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The global carbon sequestration and avoided emissions potentially achieved via blue carbon is high (∼3% of annual global greenhouse gas emissions); however, it is limited by multidisciplinary and interacting uncertainties spanning the social, governance, financial, and technological dimensions. We compiled a transdisciplinary team of experts to elucidate these challenges and identify a way forward. Key actions to enhance blue carbon as a natural climate solution include improving policy and legal arrangements to ensure equitable sharing of benefits; improving stewardship by incorporating indigenous knowledge and values; clarifying property rights; improving financial approaches and accounting tools to incorporate co-benefits; developing technological solutions for measuring blue carbon sequestration at low cost; and resolving knowledge gaps regarding blue carbon cycles. Implementing these actions and operationalizing blue carbon will achieve measurable changes to atmospheric greenhouse gas concentrations, provide multiple co-benefits, and address national obligations associated with international agreements.

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C’s actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthula species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.

Seagrass ecosystems are globally-significant ‘blue carbon’ sinks; however, there is concern that this capacity will decline if rising ocean temperatures accelerate microbial decomposition. Decomposition of plant litter is a key process in the global carbon cycle—it influences how much carbon is available for sequestration. Therefore, understanding the biogeochemistry underlying decomposition is essential to predicting the capacity of seagrass ecosystems to act as carbon sinks in the future. Here, we tracked the breakdown of standardised and natural litter of varying chemical recalcitrance (rooibos tea > seagrass leaves > green tea) combined with highly-sensitive microsensor technology to test (a) how elevated water temperatures affect short-term microbial turnover, and (b) provide novel information on how the decay dynamics of the tea litter compare to those of natural litter. We found that increased temperatures (+ 5–10 °C) boosted microbial activity for all substrates, exhibited as enhanced decay, oxygen consumption and sulphate reduction. Within the 1-month experiment, the green tea litter had a rapid Q10 response to the temperature increase, quickly exhausting the resources for microbes, while the response of the rooibos tea and seagrass litters became more apparent toward the end of the experiment. Our results suggest that the tea litters capture a range of decomposition traits and can be compared with natural litter using traditional exponential decay models. The enhanced temperature-driven organic matter turnover, even under anoxic conditions, highlights the vulnerability of fresh litter to microbial attack during the early stages of decay and the potential weakening of blue carbon accumulation rates under future climatic conditions.

The health of seagrass plants, and thereby the ecosystems they form, is linked to their associated microbial communities. However, the role of the microbiome in holobiont function and health remains poorly understood for most seagrass species and environmental pressures, and there is, therefore, a need to better understand the drivers behind the formation of and external influences on the seagrass microbiome. Using a core microbiome framework, we characterised the leaf microbiomes of 6 estuarine seagrass populations after a precipitation event to explore how the microbiomes vary across different sites and salinities over a regional spatial scale. We found that each estuary had distinct core bacterial community structures (beta-diversity), but shared a more similar fungal core community structure. We hypothesise that the differences in the bacterial members of the microbiomes among estuaries are generally the result of each estuary being influenced by unique watersheds and sources of prokaryotes. In contrast, the similarity in the core fungal communities suggests that the eukaryotic components of the microbiomes are likely under selection or result from similar colonisation pathway(s). We also found that the bacterial taxa driving the differences among estuaries were linked to the salinity of the estuary, likely due to (1) the general epibiotic nature of colonisation (i.e. watershed source and exposure) and (2) members or functional groups within the leaf microbiome assisting seagrasses in coping with the extreme salinities. These results are valuable for linking microbiomes to the resilience of seagrasses living within dynamic estuaries experiencing a range of physicochemical pressures.

More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems—salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose—an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.

Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.

