Microbiome mediating methane and nitrogen transformations in a subterranean estuary.

Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 µM, 273.31 ± 6.05 µM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.

Rapid bark-mediated tree stem methane transport occurs independently of the transpiration stream in Melaleuca quinquenervia.

Tree stem methane emissions are important components of lowland forest methane budgets. The potential for species-specific behaviour among co-occurring lowland trees with contrasting bark characteristics has not been investigated. We compare bark-mediated methane transport in two common lowland species of contrasting bark characteristics (Melaleuca quinquenervia featuring spongy/layered bark with longitudinally continuous airspaces and Casuarina glauca featuring hard/dense common bark) through several manipulative experiments. First, the progressive cutting through M. quinquenervia bark layers caused exponential increases in methane fluxes (c. 3 orders of magnitude); however, sapwood-only fluxes were lower, suggesting that upward/axial methane transport occurs between bark layers. Second, concentrated methane pulse-injections into exposed M. quinquenervia bark, revealed rapid axial methane transport rates (1.42 mm s-1 ), which were further supported through laboratory-simulated experiments (1.41 mm s-1 ). Laboratory-simulated radial CH4 diffusion rates (through bark) were c. 20-times slower. Finally, girdling M. quinquenervia stems caused a near-instantaneous decrease in methane flux immediately above the cut. By contrast, girdling C. glauca displayed persistent, though diminished, methane fluxes. Overall, the experiments revealed evidence for rapid 'between-bark' methane transport independent from the transpiration stream in M. quinquenervia, which facilitates diffusive axial transport from the rhizosphere and/or sapwood sources. This contrasts with the slower, radial 'through-bark' diffusive-dominated gas transportation in C. glauca.

All tidal wetlands are blue carbon ecosystems.

Managing coastal wetlands is one of the most promising activities to reduce atmospheric greenhouse gases, and it also contributes to meeting the United Nations Sustainable Development Goals. One of the options is through blue carbon projects, in which mangroves, saltmarshes, and seagrass are managed to increase carbon sequestration and reduce greenhouse gas emissions. However, other tidal wetlands align with the characteristics of blue carbon. These wetlands are called tidal freshwater wetlands in the United States, supratidal wetlands in Australia, transitional forests in Southeast Asia, and estuarine forests in South Africa. They have similar or larger potential for atmospheric carbon sequestration and emission reductions than the currently considered blue carbon ecosystems and have been highly exploited. In the present article, we suggest that all wetlands directly or indirectly influenced by tides should be considered blue carbon. Their protection and restoration through carbon offsets could reduce emissions while providing multiple cobenefits, including biodiversity.

Submarine Groundwater Discharge Exceeds River Inputs as a Source of Nutrients to the Great Barrier Reef.

Rivers are often assumed to be the main source of nutrients triggering eutrophication in the Great Barrier Reef (GBR). However, existing nutrient budgets suggest a major missing source of nitrogen and phosphorus sustaining primary production. Here, we used radium isotopes to resolve submarine groundwater discharge (SGD)-derived, shelf-scale nutrient inputs to the GBR. The total SGD was ∼10-15 times greater than average river inputs, with nearshore groundwater discharge accounting for ∼30% of this. Total SGD accounted for >30% of all known dissolved inorganic N and >60% of inorganic P inputs and exceeded regional river inputs. However, SGD was only a small proportion of the nutrients necessary to sustain primary productivity, suggesting that internal recycling processes still dominate the nutrient budget. With millions of dollars spent managing surface water nutrient inputs to reef systems globally, we argue for a shift in the focus of management to safeguard reefs from the impacts of excess nutrients.

Isotopic evidence for axial tree stem methane oxidation within subtropical lowland forests.

Knowledge regarding mechanisms moderating methane (CH4 ) sink/source behaviour along the soil-tree stem-atmosphere continuum remains incomplete. Here, we applied stable isotope analysis (δ13 C-CH4 ) to gain insights into axial CH4 transport and oxidation in two globally distributed subtropical lowland species (Melaleuca quinquenervia and Casuarina glauca). We found consistent trends in CH4 flux (decreasing with height) and δ13 C-CH4 enrichment (increasing with height) in relation to stem height from ground. The average lower tree stem δ13 C-CH4 (0-40 cm) of Melaleuca and Casuarina (-53.96‰ and -65.89‰) were similar to adjacent flooded soil CH4 ebullition (-52.87‰ and -62.98‰), suggesting that stem CH4 is derived mainly by soil sources. Upper stems (81-200 cm) displayed distinct δ13 C-CH4 enrichment (Melaleuca -44.6‰ and Casuarina -46.5‰, respectively). Coupled 3D-photogrammetry with novel 3D-stem measurements revealed distinct hotspots of CH4 flux and isotopic fractionation on Melaleuca, which were likely due to bark anomalies in which preferential pathways of gas efflux were enhanced. Diel experiments revealed greater δ13 C-CH4 enrichment and higher oxidation rates in the afternoon, compared with the morning. Overall, we estimated that c. 33% of the methane was oxidised between lower and upper stems during axial transport, therefore potentially representing a globally significant, yet previously unaccounted for, methane sink.

Are methane emissions from mangrove stems a cryptic carbon loss pathway? Insights from a catastrophic forest mortality.

