cycling in drylands.

In the boreal forest of Alaska, increased fire severity associated with climate change is expanding deciduous forest cover in areas previously dominated by black spruce (<em class="EmphasisTypeItalic ">Picea mariana</em>). Needle-leaf conifer and broad-leaf deciduous species are commonly associated with differences in tree growth, carbon (C) and nutrient cycling, and C accumulation in soils. Although this suggests that changes in tree species composition in Alaska could impact C and nutrient pools and fluxes, few studies have measured these linkages. We quantified C, nitrogen, phosphorus, and base cation pools and fluxes in three stands of black spruce and Alaska paper birch (<em class="EmphasisTypeItalic ">Betula neoalaskana</em>) that established following a single fire event in 1958. Paper birch consistently displayed characteristics of more rapid C and nutrient cycling, including greater aboveground net primary productivity, higher live foliage and litter nutrient concentrations, and larger ammonium and nitrate pools in the soil organic layer (SOL). Ecosystem C stocks (aboveground + SOL + 0–10 cm mineral soil) were similar for the two species; however, in black spruce, 78% of measured C was found in soil pools, primarily in the SOL, whereas aboveground biomass dominated ecosystem C pools in birch forest. Radiocarbon analysis indicated that approximately one-quarter of the black spruce SOL C accumulated prior to the 1958 fire, whereas no pre-fire C was observed in birch soils. Our findings suggest that tree species exert a strong influence over C and nutrient cycling in boreal forest and forest compositional shifts may have long-term implications for ecosystem C and nutrient dynamics.

Microbial necromass is an important source of stabilized organic matter in soil, yet the decomposition dynamics of necromass constituents have not been adequately characterized. This includes DNA, a nutrient-rich molecule that when released into the environment as extracellular DNA (eDNA) can be readily used by soil microorganisms. However, the ecological relevance of eDNA as a nutrient source for soil microorganisms is relatively unknown. To address these deficits, we performed a laboratory experiment wherein soils were amended with ¹³C-labeled eDNA and clay minerals known to interact with DNA (kaolinite and montmorillonite). The amount of eDNA-carbon remaining in the soil declined exponentially over time. Kaolinite amendment decreased eDNA decomposition rates and, after 30 days, retained a higher fraction of eDNA-carbon (∼70% remaining) than control or montmorillonite soils (∼40% remaining), indicating that clay mineral sorption can stabilize eDNA-derived carbon in soil. Sequencing of bacterial 16S rRNA genes showed that during the incubation the relative abundance of the added eDNA's sequence decreased by 98%, 92% and 99% in the control, montmorillonite, and kaolinite amended soils respectively. These results suggest that the fraction of eDNA-carbon that remained in the soil was incorporated into microbial biomass, firmly bound to soil constituents, or fragmented and no longer amenable to sequencing. In addition, the eDNA amendment affected the composition of the bacterial community. Specifically, the relative abundance of select phyla (Planctomycetes and TM7) and genera (e.g., <em>Arthrobacter</em> and <em>Nocardioides</em>) were elevated in soils that received eDNA, suggesting these groups may be particularly effective at degrading eDNA and using it for growth. Taken together, these results indicate that while eDNA is consumed by bacteria in soil, a fraction of eDNA material is resistant to decomposition, particularly when stabilized by soil minerals, suggesting a substantial amount of recalcitrant eDNA could accumulate over time.

As permafrost degrades, the amount of organic soil carbon (C) that thaws during the growing season will increase, but decomposition may be limited by saturated soil conditions common in high-latitude ecosystems. However, in some areas, soil drying is expected to accompany permafrost thaw as a result of increased water drainage, which may enhance C release to the atmosphere. We examined the effects of ecosystem warming, permafrost thaw, and soil moisture changes on C balance in an upland tundra ecosystem. This study was conducted at a water table drawdown experiment, established in 2011 and located within the Carbon in Permafrost Experimental Heating Research project, an ecosystem warming and permafrost thawing experiment in Alaska. Warming and drying increased cumulative growing season ecosystem respiration by ~20% over 3 years of this experiment. Warming caused an almost twofold increase in decomposition of a common substrate in surface soil (0–10 cm) across all years, and drying caused a twofold increase in decomposition (0–20 cm) relative to control after 3 years of drying. Decomposition of older C increased in the dried and in the combined warmed + dried plots based on soil pore space ¹⁴CO₂. Although upland tundra systems have been considered CH₄ sinks, warming and ground thaw significantly increased CH₄ emission rates. Water table depth was positively correlated with monthly respiration and negatively correlated with CH₄ emission rates. These results demonstrate that warming and drying may increase loss of old permafrost C from tundra ecosystems, but the form and magnitude of C released to the atmosphere will be driven by changes in soil moisture.