Este artículo contiene 15 páginas, 6 figuras, 1 tabla., Seagrass meadows rank among the most significant organic carbon (Corg) sinks on earth. We examined the variability in seagrass soil Corg stocks and composition across Australia and identified the main drivers of variability, applying a spatially hierarchical approach that incorporates bioregions and geomorphic settings. Top 30 cm soil Corg stocks were similar across bioregions and geomorphic settings (min-max: 20–26 Mg Corg ha−1), but meadows formed by large species (i.e., Amphibolis spp. and Posidonia spp.) showed higher stocks (24–29 Mg Corg ha−1) than those formed by smaller species (e.g., Halodule, Halophila, Ruppia, Zostera, Cymodocea, and Syringodium; 12–21 Mg Corg ha−1). In temperate coastal meadows dominated by large species, soil Corg stocks mainly derived from seagrass Corg (72 ± 2%), while allochthonous Corg dominated soil Corg stocks in meadows formed by small species in temperate and tropical estuarine meadows (64 ± 5%). In temperate coastal meadows, soil Corg stocks were enhanced by low hydrodynamic exposure associated with high mud and seagrass Corg contents. In temperate estuarine meadows, soil Corg stocks were enhanced by high contributions of seagrass Corg, low to moderate solar radiation, and low human pressure. In tropical estuarine meadows formed by small species, large soil Corg stocks were mainly associated with low hydrodynamic energy, low rainfall, and high solar radiation. These results showcase that bioregion and geomorphic setting are not necessarily good predictors of soil Corg stocks and that site-specific estimates based on local environmental factors are needed for Blue Carbon projects and greenhouse gases accounting purposes., This study was delivered as part of the Pilot Projects program of the Land Restoration Fund, supported by the Queensland Government, Deakin University, The University of Queensland, James Cook University, CSIRO, HSBC, Qantas, Australian Government Department of Industry, Science, Energy and Resources, NQ Dry Tropics, Great Barrier Reef Foundation and Greencollar. We are thankful for the funding provided by Deakin University (to PIM and MDPC), Qantas (to PIM and MDPC) and HSBC (to PIM and MDPC). MR, PY, PIM were supported through ARC Linkage grant LP160100492, and PIM and CEL were supported through ARC Linkage grant LP160100242. NJW is funded through Australian Government National Environment Science Program (Tropical Water Quality Hub). MFA was funded through an Advance Queensland Industry Research Fellowship, Queensland Government. CS was funded by ECU Higher Degree by Research Scholarship

Wetland ecosystems are critical to the regulation of the global carbon cycle, and there is a high demand for data to improve carbon sequestration and emission models and predictions. Decomposition of plant litter is an important component of ecosystem carbon cycling, yet a lack of knowledge on decay rates in wetlands is an impediment to predicting carbon preservation. Here, we aim to fill this knowledge gap by quantifying the decomposition of standardised green and rooibos tea litter over one year within freshwater and coastal wetland soils across four climates in Australia. We also captured changes in the prokaryotic members of the tea-associated microbiome during this process. Ecosystem type drove differences in tea decay rates and prokaryotic microbiome community composition. Decomposition rates were up to 2-fold higher in mangrove and seagrass soils compared to freshwater wetlands and tidal marshes, in part due to greater leaching-related mass loss. For tidal marshes and freshwater wetlands, the warmer climates had 7-16% less mass remaining compared to temperate climates after a year of decomposition. The prokaryotic microbiome community composition was significantly different between substrate types and sampling times within and across ecosystem types. Microbial indicator analyses suggested putative metabolic pathways common across ecosystems were used to breakdown the tea litter, including increased presence of putative methylotrophs and sulphur oxidisers linked to the introduction of oxygen by root in-growth over the incubation period. Structural equation modelling analyses further highlighted the importance of incubation time on tea decomposition and prokaryotic microbiome community succession, particularly for rooibos tea that experienced a greater proportion of mass loss between three and twelve months compared to green tea. These results provide insights into ecosystem-level attributes that affect both the abiotic and biotic controls of belowground wetland carbon turnover at a continental scale, while also highlighting new decay dynamics for tea litter decomposing under longer incubations. UIDB/04326/2020/ CEECINST/00114/2018 info:eu-repo/semantics/publishedVersion

High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.

Seagrass ecosystems have received a great deal of attention recently for their ability to capture and store carbon, thereby helping to mitigate climate change. However, their carbon-sink capacity could be offset somewhat if exported plant material – which accounts for ∼90% of total leaf production – undergoes microbial breakdown and is emitted into the atmosphere as a greenhouse gas. Here we measured emissions (CO2 and CH4) from the breakdown of exported seagrass plant material, focusing on beach-cast ‘wrack’. We tested two seagrass species; Zostera nigricaulis and Amphibolis antarctica, which have contrasting morphologies and chemistries. We found that both species of wrack were substantial sources of CO2, but not CH4, during the decomposition process. Biomass loss and the coinciding CO2 emissions occurred over the 30-day experiment, and the pattern of CO2 emissions over this time followed a double exponential model (R2 > 0.92). The initial flux rate was relatively high, most likely due to rapid leaching of labile compounds, then decreased substantially within the 2–9 days, and stabilizing at < 3 μmol g−1 d−1 during the remaining decomposition period. Additionally, seagrass wrack cast high up on beaches that remained dry had 72% lower emissions than wrack that was subjected to repeated wetting in the intertidal zone. This implies that relocation of seagrass wrack by coastal resource managers (e.g. from water's edge to drier dune areas) could help to reduce atmospheric CO2 emissions. Scaling up, we estimate the annual CO2-C flux from seagrass wrack globally is between 1.31 and 19.04 Tg C yr−1, which is equivalent to annual emissions of 0.63–9.19 million Chinese citizens. With climate change and increasing coastal development expected to accelerate the rate of wrack accumulation on beaches, this study provides timely information for developing coastal carbon budgets.

