Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks

The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes

Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.

Outer membrane vesicles can contribute to cellulose degradation in Teredinibacter turnerae, a cultivable intracellular endosymbiont of shipworms

Teredinibacter turnerae is a cultivable cellulolytic Gammaproeteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome of T. turnerae encodes a broad range of enzymes that deconstruct cellulose, hemicellulose, and pectin and contribute to lignocellulose digestion in the shipworm gut. However, the mechanism by which symbiont-made enzymes are secreted by T. turnerae and subsequently transported to the site of lignocellulose digestion in the shipworm gut is incompletely understood. Here, we show that T. turnerae cultures grown on carboxymethyl cellulose (CMC) produce outer membrane vesicles (OMVs) that contain a variety of proteins identified by LC-MS/MS as carbohydrate-active enzymes with predicted activities against cellulose, hemicellulose, and pectin. Reducing sugar assays and zymography confirm that these OMVs retain cellulolytic activity, as evidenced by hydrolysis of CMC. Additionally, these OMVs were enriched with TonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations suggest potential roles for OMVs in lignocellulose utilization by T. turnerae in the free-living state, in enzyme transport and host interaction during symbiotic association, and in commercial applications such as lignocellulosic biomass conversion.

Polyethylene microplastic-induced microbial shifts affected greenhouse gas emissions during litter decomposition in coastal wetland sediments

Microplastic contamination has become increasingly aggravated in coastal environments, further affecting biogeochemical processes involved with microbial community shifts. As a key biogeochemical process mainly driven by microbiota in coastal wetland sediments, litter decomposition contributes greatly to the global greenhouse gas (GHG) budget. However, under microplastic pollution, the relationship between microbial alterations and GHG emissions during litter decomposition in coastal wetlands remains largely unknown. Here, we explored the microbial mechanism by which polyethylene microplastic (PE-MP) influenced greenhouse gas (i.e., CH4, CO2 and N2O) emissions during litter decomposition in coastal sediments through a 75-day microcosm experiment. During litter decomposition, PE-MP exposure significantly decreased cumulative CH4 and CO2 emissions by 41.07% and 25.79%, respectively. However, there was no significant change in cumulative N2O emissions under PE-MP exposure. The bacterial, archaeal, and fungal communities in sediments exhibited varied responses to PE-MP exposure over time, as reflected by the altered structure and changed functional groups of the microbiota. The altered microbial functional groups ascribed to PE-MP exposure and sediment property changes might contribute to suppressing CH4 and CO2 emissions during litter decomposition. This study yielded valuable information regarding the effects of PE-MP on GHG emissions during litter decomposition in coastal wetland sediments.

Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species

Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.

Marine Bacteroidetes enzymatically digest xylans from terrestrial plants

Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.

Seagrass ecosystem adjacent to mangroves store higher amount of organic carbon of Andaman and Nicobar Islands, Andaman Sea

This study quantified the organic carbon (Corg) stocks in Thalassia hemprichii meadows that are (i) adjacent to mangroves (MG), and (ii) without mangroves (WMG), in tropical Andaman and Nicobar Islands (ANI) of India. In the top 10 cm of the sediment, Corg content was 1.8-fold higher at the MG sites than the WMG sites. The total Corg stocks (sediment + biomass) in the 144 ha of seagrass meadows at MG sites (988.74 ± 138.77 Mg C) was 1.9-fold higher than in 148 ha of WMG sites. Protection and management of T. hemprichii meadows of ANI can lead to emission avoidance of around 5447.33 (MG; 3595.12 + WMG: 1852.21) tons of CO2. The social cost of the carbon stocks in these T. hemprichii meadows is around US$ 0.30 and 0.16 million at the MG and WMG sites, respectively, showcasing the importance of ANI's seagrass ecosystems as nature-based solutions for climate change mitigation.