The role of time in ecology has a long history of investigation, but ecologists have largely restricted their attention to the influence of concurrent abiotic conditions on rates and magnitudes of important ecological processes. Recently, however, ecologists have improved their understanding of ecological processes by explicitly considering the effects of antecedent conditions. To broadly help in studying the role of time, we evaluate the length, temporal pattern, and strength of memory with respect to the influence of antecedent conditions on current ecological dynamics. We developed the stochastic antecedent modelling (SAM) framework as a flexible analytic approach for evaluating exogenous and endogenous process components of memory in a system of interest. We designed SAM to be useful in revealing novel insights promoting further study, illustrated in four examples with different degrees of complexity and varying time scales: stomatal conductance, soil respiration, ecosystem productivity, and tree growth. Models with antecedent effects explained an additional 18–28% of response variation compared to models without antecedent effects. Moreover, SAM also enabled identification of potential mechanisms that underlie components of memory, thus revealing temporal properties that are not apparent from traditional treatments of ecological time-series data and facilitating new hypothesis generation and additional research.

<section id="abstract" class="article-section article-section--abstract article-tools__article-section--is-active"> <div class="article-section__content mainAbstract"> Isotopic methods offer great potential for partitioning trace gas fluxes such as soil respiration into their different source contributions. Traditional partitioning methods face challenges due to variability introduced by different measurement methods, fractionation effects, and end-member uncertainty. To address these challenges, we describe a hierarchical Bayesian (HB) approach for isotopic partitioning of soil respiration that directly accommodates such variability. We apply our HB method to data from an experiment conducted in a shortgrass steppe ecosystem, where decomposition was previously shown to be stimulated by elevated CO₂. Our approach simultaneously fits Keeling plot (KP) models to observations of soil or soil-respired <em>δ</em>¹³C and [CO₂] obtained via chambers and gas wells, corrects the KP intercepts for apparent fractionation (Δ) due to isotope-specific diffusion rates and/or method artifacts, estimates method- and treatment-specific values for Δ, propagates end-member uncertainty, and calculates proportional contributions from two distinct respiration sources (“old” and “new” carbon). The chamber KP intercepts were estimated with greater confidence than the well intercepts and compared to the theoretical value of 4.4‰, our results suggest that Δ varies between 2 and 5.2‰ depending on method (chambers versus wells) and CO₂ treatment. Because elevated CO₂ plots were fumigated with ¹³C-depleted CO₂, the source contributions were tightly constrained, and new C accounted for 64% (range = 55–73%) of soil respiration. The contributions were less constrained for the ambient CO₂ treatments, but new C accounted for significantly less (47%, range = 15–82%) of soil respiration. Our new HB partitioning approach contrasts our original analysis (higher contribution of old C under elevated CO₂) because it uses additional data sources, accounts for end-member bias, and estimates apparent fractionation effects. </div> </section>&nbsp; <section id="jgrg20329-sec-0001" class="article-section article-body-section"></section>

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (<i>nifH</i>), and denitrifying (<i>nirS, nirK, nosZ</i>) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the <i>nirK</i>-harboring bacterial community. A highly divergent <i>nirK</i>-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

