Sulfide Intrusion and Detoxification in the Seagrass Zostera marina

Sulfide intrusion of seagrass Thalassia hemprichii along a eutrophication gradient with carbonate and terrigenous sediments in tropical coastal sea

Seagrasses growing in different eutrophic states in carbonate and terrigenous sediments may exhibit contrasting sulfide intrusion and responses; however, limited information is available. In this study, sulfide intrusion in the tropical typical seagrass Thalassia hemprichii along a eutrophication gradient in carbonate and terrigenous sediments on Hainan Island, South China Sea, was investigated using combined elements, stable isotopes, and photobiology. The sediment porewater sulfide concentration increased with rising nutrient levels, with porewater sulfide as 223.92 ± 25.34 μmol/L when the dissolved inorganic nitrogen concentration was 10.83 ± 0.60 μmol/L and the dissolved inorganic phosphate concentration was 0.39 ± 0.01 μmol/L. The nutrient input significantly enhanced sulfide intrusion in seagrass, resulting in reduced δ34S values in roots from 12.78 ± 1.16 to 2.69 ± 0.46 ‰, with leaf δ15N as the greatest explanatory factor. In addition, sulfide intrusion inhibited photosynthesis more strongly in seagrass growing in carbonate sediments than in terrigenous sediments because of the low iron content in carbonate sediments (almost 50 % of the iron content in terrigenous sediments), reducing rETRmax and Ek by 43.08 % and 36.42 %, respectively. Therefore, the synergistic effects of nutrient input, sulfide concentration, sediment substrate, and iron content affected the sulfide intrusion in seagrass.

Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success

Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.

More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics

We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.

Pillucina vietnamica influence on mitigating nutrients stress in tropical seagrass Thalassia hemprichii

Anthropogenic eutrophication threatens to seagrass ecosystems particularly by increasing sulfide toxicity. This study aimed to investigate whether seagrass-lucinid mutualism can decrease the negative effects of nutrients on seagrass Thalassia hemprichii in tropical coastal ecosystems. A 6-week manipulative field experiment was conducted to explore the effects of nutrient and Pillucina vietnamica addition to sediments on morphological and physiological characteristics of T. hemprichii as well as on microbial communities in sediments. Our results showed that nutrient addition caused serious sulfide accumulation, enhanced sedimental sulfur-oxidizing bacteria abundance. P. vietnamica significantly increased leaf length and width, root length and diameter, shoot number, underground tissues C content of seagrasses. The presence of P. vietnamica significantly decreased the negative effects of nutrients by decreasing sulfide concentration of porewater, improving the communities of Actinobacteriota, Bacteroidota and Firmicutes, and increasing root diameter of T. hemprichii. Our results indicated that nutrients negatively affected seagrass T. hemprichii, while seagrass-lucinid mutualism can mitigate nutrients stress. Monitoring seagrasses, lucinid and microorganisms can be used as a potential management tool to evaluate the healthy status of seagrass ecosystems, provide the crucial basis for threatened seagrasses conservation and management in tropical coastal eutrophicated ecosystems with global climate change.

The methylome of clonal seagrass shoots shows age-associated variation and differentiation of roots from other tissues

Factors influencing variance of DNA methylation in vegetatively reproducing plants, both terrestrial plants and aquatic seagrasses, is just beginning to be understood. Improving our knowledge of these mechanisms will increase understanding of transgenerational epigenetics in plant clones, of the relationship between DNA methylation and seagrass development, and of the drivers of epigenetic variation, which may underly acclimation in clonally reproducing plants. Here, we sampled leaves, rhizomes and roots of three physically and spatially separated ramet sections from a clonally propagated field of the seagrass Zostera marina. Using reduced methylome sequencing, we studied variations in the methylome of seagrass Zostera marina between the sampled tissue types and across age groups. Our analysis of ramets of different ages showed variations in methylation between older and younger samples in both specific methylation patterns and global methylation levels. Our analysis of tissue types showed a marked differentiation of the roots from the rhizomes and leaves, which showed more similar methylation patterns. These findings are in agreement with the strong connection of DNA methylation and plant development and tissue differentiation. We also suggest an effect of differential environmental exposures on the methylome of the younger versus the older ramets due to the forming of molecular stress memories.