For millennia, coastal and marine ecosystems have adapted and flourished in the Red Sea’s unique environment. Surrounded by deserts on all sides, the Red Sea is subjected to high dust inputs and receives very little freshwater input, and so harbors a high salinity. Coral reefs, seagrass meadows, and mangroves flourish in this environment and provide socio-economic and environmental benefits to the bordering coastlines and countries. Interestingly, while coral reef ecosystems are currently experiencing rapid decline on a global scale, those in the Red Sea appear to be in relatively better shape. That said, they are certainly not immune to the stressors that cause degradation, such as increasing ocean temperature, acidification and pollution. In many regions, ecosystems are already severely deteriorating and are further threatened by increasing population pressure and large coastal development projects. Degradation of these marine habitats will lead to environmental costs, as well as significant economic losses. Therefore, it will result in a missed opportunity for the bordering countries to develop a sustainable blue economy and integrate innovative nature-based solutions. Recognizing that securing the Red Sea ecosystems’ future must occur in synergy with continued social and economic growth, we developed an action plan for the conservation, restoration, and growth of marine environments of the Red Sea. We then investigated the level of resources for financial and economic investment that may incentivize these activities. This study presents a set of commercially viable financial investment strategies, ecological innovations, and sustainable development opportunities, which can, if implemented strategically, help ensure long-term economic benefits while promoting environmental conservation. We make a case for investing in blue natural capital and propose a strategic development model that relies on maintaining the health of natural ecosystems to safeguard the Red Sea’s sustainable development.

Intensive macroalgal blooms, a source of labile organic carbon (LOC) induced by coastal nutrient loading in some seagrass ecosystems, create ideal conditions for enhanced recalcitrant organic carbon (ROC) loss via the cometabolism effect. Here, we carried out a 62-day laboratory experiment to see if density-dependent addition of macroalgal biomass can influence the seagrass decomposition process, including seagrass detritus carbon chemistry, greenhouse emissions, and bacterial communities. We found that higher density macroalgal addition stimulated microbes to decompose ∼20% more of the seagrass biomass compared to other treatments, which was also reflected in enhanced (∼twofold) greenhouse gas emissions. Although the composition of the seagrass-associated microbiome communities was unaffected by the addition of macroalgae, we showed that high macroalgal addition caused a relative depletion in the ROC as lignin and lipid compounds, as well as δ13C depletion and δ15N enrichment of the seagrass detritus. These results suggest that macroalgal blooms may stimulate the remineralization of recalcitrant components of seagrass detritus via cometabolism, possibly through providing available energy or resources for the synthesis of ROC-degrading enzymes within the resident microbial population. This study provides evidence that cometabolism can be a mechanism for leading to reduced seagrass blue carbon sequestration and preservation.

Coastal ecosystems are under increasing pressure from land-derived eutrophication in most developed coastlines worldwide. Here, we tested for 277 days the effects of a nutrient pulse on blue carbon retention and cycling within an Australian temperate coastal system. After 56 days of exposure, saltmarsh and mangrove plots subject to a high-nutrient treatment (~20 g N m−2 yr−1 and ~2 g P m−2 yr−1) had ~23% lower superficial soil carbon stocks. Mangrove plots also experienced a ~33% reduction in the microbe Amplicon Sequence Variant richness and a shift in community structure linked to elevated ammonium concentrations. Live plant cover, tea litter decomposition, and soil carbon fluxes (CO2 and CH4) were not significantly affected by the pulse. Before the end of the experiment, soil carbon- and nitrogen-cycling had returned to control levels, highlighting the significant but short-lived impact that a nutrient pulse can have on the carbon sink capacity of coastal wetlands.