One of the primary challenges of our time is to feed a growing and more demanding world population with reduced external inputs and minimal environmental impacts, all under more variable and extreme climate conditions in the future^{<a id="ref-link-1" title="Foley, J. A. et al. Solutions for a cultivated planet. Nature 478, 337-342 (2011)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref1">1</a>, <a id="ref-link-2" title="Lobell, D. B. et al. Prioritizing climate change adaptation needs for food security in 2030. Science 319, 607-610 (2008)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref2">2</a>, <a id="ref-link-3" title="Godfray, H. C. J. &amp; Garnett, T. Food security and sustainable intensification. Phil. Trans. R. Soc. B 369, 20120273 (2014)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref3">3</a>, <a id="ref-link-4" title="Tilman, D., Balzer, C., Hill, J. &amp; Befort, B. L. Global food demand and the sustainable intensification of agriculture. Proc. Natl Acad. Sci. USA 108, 20260-20264 (2011)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref4">4</a>}. Conservation agriculture represents a set of three crop management principles that has received strong international support to help address this challenge^{<a id="ref-link-5" title="FAO. Save and Grow: A Policymaker/'s Guide to the Sustainable Intensification of Smallholder Crop Production 1-37 (FAO, 2011)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref5">5</a>, <a id="ref-link-6" title="Hobbs, P. R., Sayre, K. &amp; Gupta, R. The role of conservation agriculture in sustainable agriculture. Phil. Trans. R. Soc. B 363, 543-555 (2008)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref6">6</a>}, with recent conservation agriculture efforts focusing on smallholder farming systems in sub-Saharan Africa and South Asia^{<a id="ref-link-7" title="Stevenson, J. R., Serraj, R. &amp; Cassman, K. G. Evaluating conservation agriculture for small-scale farmers in sub-Saharan Africa and South Asia. Agric. Ecosyst. Environ. 187, 1-10 (2014)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref7">7</a>}. However, conservation agriculture is highly debated, with respect to both its effects on crop yields^{<a id="ref-link-8" title="Giller, K. E., Witter, E., Corbeels, M. &amp; Tittonell, P. Conservation agriculture and smallholder farming in Africa: the heretics/' view. Field Crops Res. 114, 23-34 (2009)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref8">8</a>, <a id="ref-link-9" title="Rusinamhodzi, L. et al. A meta-analysis of long-term effects of conservation agriculture on maize grain yield under rain-fed conditions. Agron. Sust. Dev. 31, 657-673 (2011)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref9">9</a>, <a id="ref-link-10" title="Brouder, S. M. &amp; Gomez-Macpherson, H. The impact of conservation agriculture on smallholder agricultural yields: a scoping review of the evidence. Agric. Ecosyst. Environ. 187, 11-32 (2014)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref10">10</a>} and its applicability in different farming contexts^{<a id="ref-link-11" title="Stevenson, J. R., Serraj, R. &amp; Cassman, K. G. Evaluating conservation agriculture for small-scale farmers in sub-Saharan Africa and South Asia. Agric. Ecosyst. Environ. 187, 1-10 (2014)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref7">7</a>, <a id="ref-link-12" title="Andersson, J. A. &amp; Giller, K. E. in Contested Agronomy: Agricultural Research in a Changing World (eds Sumberg, J. &amp; Thompson, J.) Ch. 2 22-46 (Earthscan, 2012)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref11">11</a>, <a id="ref-link-13" title="Giller, K. E. et al. A research agenda to explore the role of conservation agriculture in African smallholder farming systems. Field Crops Res. 124, 468-472 (2011)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref12">12</a>, <a id="ref-link-14" title="Friedrich, T., Derpsch, R. &amp; Kassam, A. Overview of the global spread of conservation agriculture. Field Actions Sci. Rep. 6, 1941 (2012)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref13">13</a>}. Here we conduct a global meta-analysis using 5,463 paired yield observations from 610 studies to compare no-till, the original and central concept of conservation agriculture, with conventional tillage practices across 48 crops and 63 countries. Overall, our results show that no-till reduces yields, yet this response is variable and under certain conditions no-till can produce equivalent or greater yields than conventional tillage. Importantly, when no-till is combined with the other two conservation agriculture principles of residue retention and crop rotation, its negative impacts are minimized. Moreover, no-till in combination with the other two principles significantly increases rainfed crop productivity in dry climates, suggesting that it may become an important climate-change adaptation strategy for ever-drier regions of the world. However, any expansion of conservation agriculture should be done with caution in these areas, as implementation of the other two principles is often challenging in resource-poor and vulnerable smallholder farming systems, thereby increasing the likelihood of yield losses rather than gains. Although farming systems are multifunctional, and environmental and socio-economic factors need to be considered^{<a id="ref-link-15" title="Godfray, H. C. et al. Food security: the challenge of feeding 9 billion people. Science 327, 812-818 (2010)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref14">14</a>, <a id="ref-link-16" title="Sachs, J. et al. Monitoring the world/'s agriculture. Nature 466, 558-560 (2010)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref15">15</a>, <a id="ref-link-17" title="Palm, C., Blanco-Canqui, H., DeClerck, F., Gatere, L. &amp; Grace, P. Conservation agriculture and ecosystem services: An overview. Agric. Ecosyst. Environ. 187, 87-105 (2014)" href="http://www.nature.com/nature/journal/v517/n7534/full/nature13809.html#ref16">16</a>}, our analysis indicates that the potential contribution of no-till to the sustainable intensification of agriculture is more limited than often assumed.

