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Tree stem mediated methane emissions represent a potentially important yet poorly constrained source of atmospheric methane. Here we present the first ever quantification of tree stem methane emissions from Melaleuca quinquenervia, a widespread iconic Australian lowland tree and globally invasive species. Under two distinct hydrological conditions (wet and dry) we captured 431 tree stem flux measurements encompassing six different vertical stem heights along a 50 m topo-gradient transect, separated into three distinct hydrological zones (upper, transitional and lower). The tree stem methane fluxes closely reflected local topography/hydrology and ranged from − 30.0 to 123,227 µmol m−2 day−1, with the maximum values amongst the highest values reported to date. The highest methane emissions were observed during wet conditions, within the inundated lower zone and from near the tree stem bases and water table. The average methane flux per tree (scaled to 1 m of stem) for the transitional and lower zones was 52-fold and 46-fold higher during wet conditions compared to dry, whereas the upper zone emissions changed little between seasons. Adjacent soil fluxes followed similar trends along the hydrology gradient with the upper zone tree stem emissions offsetting the adjacent soil methane sink capacity. A clear trend of sharply decreasing methane emissions with stem-height suggests a soil methane origin. A 45-h time-series of two trees within the lower zone revealed three to fourfold diel variability, with elevated morning-time fluxes. Overall, the study revealed that seasonal hydrological conditions and topo-gradient substantially regulated the methane emissions from M. quinquenervia and that this previously overlooked pathway should be accounted for within wetland methane budgets, especially during inundated conditions.

A combination of elemental analysis, bulk stable isotope analysis (bulk SIA) and compound-specific stable isotope analysis of amino acids (CSIA-AA) was used to assess and monitor carbon (C), nitrogen (N) and sulfur (S) cycling of a mangrove ecosystem that suffered mass dieback of trees in the Gulf of Carpentaria, Australia in 2015–2016, attributed to an extreme drought event. Three field campaigns were conducted 8, 20 and 32 months after the event over a period from 2016 to 2018 to obtain biological time-series data. Invertebrates and associated organic matter including mangroves and sediments from the impacted ecosystem showed enrichment in 13C, 15N and 34S relative to those from an adjacent unimpacted reference ecosystem, likely indicating lower mangrove carbon fixation, lower nitrogen fixation and lower sulfate reduction in the impacted ecosystem. For example, invertebrates representing the feeding types of grazing, leaf feeding and algae feeding were more 13C enriched at the impacted site, by 1.7 ‰–4.1 ‰, and these differences did not change over the period from 2016 to 2018. The CSIA-AA data indicated widespread 13C enrichment across five essential amino acids and all groups sampled (except filter feeders) within the impacted site. The seedling density increased from 0.2 m−2 in 2016 to 7.1 m−2 in 2018 in the impacted forest, suggesting recovery of the vegetation. Recovery of CNS cycling, however, was not evident even after 32 months, suggesting a biogeochemical legacy of the mortality event. Continued monitoring of the post-dieback forest is required to predict the long-term trajectory of ecosystem recovery. This study shows that time-series SIA can track biogeochemical changes over time and evaluate recovery of an impacted ecosystem from an extreme event.

A massive mangrove dieback event occurred in 2015–2016 along ∼1000 km of pristine coastline in the Gulf of Carpentaria, Australia. Here, we use sediment and wood chronologies to gain insights into geochemical and climatic changes related to this dieback. The unique combination of low rainfall and low sea level observed during the dieback event had been unprecedented in the preceding 3 decades. A combination of iron (Fe) chronologies in wood and sediment, wood density and estimates of mangrove water use efficiency all imply lower water availability within the dead mangrove forest. Wood and sediment chronologies suggest a rapid, large mobilization of sedimentary Fe, which is consistent with redox transitions promoted by changes in soil moisture content. Elemental analysis of wood cross sections revealed a 30- to 90-fold increase in Fe concentrations in dead mangroves just prior to their mortality. Mangrove wood uptake of Fe during the dieback is consistent with large apparent losses of Fe from sediments, which potentially caused an outwelling of Fe to the ocean. Although Fe toxicity may also have played a role in the dieback, this possibility requires further study. We suggest that differences in wood and sedimentary Fe between living and dead forest areas reflect sediment redox transitions that are, in turn, associated with regional variability in groundwater flows. Overall, our observations provide multiple lines of evidence that the forest dieback was driven by low water availability coinciding with a strong El Niño–Southern Oscillation (ENSO) event and was associated with climate change.

Comprehensive aquifer characterization requires the development of a three-dimensional (3D) geological model and estimation of hydraulic and hydro-geochemical properties. This can be used to discern the governing processes of groundwater flow and chemistry, and plan pertinent groundwater management approaches. This study evaluated the influence of geological settings and groundwater flow on the groundwater development potential and chemistry in a Quaternary aquifer system in the Raya Valley, Ethiopia. Surface geology, digital elevations, groundwater-level measurements, and data from drill logs, pumping tests and vertical electrical soundings were combined to characterize the physical properties of the aquifer system. 3D geological and hydrogeological models were developed and used to delineate subsurface formations and to quantify groundwater flow. The aquifer was characterized as a heterogeneous and anisotropic unconfined system. The available groundwater volume was estimated to be 80 ± 1 km3 with a maximum sustainable yield of 530,409 ± 16,800 m3/day. The use of geochemical models and principal component analysis revealed that the origin and geochemical composition of the groundwater were spatially variable. Rock weathering, mineral dissolution, ion-exchange and anthropogenic activities were the major processes governing the hydro-geochemical characteristics of the aquifer, while evaporation processes caused groundwater salinity enrichment. However, even though mineral saturation of the groundwater at specific locations was highly influenced by the geologic matrix, advective groundwater transport led to areas with mixed groundwater chemistry. The observed and modelled complexity of this aquifer system suggests that such evaluations are important to design appropriate groundwater management strategies in heterogeneous and structurally complex aquifer systems.