The contribution of wetland plant litter to soil carbon pool: Decomposition rates and priming effects

Plant litter input is an important driver of soil/sediment organic carbon (SOC) turnover. A large number of studies have targeted litter-derived C input tracing at a global level. However, little is known about how litter carbon (C) input via various plant tissues affects SOC accumulation and mineralization. Here, we conducted laboratory incubation to investigate the effects of leaf litter and stem litter input on SOC dynamics using the natural ¹³C isotope technique. A 122-day laboratory incubation period showed that litter input facilitated SOC accumulation. Leaf and stem litter inputs increased soil total organic carbon content by 37.6% and 15.5%, respectively. Leaf litter input had a higher contribution to SOC accumulation than stem litter input. Throughout the incubation period, the δ¹³C values of stem litter and leaf litter increased by 1.5‰ and 3.3‰, respectively, while δ¹³CO₂ derived from stem litter and δ¹³CO₂ derived from leaf litter decreased by 4.2‰ and 6.1‰, respectively, suggesting that the magnitude of δ¹³C in litter and δ¹³CO₂ shifts varied, depending on litter tissues. The cumulative CO₂-C emissions of leaf litter input treatments were 27.56%-42.47% higher than those of the stem litter input treatments, and thus leaf litter input promoted SOC mineralization more than stem litter input. Moreover, the proportion of increased CO₂-C emissions to cumulative CO₂-C emissions (57.18%-92.12%) was greater than the proportion of litter C input to total C (18.7%-36.8%), indicating that litter input could stimulate native SOC mineralization, which offsets litter-derived C in the soil. Overall, litter input caused a net increase in SOC accumulation, but it also accelerated the loss of native SOC. These findings provide a reliable basis for assessing SOC stability and net C sink capacity in wetlands.

Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae)

The bivalve families Teredinidae and Xylophagaidae include voracious consumers of wood in shallow and deep-water marine environments, respectively. The taxa are sister clades whose members consume wood as food with the aid of intracellular cellulolytic endosymbionts housed in their gills. This combination of adaptations is found in no other group of animals and was likely present in the common ancestor of both families. Despite these commonalities, the two families have followed dramatically different evolutionary paths with respect to anatomy, life history and distribution. Here we present 42 new mitochondrial genome sequences from Teredinidae and Xylophagaidae and show that distinct trajectories have also occurred in the evolution and organization of their mitochondrial genomes. Teredinidae display significantly greater rates of amino acid substitution but absolute conservation of protein-coding gene order, whereas Xylophagaidae display significantly less amino acid change but have undergone numerous and diverse changes in genome organization since their divergence from a common ancestor. As with many bivalves, these mitochondrial genomes encode two ribosomal RNAs, 12 protein coding genes, and 22 tRNAs; atp8 was not detected. We further show that their phylogeny, as inferred from amino acid sequences of 12 concatenated mitochondrial protein-coding genes, is largely congruent with those inferred from their nuclear genomes based on 18S and 28S ribosomal RNA sequences. Our results provide a robust phylogenetic framework to explore the tempo and mode of mitochondrial genome evolution and offer directions for future phylogenetic and taxonomic studies of wood-boring bivalves.

Over 100-Year Preservation and Temporal Fluctuations of Cell Wall Polysaccharides in Marine Sediments

Polysaccharides constitute an important carbon pool in marine systems, but much is still unknown about the fate and degradation of these compounds. They are derived partly from production in situ, and in coastal areas, they are partly terrestrially derived, originating from freshwater runoff from land. The aim of this study was to test the applicability of high-throughput polysaccharide profiling for plant and algal cell-wall compounds in dated sediment cores from a coastal marine environment, to examine the preservation of cell-wall polysaccharides and explore their potential as proxies for temporal environmental changes. Preserved compounds and remains of organisms are routinely used as paleoenvironmental proxies as the amount and composition of different compounds that can provide insight into past environmental conditions, and novel means for reporting environmental changes are highly sought.