No-till agriculture represents a relatively widely adopted management system that aims to reduce soil erosion, decrease input costs, and sustain long-term crop productivity. However, its impacts on crop yields are variable, and an improved understanding of the factors limiting productivity is needed to support evidence-based management decisions. We conducted a global meta-analysis to evaluate the influence of various crop and environmental variables on no-till relative to conventional tillage yields using data obtained from peer-reviewed publications (678 studies with 6005 paired observations, representing 50 crops and 63 countries). Side-by-side yield comparisons were restricted to studies comparing conventional tillage to no-till practices in the absence of other cropping system modifications. Crop category was the most important factor influencing the overall yield response to no-till followed by aridity index, residue management, no-till duration, and N rate. No-till yields matched conventional tillage yields for oilseed, cotton, and legume crop categories. Among cereals, the negative impacts of no-till were smallest for wheat (−2.6%) and largest for rice (−7.5%) and maize (−7.6%). No-till performed best under rainfed conditions in dry climates, with yields often being equal to or higher than conventional tillage practices. Yields in the first 1–2 years following no-till implementation declined for all crops except oilseeds and cotton, but matched conventional tillage yields after 3–10 years except for maize and wheat in humid climates. Overall, no-till yields were reduced by 12% without N fertilizer addition and 4% with inorganic N addition. Our study highlights factors contributing to and/or decreasing no-till yield gaps and suggests that improved targeting and adaptation, possibly including additional system modifications, are necessary to optimize no-till performance and contribute to food production goals. In addition, our results provide a basis for conducting trade-off analyses to support the development of no-till crop management and international development strategies based on available scientific evidence.

<p id="p-2" class="flushleft">Alexander Fleming famously warned that the ignorant may someday misuse his life-saving discovery—penicillin—and select for resistant bacteria (<a id="xref-ref-1-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-1">1</a>). This was prescient given the widespread use of subtherapeutic antibiotics by food-animal producers today. According to the findings of Van Boeckel et al. (<a id="xref-ref-2-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-2">2</a>) in PNAS, the proliferation of ignorance is only poised to increase. Using global datasets of veterinary antibiotic use, livestock densities, and economic projections of meat demand, Van Boeckel et al. (<a id="xref-ref-2-2" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-2">2</a>) estimate that from 2010 to 2030 antibiotic use in food-animal production will increase by 67%, from 63,151 ± 1,560 tons to 105,596 ± 3,605 tons.</p> <p id="p-3">The study by Van Boeckel et al. (<a id="xref-ref-2-3" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-2">2</a>) is the first to estimate global use of antibiotics in livestock production, and to disaggregate that global figure into estimates for each of 228 countries. However, their estimate is based on data from only 32 countries. Using a clear framework and a state-of-the-art Bayesian statistical model, the authors extrapolate from the most reliable data available to arrive at the global sum. This is an admirable approach to a difficult problem, but it raises a question: Why not derive the values more simply, by summing data from all 228 countries, using the actual records of antibiotic use in livestock production? After all, this is how we quantify global fossil fuel use (<a id="xref-ref-3-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-3">3</a>), livestock production and trade (<a id="xref-ref-4-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-4">4</a>, <a id="xref-ref-5-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-5">5</a>), and the use of fertilizers in agriculture (<a id="xref-ref-4-2" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-4">4</a>). For many assessments of global economic activity, including these, the actual data exist. However, for antibiotics in livestock production, a statistical model is the best option because comprehensive data on the use of antibiotics in livestock production are not available. Most countries do not record the sale and use of antibiotics, in part because practitioners may be reluctant to release those data. Despite this limitation, Van Boeckel et al. (<a id="xref-ref-2-4" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-2">2</a>) provide the first global assessment of antibiotic use in livestock production. Their estimate is important: The figure is large and has been notoriously difficult to extract (<a id="xref-ref-6-1" class="xref-bibr" href="http://www.pnas.org/content/112/18/5554.full#ref-6">6</a>), and it sets the stage for understanding the global impacts of profligate use of these powerful drugs.</p>