The magnitude of the terrestrial carbon (C) sink may be overestimated globally due to the difficulty of accounting for all C losses across heterogeneous landscapes. More complete assessments of net landscape C balances (NLCB) are needed that integrate both emissions by fire and transfer to aquatic systems, two key loss pathways of terrestrial C. These pathways can be particularly significant in the wet-dry tropics, where fire plays a fundamental part in ecosystems and where intense rainfall and seasonal flooding can result in considerable aquatic C export (sigma F-aq). Here, we determined the NLCB of a lowland catchment (similar to 140 km(2)) in tropical Australia over 2 years by evaluating net terrestrial productivity (NEP), fire-related C emissions and sigma F-aq (comprising both downstream transport and gaseous evasion) for the two main landscape components, that is, savanna woodland and seasonal wetlands. We found that the catchment was a large C sink (NLCB 334 Mg C km(-2) year(-1)), and that savanna and wetland areas contributed 84% and 16% to this sink, respectively. Annually, fire emissions (-56 Mg C km(-2) year(-1)) and sigma F-aq (-28 Mg C km(-2) year(-1)) reduced NEP by 13% and 7%, respectively. Savanna burning shifted the catchment to a net C source for several months during the dry season, while sigma F-aq significantly offset NEP during the wet season, with a disproportionate contribution by single major monsoonal events-up to 39% of annual sigma F-aq was exported in one event. We hypothesize that wetter and hotter conditions in the wet-dry tropics in the future will increase sigma F-aq and fire emissions, potentially further reducing the current C sink in the region. More long-term studies are needed to upscale this first NLCB estimate to less productive, yet hydrologically dynamic regions of the wet-dry tropics where our result indicating a significant C sink may not hold.

Coastal waters are known to emit globally significant quantities of CH4, a potent greenhouse gas, but the potential of the rapid and ongoing human alterations to coastal areas to alter these emissions remains undefined. Here we addressed this gap by quantifying water-to-air CH4 fluxes and δ13C-CH4 values in sub-tropical estuaries at Low (n = 3), Moderate (n = 2), and High (n = 3) levels of human modification (agricultural land use, wastewater discharge), and sediment-to-water CH4 fluxes from the major benthic habitats in representative Low, Moderate, and High systems. An increase in water-to-air CH4 fluxes from 9.7 µmol m−2 d−1 (Low) to 28 µmol m−2 d−1 (Moderate) to 47 µmol m−2 d−1 (High) was accompanied by a shift from hydrogenotrophic to acetoclastic production pathways. Unexpectedly, benthic CH4 production, which ranged from −48 µmol m−2 d−1 to +180 µmol m−2 d−1 between habitats, estuaries, and seasons, was not the primary driver of this shift. Sediments produced more CH4 (∼600%) than emitted from the Low estuary, ∼90% of CH4 emitted from the Moderate estuary, but only 9% of CH4 emitted from the High estuary. Instead, a combination of wastewater, groundwater, and apparent water column production caused a ∼ 3-fold increase in estuary CH4 emissions. Our findings indicate that human alterations to the source, rate, and pathways of CH4 production are driving a net increase in emissions from estuaries, demonstrating a need to redefine how we quantify ‘anthropogenic’ CH4 emissions.

Tree stem methane emissions are gaining increasing attention as an overlooked atmospheric source pathway. Existing methods for measuring tree stem greenhouse gas fluxes and isotopes may provide robust integrated emission estimates, but due to their coarse resolution, the capacity to derive insights into fine-scale dynamics of tree stem emissions is limited. We demonstrate and field test an alternative method that is Small, Nimble, In situ and allows for Fine-scale Flux (‘SNIFF’) measurements, on complex and contrasting stem surfaces. It is lightweight and therefore suitable to remote field locations enabling real-time data observations allowing for field-based, data driven sampling regimes. This method facilitated novel results capturing fine-scale vertical and radial methane flux measurements (5 cm increments) and revealed: (1) 86–89% of methane emissions emanated from the lower 30 cm of sampled wetland tree species; (2) clear vertical and horizontal trends in δ13C-CH4 possibly due to fractionation associated with oxidation and/or mass-dependant fractionation during diffusive transport; and (3) the occurrence of substantial radial heterogeneity. We also compared a variety of up-scaling approaches to estimate methane flux per tree, including novel smartphone 3D photogrammetry that resulted in substantially higher stem surface area estimations (> 16 to 36%) than traditional empirical methods. Utilising small chambers with high radial and vertical resolution capabilities may therefore facilitate more robust future assessments into the drivers, pathways, oxidation sinks and magnitude of tree stem greenhouse gas emissions, and compliment previous broad-scale sampling techniques.

Combined pressures from inland agricultural intensification and coastal development are dramatically altering estuaries’ structure and function. Despite the established global significance of estuarine carbon (C) cycling, the impact of growing anthropogenic stress on coastal C inputs and exports is unclear. To address this gap, we evaluated the magnitude and drivers of estuary C fluxes in eight sub-tropical estuaries at Low (n = 3), Moderate (n = 2), and High (n = 3) levels of nutrient enrichment. We measured changes in the concentration and isotopic composition (δ13C) of the major C pools (organic and inorganic) and gaseous product of C turnover (CO2) over wet and dry seasons. Over both sampling periods estuaries classified Moderate and High emitted far more CO2 (37 ± 10 mmol m−2 d−1) than those classified Low (6.3 ± 4 mmol m−2 d−1). However, estuaries with both high nutrients and high turbidity produced less CO2, and thus exported more DIC, than expected from hydrodynamics (freshwater flushing time). Differences in estuary phytoplankton biomass (Chla concentrations) corresponded with differences in the biological CO2 production (respiration) rates estimated from δ13C-DIC variations, although respiration rates were higher than predicted based on hydrodynamics (surface area/discharge) in high nutrient, low turbidity systems. Together these findings demonstrate that land-use intensification can alter both the source and the production of estuary CO2, and suggest that the direction of this shift can depend on ancillary factors like turbidity as well as nutrient enrichment. Evidence that human alterations to coastal ecosystems can shift the balance between DIC downstream export and CO2 emissions outside of the range predicted by hydrodynamic factors like residence time, surface area, and discharge has implications for global C models.