Estimating the integrated degradation rates of woody debris at the scale of a Mediterranean coastal catchment

Woody debris is found in all habitats of the land-sea continuum. While isolated experimental studies of wood degradation exist, few programs have observed the dynamics of wood degradation, in situ across this gradient. Since 2014, we have been conducting a series of long-term observations of wood decay in three characteristic areas of a Mediterranean Sea coastal watershed: forest leaf litter ('Forest'), river bed ('River') and the near-shore marine environment ('Sea'). The study sites are within the Massane River watershed (France) whose headwaters are in a protected beech tree (Fagus sylvatica) dominated forest. Branch sections from a recently fallen beech tree and standardized blocks of Norway spruce (Picea abies) were installed in all three environments. The proportion of remaining mass and volumetric mass of the individual wood samples were determined periodically over 4.2 years. Regardless of wood type, there were marked differences in the decay dynamics. Mass losses at the Forest and River sites were well-described by continuous negative exponential models. At the Sea site, there was a short latency period followed by rapid degradation for the wood fraction exploited by shipworms; in this case, a Weibull-type function was fitted to the data. Integrated mass loss rates at the coastal location were 6 to 20 times faster than in the other two environments. Our study suggests that the early dynamics of wood degradation in a land-sea meta-ecosystem are dominated by the marine invertebrate community. This means woody debris, once it reaches the sea, is likely to break down rapidly within near shore coastal habitats. These results highlight the need to quantify the mass transport dynamics between local ecosystems.

Estimation of carbon pools in the biomass and soil of mangrove forests in Sirik Azini creek, Hormozgan province (Iran)

Despite the increasing interest in mangroves as one of the most carbon-rich ecosystems, arid mangroves are still poorly investigated. We aimed to improve the knowledge of biomass and soil carbon sequestration for an arid mangrove forest located at the Azini creek, Sirik, Hormozgan Province (Iran). We investigated the biomass and organic carbon stored in the above and belowground biomass for three different regions selected based on the composition of the principal species: (1) Avicennia marina, (2) mixed forest of A. marina and Rhizophora mucronata, and (3) R. mucronata. Topsoil organic carbon storage to 30 cm depth was also estimated for each analyzed area. Biomass carbon storage, considering both aboveground (AGB) and belowground biomass (BGB), was significantly different between the cover areas. Overall, the mean forest biomass (MFB) was 283.1 ± 89 Mg C ha-1 with a mean C stored in the biomass of 128.9 ± 59 Mg C ha-1. Although pure Rhizophora stand showed the lowest value of above and below tree carbon (AGC + BGC); 17.6 ± 1.9 Mg C ha-1), soil organic carbon stock in sites under Rhizophora spp. was significantly higher than in the site with pure stand of Avicennia spp. Overall, forest soil stored the highest proportion of Sirik mangrove ecosystem organic carbon (59%), with a mean value of 188.3 ± 27 Mg C ha-1. These results will contribute to broaden the knowledge and the dataset available, reducing the uncertainties related to estimates and modeling of carbon pools in arid mangrove ecosystem, which also represent an important climatic threshold of mangrove worldwide distribution.

Seagrass contributes substantially to the sedimentary lignin pool in an estuarine seagrass meadow