Terrestrial plant and soil respiration, or ecosystem respiration (R_eco), represents a major CO₂ flux in the global carbon cycle. However, there is disagreement in how R_eco will respond to future global changes, such as elevated atmosphere CO₂ and warming. To address this, we synthesized six years (2007–2012) of R_eco data from the Prairie Heating And CO₂ Enrichment (PHACE) experiment. We applied a semi-mechanistic temperature–response model to simultaneously evaluate the response of R_eco to three treatment factors (elevated CO₂, warming, and soil water manipulation) and their interactions with antecedent soil conditions [e.g., past soil water content (SWC) and temperature (SoilT)] and aboveground factors (e.g., vapor pressure deficit, photosynthetically active radiation, vegetation greenness). The model fits the observed R_eco well (<em>R</em>²= 0.77). We applied the model to estimate annual (March–October) R_eco, which was stimulated under elevated CO₂ in most years, likely due to the indirect effect of elevated CO₂ on SWC. When aggregated from 2007 to 2012, total six-year R_eco was stimulated by elevated CO₂ singly (24%) or in combination with warming (28%). Warming had little effect on annual R_eco under ambient CO₂, but stimulated it under elevated CO₂ (32% across all years) when precipitation was high (e.g., 44% in 2009, a ‘wet’ year). Treatment-level differences in R_eco can be partly attributed to the effects of antecedent SoilT and vegetation greenness on the apparent temperature sensitivity of R_eco and to the effects of antecedent and current SWC and vegetation activity (greenness modulated by VPD) on R_eco base rates. Thus, this study indicates that the incorporation of both antecedent environmental conditions and aboveground vegetation activity are critical to predicting R_eco at multiple timescales (subdaily to annual) and under a future climate of elevated CO₂ and warming.

Large quantities of organic carbon are stored in frozen soils (permafrost) within Arctic and sub-Arctic regions. A warming climate can induce environmental changes that accelerate the microbial breakdown of organic carbon and the release of the greenhouse gases carbon dioxide and methane. This feedback can accelerate climate change, but the magnitude and timing of greenhouse gas emission from these regions and their impact on climate change remain uncertain. Here we find that current evidence suggests a gradual and prolonged release of greenhouse gas emissions in a warming climate and present a research strategy with which to target poorly understood aspects of permafrost carbon dynamics.