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula virulence and ecology. Given these uncertainties, we investigated Labyrinthula from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate of Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula’s actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialised substrate affinity and the scarcity of characterised protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between Labyrinthula species and its host substrate.

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.

Microbes are the ‘gatekeepers’ of the marine carbon cycle, yet the mechanisms for how microbial metabolism drives carbon sequestration in coastal ecosystems are still being defined. The proximity of coastal habitats to runoff and disturbance creates ideal conditions for microbial priming, i.e., the enhanced remineralisation of stored carbon in response to fresh substrate availability and oxygen introduction. Microbial priming, therefore, poses a risk for enhanced CO2 release in these carbon sequestration hotspots. Here we quantified the existence of priming in seagrass sediments and showed that the addition of fresh carbon stimulated a 1.7- to 2.7-fold increase in CO2 release from recent and accumulated carbon deposits. We propose that priming taking place at the sediment surface is a natural occurrence and can be minimised by the recalcitrant components of the fresh inputs (i.e., lignocellulose) and by reduced metabolism in low oxygen and high burial rate conditions. Conversely, priming of deep sediments after the reintroduction to the water column through physical disturbances (e.g., dredging, boat scars) would cause rapid remineralisation of previously preserved carbon. Microbial priming is identified as a process that weakens sediment carbon storage capacity and is a pathway to CO2 release in disturbed or degraded seagrass ecosystems; however, increased management and restoration practices can reduce these anthropogenic disturbances and enhance carbon sequestration capacity.

Mechanistic models rely on specification of parameters representing biophysical traits and process rates such as phytoplankton, zooplankton and seagrass growth and respiration rates, organism sizes, stoichiometry, light, temperature and nutrient responses, nutrient-specific excretion rates and detrital stoichiometry and decay rates. Choosing suitable values for these parameters is difficult. Current practise is problematic. This paper presents a resource designed to facilitate an evidence-based approach to parameterisation of aquatic ecosystem models. An online tool is provided which collates relevant, published biological trait and biogeochemical rate observations from many sources and allows users to explore, filter and convert these data in a consistent, reproducible way, to find parameter values and calculate probability distributions. Using this information within a traditional or Bayesian paradigm should provide improved understanding of the uncertainty and predictive capacity of aquatic ecosystem models and provide insight into current sources of structural error in models.

© 2017 Marine disease ecology is a growing field of research, particularly for host organisms negatively impacted by a changing climate and anthropogenic activities. A decrease in health and increase in susceptibility to disease has been hypothesised as the mechanism behind wide-spread seagrass die-offs related to wasting disease in the past. However, seagrass wasting disease and the causative pathogen, Labyrinthula, have been vastly understudied in the southern hemisphere. Our aim was to build on the current knowledge of Australian Labyrinthula descriptions and phylogeny, while also providing a first look at wasting disease ecology in Australia. Five seagrass species along a 750 km stretch of coastline in southeastern Australia were sampled. The resulting 38 Labyrinthula isolates represented a diversity of morphotypes and five haplotypes of varying phylogenetic clade positions and virulence. The haplotypes clustered with previously-described phylogenetic clades containing isolates from Asia, USA and Europe. Pathogenicity tests confirmed, for the first time, the presence of at least two pathogenic haplotypes in Australia. While historically there have been no reports of wasting disease-related seagrass habitat loss, the presence of pathogenic Labyrinthula highlights the need for disease monitoring and research to understand seagrass wasting disease ecology in Australia.

It is global practice to construct wetlands in urban environments to treat pollutants from stormwater and overland runoff. However, constructed wetlands can also trigger climatic consequences by releasing a considerable amount of greenhouse gas emissions via diffusion and ebullition. While diffusive emissions are broadly measured, assessing the extent of ebullitive emissions is less common. This is due to the stochastic nature of ebullitive emissions and the complexity in their measurement. In addition, the soil microbiome community involved in greenhouse gas transport pathway has been generally understudied in Constructed wetlands although widely recognized in natural wetlands. Here we investigated diffusive and ebullitive CO2 and CH4 and ebullitive N2O emissions and the prokaryotic community from four municipal Surface Flow Constructed wetlands in southeast Australia over a 4-week period. We found that the total Global Warming Potential over a 100-year horizon of diffusive and ebullitive emissions was 0.44 kg CO2-equivalents m-2 day-1, which is 3-fold higher than the European estimates that accounted for diffusive emissions alone. Among the microbial functional groups that drove the main differences in β-diversity, putative methanotrophs represented the 3.6%, nitrogen-cycling microbes the 44.5% and sulfate/iron cycling microbes the 13.5%, indicating that several taxa, other than methanogens, can be key in microbial dynamics, nutrient turnover and in the shift in the production of greenhouse gas thus amplifying the role of constructed wetlands as sources of CH4. We present evidence that Constructed wetlands can be major sources of greenhouse gases, particularly ebullitive CH4 that accounted for more than two-thirds of the total emissions. As such, ebullitive flux rate measurements are critical to assemble national greenhouse gas budgets, particularly from Constructed wetlands.