Flavonoids and anthocyanins in seagrasses: implications for climate change adaptation and resilience

Seagrasses are a paraphyletic group of marine angiosperms and retain certain adaptations from the ancestors of all embryophytes in the transition to terrestrial environments. Among these adaptations is the production of flavonoids, versatile phenylpropanoid secondary metabolites that participate in a variety of stress responses. Certain features, such as catalytic promiscuity and metabolon interactions, allow flavonoid metabolism to expand to produce novel compounds and respond to a variety of stimuli. As marine environments expose seagrasses to a unique set of stresses, these plants display interesting flavonoid profiles, the functions of which are often not completely clear. Flavonoids will likely prove to be effective and versatile agents in combating the new host of stress conditions introduced to marine environments by anthropogenic climate change, which affects marine environments differently from terrestrial ones. These new stresses include increased sulfate levels, changes in salt concentration, changes in herbivore distributions, and ocean acidification, which all involve flavonoids as stress response mechanisms, though the role of flavonoids in combatting these climate change stresses is seldom discussed directly in the literature. Flavonoids can also be used to assess the health of seagrass meadows through an interplay between flavonoid and simple phenolic levels, which may prove to be useful in monitoring the response of seagrasses to climate change. Studies focusing on the genetics of flavonoid metabolism are limited for this group, but the large chalcone synthase gene families in some species may provide an interesting topic of research. Anthocyanins are typically studied separately from other flavonoids. The phenomenon of reddening in certain seagrass species typically focuses on the importance of anthocyanins as a UV-screening mechanism, while the role of anthocyanins in cold stress is discussed less often. Both of these stress response functions would be useful for adaptation to climate change-induced deviations in tidal patterns and emersion. However, ocean warming will likely lead to a decrease in anthocyanin content, which may impact the performance of intertidal seagrasses. This review highlights the importance of flavonoids in angiosperm stress response and adaptation, examines research on flavonoids in seagrasses, and hypothesizes on the importance of flavonoids in these organisms under climate change.

Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses

Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE

Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.

Insights into response of seagrass (Zostera marina) to sulfide exposure at morphological, physiochemical and molecular levels in context of coastal eutrophication and warming

Sulfide in sediment porewaters, is toxic to rooted macrophytes in both marine and freshwater environments. Current research on sulfide stress in seagrasses primarily focuses on morphological and physiological aspects, with little known about the molecular response and resistance mechanisms. This study first investigated the damage caused by sulfide to eelgrass (Zostera marina L.) using transcriptomic, metabolomic, and other physiological and biochemical indicators and explored the potential resistance of eelgrass at molecular level through laboratory simulated and in-situ sulfide stress experiments. Comprehensive results showed that sulfide stress severely inhibited the growth, photosynthesis, and antioxidant enzyme activities of eelgrass. Importantly, transcriptome analysis revealed significant activation of pathways related to carbohydrate and sulfur metabolism. This activation served a dual purpose: providing an energy source for eelgrass stress response and achieving detoxification through accelerated sulfur metabolism-a potential resistance mechanism. The toxicity of sulfide increased with rising temperature as evidenced by a decrease in EC50. Results from recovery experiments indicated that when Fv/Fm reduced to about 0 under sulfide stress, the growth and photosynthesis of eelgrass recovered to normal level after timely removal of sulfide. However, prolonged exposure to sulfide resulted in failure to recover, leading ultimately to plant death. This study not only enhances our understanding of the molecular-level impacts of sulfide on seagrasses but also provides guidance for the management and ecological restoration of seagrass meadows under sulfide stress.

The metabolic network response and tolerance mechanism of Thalassia hemprichii under high sulfide based on widely targeted metabolome and transcriptome

Costal eutrophication leads to increased sulfide levels in sediments, which has been identified as a major cause of the global decline in seagrass beds. The seagrass Thalassia hemprichii, a dominant tropical species in the Indo-Pacific, is facing a potential threat from sulfide, which can be easily reduced from sulfate in porewater under the influence of global climate change and eutrophication. However, its metabolic response and tolerance mechanisms to high sulfide remain unclear. Thus, the current study investigated the physiological responses and programmed metabolic networks of T. hemprichii through a three-week mesocosm experiment, integrating physiology, stable isotope, widely targeted metabolomics, transcriptomics, and microbial diversity assessments. High sulfide reduced the sediment microbial diversity, while increased sediment sulfate reduced bacterial abundance and δ34S. The exposure to sulfide enhanced root δ34S while decreased leaf δ34S in T. hemprichii. High sulfide was shown to inhibit photosynthesis via damaging PSII, which further reduced ATP production. In response, abundant up-regulated differentially expressed genes in energy metabolism, especially in oxidative phosphorylation, were activated to compensate high energy requirement. High sulfide also promoted autophagy by overexpressing the genes related to phagocytosis and phagolysosome. Meanwhile, metabolomic profiling revealed that the contents of many primary metabolites, such as carbohydrates and amino acids, were reduced in both leaves and roots, likely to provide more energy and synthesize stress-responsive secondary metabolites. Genes related to nitrate reduction and transportation were up-regulated to promote N uptake for sulfide detoxification. High sulfide levels specifically enhanced thiamine in roots, while increased jasmonic acid and flavonoid levels in leaves. The distinct differences in metabolism between roots and leaves might be related to sulfide levels and the growth-defense trade-off. Collectively, our work highlights the specific mechanisms underlying the response and tolerance of T. hemprichii to high sulfide, providing new insights into seagrass strategies for resisting sulfide.