Extreme climatic events can trigger sudden but often long‐lasting impacts in ecosystems by causing near to complete mortality of foundation (habitat‐forming) species. The magnitude and frequency of such events are expected to rise due to anthropogenic climate change, but the impacts that such events have on many foundation species and the ecosystems that they support remains poorly understood. In many cases, manipulative experimentation is extremely challenging and rarely feasible at a large scale. In late 2015 to early 2016, an extensive area of mangrove forest along ∼ 1000 km of coastline in the Gulf of Carpentaria, Australia, experienced severe dieback, an event associated with climatic extremes. To assess the effect this dieback event had on the mangrove ecosystem, we assessed benthic faunal assemblages and food web structure using stable carbon and nitrogen isotopes in a comparative experiment of impacted forest and adjacent unimpacted forest. Eighteen months after the dieback, the forest that suffered dieback contained significantly fewer crabs that rely on mangrove litter food source but more crabs that rely on microphytobenthos food source than the unimpacted forest. However, the infaunal biomass was largely unaffected by the mortality effect. This is most likely because microphytobenthos was largely unaffected and consequently, this buffered the food web responses. However, overall, the habitat value for mangrove ecosystem services most likely decreased due to lower physical habitat complexity following tree mortality. Longer‐term monitoring could lead to better understanding of biological effects of this extreme event and underlying biological mechanisms that drive changes and recovery.

Atmospheric concentrations of methane have increased ∼2.4 fold since the industrial revolution with wetlands and inland waters representing the largest source of methane to the atmosphere. Substantial uncertainties remain in global methane budgets, due in part to the lack of adequate techniques and detailed measurements to assess ebullition in aquatic environments. Here, we present details of a low cost (∼$120 US per unit) ebullition sensor that autonomously logs both volumetric ebullition rate and methane concentrations. The sensor combines a traditional funnel bubble trap with an Arduino logger, a pressure sensor, thermal conductivity methane sensor, and a solenoid valve. Powered by three AA batteries, the sensor can measure autonomously for three months when programmed for a sampling frequency of 30 min. For field testing, four sensors were deployed for six weeks in a small lake. While ebullition was spatially and temporally variable, a distinct diurnal trend was observed with the highest rates from mid-morning to early afternoon. Ebullition rates were similar for all four sensors when integrated over the sampling period. The widespread deployment of low cost automated ebullition sensors such as the iAMES described here will help constrain one of the largest uncertainties in the global methane budget.

Mangrove soil carbon stocks are known to decrease following forest loss due to respiration and enhanced soil CO2 emissions. However, changes in carbon outwelling to the coastal ocean due to mangrove forest disturbance have not been considered. In December 2015, an extremely large mangrove dieback event (∼7000 hectares, spanning 1000 km of coastline) occurred in the Gulf of Carpentaria, Australia. To assess the effect this dieback event had on carbon outwelling, we used radium isotopes and dissolved carbon measurements (dissolved organic carbon, DOC, dissolved inorganic carbon, DIC, and total alkalinity, TAlk) to estimate cross-shelf carbon transport from living and dead mangrove areas and to calculate the carbon losses from living and dead forest soils via SGD. Radium distributions imply cross shelf eddy diffusivity of 107.5 ± 26.9 and 104.6 ± 23.9 m−2 s−1 from dead and living areas and radium water ages reveal that mangrove carbon reaches 10 km offshore within 7 days. Outwelling rates from living and dead areas were explained by soil carbon losses via SGD. This study suggests a decrease in carbon outwelling to the ocean from dead forest areas compares to living areas by 0–12% for DOC, 50–52% for DIC and by 37–51% for TAlk ∼8 months after the dieback event occurred. Changes to oceanic carbon outwelling rates following mangrove loss are likely driven by a gradual depletion of carbon stocks from the sediment profile.

Mangroves sequester large amounts of carbon in soils but limited information is available on carbon losses from tropical mangrove systems. Here we quantify carbon outwelling, CO2 emissions and pore-water exchange rates from two nearby (∼2 km apart) tropical mangrove creeks located in different geomorphic settings on the island of Palau, Micronesia during the monsoon storm season. On average, POC and pCO2 were >100% higher and DOC, DIC and TA were 62%, 25%, 16% higher, respectively, from Creek 1 (located within a semi-enclosed bay) than from Creek 2 (located along the coast adjacent to fringing reefs). Both creeks were net exporters of DIC, DOC, POC, TA and emitters of CO2. However, outwelling rates of POC, DIC and DOC and CO2 emissions were 27-fold, 8-fold, 4-fold and 3-fold higher at Creek 1. DIC outwelling (37%) and CO2 emissions (39%) were the major terms contributing to total carbon losses at Creek 1, whilst CO2 emission (61%) was the major contributor at Creek 2. Monsoon storms appeared to explain the organic carbon dynamics whilst tidal pumping appears to drive the inorganic carbon dynamics at both creeks. Our data demonstrates the considerable heterogeneity of mangroves creeks that are in close proximity and subject to similar weather conditions but in differing geomorphological settings.

Coastal lagoons are dynamic aquatic systems that are susceptible to eutrophication due to long residence times and high inputs of nutrients. We hypothesise that groundwater-derived nutrients make a significant contribution to primary production, eutrophication and carbon cycling in these systems. Here, we report results from seasonal (pre-bloom, bloom and post bloom), nutrient, pCO2 and 222Rn (a natural groundwater tracer) surveys in a coastal lagoon that frequently experiences macroalgae blooms (Avoca Lagoon, Australia). Groundwater inputs of DIN and DIP deliver the nutrient load equivalent to the entire lagoon inventory in 1.6 to 3.5 days and 1.7 and 6 days respectively, indicating groundwater was a major source of inorganic nutrients to the system. Lagoon pCO2 displayed significant spatial and temporal variability, with the average pCO2 shifting from 1717 μatm during pre-bloom, to 137 μatm during the bloom and 3056 μatm post bloom. Radon-222 displayed a significant positive relationship with dissolved inorganic nitrogen (DIN) and pCO2 during the pre-bloom period. This suggests a hydrological dominance of surface water DIN and pCO2 during the pre-bloom period. During the bloom period, DIN displayed a positive relationship with pCO2 and negative relationship with dissolved oxygen, indicating a strong biological control over the nutrient pool. Phosphate did not appear to be controlled by either groundwater inputs, or ecosystem metabolism throughout the study. While groundwater discharge stimulated primary production through nutrient inputs (thus reducing surface water CO2), it also directly delivered significant quantities of CO2 to surface waters. The net effect of groundwater inputs of nutrients and dissolved carbon into the lagoon was a stimulation of CO2 fluxes to the atmosphere.