Shallow coastal ecosystems are reservoirs of carbon derived from allochthonous organic matter and autochthonous organic matter produced by microalgae and macrophytes. Carbon stored in vegetated coastal ecosystems has attracted broad attention as an important component of carbon sinks. Characterizing the source of carbon in sediments is essential for quantifying the carbon-sequestration function of shallow coastal ecosystems. In this study, we investigated the origins of organic matter using organic biomarkers (lignin phenols, fatty acids, cutin acids, diacids, and ω-hydroxy acids) in surface sediments in a seagrass-dominated lagoon (Furen Lagoon, Japan). Biomarkers derived from allochthonous vascular plants, such as long-chain fatty acids, showed higher concentrations near river mouths. Furthermore, biomarker signals indicated that sedimentary organic carbon originated in large part from degraded allochthonous vascular plants including roots. A Bayesian mixing model using the ratios of syringyl phenols to vanillyl phenols and cinnamyl phenols to vanillyl phenols indicated that up to about 65% of lignin in the sediments was derived from seagrass. This result indicates a substantial contribution of seagrass to the sedimentary lignin pool in an estuarine seagrass meadow. However, the percent contribution of seagrass to the lignin pool varied, with higher values near a tidal inlet and relatively low values near river mouths. Vertical profiles of organic biomarkers varied with the differences in degradability of organic compounds. Specifically, long-chain fatty acids decreased with increasing depth more than the other compounds, suggesting that they degraded more easily. Conversely, we observed a tendency for lignin phenols to be selectively preserved in the vertical sediment profiles. Our results show that sediment organic biomarkers can provide diverse information such as the composition and origins of organic carbon, the contribution of seagrass derived lignin, and the varying degrees of decomposition. This approach should bring new insights to the estimation of carbon in future blue carbon studies.

Ecosystem type drives tea litter decomposition and associated prokaryotic microbiome communities in freshwater and coastal wetlands at a continental scale

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.

How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes

Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.

Food-web comparisons between two shallow vegetated habitat types in the Baltic Sea

Coastal vegetated habitats maintain highly diverse communities, where the contribution of macrophyte production is significant for macroinvertebrate primary consumers. In the brackish-waters of the Baltic Sea, the taxonomical diversity of different macrophytes includes both marine and limnic species. To study the basal food-web differences of two key vegetated habitat types, either dominated by a perennial brown macroalgae (Fucus vesiculosus) or by angiosperm plants, ¹³C and ¹⁵N compositions of different primary producers and macroinvertebrate consumers were examined, and their diets were estimated by Bayesian mixing models. Carbon isotope diversity of primary producers was high especially in the hard-bottom Fucus-dominated habitats, which was also reflected in a larger consumer isotope niche. However, consumer isotope niche among sites was similar within the same habitat type. Our models indicated that the perennial macrophyte dietary median contribution was about 25% for deposit feeders and omnivores in both habitat types, while epigrazers preferred filamentous algae (30-60%). The niche positions of the abundant clams L. balthica, M. arenaria and C. glaucum differed between the two habitats, but they showed only small (<10% units) differences in their macrophyte dietary contributions. The isotopic compositions of the dominating primary producer assemblage reflected significantly in the isotope niche structure of the associated primary consumers.

Autochthonous production contributes to the diet of wood-boring invertebrates in temperate shallow water

Marine wood-boring invertebrates rapidly fragment coarse woody debris in the sea. These wood borers have the ability to digest wood cellulose, but other potential food sources have been less investigated. To assess the contribution of each potential food source to the diet of wood borers, we traced seasonal and environmental changes in δ¹³C of shipworms cultured under the same experimental conditions and related these changes to variations in δ¹³C of potential food sources, i.e., wood log and particulate organic matter (POM) by using multiple linear regression models rather than the Bayesian mixing model. Based on the standardized partial regression coefficients in the model, it became clear that wood-derived organic carbon was the main carbon source for the teredinids, and POM also accounted for 37.9% of the teredinids' carbon source. Furthermore, we clarified variations in supplemental nitrogen sources for the teredinids: one species depended on both POM and wood log, whereas the other three species depended on either POM or wood log for their nitrogen source. δ¹³C values of another wood-boring bivalve of Martesia (Pholadidae) increase as it grows, which suggests that the bivalve switches its feeding strategy from xylophagous to filter feeding as it grows. Wood borers are known to accelerate the transfer of organic materials derived from wood logs to marine ecosystems. However, this study suggests that autochthonous production strongly contribute to the diet of marine wood borers, helping them to decompose wood logs in temperate shallow water.