Predicting tree biomass and growth increments via allometric equations is routine in forestry, but this approach is problematic in old-growth forests unless equations are derived from trees spanning the full size range. Using intensive measurements of 27 standing <em>Eucalyptus regnans</em> trees 61.1–99.8 m tall and 80–430 years old in Tasmania, Victoria, and New Zealand, we develop allometric equations to predict aboveground attributes, including biomass and annual growth increments, of trees &gt;60 m tall using ground-based measurements. Power functions of diameter underestimate biomass growth increments unless measurements are made above buttressing on the lower trunk. Growth anomalies apparent in several trees suggest that wounded <em>E. regnans</em>expend considerable energy to outgrow decay fungi and prevent structural collapse. Despite declining growth efficiency – defined as biomass growth per unit mass of photosynthetic tissues – with increasing tree size and age, biomass growth increments of <em>E. regnans</em> increase as trees enlarge with age until extrinsic forces cause mortality. The largest living <em>E. regnans</em> has an aboveground biomass of 215 Mg and a growth increment of 0.784 Mg year⁻¹, not accounting for mass loss due to decay. An even larger <em>E. regnans</em>tree – killed by fire in 2003 – had an aboveground biomass of ∼270 Mg, an estimated growth increment of ∼1 Mg year⁻¹, and was ∼480 years old at the end of its life. Prior to a stand-replacing fire in 2009, Australia’s tallest forest had a maximum aboveground biomass of 1504 Mg ha⁻¹ and a maximum aboveground carbon mass of 706 Mg ha⁻¹.

Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.

<div dir="ltr" data-angle="0" data-font-name="g_font_21_0" data-canvas-width="215.6235865445137">The causes of the Pleistocene extinctions of large numbers of megafaunal species in the Northern Hemisphere remain unclear. A range of evidence points to human hunting, climate change, or a combination of both. Using ancient DNA and detailed paleoclimate data, Cooper et al . report a close relationship between Pleistocene megafau-nal extinction events and rapid warming events at the start</div> <div dir="ltr" data-angle="0" data-font-name="g_font_21_0" data-canvas-width="204.2591669979572">of interstadial periods. Their analysis strengthens the case for climate change as the key driver of megafaunal extinctions, with human impacts playing a secondary role.</div>

Soils are important sources and sinks of three greenhouse gases (GHGs): carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). However, it is unknown whether semiarid landscapes are important contributors to global fluxes of these gases, partly because our mechanistic understanding of soil GHG fluxes is largely derived from more humid ecosystems. We designed this study with the objective of identifying the important soil physical and biogeochemical controls on soil GHG fluxes in semiarid soils by observing seasonal changes in soil GHG fluxes across a three million year substrate age gradient in northern Arizona. We also manipulated soil nitrogen (N) and phosphorus availability with 7 years of fertilization and used regression tree analysis to identify drivers of unfertilized and fertilized soil GHG fluxes. Similar to humid ecosystems, soil N₂O flux was correlated with changes in N and water availability and soil CO₂ efflux was correlated with changes in water availability and temperature. Soil CH₄ uptake was greatest in relatively colder and wetter soils. While fertilization had few direct effects on soil CH₄ flux, soil nitrate was an important predictor of soil CH₄ uptake in unfertilized soils and soil ammonium was an important predictor of soil CH₄ uptake in fertilized soil. Like in humid ecosystems, N gas loss via nitrification or denitrification appears to increase with increases in N and water availability during ecosystem development. Our results suggest that, with some exceptions, the drivers of soil GHG fluxes in semiarid ecosystems are often similar to those observed in more humid ecosystems.

Permafrost thaw can alter the soil environment through changes in soil moisture, frequently resulting in soil saturation, a shift to anaerobic decomposition, and changes in the plant community. These changes, along with thawing of previously frozen organic material, can alter the form and magnitude of greenhouse gas production from permafrost ecosystems. We synthesized existing methane (CH4) and carbon dioxide (CO2) production measurements from anaerobic incubations of boreal and tundra soils from the geographic permafrost region in order to evaluate large-scale controls of anaerobic CO2 and CH4 production and compare the relative importance of landcape-level factors (e.g., vegetation type and landscape position), soil properties (e.g., pH, depth and soil type), and soil environmental conditions (e.g., temperature and relative water table position). We found five-fold higher maximum CH4 production per gram soil carbon from organic soils than mineral soils. Maximum CH4 production from soils in the active layer (ground that thaws and refreezes annually) was nearly four times that of permafrost per gram soil carbon, and CH4 production per gram soil carbon was two times greater from sites without permafrost than sites with permafrost. Maximum CH4 and median anaerobic CO2 production decreased with depth, while CO2:CH4 production increased with depth. Maximum CH4 production was highest in soils with herbaceous vegetation and soils that were either consistently or periodically inundated. This synthesis identifies the need to consider biome, landscape position, and vascular/moss vegetation types when modeling CH4 production in permafrost ecosystems and suggests the need for longer-term anaerobic incubations to fully capture CH4 dynamics. Our results demonstrate that as climate warms in arctic and boreal regions, rates of anaerobic CO2 and CH4 production will increase, not only as a result of increased temperature, but also from shifts in vegetation and increased ground saturation that will accompany permafrost thaw. This article is protected by copyright. All rights reserved