This paper presents the first aquatic CO2 and CH4 flux estimates from a macro-tidal mangrove creek located in the 0–5° latitude band, where ∼30% of the world’s mangroves occur. High resolution dissolved CO2, CH4 and 222Rn (a natural pore-water tracer) concentrations were measured over a spring-neap tidal cycle from a mangrove tidal creek located in North Brazil (∼0.8°S). Surface water pCO2, CH4 and 222Rn ranged from 592 to 15,361 μatm, 58 to 1469 nM, and 585 to 16,583 dpm m−3 with considerable temporal variability observed semi diurnally (i.e. hourly) and over the spring-neap cycle (i.e. weekly). Tidally-driven pore-water exchange (tidal pumping) drove surface water pCO2 and CH4, leading to high concentrations at low-tide (semi-diurnal variability). Higher pCO2 and CH4 were also observed after the inundation of the upper inter-tidal flat, with peak values coinciding with the “first flush” of aged pore-waters. We hypothesise that additional pore-water exchanges occur during forest inundation in macro-tidal mangrove systems, controlling mangrove creek water pCO2 and CH4 over spring-neap cycles. Estimated CO2 and CH4 water-atmosphere fluxes were 174 ± 129 mmol m−2 d−1 and 855 ± 406 μmol m−2 d−1, respectively. These emissions are amongst the highest reported for mangrove systems worldwide and suggests that the most recent global estimates based mostly on data from higher latitudes may have underestimated the role of mangroves in greenhouse gas emissions.

Hypersaline tidal flats (HTFs) are coastal ecosystems with freshwater deficits often occurring in arid or semi-arid regions near mangrove supratidal zones with no major fluvial contributions. Here, we estimate that organic carbon (OC), total nitrogen (TN) and total phosphorus (TP) were buried at rates averaging 21 (±6), 1.7 (±0.3) and 1.4 (±0.3) gm-2yr-1, respectively, during the previous century in three contrasting HTF systems, one in Brazil (eutrophic) and two in Australia (oligotrophic). Although these rates are lower than those from nearby mangrove, saltmarsh and seagrass systems, the importance of HTFs as sinks for OC, TN and TP may be significant given their extensive coverage. Despite the measured short-term variability between net air–saltpan CO2 influx and emission estimates found during the dry and wet season in the Brazilian HTF, the only site with seasonal CO2 flux measurements, the OC sedimentary profiles over several decades suggest efficient OC burial at all sites. Indeed, the stable isotopes of OC and TN (δ13C and δ15N) along with C:N ratios show that microphytobenthos are the major source of the buried OC in these HTFs. Our findings highlight a previously unquantified carbon as well as a nutrient sink and suggest that coastal HTF ecosystems could be included in the emerging blue carbon framework.

The small-scale spatial variability in dissolved carbon dioxide (CO2) and water-air CO2 flux dynamics were investigated within first-order catchments of the upper Blue Mountains Plateau (New South Wales, Australia). Water samples were collected at 81 locations during winter and summer over two consecutive years across seven aquatic ecosystem types: wetland, impoundment, lake, tributary stream, mainstem, escarpment complex, and urban-aquatic interface. Dissolved [CO2] ranged from 15 to 880 μM (94 to 4760%Sat), and dissolved [O2] from 0 to 350 μM (0 to 101%Sat). CO2 supersaturation was typically highest in wetlands and vegetated impoundments of the upper plateau, and decreased downstream approaching atmospheric equilibrium at the escarpment waterfalls. Gas transfer velocities ranged from 0.18 m d−1 in lentic waters to 292 m d−1 at the bottom of waterfalls due to bubble-mediated transfer. The first- and second-order streams represented only 4.8% of the total open water area yet contributed to 61% of the total water-air CO2 outgassing. The lake, escarpment and mainstem group systems had narrow diel and seasonal CO2 concentration variability, while wetlands and vegetated impoundments had the widest ranges. Our high resolution spatio-temporal sampling was essential to identifying CO2 outgassing hotspots in these geomorphically diverse catchments. Overall, >95% of excess dissolved CO2 traversing the upper Blue Mountains Plateau was outgassed to the atmosphere.

Coastal vegetated habitats, including mangroves, saltmarshes and seagrasses, mitigate climate change by storing atmospheric carbon. Previous blue carbon research has mainly focused on organic carbo...

Nutrient and pesticide pollution are among the major threats to groundwater quality in agriculturally impacted aquifers. Understanding their legacy effects and drivers are important to protect aquifers from exposures to contamination. However, the complexities of groundwater flowpaths make it difficult to predict the time-scales of groundwater flow and contaminant transport. To determine these controls of groundwater nutrient and pesticides in an aquifer system underlying an intensive agricultural area in the Great Barrier Reef catchment, Australia, we sampled tritium (3H) to estimate groundwater-age, nutrient and pesticide concentrations to investigate groundwater contamination, and nitrogen (ẟ15N-NO3−) and oxygen (ẟ18O-NO3−) isotopes to determine groundwater nitrate dynamics. We, then, constructed high-resolution 3D geological and groundwater flow models of the aquifer system to determine the role of the geologic heterogeneity on the observed nutrient and pesticide concentrations. Groundwater 3H derived ages, and nutrient and pesticide concentrations did not follow distinct spatial trends. ẟ15N-NO3− and ẟ18O-NO3− values indicated that nitrification and denitrification processes influenced nitrate dynamics in the aquifer system; however, they were not solely able to explain the entire 3D variability. The 3D geologic modelling identified possible preferential flowpaths and perched systems, which helped to explain the observed groundwater-age, nutrient and pesticide variabilities. Old-groundwater (~100-years) was found in shallow depths ( 25 m), below perched and locally confined systems. Downward increasing groundwater-age, and decreasing nutrient and pesticide concentrations were detected in the unconfined aquifer, while old-groundwater (~160-years) and lower nitrate (