Mangrove ecological services at the forefront of coastal change in the French overseas territories

Mangroves are located at the land-sea interface and are therefore confronted with human settlement in the coastal areas and associated pressures and uses. This unique habitat provides important ecosystem services to coastal communities worldwide, but the global decline of their surface area and their degradation over the past decades has put coastal communities even more at risk from the effects of climate change. This paper aims to present the first ecosystem services valuation of the mangroves of the French overseas Territories. We provide the economic value of mangroves for coastal protection, carbon sequestration, water purification and fish biomass production. We coupled a geospatial analysis of mangrove's distribution with the characterisation of land artificialisation behind mangroves. Then we developed a vulnerability index based on multiple indicators of exposure to environmental and anthropogenic stressors, mangroves' sensitivity to pressures, and mangroves' adaptive capacity to adjust their production functions accordingly. We estimated the monetary value of regulation and support services provided by mangroves in French overseas territories to be on average EUR 1.6 billion annually, 60% of which is carbon sequestration, 28% coastal protection, 7% water purification and 6% fish biomass production. When considering mangroves services without the vulnerability adjustment, the total value for those services would reach EUR 2 billion per year. Although much of the spatio-temporal variability in mangrove functioning could not be considered given the spatial scale of our study, these results demonstrate the value and socio-economic importance of mangroves to face and adapt from the effects of coastal change, at local and national scales, but also highlight the loss of services due to their vulnerability. This paper emphasises on the value of ecosystem services provided by mangroves to face coastal change so that a service-based approach to conservation would plead for increased national investment into their protection.

Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

BACKGROUND

Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh.

RESULTS

Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed.

CONCLUSIONS

Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments. Video Abstract.

Macroalgal Blooms Trigger the Breakdown of Seagrass Blue Carbon

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.

Deciphering organic matter sources and ecological shifts in blue carbon ecosystems based on molecular fingerprinting

Blue carbon ecosystems (BCE) play an essential role in the global carbon cycle by removing atmospheric carbon dioxide and storing it as organic carbon (OC) in biomass and sediments. However, organic matter (OM) deposition and degradation/preservation processes are poorly understood, especially on the long-term and at molecular scales. We analysed sediment samples from six cores collected in tidal marshes, mangroves and seagrasses (up to 150 cm long cores spanning up to 10,000 yrs of OC accumulation) from Spencer Gulf (South Australia), by pyrolysis (Py-GC-MS and THM-GC-MS), and we compared the results with elemental and stable isotope data, to decipher OM provenance and to assess degradation/preservation dynamics. The results showed that: (1) the major biopolymers preserved were polysaccharides, polyphenolic moieties (lignin and tannin) and polymethylenic moieties (e.g. cutin, suberin, chlorophyll) with smaller apportions of proteins and resins; (2) the OM originates predominantly from vascular plant materials (in particular lignocellulose) that have been well-preserved, even in some of the oldest sediments; (3) mangroves were found to be the most efficient OC sinks, partially explained by syringyl lignin preservation; (4) seagrasses were shown to store polysaccharide-enriched OM; (5) large proportions of polycyclic aromatic hydrocarbons (PAHs) in surficial tidal marsh and mangrove sediments probably reflect pyrogenic OM from industrial combustion, and; (6) "ecosystem shifts", i.e. mangrove encroachment in tidal marsh and transition from seagrass to mangrove, were detected. Deposition environment and source vegetation control OC sequestration and there is no specific recalcitrant form of OM that is selectively preserved. For the first time, we demonstrate how analytical pyrolysis in combination with stable isotope analysis can be used to reconstruct (palaeo-)ecological shifts between different BCE. This study improves our knowledge on OC accumulation dynamics and the response of BCE to environmental change, which can inform the implementation of strategies for climate change mitigation.