Elevated atmospheric CO₂ concentrations increase plant productivity and affect soil microbial communities, with possible consequences for the turnover rate of soil carbon (C) pools and feedbacks to the atmosphere. In a previous analysis (Van Groenigen <em>et al</em>., 2014), we used experimental data to inform a one-pool model and showed that elevated CO₂ increases the decomposition rate of soil organic C, negating the storage potential of soil. However, a two-pool soil model can potentially explain patterns of soil C dynamics without invoking effects of CO₂ on decomposition rates. To address this issue, we refit our data to a two-pool soil C model. We found that CO₂ enrichment increases decomposition rates of both fast and slow C pools. In addition, elevated CO₂ decreased the carbon use efficiency of soil microbes (CUE), thereby further reducing soil C storage. These findings are consistent with numerous empirical studies and corroborate the results from our previous analysis. To facilitate understanding of C dynamics, we suggest that empirical and theoretical studies incorporate multiple soil C pools with potentially variable decomposition rates.

Soil organic carbon (SOC) mass and its constituents, chemistry, and isotopic signatures (Δ¹⁴C, δ¹³C) were examined for two different loblolly pine (<em>Pinus taeda</em> L.) research installations located in north-central Florida. Both studies were designed as split-plots with the whole plots as different levels of fertilization and herbicide application (cultural intensity), and full-sib families of loblolly pine were the splits. The cultural intensities and the families of loblolly pine were different at each site and so each site was analyzed separately. The plantations were aged 9 or 10 years at the time of soil sampling. At both sites, the overall mass of SOC to a depth of 0–30 cm was unresponsive to the level of family growth or cultural intensity and did not show a trend with aboveground biomass. The SOC pool was further separated into live roots and wood; and density fractionation was used to separate the SOC sample into a light fraction (LF) (&lt;1.7 g cm⁻³) and heavy fraction (HF) with the LF dissected further for charcoal and dead roots. Higher fertilization levels generally depressed fine root (&lt;1 mm) biomass, but whether the effect was significant varied with family and soil horizon. The HF was a relatively small component (&lt;5%) of SOC in these sandy textured soils, but at one of the two sites, the HF was significantly increased with more intensive silviculture and for the faster growing family. The Δ¹⁴C value of the LF-SOC for one slow growing family under low culture (136 ± 11‰) differed from the faster growing low culture plot, and its relationship to the atmospheric Δ¹⁴C record suggested that the LF-SOC likely originated prior to stand establishment. The LF chemistry was determined with solid-state ¹³C nuclear magnetic resonance (NMR) and cultural intensity did not significantly affect SOC chemistry. However, the family effect was significant for carbohydrates at one site, and for lignin and lipids at the other site. Overall, these results suggest that tree genetics in managed forests can influence SOC chemistry and that the relatively small fractions of SOC can change with management intensity; however, the effect of cultural intensity is minimal for the largest components of SOC and there is no clear relationship between SOC dynamics and aboveground production under the management regimes, and stand ages, examined with these two research installations.