Water-to-air carbon dioxide fluxes from tropical coastal waters are an important but understudied component of the marine carbon budget. Here, we investigate drivers of carbon dioxide partial pressure (pCO2) in a relatively pristine mangrove-seagrass embayment on a tropical island (Bali, Indonesia). Observations were performed over eight underway seasonal surveys and a fixed location time series for 55 h. There was a large spatial variability of pCO2 across the continuum of mangrove forests, seagrass meadows and the coastal ocean. Overall, the embayment waters surrounded by mangroves released CO2 to the atmosphere with a net flux rate of 18.1 ± 5.8 mmol m-2 d-1. Seagrass beds produced an overall CO2 net flux rate of 2.5 ± 3.4 mmol m-2 d-1, although 2 out of 8 surveys revealed a sink of CO2 in the seagrass area. The mouth of the bay where coral calcification occurs was a minor source of CO2 (0.3 ± 0.4 mmol m-2 d-1). The overall average CO2 flux to the atmosphere along the transect was 9.8 ± 6.0 mmol m-2 d-1, or 3.6 × 103 mol d-1 CO2 when upscaled to the entire embayment area. There were no clear seasonal patterns in contrast to better studied temperate systems. pCO2 significantly correlated with antecedent rainfall and the natural groundwater tracer radon (222Rn) during each survey. We suggest that the CO2 source in the mangrove dominated upper bay was associated with delayed groundwater inputs, and a shifting CO2 source-sink in the lower bay was driven by the uptake of CO2 by seagrass and mixing with oceanic waters. This differs from modified landscapes where potential uptake of CO2 is weakened due to the degradation of seagrass beds, or emissions are increased due to drainage of coastal wetlands.

Our understanding of how wet-dry tropical catchments process water and solutes remains limited. In this study, we attempt to gain understanding of water and dissolved organic carbon (DOC) transport, storage, and mixing in a 126 km(2) catchment of northern Australia. We developed a coupled, tracer-aided, conceptual rainfall-runoff model (SAVTAM) that simultaneously calculates water, isotope, and DOC-based processes at a daily time step. The semidistributed model can account for the marked hydrological distinction between savanna woodlands and adjacent seasonal wetlands. Using the calibrated model, we tracked the fluxes and derived the age of water in fluxes and storages. Model output matched the seasonal variability, controlled by seasonal rainfall, which switched on and off water and carbon flow pathways from the savanna to seasonal wetlands and ultimately to the perennial river. Such hydrological connectivity is modulated by the karst aquifer system that continuously contributes older waters (decades to century old) to maintain relatively stable and older streamflow during the dry season (average stream water age = 9.7 to 16.2 years). Such older waters occur despite a rapid, monsoon-driven streamflow response. The DOC fluxes were largely sourced from the wetland and riparian forest that transported DOC in the order of 1.9 t C km(-2) year(-1) to the stream, which was on average 90% of the total simulated DOC exports of 2 t C.km(-2).year(-1). We conclude that coupled simulation of water and biogeochemistry is necessary to generate a more complete picture of catchment functioning, particularly in the tropics.

Mangroves provide vital ecosystem services at the dynamic interface between land and oceans. Recent reports of mangrove mortality suggest that mangroves may be adversely affected by climate change. Here, we review historical mortality events from natural causes (all mortality other than deforestation, land use change and pollution) and provide a global assessment of mortality drivers. Since the 1960's approximately 36,000 ha of mangrove mortality has been reported (0.2% of total mangrove cover in 2011) in 47 peer reviewed articles. Due to the uneven global distribution of research effort, it is likely that mangrove mortality events go unreported in many countries. It is therefore difficult to assess temporal changes in mortality due to the small number of reports and increasing effort in observations in recent years. From the published literature, approximately 70% of reported mangrove loss from natural causes has occurred as a result of low frequency, high intensity weather events, such as tropical cyclones and climatic extremes. Globally, tropical cyclones have caused the greatest area of mangrove mortality, equivalent to 45% of the reported global mangrove mortality area from events over six decades. However, recent large-scale mortality events associated with climatic extremes in Australia account for 22% of all reported historical forest loss. These recent mortality events suggest the increasing importance of extreme climatic events, and highlight that mangroves may be important sentinels of global climate change. Increasing frequency, intensity and destructiveness of cyclones as well as climatic extremes, including low and high sea level events and heat waves, have the potential to directly influence mangrove mortality and recovery, particularly in mid latitudes.

Silvicultural thinning treatments to restore whitebark pine (Pinus albicaulis) are widely used in subalpine forests throughout the western United States (US) and Canada. The objectives of these treatments are to (1) improve the condition of whitebark pine at all ages, (2) to improve seedling recruitment processes, and (3) mitigate the damage caused by mountain pine beetle (MPB; Dendroctonus ponderosae) and white pine blister rust (WPBR; caused by the fungus Cronartium ribicola). However, there is some disagreement about the ecological basis of restoration and a paucity of information on the effects these activities – few treatments have been monitored to assess their success. We investigated the ecological effects of silvicultural restoration treatments in whitebark pine forests and evaluated their success by retrospectively sampling five treatment sites in the western US 6–10 years after implementation. We found strong evidence of growth release at a site previously characterized by closed-canopy stands. Growth responses in more open, park-like stands, however, were variable: we found weak growth increases at one site, weak growth decreases at another and no response at two other sites. At the site with strong growth increases, trees with previous damage from WPBR infection had growth increases similar to uninfected trees. We found low rates of whitebark pine seedling recruitment overall, and no increase in whitebark pine recruitment associated with treatments at any site. However, at one site, treated stands had higher regeneration of non-target species than did untreated stands. Post-treatment mortality (mostly from the late 2000s MPB outbreak) was significantly lower in the treated stand at the closed-canopy site; at the other sites, there was no difference in mortality between treated and untreated stands. The treatments had little detectable effect on short-term growth-climate relationships, although our analyses revealed that whitebark pine growth at our sites was more temperature limited than water limited. While some management goals were achieved, many were not, and there were some unintended consequences. Our results call for a closer examination of the ecological basis of silvicultural restoration treatments in whitebark pine and an expanded use of adaptive management.