Growing evidence indicates that tree-stem methane (CH4 ) emissions may be an important and unaccounted-for component of local, regional and global carbon (C) budgets. Studies to date have focused on upland and freshwater swamp-forests; however, no data on tree-stem fluxes from estuarine species currently exist. Here we provide the first-ever mangrove tree-stem CH4 flux measurements from  >50 trees (n = 230 measurements), in both standing dead and living forest, from a region suffering a recent large-scale climate-driven dieback event (Gulf of Carpentaria, Australia). Average CH4 emissions from standing dead mangrove tree-stems was 249.2 ± 41.0 µmol m-2  d-1 and was eight-fold higher than from living mangrove tree-stems (37.5 ± 5.8 µmol m-2  d-1 ). The average CH4 flux from tree-stem bases (c. 10 cm aboveground) was 1071.1 ± 210.4 and 96.8 ± 27.7 µmol m-2  d-1 from dead and living stands respectively. Sediment CH4 fluxes and redox potentials did not differ significantly between living and dead stands. Our results suggest both dead and living tree-stems act as CH4 conduits to the atmosphere, bypassing potential sedimentary oxidation processes. Although large uncertainties exist when upscaling data from small-scale temporal measurements, we estimated that dead mangrove tree-stem emissions may account for c. 26% of the net ecosystem CH4 flux.

iAMES: An inexpensive, Automated Methane Ebullition Sensor.

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.

Improving the measurement of nitrogen stable isotopes in organic materials containing high C:N ratios using a 5A molecular sieve column.

The nitrogen stable isotope composition (δ15N) of plant materials has numerous applications. Plant materials like bark can have a very high C:N ratio. Incomplete C combustion in such samples interferes with the δ15N measurement due to CO production. We modified the standard setup for δ15N measurement using an elemental analyzer (EA) coupled to an isotope ratio mass spectrometer (IRMS) by incorporating a 5A molecular sieve column, which better separates N2 from CO. We compared this new modified setup and the standard one for the measurement of bark samples. Precision and accuracy for δ15N in standards with low C:N ratio were equivalent for the two methods. However, for bark the results obtained with the new method had better precision and accuracy than the standard method. Replicates are nevertheless recommended with the new method to ensure confidence in the results.•During elemental analysis, incomplete combustion of material with high C:N ratio can lead to CO formation, which interferes with δ15N IRMS measurements.•Here we use a 5A molsieve column to remove the CO interference in δ15N measurements Precision and accuracy on δ15N measurements of samples with high C content are significantly improved.

Groundwater discharge and bank overtopping drive large carbon exports from Indian Sundarban mangroves.

The Sundarbans represent the largest mangrove system on Earth, covering >10,000 km2. These mangroves can export a vast amount of aquatic carbon that can be potentially sequestered for millennia. However, the mechanisms that drive these processes remain poorly constrained. Here, we estimate porewater-driven carbon exchange between the Sundarbans and the Bay of Bengal using high-resolution time series and a radon groundwater mass balance approach spanning a neap-spring tidal cycle. Submarine groundwater discharge (SGD) increased from neap to spring tides by 352 % up to a maximum of 65.6 cm d-1 largely driven by creek bank overtopping after the mid-tide. Exports of dissolved organic and inorganic carbon and alkalinity doubled between neap and spring, likely due to the 'first flush' of older porewater in the mangrove flats. Groundwater discharge was a significant driver of the net carbon export, contributing up to 86.7 % of DIC and 74.0 % of alkalinity during the spring tide while contributing a lower proportion of DOC (4 %-23 %). If these results are representative of the Sundarbans more broadly, carbon fluxes from the Sundarbans would be more than an order of magnitude higher than some of the world's largest rivers on an areal basis, highlighting the importance of Sundarbans mangroves to global oceanic carbon budgets.

Bark-dwelling methanotrophic bacteria decrease methane emissions from trees.

Tree stems are an important and unconstrained source of methane, yet it is uncertain whether internal microbial controls (i.e. methanotrophy) within tree bark may reduce methane emissions. Here we demonstrate that unique microbial communities dominated by methane-oxidising bacteria (MOB) dwell within bark of Melaleuca quinquenervia, a common, invasive and globally distributed lowland species. In laboratory incubations, methane-inoculated M. quinquenervia bark mediated methane consumption (up to 96.3 µmol m-2 bark d-1) and reveal distinct isotopic δ13C-CH4 enrichment characteristic of MOB. Molecular analysis indicates unique microbial communities reside within the bark, with MOB primarily from the genus Methylomonas comprising up to 25 % of the total microbial community. Methanotroph abundance was linearly correlated to methane uptake rates (R2 = 0.76, p = 0.006). Finally, field-based methane oxidation inhibition experiments demonstrate that bark-dwelling MOB reduce methane emissions by 36 ± 5 %. These multiple complementary lines of evidence indicate that bark-dwelling MOB represent a potentially significant methane sink, and an important frontier for further research.

The legacy and drivers of groundwater nutrients and pesticides in an agriculturally impacted Quaternary aquifer system.

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 (<15 m) where perched systems were identified. In areas with preferential flowpaths, young-groundwater (⁓1-year) with significant nitrate (~12 mg-N/L) and pesticides (up to 315 ng/L) concentrations were detected at deeper 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 (<3 mg-N/L) and pesticides (<2 ng/L) concentrations were detected in the confined systems. This study demonstrates the importance of understanding both the geology and the hydrogeology of an area before deploying monitoring studies and/or making conclusions from tritium, nutrient and pesticide data alone.

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient.

In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 µM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 µM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 µM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%- 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O2, NO3-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane-a potent greenhouse gas.