Ranking the risk of CO2 emissions from seagrass soil carbon stocks under global change threats

Seagrass meadows are natural carbon storage hotspots at risk from global change threats, and their loss can result in the remineralization of soil carbon stocks and CO2 emissions fueling climate change. Here we used expert elicitation and empirical evidence to assess the risk of CO2 emissions from seagrass soils caused by multiple human-induced, biological and climate change threats. Judgments from 41 experts were synthesized into a seagrass CO2 emission risk score based on vulnerability factors (i.e., spatial scale, frequency, magnitude, resistance and recovery) to seagrass soil organic carbon stocks. Experts perceived that climate change threats (e.g., gradual ocean warming and increased storminess) have the highest risk for CO2 emissions at global spatial scales, while direct threats (i.e., dredging and building of a marina or jetty) have the largest CO2 emission risks at local spatial scales. A review of existing peer-reviewed literature showed a scarcity of studies assessing CO2 emissions following seagrass disturbance, but the limited empirical evidence partly confirmed the opinion of experts. The literature review indicated that direct and long-term disturbances have the greatest negative impact on soil carbon stocks per unit area, highlighting that immediate management actions after disturbances to recover the seagrass canopy can significantly reduce soil CO2 emissions. We conclude that further empirical evidence assessing global change threats on the seagrass carbon sink capacity is required to aid broader uptake of seagrass into blue carbon policy frameworks. The preliminary findings from this study can be used to estimate the potential risk of CO2 emissions from seagrass habitats under threat and guide nature-based solutions for climate change mitigation

Fingerprinting blue carbon: Rationale and tools to determine the source of organic carbon in marine depositional environments

Blue carbon is the organic carbon in oceanic and coastal ecosystems that is captured on centennial to millennial timescales. Maintaining and increasing blue carbon is an integral component of strategies to mitigate global warming. Marine vegetated ecosystems (especially seagrass meadows, mangrove forests, and tidal marshes) are blue carbon hotspots and their degradation and loss worldwide have reduced organic carbon stocks and increased CO2 emissions. Carbon markets, and conservation and restoration schemes aimed at enhancing blue carbon sequestration and avoiding greenhouse gas emissions, will be aided by knowing the provenance and fate of blue carbon. We review and critique current methods and the potential of nascent methods to track the provenance and fate of organic carbon, including: bulk isotopes, compound-specific isotopes, biomarkers, molecular properties, and environmental DNA (eDNA). We find that most studies to date have used bulk isotopes to determine provenance, but this approach often cannot distinguish the contribution of different primary producers to organic carbon in depositional marine environments. Based on our assessment, we recommend application of multiple complementary methods. In particular, the use of carbon and nitrogen isotopes of lipids along with eDNA have a great potential to identify the source and quantify the contribution of different primary producers to sedimentary organic carbon in marine ecosystems. Despite the promising potential of these new techniques, further research is needed to validate them. This critical overview can inform future research to help underpin methodologies for the implementation of blue carbon focused climate change mitigation schemes

Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN

Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In P. aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues

Reviews and syntheses: 210Pb-derived sediment and carbon accumulation rates in vegetated coastal ecosystems – setting the record straight

Vegetated coastal ecosystems, including tidal marshes, mangroves and seagrass meadows, are being increasingly assessed in terms of their potential for carbon dioxide sequestration worldwide. However, there is a paucity of studies that have effectively estimated the accumulation rates of sediment organic carbon (Corg), also termed blue carbon, beyond the mere quantification of Corg stocks. Here, we discuss the use of the 210Pb dating technique to determine the rate of Corg accumulation in these habitats. We review the most widely used 210Pb dating models to assess their limitations in these ecosystems, often composed of heterogeneous sediments with varying inputs of organic material, that are disturbed by natural and anthropogenic processes resulting in sediment mixing and changes in sedimentation rates or erosion. Through a range of simulations, we consider the most relevant processes that impact the 210Pb records in vegetated coastal ecosystems and evaluate how anomalies in 210Pb specific activity profiles affect sediment and Corg accumulation rates. Our results show that the discrepancy in sediment and derived Corg accumulation rates between anomalous and ideal 210Pb profiles is within 20% if the process causing such anomalies is well understood. While these discrepancies might be acceptable for the determination of mean sediment and Corg accumulation rates over the last century, they may not always provide a reliable geochronology or historical reconstruction. Reliable estimates of Corg accumulation rates might be difficult at sites with slow sedimentation, intense mixing and/or that are affected by multiple sedimentary processes. Additional tracers or geochemical, ecological or historical data need to be used to validate the 210Pb-derived results. The framework provided in this study can be instrumental in reducing the uncertainties associated with estimates of Corg accumulation rates in vegetated coastal sediments

Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing

Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples

Assessing the risk of carbon dioxide emissions from blue carbon ecosystems

“Blue carbon” ecosystems, which include tidal marshes, mangrove forests, and seagrass meadows, have large stocks of organic carbon (Corg) in their soils. These carbon stocks are vulnerable to decomposition and – if degraded – can be released to the atmosphere in the form of CO2. We present a framework to help assess the relative risk of CO2 emissions from degraded soils, thereby supporting inclusion of soil Corg into blue carbon projects and establishing a means to prioritize management for their carbon values. Assessing the risk of CO2 emissions after various kinds of disturbances can be accomplished through knowledge of both the size of the soil Corg stock at a site and the likelihood that the soil Corg will decompose to CO2

Commissioning and quality assurance for VMAT delivery systems: An efficient time-resolved system using real-time EPID imaging.