CO2 and CH4 emissions from estuaries of the Southern Hemisphere are greatly under-represented in global estuary emission estimates. This study quantifies seasonal pCO2 and CH4 concentrations and emissions along the salinity gradient of three tropical mangrove-dominated estuaries in Australia. A combination of approaches (i.e. carbon stable isotopes, groundwater inputs, riverine contribution, freshwater flushing times) was used to assess the spatial and seasonal variable factors that controlled the estuary surface water CO2 and CH4 concentrations and hence emissions. Overall, CO2 and CH4 emissions ranged from 21.6 to 110.4 mmol m−2 d−1 and 40.3 to 1047.1 μmol m−2 d−1, respectively, and were within or at the high end compared to estuaries in Australia and globally. In the Johnstone River estuary, high emissions were predominantly driven by groundwater and riverine carbon inputs with exports of CO2 and CH4 to the ocean expected in the wet season. In the Fitzroy River estuary and Constant Creek estuary, in situ production and terrestrial carbon inputs were likely the main factors controlling CO2 and CH4 emissions. The contribution of riverine CO2 may be more important to overall CO2 emissions than the riverine CH4 to overall CH4 emissions in estuaries. The relative contribution of in situ production, the exchange with adjacent coastal habitats (i.e. mangroves, inter-tidal flats), and terrestrial, riverine and groundwater inputs in the wet and in the dry season determined whether CO2 and CH4 were fully ventilated within the estuaries or exported to the open ocean. The revised global estimate for estuary CO2 emission of the latitude 0 to 23.5 °S is 52.1 ± 16.1 mmol m−2 d−1, which is 15% higher than a recent estimate of this latitudinal region.

Mangrove forests can be a source or a sink of nitrous oxide (N2O) to the atmosphere, but seasonal mangrove N2O dynamics are not well understood. We used continuous high-resolution N2O concentration data to construct seasonal budgets of N2O in two tropical mangrove-lined creeks for both the wet and dry seasons. Furthermore we used N stable isotope analysis to constrain the pathways of N2O production and consumption within these creeks. Calculated water-air fluxes were within a range typical of undisturbed mangroves, however obvious seasonal differences in N2O dynamics were observed at the two sites. The mangrove systems were a net source of N2O to the atmosphere during the dry season and a net sink during the wet season. In the wet season we propose that increased allochthonous carbon enhances N2O consumption by denitrification. Combining the seasonal fluxes, the Fitzroy mangrove system, which received a continual input of allochthonous nitrate (NO3−), was a net source of N2O, while the Burdekin mangrove system was close to a net N2O balance. Interpreted in the context of DIN and N2O concentrations, the N2O isotopic values observed in the dry season point to fungal denitrification as the most likely pathway of N2O production. This study shows that subtle shifts in seasonal nutrient supply regulate mangrove N2O production and consumption.

Groundwater is a primary source of dissolved CO2 and CH4 in Amazonian headwaters, yet in higher order rivers, a groundwater/pore-water source is difficult to constrain due to the high spatial and temporal heterogeneity of pore-water exchange. Here, we report coupled, high resolution measurements of pCO2, CH4, and 222Rn (a natural pore-water and groundwater tracer) during receding waters in the three major water types of the Central Amazon Basin: black (Negro River); clear (Tapajós River); white (Madeira River). Considerable spatial heterogeneity was observed in pCO2, CH4, and 222Rn concentrations ranging from 460 ?atm to 8030 ?atm, 7 nM to 281 nM, and 713 dpm m?3 to 8516 dpm m?3, respectively. The significant correlations between pCO2 and CH4 to 222Rn in the black and clear waters suggests that pore-water further enhanced CO2 supersaturation by 18?47% and is a driver of CH4 dynamics in these waters.

Aquatic carbon exports are an understudied component of catchment carbon budgets. For drained agroecosystems, the role of this aquatic pathway in offsetting the terrestrial carbon sink is unknown. Here, we present findings on the complete annual carbon budget of a subtropical agricultural floodplain in Australia. We quantified net ecosystem exchange (NEE) using eddy covariance, and aquatic carbon fluxes from drainage canals over an annual cycle, including atmospheric exchange of aquatic CO2 and CH4, as well as lateral exports of dissolved organic, inorganic and particulate carbon. The floodplain was a large atmospheric CO2 sink, with an annual NEE of −900 g C m−2 yr−1 driven by the sugarcane growing season. Aquatic carbon fluxes were estimated at 24, 16, and 0.05 g C m−2 yr−1 for lateral export, CO2 and CH4 evasion, respectively. Between 70% and 91% of aquatic carbon was lost during flood events which occurred only 12% of the time. From these measurements and estimates of other carbon inputs and outputs from farm operations, the net ecosystem carbon budget was close to neutral at −100 (error range −289 to 215) g C m−2 yr−1. Compared to other drained wetlands, the aquatic carbon flux was a minor component of the carbon budget.

