Summary Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH4 emissions and trace their potential origin. We identified the need: (1) for both long‐term, high‐frequency measurements of stem CH4 emissions to understand the fine‐scale processes, alongside rapid large‐scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (3) to develop a mechanistic model including passive and active transport of CH4 from the soil–tree–atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH4 emissions, and allow for the integration of pathways and mechanisms of CH4 production and emissions into process‐based models. These advances will facilitate the upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local to global CH4 budget.

[1] Through rapid reactions with ozone, which can initiate the formation of secondary organic aerosols, the emission of sesquiterpenes from vegetation in Amazonia may have significant impacts on tropospheric chemistry and climate. Little is known, however, about sesquiterpene emissions, transport, and chemistry within plant canopies owing to analytical difficulties stemming from very low ambient concentrations, high reactivities, and sampling losses. Here, we present ambient sesquiterpene concentration measurements obtained during the 2010 dry season within and above a primary tropical forest canopy in Amazonia. We show that by peaking at night instead of during the day, and near the ground instead of within the canopy, sesquiterpene concentrations followed a pattern different from that of monoterpenes, suggesting that unlike monoterpene emissions, which are mainly light dependent, sesquiterpene emissions are mainly temperature dependent. In addition, we observed that sesquiterpene concentrations were inversely related with ozone (with respect to time of day and vertical concentration), suggesting that ambient concentrations are highly sensitive to ozone. These conclusions are supported by experiments in a tropical rain forest mesocosm, where little atmospheric oxidation occurs and sesquiterpene and monoterpene concentrations followed similar diurnal patterns. We estimate that the daytime dry season ozone flux of −0.6 to −1.5 nmol m −2 s −1 due to in-canopy sesquiterpene reactivity could account for 7%-28% of the net ozone flux. Our study provides experimental evidence that a large fraction of total plant sesquiterpene emissions (46%-61% by mass) undergo within-canopy ozonolysis, which may benefit plants by reducing ozone uptake and its associated oxidative damage.

[1] Amazon forests are potentially globally significant sources or sinks for atmospheric carbon dioxide. In this study, we characterize the spatial trends in carbon storage and fluxes in both live and dead biomass (necromass) in two Amazonian forests, the Biological Dynamic of Forest Fragments Project (BDFFP), near Manaus, Amazonas, and the Tapajós National Forest (TNF) near Santarém, Pará. We assessed coarse woody debris (CWD) stocks, tree growth, mortality, and recruitment in ground-based plots distributed across the terra firme forest at both sites. Carbon dynamics were similar within each site, but differed significantly between the sites. The BDFFP and the TNF held comparable live biomass (167 ± 7.6 MgCÁha À1 versus 149 ± 6.0 MgCÁha À1 , respectively), but stocks of CWD were 2.5 times larger at TNF (16.2 ± 1.5 MgCÁha À1 at BDFFP, versus 40.1 ± 3.9 MgCÁha À1 at TNF). A model of current forest dynamics suggests that the BDFFP was close to carbon balance, and its size class structure approximated a steady state. The TNF, by contrast, showed rapid carbon accrual to live biomass (3.24 ± 0.22 MgCÁha À1 Áa À1 in TNF, 2.59 ± 0.16 MgCÁha À1 Áa À1 in BDFFP), which was more than offset by losses from large stocks of CWD, as well as ongoing shifts of biomass among size classes. This pattern in the TNF suggests recovery from a significant disturbance. The net loss of carbon from the TNF will likely last 10-15 years after the initial disturbance (controlled by the rate of decay of coarse woody debris), followed by uptake of carbon as the forest size class structure and composition continue to shift. The frequency and longevity of forests showing such disequilibruim dynamics within the larger matrix of the Amazon remains an essential question to understanding Amazonian carbon balance.

An experimental forest ecosystem drought Drought is affecting many of the world’ s forested ecosystems, but it has proved challenging to develop an ecosystem-level mechanistic understanding of the ways that drought affects carbon and water fluxes through forest ecosystems. Werner et al . used an experimental approach by imposing an artificial drought on an entire enclosed ecosystem: the Biosphere 2 Tropical Rainforest in Arizona (see the Perspective by Eisenhauer and Weigelt). The authors show that ecosystem-scale plant responses to drought depend on distinct plant functional groups, differing in their water-use strategies and their position in the forest canopy. The balance of these plant functional groups drives changes in carbon and water fluxes, as well as the release of volatile organic compounds into the atmosphere. —AMS