PURPOSE: An ideal commissioning and quality assurance (QA) program for Volumetric Modulated Arc Therapy (VMAT) delivery systems should assess the performance of each individual dynamic component as a function of gantry angle. Procedures within such a program should also be time-efficient, independent of the delivery system and be sensitive to all types of errors. The purpose of this work is to develop a system for automated time-resolved commissioning and QA of VMAT control systems which meets these criteria. METHODS: The procedures developed within this work rely solely on images obtained, using an electronic portal imaging device (EPID) without the presence of a phantom. During the delivery of specially designed VMAT test plans, EPID frames were acquired at 9.5 Hz, using a frame grabber. The set of test plans was developed to individually assess the performance of the dose delivery and multileaf collimator (MLC) control systems under varying levels of delivery complexities. An in-house software tool was developed to automatically extract features from the EPID images and evaluate the following characteristics as a function of gantry angle: dose delivery accuracy, dose rate constancy, beam profile constancy, gantry speed constancy, dynamic MLC positioning accuracy, MLC speed and acceleration constancy, and synchronization between gantry angle, MLC positioning and dose rate. Machine log files were also acquired during each delivery and subsequently compared to information extracted from EPID image frames. RESULTS: The largest difference between measured and planned dose at any gantry angle was 0.8% which correlated with rapid changes in dose rate and gantry speed. For all other test plans, the dose delivered was within 0.25% of the planned dose for all gantry angles. Profile constancy was not found to vary with gantry angle for tests where gantry speed and dose rate were constant, however, for tests with varying dose rate and gantry speed, segments with lower dose rate and higher gantry speed exhibited less profile stability. MLC positional accuracy was not observed to be dependent on the degree of interdigitation. MLC speed was measured for each individual leaf and slower leaf speeds were shown to be compensated for by lower dose rates. The test procedures were found to be sensitive to 1 mm systematic MLC errors, 1 mm random MLC errors, 0.4 mm MLC gap errors and synchronization errors between the MLC, dose rate and gantry angle controls systems of 1°. In general, parameters measured by both EPID and log files agreed with the plan, however, a greater average departure from the plan was evidenced by the EPID measurements. CONCLUSION: QA test plans and analysis methods have been developed to assess the performance of each dynamic component of VMAT deliveries individually and as a function of gantry angle. This methodology relies solely on time-resolved EPID imaging without the presence of a phantom and has been shown to be sensitive to a range of delivery errors. The procedures developed in this work are both comprehensive and time-efficient and can be used for streamlined commissioning and QA of VMAT delivery systems

Cosmological equations and Thermodynamics on Apparent Horizon in Thick Braneworld

We derive the generalized Friedmann equation governing the cosmological evolution inside the thick brane model in the presence of two curvature correction terms: a four-dimensional scalar curvature from induced gravity on the brane, and a five-dimensional Gauss-Bonnet curvature term. We find two effective four-dimensional reductions of the Friedmann equation in some limits and demonstrate that they can be rewritten as the first law of thermodynamics on the apparent horizon of thick braneworld.Comment: 25 pages, no figure, a definition corrected, several references added, more motivation and discussio

Unravelling the complex speciation of halozincate ionic liquids using X-ray spectroscopies and calculations

Using a combination of liquid-phase experimental X-ray spectroscopy experiments and small-scale calculations we have gained new insights into the speciation of halozincate anions in ionic liquids (ILs). Both core and valence X-ray photoelectron spectroscopy (XPS) were performed directly on the liquid-phase ILs, supplemented by Zn 1s X-ray absorption near edge structure (XANES) spectroscopy. Density functional theory (DFT) calculations were carried out on both 1- and 2- halozincate anions, in both a generalised solvation model SMD (Solvation Model based on Density) and the gas phase, to give XP spectra and total energy differences; time-dependent DFT was used to calculate XA spectra. Speciation judgements were made using a combination of the shape and width of experimental spectra, and visual matches to calculated spectra. For 2- halozincate anions, excellent matches were found between experimental and calculated XP spectra, clearly showing that only 2- halozincate anions were present at all zinc halide mole fraction, x, studied. At specific x (0.33, 0.50, 0.60) only one halozincate anion was present; equilibria of different halozincate anions at those x were not observed. All findings show that chlorozincate anion and bromozincate anion speciation matched at the same x. Based on the results, predictions are made of the halozincate anion speciation for all x up to 0.67. Caution is advised when using differences in calculated total energies obtained from DFT to judge halozincate anion speciation, even when the SMD was employed, as predictions based on total energy differences did not always match the findings from experimental and calculated spectra. Our findings clearly establish that the combination of high-quality experimental data from multiple spectroscopies and a wide range of calculated structures are essential to have high confidence in halozincate anion speciation identification