We investigated coral reef carbonate chemistry dynamics and metabolic rates using an automated system that measured total alkalinity (TA, 30 min intervals), pH on the total scale (pHT, 10 min intervals) and the partial pressure of carbon dioxide (pCO2, 1 min intervals) over 2 weeks at Heron Island (Great Barrier Reef, Australia). The calculation of pHT (using the pCO2 and TA pair) and pCO2 (using the pH and TA pair) had similar values to the measured pHT and pCO2 values. In contrast, calculated TA from the pCO2-pH pair showed a large discrepancy with measured TA (average difference between measured and calculated TA = 52 μmol kg−1). High frequency sampling allowed for detailed analysis of the observations and an assessment of optimum sampling intervals required to characterise the net ecosystem calcification (NEC) and production (NEP) using a slack water approach. Depending on the sampling interval (30 min–2 h time steps) used for calculations, the estimated daily NEC and NEP could differ by 12% and 30%, respectively. Abrupt changes in both NEC and NEP were observed at dawn and dusk, with positive NEC during these periods despite negative NEP. Integrating NEC and NEP over a full diel cycle using 1 or 2 h integration time steps resulted in small differences of 2–7% for NEC and 1–3% for NEP. A diel hysteresis pattern rather than a simple linear relationship was observed between the aragonite saturation state (Ωar) and NEC. The observed hysteresis supports recent studies suggesting that short-term observations of seawater Ωar may not be a good predictor of long-term changes in NEC due to ocean acidification. The slope of the DIC to TA relationship was slightly higher (0.33) in 2014 than in an earlier study in 2012 (0.30). The automated, high frequency sampling approach employed here can deliver high precision data and can be used at other coral reef research stations to reveal long-term changes in NEC and NEP potentially driven by ocean acidification, eutrophication or other local changes.

Large uncertainties remain in global estuarine CO2 and CH4 emissions estimates due to spatial heterogeneity, differences in methodologies and insufficient data at key locations. This study utilised novel techniques to integrate high-resolution temporal measurements of dissolved CO2 and CH4 and gas transfer velocity, within an urbanised subtropical estuary (Coffs Creek, Australia). An intensive four-station 25hr moving time series approach accounted for diurnal, tidal and spatial trends along an estuarine salinity gradient. Using 185 floating chamber measurements, results revealed major differences in emission rates over short distances. Average CO2 emission rates ranged from 16.7 to 84.4 mmol m−2 day−1 from lower to upper estuary respectively (averaged 49.0 mmol m−2 day−1). The CH4 emissions ranged from 38.8 to 193.4 μmol m−2 day−1 (averaged 115.0 μmol m−2 day−1), equating to 2.4% of the average CO2 emissions, when converted to global warming potential CO2 equivalent (over 100 years). Conservative mixing plots revealed a mid-estuary source of groundwater and porewater exchange that corresponded with a source of pCO2 and pCH4 in the mangrove lined portion of the estuary. Between the mouth and upper-estuary, a 230-fold change in gas transfer velocity (k600) (0.1–25.9 cm hr−1), 130-fold change in CO2 fluxes (1.6–202.6 mmol m−2 day−1) and 260-fold change of CH4 fluxes were observed (2.6–671.1 μmol m−2 day−1). Current velocity was the most important driver of k600 in the lower estuary (r2 = 0.37, p

The growing importance of resolving ecosystem carbon budgets has resulted in more studies integrating terrestrial and aquatic carbon fluxes. Although recent estimates highlight the importance of inland waters in global carbon budgets, the extent to which aquatic pathways contribute to the net ecosystem carbon budget (NECB) of different ecosystems remains poorly understood. Here, we provide a cross-ecosystem review of annual carbon budgets integrating terrestrial and aquatic fluxes. Large variability in the proportion of aquatic carbon offset to terrestrial net ecosystem productivity (NEP) was observed, with aquatic offsets ranging from

We investigated whether submarine groundwater discharge (SGD) traced by radon (222Rn, a natural groundwater tracer) may drive carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) in surface waters in Chowder Bay, a marine embayment in Sydney Harbour, Australia. A radon mass balance revealed significant groundwater discharge rates into the bay (8.7 ± 5.8 cm d−1). The average CO2, CH4, and N2O concentrations in the subterranean estuary were 3.5, 7.2, and 2.8 times higher than the average surface water concentrations, indicating the possibility of coastal groundwater as a source of greenhouse gases to the bay. SGD-derived fluxes of greenhouse gases were 5.02 ± 2.28 mmol m−2 d−1, 5.63 ± 2.55 μmol m−2 d−1, and 1.72 ± 0.78 μmol m−2 d−1 for CO2, CH4 and N2O, respectively. The average CO2 evasion rate from surface water was 2.29 ± 0.46 mmol m−2 d−1 while CH4 and N2O evasion rates were 12.89 ± 3.05 and 1.23 ± 0.25 μmol m−2 d−1 respectively. Therefore, groundwater-derived greenhouse gas fluxes accounted for >100% CO2 and N2O and ∼43% of CH4 surface water evasion, indicating SGD is likely an important source of greenhouse gases to surface waters. However, this may be due to observations being performed near the SGD source, which may overestimate its contribution to the wider Sydney Harbour. Over a 20-year time frame, the combined emissions of CH4 and N2O from surface waters to the atmosphere accounted for 25% of the total CO2-equivalent emissions. Although this study gives preliminary insight into SGD and greenhouse gas dynamics in Sydney Harbour, more spatial and temporal resolution sampling is required to fully constrain these processes.

Temperate Highland Peat Swamps on Sandstone (THPSS) are upland wetlands, similar to fens in the Northern Hemisphere and are found at the headwaters of low-order streams on the plateaus of Eastern Australia. They are classified as endangered ecological communities under State and National legislation. Previous works have identified particular geomorphic characteristics that are important to carbon storage in these low energy sediment accumulation zones. Changes in the geomorphic structure of THPSS, such as channelisation, may have profound implications for carbon storage. To assess the effect of channelisation on carbon budgets in these ecosystems it is essential to identify and quantify differences in carbon export, emissions and stocks of carbon of intact swamps and those that have become channelised. We undertook seasonal sampling of the perched swamp aquifers and surface waters of two intact swamps and two channelised fills in the Blue Mountains of New South Wales, Australia, to investigate differences in carbon exports and emissions between the two swamp types. We found that channelised fills' mean CO 2 emissions were almost four times higher than intact swamps with mean CH 4 emissions up to five times higher. Annual fluvial carbon exports for channelised fills were up to 18 times that of intact swamps. Channelised fill exports and emissions can represent up to 2% of the total swamp carbon stocks per annum which is 40 times higher than the intact swamps. This work clearly demonstrates that changes in geomorphic structure brought about by incision and channelisation results in profound changes to the carbon storage function of THPSS.