Wetlands have a major influence on the global carbon cycle, with capacity to act as carbon ‘sinks’ or ‘sources’. The source-sink capacity of wetlands is governed by microbially-mediated biogeochemical processes, which are furthermore regulated by environmental conditions. With growing interest in nature-based climate solutions, policymakers and resource managers seek information on ways how wetlands can be managed to maximize carbon drawdown. Here, we explored how rehabilitation (i.e., fencing and grazing removal) influences greenhouse gas (GHG) emissions and soil biogeochemistry (microbial communities and soil quality) from semi-arid, rain-filled freshwater wetlands in south-eastern Australia. Specifically, we investigated the carbon and microbes response under major local environmental factors, such as vegetation type (graminoids vs eucalyptus tree) and seasonal hydroperiod (spring vs autumn), across wetlands that are currently used for grazing or cropping and those that have been under fencing rehabilitation for up to 20 years. We found that rehabilitation did not reduce CO2 and CH4 emissions, rather CH4 flux rates were elevated when the wetlands were flooded (spring). Anaerobic conditions from spring waterlogged soils also increased microbial diversity by 2.6-fold, and influenced the relative abundance of putative methane oxidizers (Nitrososphaerales and Mixococcales) and methanogenic archaea (Methanomicrobia, Methanobacteria). Organic matter quality (measured as C:N ratio) was reduced by the removal of grazing pressure in eucalyptus-dominated sites only. Soil quality, influenced by vegetation type, also had a significant impact on relative abundance of putative nitrogen and carbon cyclers. Overall, our results suggest that fencing rehabilitation in semi-arid rain-filled wetlands had a minor impact on microbial dynamics and carbon processes, overshadowed by the influence of the water table and vegetation type. Focusing future research on spatial and temporal patterns of carbon and microbe rehabilitation responses will help managers devise the most effective rehabilitation practice within a particular geographical area.

To promote the sequestration of blue carbon, resource managers rely on best-management practices that have historically included protecting and restoring vegetated coastal habitats (seagrasses, tidal marshes, and mangroves), but are now beginning to incorporate catchment-level approaches. Drawing upon knowledge from a broad range of environmental variables that influence blue carbon sequestration, including warming, carbon dioxide levels, water depth, nutrients, runoff, bioturbation, physical disturbances, and tidal exchange, we discuss three potential management strategies that hold promise for optimizing coastal blue carbon sequestration: (1) reducing anthropogenic nutrient inputs, (2) reinstating top-down control of bioturbator populations, and (3) restoring hydrology. By means of case studies, we explore how these three strategies can minimize blue carbon losses and maximize gains. A key research priority is to more accurately quantify the impacts of these strategies on atmospheric greenhouse-gas emissions in different settings at landscape scales.

Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.

Este artículo contiene 10 páginas, 3 tablas, 2 figuras., Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservation and restoration. Australia contributes 5–11% of the C stored in VCE globally (70–185 Tg C in aboveground biomass, and 1,055–1,540 Tg C in the upper 1m of soils). Potential CO2 emissions from current VCE losses are estimated at 2.1–3.1 Tg CO2-e yr-1, increasing annual CO2 emissions from land use change in Australia by 12–21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions., This project was supported by the CSIRO Marine and Coastal Carbon Biogeochemical Cluster, CSIRO Oceans and Atmosphere, the ECU Faculty Research Grant Scheme and Early Career Research Grant Schemes, UTS Plant Functional Biology and Climate Change Cluster, NSW Southeast Local Land Services, Department of Environment, Land, Water and Planning (DELWP), Parks Victoria, Victorian Coastal Catchment Management Authorities (GHCMA, CCMA, PPWCMA, WGCMA, EGCMA), University of Queensland Centennial Scholarship, Hodgkin Trust Scholarship, Australian Institute of Nuclear Science and Engineering, Northern Territory Government Innovation Grant, Australian Research Council (DE130101084, DE140101733, DE150100581, DE160100443, DE170101524, DP150103286, DP150102092, DP160100248, DP160100248, DP180101285, LE140100083, LE170100219, LP150100519, LP160100242 and LP110200975), the Generalitat de Catalunya (MERS 2014 SGR-1356), the ICTA ‘Unit of Excellence’ (MinECo, MDM2015-0552), Obra Social “LaCaixa”, SUMILEN, CTM 2013-47728-R, Ministry of Economy and Competitiveness and UKM-DIP-2017- 005.