Unprecedented rates of climate warming over the past century have resulted in increased forest stress and mortality worldwide. Decreased tree growth in association with increasing temperatures is generally accepted as a signal of temperature-induced drought stress. However, variations in tree growth alone do not reveal the physiological mechanisms behind recent changes in tree growth. Examining stable carbon isotope composition of tree rings in addition to tree growth can provide a secondary line of evidence for physiological drought stress. In this study, we examined patterns of black spruce growth and carbon isotopic composition in tree rings in response to climate warming and drying in the boreal forest of interior Alaska. We examined trees at three nested scales: landscape, toposequence, and a subsample of trees within the toposequence. At each scale, we studied the potential effects of differences in microclimate and moisture availability by sampling on northern and southern aspects. We found that black spruce radial growth responded negatively to monthly metrics of temperature at all examined scales, and we examined ∆¹³C responses on a subsample of trees as representative of the wider region. The negative ∆¹³C responses to temperature reveal that black spruce trees are experiencing moisture stress on both northern and southern aspects. Contrary to our expectations, ∆¹³C from trees on the northern aspect exhibited the strongest drought signal. Our results highlight the prominence of drought stress in the boreal forest of interior Alaska. We conclude that if temperatures continue to warm, we can expect drought-induced productivity declines across large regions of the boreal forest, even for trees located in cool and moist landscape positions.

Forests sequester carbon from the atmosphere, helping mitigate climate change. In fire-prone forests, burn events result in direct and indirect emissions of carbon. High fire-induced tree mortality can cause a transition from a carbon sink to source, but thinning and prescribed burning can reduce fire severity and carbon loss when wildfire occurs. However, treatment implementation requires carbon removal and emissions to reduce high-severity fire risk. The carbon removed and emitted during treatment may be resequestered by subsequent tree growth, although there is much uncertainty regarding the length of time required. To assess the long-term carbon dynamics of thinning and burning treatments, we quantified the 10-year post-treatment carbon stocks and 10-year net biome productivity (NBP) from a full-factorial experiment involving three levels of thinning and two levels of burning in a mixed-conifer forest in California’s Sierra Nevada. Our results indicate that (1) the understory thin treatment, that retained large trees, quickly recovered the initial carbon emissions (NBP = 31.4 ± 4.2 Mg C ha⁻¹), (2) the carbon emitted from prescribed fire in the burn-only treatment was resequestered within the historical fire return interval (NBP = 32.8 ± 3.5 Mg C ha⁻¹), and (3) the most effective treatment for reducing fire risk, understory thin and burn, had negative NBP (−6.0 ± 4.5 Mg C ha⁻¹) because of post-fire large tree mortality. Understory thinning and prescribed burning can help stabilize forest carbon and restore ecosystem resilience, but this requires additional emissions beyond only thinning or only burning. Retaining additional mid-sized trees may reduce the carbon impacts of understory thinning and burning.

Dissolved organic C (DOC) leached from leaf litter contributes to the C pool of stream ecosystems and affects C cycling in streams. We studied how differences in leaf-litter chemistry affect the optical properties and decomposition of DOC. We used 2 species of cottonwoods (Populus) and their naturally occurring hybrids that differ in leaf-litter phytochemistry and decomposition rate. We measured DOC and nutrient concentration in leaf leachates and determined the effect of DOC quality on heterotrophic respiration in 24-h incubations with stream sediments. Differences in DOC composition and quality were characterized with fluorescence spectroscopy. Rapidly decomposing leaves with lower tannin and lignin concentrations leached ∼40 to 50% more DOC and total dissolved N than did slowly decomposing leaves. Rates of heterotrophic respiration were 25 to 50% higher on leachate from rapidly decomposing leaf types. Rates of heterotrophic respiration were related to metrics of aromaticity. Specifically, rates of respiration were correlated negatively with the Fluorescence Index and positively with Specific Ultraviolet Absorbance (SUVA254) and T280 tryptophan-like fluorescence peak. These results reveal that leaf-litter DOC is distinctly different from ambient streamwater DOC. The relationships between optical characteristics of leaf leachate and bioavailability are opposite those found in streamwater DOC. Differences in phytochemistry among leaf types can influence stream ecosystems with respect to DOC quantity, composition, and rates of stream respiration. These patterns suggest that the relationship between the chemical structure of DOC and its biogeochemistry is more complex than previously recognized. These unique properties of leaflitter DOC will be important when assessing the effects of terrestrial C on aquatic ecosystems, especially during leaf fall.