Continuous high-resolution surface water pCO2 and δ13C-CO2 and 222Rn (dry season only) were measured over two tidal cycles in the wet and dry season in three tropical tidal mangrove creeks on the north-eastern coast of Queensland, Australia. Mangrove surface water pCO2 followed a clear tidal pattern (ranging from 387 to 13,031 µatm) with higher pCO2-values in the wet season than in the dry season. The δ13C-CO2 in the mangrove waters ranged from −21.7 to −8.8‰ and was rather indicative of a mixed source than a distinct mangrove signature. Surface water CO2 was likely driven by a combination of mangrove and external carbon sources, e.g. exchange with groundwater/pore water enriched in 13C, or terrestrial carbon inputs with a significant contribution of C4-vegetation (sugar cane) source. The kinetic and equilibrium fractionation during the gas exchange at the water-atmosphere interface may have further caused a 13C-enrichment of the CO2 pool in the mangrove surface waters. Average CO2 evasion rates (58.7–277.6 mmol m−2 d−1) were calculated using different empirical gas transfer velocity models. Using our high-resolution time series data and previously published data, the average CO2 flux rate in mangrove ecosystems was estimated to be 56.5 ± 8.9 mmol m−2 d−1, which corresponds to a revised global mangrove CO2 emission of 34.1 ± 5.4 Tg C per year.

Few studies exist on the contribution of subterranean estuaries (STEs) to the oceanic uranium (U) budget. Here, we estimate the dissolved U fluxes out of a quartz sand STE located on the east coast of Australia. Our results indicate that the advective flow of seawater in permeable sands enhances cycling of U in the STE. Dissolved U concentrations ranged from 25 nM in the STE to an effective zero salinity end-member of 3.8 nM in the surface estuary. The dissolved U (salinity corrected) concentrations were positively correlated to Fe (r2 = 0.49 p

We thank Patricia A. Soranno, Stephen V. Smith, and an anonymous reviewer for their advice in revising this paper. PM was supported by an Australian Research Council DECRA Fellowship (DE130101084) and a Linkage Project (LP160100242). OS was supported by the CSIRO Flagship Marine and Coastal Carbon Biogeochemical Cluster and an ARC DECRA (DE170101524). DM was supported by an ARC DECRA Fellowship (DE150100581). CMD was supported by baseline funding from KAUST.

The oceans are a major source of the potent greenhouse gas nitrous oxide (N 2 O) to the atmosphere. However, little information is available on how estuaries and the coastal ocean may contribute to N 2 O budgets, and on the drivers of N 2 O in aquatic environments. This study utilised five time series stations along the freshwater to marine continuum in a sub-tropical estuary in Australia (Coffs Creek, Australia). Each time series station captured N 2 O, radon ( 222 Rn, a natural submarine groundwater discharge tracer), dissolved nitrogen, and dissolved organic carbon (DOC) concentrations for a minimum of 25 h. The use of automated time series observations enabled spatial and tidal-scale variability of N 2 O to be captured. Groundwater was highly enriched in N 2 O (up to 306 nM) compared to the receiving surface water. Dissolved N 2 O supersaturation as high as 386% (27.4 nM) was observed in the upstream freshwater and brackish water areas which represented only a small (∼13%) proportion of the total estuary area. A large area of N 2 O undersaturation (as low as 53% or 3.9 nM) was observed in the mangrove-dominated lower estuary. This undersaturated area likely resulted from N 2 O consumption due to nitrate/nitrite (NO x ) limitation in mangrove sediments subject to shallow porewater exchange. Overall, the estuary was a minor source of N 2 O to the atmosphere as the lower mangrove-dominated estuary sink of N 2 O counteracted groundwater-dominated source of N 2 O in the upper estuary. Average area-weighted N 2 O fluxes at the water-air interface approached zero (0.2–0.7 μmol m −2 d −1 , depending on piston velocity model used), and were much lower than nitrogen-rich Northern Hemisphere estuaries that are considered large sources of N 2 O to the atmosphere. This study revealed a temporally and spatially diverse estuary, with areas of N 2 O production and consumption related to oxygen and total dissolved nitrogen availability, submarine groundwater discharge, and uptake within mangroves.

Distributions of short-lived radium isotopes (224Ra and 223Ra) were investigated on the Gold Coast waterways, one of the largest residential estuarine canal systems on Earth, in an attempt to estimate radium-derived residence times and obtain insights into sources of radium isotopes. Surface and bottom canal waters were sampled in 61 locations over ~300 km of waterways. Radium isotope activities were 12-fold higher in groundwater than estuarine waters. Surprisingly, radium activities were usually higher in surface waters than bottom waters implying a radium source associated with tidal pumping in artificial beach sediments. Estimated radium ages were usually younger within artificial canal surface waters than in the natural estuarine waterways. This study shows that the tidally driven groundwater radium source can be enhanced by the extended canal shoreline.

Mangroves are among the most carbon-rich ecosystems on Earth and can sequester carbon in sediments over long timescales. Here we assess whether century-old buried carbon may be remineralized and exported by measuring Δ14C in the exported dissolved inorganic carbon (DIC) as well as sediment Δ14C profiles in a subtropical mangrove. Pore water exchange released isotopically depleted, old DIC to surface waters. Keeling plots revealed that the source of DIC to surface waters had a δ13C-DIC value of −29.4 ±1.9‰ and Δ14C-DIC value of −73±9‰. The respired and exported carbon comes from an average depth of ~40 cm, equivalent to ~100 years of sediment accumulation. Therefore, century-old sequestered carbon is still susceptible to remineralization and tidal export to the coastal ocean via pore water exchange or submarine groundwater discharge. We suggest that the timescales over which blue carbon burial is assessed should consider carbon losses via pore water exchange.