Wetlands are among the earth's most efficient ecosystems for carbon sequestration, but can also emit potent greenhouse gases (GHGs) depending on how they are managed. Global management strategies have sought to maximize carbon drawdown by wetlands by manipulating wetland hydrology to inhibit bacterially-mediated emissions. However, it has recently been hypothesized within wetlands that viruses have the potential to dictate the magnitude and direction of GHG emissions by attacking prokaryotes involved in the carbon cycle. Here we tested this hypothesis in a whole-ecosystem manipulation by hydrologically-restoring a degraded wetland (‘rewetting’) and investigated the changes in GHG emissions, prokaryotes, viruses, and virus-host interactions. We found that hydrological restoration significantly increased prokaryotic diversity, methanogenic Methanomicrobia, as well as putative iron/sulfate-cyclers (Geobacteraceae), nitrogen-cyclers (Nitrosomonadaceae), and fermentative bacteria (Koribacteraceae). These results provide insights into successional microbial community shifts during rehabilitation. Additionally, in response to watering, viral-induced prokaryotic mortality declined by 77%, resulting in limited carbon released by viral shunt that was significantly correlated with the 2.8-fold reduction in wetland carbon emissions. Our findings highlight, for the first time, the potential implications of viral infections in soil prokaryotes on wetland greenhouse gas dynamics and confirm the importance of wetland rehabilitation as a tool to offset carbon emissions.

Seagrass biomass represents an important source of organic carbon that can contribute to long-term sediment carbon stocks in coastal ecosystems. There is little empirical data on the long-term microbial decomposition of seagrass detritus, despite this process being one of the key drivers of carbon-cycling in coastal ecosystems, that is, it influences the amount and quality of carbon available for sequestration. Here, our goal was to investigate how litter quality (leaf vs. rhizome/root) and the microbial communities involved in organic matter remineralisation shift over a 2-year field decomposition study north of Sydney, Australia using the temperate seagrass Zostera muelleri. The sites varied in bulk sediment characteristics and the sediment-associated microbial communities, but these variables overall had little influence on long-term seagrass decomposition rates or seagrass-associated microbiomes. The results showed a clear succession of bacterial and archaeal communities for both tissues types from r-strategists such as α- and γ-proteobacteria to K-strategies, including δ-proteobacteria, Bacteroidia and Spirochaetes. We used a new mathematical model to capture how decay rates varied over time and found that two decomposition events occurred for some seagrass leaf samples, possibly due to exudate input from living seagrass roots growing into the litter bag. The new model also indicated that conventional single exponential models overestimate long-term decay rates, and we detected for the first time the refractory, or stable, phase of decomposition for rhizome/root biomass. The stable phase began at approximately 20% mass remaining and after 600 days, and the persistence of rhizome/root biomass was attributed to the anoxic conditions and the preservation of refractory organic matter. While we predict that rhizome/root biomass will contribute more to the long-term sediment carbon stocks, the preservation of leaf carbon may be enhanced at locations were sedimentation is high and burial in anoxic conditions is rapid and constant.