Nutrient loading diminishes the dissolved organic carbon drawdown capacity of seagrass ecosystems

Seawater dissolved organic carbon (DOC) in seagrass meadows is gaining attention for its role in carbon sequestration. Abundant refractory compounds in DOC are exported by seagrass meadows to the deep sea, thereby contributing to long-term carbon drawdown. DOC lability and bacterioplankton communities are key determining factors in this carbon sequestration process, and it has been hypothesized that these may be affected by nutrient loading - however, scientific evidence is so far weak. Here, we studied the response of DOC composition and bacterioplankton communities to nutrient loading in seagrass meadows of the South China Sea. We found that increasing nutrient loads enhanced nitrogen and phosphorus concentrations in DOC, which promoted algae blooms (i.e. epiphyte, phytoplankton and macroalgae) in seagrass meadows, and presumably increased the lability of DOC and its bioavailability to microbes. Also, the relative abundance of K-strategist bacterioplankton communities with the potential to degrade refractory compounds (Acidimicrobiia, Verrucomicrobiales and Micrococcales) increased in the seagrass meadows exposed to high nutrient loads. These results suggest that high nutrient loading can enhance labile DOC composition, and thus increase refractory DOC remineralization rate, thereby weakening the DOC contribution potential of seagrass meadows to long-term carbon sequestration.

Carbon Balance in Salt Marsh and Mangrove Ecosystems: A Global Synthesis

Mangroves and salt marshes are among the most productive ecosystems in the global coastal ocean. Mangroves store more carbon (739 Mg CORG ha−1) than salt marshes (334 Mg CORG ha−1), but the latter sequester proportionally more (24%) net primary production (NPP) than mangroves (12%). Mangroves exhibit greater rates of gross primary production (GPP), aboveground net primary production (AGNPP) and plant respiration (RC), with higher PGPP/RC ratios, but salt marshes exhibit greater rates of below-ground NPP (BGNPP). Mangroves have greater rates of subsurface DIC production and, unlike salt marshes, exhibit active microbial decomposition to a soil depth of 1 m. Salt marshes release more CH4 from soil and creek waters and export more dissolved CH4, but mangroves release more CO2 from tidal waters and export greater amounts of particulate organic carbon (POC), dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC), to adjacent waters. Both ecosystems contribute only a small proportion of GPP, RE (ecosystem respiration) and NEP (net ecosystem production) to the global coastal ocean due to their small global area, but contribute 72% of air–sea CO2 exchange of the world’s wetlands and estuaries and contribute 34% of DIC export and 17% of DOC + POC export to the world’s coastal ocean. Thus, both wetland ecosystems contribute disproportionately to carbon flow of the global coastal ocean.

Discerning natural and anthropogenic organic matter inputs to salt marsh sediments of Ria Formosa lagoon (South Portugal)

Sedimentary organic matter (OM) origin and molecular composition provide useful information to understand carbon cycling in coastal wetlands. Core sediments from threors' Contributionse transects along Ria Formosa lagoon intertidal zone were analysed using analytical pyrolysis (Py-GC/MS) to determine composition, distribution and origin of sedimentary OM. The distribution of alkyl compounds (alkanes, alkanoic acids and alkan-2-ones), polycyclic aromatic hydrocarbons (PAHs), lignin-derived methoxyphenols, linear alkylbenzenes (LABs), steranes and hopanes indicated OM inputs to the intertidal environment from natural-autochthonous and allochthonous-as well as anthropogenic. Several n-alkane geochemical indices used to assess the distribution of main OM sources (terrestrial and marine) in the sediments indicate that algal and aquatic macrophyte derived OM inputs dominated over terrigenous plant sources. The lignin-derived methoxyphenol assemblage, dominated by vinylguaiacol and vinylsyringol derivatives in all sediments, points to large OM contribution from higher plants. The spatial distributions of PAHs (polyaromatic hydrocarbons) showed that most pollution sources were mixed sources including both pyrogenic and petrogenic. Low carbon preference indexes (CPI > 1) for n-alkanes, the presence of UCM (unresolved complex mixture) and the distribution of hopanes (C₂₉-C₃₆) and steranes (C₂₇-C₂₉) suggested localized petroleum-derived hydrocarbon inputs to the core sediments. Series of LABs were found in most sediment samples also pointing to domestic sewage anthropogenic contributions to the sediment OM.