Recent field observations indicate that in many forest ecosystems, plants use water that may be isotopically distinct from soil water that ultimately contributes to streamflow. Such an assertion has been met with varied reactions. Of the outstanding questions, we examine whether ecohydrological separation of water between trees and streams results from a separation in time, or in space. Here we present results from a 9‐month drought and rewetting experiment at the 26,700‐m3 mesocosm, Biosphere 2‐Tropical Rainforest biome. We test the null hypothesis that transpiration and groundwater recharge water are sampled from the same soil volume without preference for old nor young water. After a 10‐week drought, we added 66 mm of labeled rainfall with 152‰ δ2H distributed over four events, followed by background rainfall (−60‰ δ2H) distributed over 13 events. Our results show that mean transit times through groundwater recharge and plant transpiration were markedly different: groundwater recharge was 2–7 times faster (~9 days) than transpired water (range 17–62 days). The “age” of transpired water showed strong dependence on species and was linked to the difference between midday leaf water potential and soil matric potential. Moreover, our results show that trees used soil water (89% ±6) and not the “more mobile” (represented by “zero tension” seepage) water (11% ±6). The finding, which rejects our null hypothesis, is novel in that this partitioning is established based on soil water residence times. Our study quantifies mean transit times for transpiration and seepage flows under dynamic conditions.

72Zero-order drainage basins, and their constituent hillslopes, are the fundamental geomorphic unit 73 comprising much of Earth's uplands. The convergent topography of these landscapes generates 74 spatially variable substrate and moisture content, facilitating biological diversity and influencing 75 how the landscape filters precipitation and sequesters atmospheric carbon dioxide. In light of 76 these significant ecosystem services, refining our understanding of how these functions are 77 affected by landscape evolution, weather variability, and long-term climate change is imperative. 78 In this paper we introduce the Landscape Evolution Observatory (LEO): a large-scale 79 controllable infrastructure consisting of three replicated artificial landscapes (each 330 m 2 80 surface area) within the climate-controlled Biosphere 2 facility in Arizona, USA. At LEO, 81 experimental manipulation of rainfall, air temperature, relative humidity, and wind speed are 82 possible at unprecedented scale. The Landscape Evolution Observatory was designed as a 83 community resource to advance understanding of how topography, physical and chemical 84 properties of soil, and biological communities coevolve, and how this coevolution affects water, 85 carbon, and energy cycles at multiple spatial scales. With well-defined boundary conditions and 86 an extensive network of sensors and samplers, LEO enables an iterative scientific approach that 87 includes numerical model development and virtual experimentation, physical experimentation, 88 data analysis, and model refinement. We plan to engage the broader scientific community 89 through public dissemination of data from LEO, collaborative experimental design, and 90 community-based model development. 91 coevolution 93 94 95 1. Introduction 96Hillslopes and their adjacent hollows (i.e., zero-order drainage basins, or ZOBs) 97 constitute a large fraction of upland areas over Earth's surface and provide critical ecosystem 98 services. Within ZOBs there is exchange of water, carbon dioxide, and energy with the 99 atmosphere and transport of soil, water, and solutes into fluvial drainage networks-processes 100 that link ZOBs with the climate system and downstream water quantity and quality. The time-101 varying rates of these exchange and transport processes are integrated responses to many 102 physical and biological phenomena that occur from below the base of the soil profile to the 103 vertical extent of the atmospheric boundary layer (e.g., see discussion by Chorover et al., 2011). 104 Zero-order basins evolve as climate varies, soils form and erode, and biological 105 communities establish, compete, and change in response to environmental stimuli. Across 106 spatial and topographic gradients, these interacting processes may result in consistently 107 observable correlations between temperature and precipitation dynamics, soil depth and hillslope 108 length, and plant biomass accumulation (e.g., Rasmussen et al., 2011; Pelletier et al., 2013). 109 Coupled soil-production and ...

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Isoprene is the most abundant volatile hydrocarbon emitted by many tree species and has a major impact on tropospheric chemistry, leading to formation of pollutants and enhancing the lifetime of methane, a powerful greenhouse gas. Reliable estimates of global isoprene emission from different ecosystems demand a clear understanding of the processes of both production and consumption. Although the biochemistry of isoprene production has been studied extensively and environmental controls over its emission are relatively well known, the study of isoprene consumption in soil has been largely neglected.Here, we present results on the production and consumption of isoprene studied by measuring the following different components: (1) leaf and soil and (2) at the whole ecosystem level in two distinct enclosed ultraviolet light-depleted mesocosms at the Biosphere 2 facility: a cottonwood plantation with trees grown at ambient and elevated atmospheric CO 2 concentrations and a tropical rainforest, under well watered and drought conditions. Consumption of isoprene by soil was observed in both systems. The isoprene sink capacity of litter-free soil of the agriforest stands showed no significant response to different CO 2 treatments, while isoprene production was strongly depressed by elevated atmospheric CO 2 concentrations. In both mesocosms, drought suppressed the sink capacity, but the full sink capacity of dry soil was recovered within a few hours upon rewetting. We conclude that soil uptake of atmospheric isoprene is likely to be modest but significant and needs to be taken into account for a comprehensive estimate of the global isoprene budget. More studies investigating the capacity of soils to uptake isoprene in natural conditions are clearly needed.