Wetland ecosystems have a disproportionally large influence on the global carbon cycle. They can act as carbon sinks or sources depending upon their location, type, and condition. Rehabilitation of wetlands is gaining popularity as a nature-based approach to helping mitigate climate change; however, few studies have empirically tested the carbon benefits of wetland restoration, especially in freshwater environments. Here we investigated the effects of passive rehabilitation (i.e. fencing and agricultural release) of 16 semi-arid rain-filled freshwater wetlands in southeastern Australia. Eight control sites were compared with older (>10 year) or newer (2–5 year) rehabilitated sites, dominated by graminoids or eucalypts. Carbon stocks (soils and plant biomass), and emissions (carbon dioxide - CO2; and methane - CH4) were sampled across three seasons, representing natural filling and drawdown, and soil microbial communities were sampled in spring. We found no significant difference in soil carbon or greenhouse gas emissions between rehabilitated and control sites, however, plant biomass was significantly higher in older rehabilitated sites. Wetland carbon stocks were 19.21 t Corg ha−1 and 2.84 t Corg ha−1 for soils (top 20 cm; n = 137) and plant biomass (n = 288), respectively. Hydrology was a strong driver of wetland greenhouse gas emissions. Diffusive fluxes (n = 356) averaged 117.63 mmol CO2 m2 d−1 and 2.98 mmol CH4 m2 d−1 when wet, and 124.01 mmol CO2 m2 d−1 and –0.41 mmol CH4 m2 d−1 when dry. Soil microbial community richness was nearly 2-fold higher during the wet phase than the dry phase, including relative increases in Nitrososphaerales, Myxococcales and Koribacteraceae and methanogens Methanobacteriales. Vegetation type significantly influenced soil carbon, aboveground carbon, and greenhouse gas emissions. Overall, our results suggest that passive rehabilitation of rain-filled wetlands, while valuable for biodiversity and habitat provisioning, is ineffective for increasing carbon gains within 20 years. Carbon offsetting opportunities may be better in systems with faster sediment accretion. Active rehabilitation methods, particularly that reinstate the natural hydrology of drained wetlands, should also be considered.

© Inter-Research 2018. Marine heterotrophic protists of the Labyrinthulomycota are of interest for their biotechnological (e.g. thraustochytrid production of lipids) and ecological (e.g. wasting disease and rapid blight by pathogens of the genus Labyrinthula) applications; culture-based laboratory studies are a central technique of this research. However, maintaining such microorganism cultures can be labour- and cost-intensive, with a high risk of culture contamination and die-off over time. Deep-freeze storage, or cryopreservation, can be used to maintain culture back-ups, as well as to preserve the genetic and phenotypic properties of the microorganisms; however, this method has not been tested for the ubiquitous marine protists Labyrinthula spp. In this study, we trialled 12 cryopreservation protocols on 3 Labyrinthula sp. isolates of varying colony morphological traits. After 6 mo at -80°C storage, the DMSO and glycerol protocols were the most effective cryoprotectants compared to methanol (up to 90% success vs. 50% success, respectively). The addition of 30% horse serum to the cryoprotectant solution increased Labyrinthula sp. growth success by 20-30%. We expect that these protocols will provide extra security for culture-based studies, as well as opportunities for long-term research on key Labyrinthula sp. isolates.

© 2018, The Chinese Society of Oceanography and Springer-Verlag GmbH Germany, part of Springer Nature. Dissolved organic matter (DOM) represents a significant source of nutrients that supports the microbial-based food web in seagrass ecosystems. However, there is little information on how the various fractions of DOM from seagrass leaves contributed to the coastal biogeochemical cycles. To address this gap, we carried out a 30-day laboratory chamber experiment on tropical seagrasses Thalassia hemprichii and Enhalus acoroides. After 30 days of incubation, on average 22% carbon (C), 70% nitrogen (N) and 38% phosphorus (P) of these two species of seagrass leaf litter was released. The average leached dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP) of these two species of seagrass leaf litter accounted for 55%, 95% and 65% of the total C, N and P lost, respectively. In the absence of microbes, about 75% of the total amount of DOC, monosaccharides (MCHO), DON and DOP were quickly released via leaching from both seagrass species in the first 9 days. Subsequently, little DOM was released during the remainder of the experiment. The leaching rates of DOC, DON and DOP were approximately 110, 40 and 0.70 µmol/(g·d). Leaching rates of DOM were attributed to the nonstructural carbohydrates and other labile organic matter within the seagrass leaf. Thalassia hemprichii leached more DOC, DOP and MCHO than E. acoroides. In contrast, E. acoroides leached higher concentrations of DON than T. hemprichii, with the overall leachate also having a higher DON: DOP ratio. These results indicate that there is an overall higher amount of DOM leachate from T. hemprichii than that of E. acoroides that is available to the seagrass ecosystem. According to the logarithmic model for DOM release and the in situ leaf litter production (the Xincun Bay, South China Sea), the seagrass leaf litter of these two seagrass species could release approximately 4×103 mol/d DOC, 1.4×103 mol/d DON and 25 mol/d DOP into the seawater. In addition to providing readily available nutrients for the microbial food web, the remaining particulate organic matter (POM) from the litter would also enter microbial remineralization processes. What is not remineralized from either DOM or POM fractions has potential to contribute to the permanent carbon stocks.

Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH4 + and PO4 3− content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.

Like both terrestrial plants and other benthic marine organisms, seagrasses host abundant and diverse communities of microorganisms. These microbes fundamentally influence seagrass physiology and health, while also regulating the biogeochemical dynamics of entire seagrass meadows. Discrete populations of bacteria, fungi, microalgae, archaea and viruses inhabit seagrass leaves, roots and rhizomes and the surrounding sediments. The plethora of ecological interactions taking place between seagrasses and this microbiome span the continuum of symbiotic relationships from mutualism to parasitism. Indeed, the metabolic activities of some seagrass associated microbes, such as diazotrophic and sulphur oxidizing bacteria, govern the local chemical environment in ways that facilitate seagrass survival. On the other hand, pathogens, such as the protozoan parasite Labyrinthula cause disease outbreaks that can lead to mass seagrass die offs. While the role of the seagrass microbiome in defining the success of seagrass habitats is becoming increasingly apparent, there is still much to be learnt. For instance, the development of an understanding of how seagrass associated microbes may buffer or augment the negative impacts of growing environmental pressures will be valuable for informing decisions regarding the management and conservation of threatened seagrass habitats. In this chapter we will synthesise the current state of knowledge on the microbiology of seagrasses, with a goal of conveying the often overlooked importance of the seagrass microbiome in governing seagrass health and the biogeochemical stability of seagrass ecosystems.

Through litter decomposition enormous amounts of carbon is emitted to the atmosphere. Numerous large-scale decomposition experiments have been conducted focusing on this fundamental soil process in order to understand the controls on the terrestrial carbon transfer to the atmosphere. However, previous studies were mostly based on site-specific litter and methodologies, adding major uncertainty to syntheses, comparisons and meta-analyses across different experiments and sites. In the TeaComposition initiative, the potential litter decomposition is investigated by using standardized substrates (Rooibos and Green tea) for comparison of litter mass loss at 336 sites (ranging from -9 to +26 °C MAT and from 60 to 3113 mm MAP) across different ecosystems. In this study we tested the effect of climate (temperature and moisture), litter type and land-use on early stage decomposition (3 months) across nine biomes. We show that litter quality was the predominant controlling factor in early stage litter decomposition, which explained about 65% of the variability in litter decomposition at a global scale. The effect of climate, on the other hand, was not litter specific and explained

Many marine ecosystems have the capacity for long-term storage of organic carbon (C) in what are termed "blue carbon" systems. While blue carbon systems (saltmarsh, mangrove, and seagrass) are efficient at long-term sequestration of organic carbon (C), much of their sequestered C may originate from other (allochthonous) habitats. Macroalgae, due to their high rates of production, fragmentation, and ability to be transported, would also appear to be able to make a significant contribution as C donors to blue C habitats. In order to assess the stability of macroalgal tissues and their likely contribution to long-term pools of C, we applied thermogravimetric analysis (TGA) to 14 taxa of marine macroalgae and coastal vascular plants. We assessed the structural complexity of multiple lineages of plant and tissue types with differing cell wall structures and found that decomposition dynamics varied significantly according to differences in cell wall structure and composition among taxonomic groups and tissue function (photosynthetic vs. attachment). Vascular plant tissues generally exhibited greater stability with a greater proportion of mass loss at temperatures > 300 degrees C (peak mass loss -320 degrees C) than macroalgae (peak mass loss between 175-300 degrees C), consistent with the lignocellulose matrix of vascular plants. Greater variation in thermogravimetric signatures within and among macroalgal taxa, relative to vascular plants, was also consistent with the diversity of cell wall structure and composition among groups. Significant degradation above 600 degrees C for some macroalgae, as well as some belowground seagrass tissues, is likely due to the presence of taxon-specific compounds. The results of this study highlight the importance of the lignocellulose matrix to the stability of vascular plant sources and the potentially significant role of refractory, taxon-specific compounds (carbonates, long-chain lipids, alginates, xylans, and sulfated polysaccharides) from macroalgae and seagrasses for their long-term sedimentary C storage. This study shows that marine macroalgae do contain refractory compounds and thus may be more valuable to long-term carbon sequestration than we previously have considered.