Seagrass-Associated Biodiversity Influences Organic Carbon in a Temperate Meadow

There is increasing interest in the role that seagrasses play in storing carbon in the context of climate mitigation, but many knowledge gaps in the factors controlling this storage exist. Here, we provide a small case study that examines the role of infaunal biodiversity in influencing seagrass and the carbon stored in its sediments. A total of 25 species of invertebrate were recorded in an intertidal Zostera marina meadow, where these species were dominated by polychaete worms with no bivalves present. We find organic carbon storage (within the top 20 cm) measured by AFDW to be highly variable within a small area of seagrass meadow ranging from 2961 gC.m−2 to 11,620 gC.m−2 with an average (±sd) of 64602 ± 3274 gC.m−2. Our analysis indicates that infaunal communities are significantly and negatively correlated with this sediment organic carbon. However, this effect is not as influential as hypothesised, and the relatively small sample size of the present study limits its ability to provide strong causality. Other factors, such as algal abundance, curiously had a potentially stronger influence on the carbon in the upper sediments. The increasing richness of infauna is likely reducing the build-up of organic carbon, reducing its ecosystem service role. We believe this to likely be the result of bioturbation by specific species such as Arenicola marina and Ampharete acutifrons. A change in sediment organic carbon suggests that these species could be key drivers of bioturbator-initiated redox-driven organic matter turnovers, influencing the microbial processes and remobilizing sediment compounds. Bioturbators should be considered as a limitation to Corg storage when managing seagrass Corg stocks; however, bioturbation is a natural process that can be moderated when an ecosystem is less influenced by anthropogenic change. The present study only provides small-scale correlative evidence with a range of surprising results; confirming these results within temperate seagrasses requires examining this process at large spatial scales or with targeted experiments.

Impact of persistently high sea surface temperatures on the rhizobiomes of Zostera marina in a Baltic Sea benthocosms

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass-microorganism interactions is needed to leverage knowledge on host-microbe interactions in seagrasses.

Detrimental impact of sulfide on the seagrass Zostera marina in dark hypoxia

Sulfide poisoning, hypoxia events, and reduced light availability pose threats to marine ecosystems such as seagrass meadows. These threats are projected to intensify globally, largely due to accelerating eutrophication of estuaries and coastal environments. Despite the urgency, our current comprehension of the metabolic pathways that underlie the deleterious effects of sulfide toxicity and hypoxia on seagrasses remains inadequate. To address this knowledge gap, I conducted metabolomic analyses to investigate the impact of sulfide poisoning under dark-hypoxia in vitro conditions on Zostera marina, a vital habitat-forming marine plant. During the initial 45 minutes of dark-hypoxia exposure, I detected an acclimation phase characterized by the activation of anaerobic metabolic pathways and specific biochemical routes that mitigated hypoxia and sulfide toxicity. These pathways served to offset energy imbalances, cytosolic acidosis, and sulfide toxicity. Notably, one such route facilitated the transformation of toxic sulfide into non-toxic organic sulfur compounds, including cysteine and glutathione. However, this sulfide tolerance mechanism exhibited exhaustion post the initial 45-minute acclimation phase. Consequently, after 60 minutes of continuous sulfide exposure, the sulfide toxicity began to inhibit the hypoxia-mitigating pathways, culminating in leaf senescence and tissue degradation. Utilizing metabolomic approaches, I elucidated the intricate metabolic responses of seagrasses to sulfide toxicity under in vitro dark-hypoxic conditions. My findings suggest that future increases in coastal eutrophication will compromise the resilience of seagrass ecosystems to hypoxia, primarily due to the exacerbating influence of sulfide.

Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments

Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope (³⁴S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.

Defense System of the Manila Clam Ruditapes philippinarum under High-Temperature and Hydrogen Sulfide Conditions

Hydrogen sulfide (H₂S) acts as an environmental toxin. Despite its toxicity, little is known about the defense strategies of marine bivalves against it. Thus, the tolerance, behavioral characteristics, and physiological response strategies against H₂S treatment in the sentinel organism Manila clam Ruditapes philippinarum were examined. We monitored the survival and behavioral status of Manila clams exposed to different combinations of temperature and H₂S. The physiological response strategies were examined by measuring the enzymatic activity of cytochrome C oxidase (CCO), fumarate reductase (FRD), superoxide dismutase (SOD), and catalase enzymes (CAT). Moreover, adverse effects of H₂S on the tissue and cell structure of Manila clams were also examined under a transmission electron microscope. Manila clams responded to H₂S stress through behavioral and chemical defenses. With exposure to H₂S alone, Manila clams primarily enhanced aerobic respiratory metabolic pathways in the beginning stages by opening the shell and increasing the CCO activity to obtain more oxygen; with increasing exposure time, when aerobic respiration was inhibited, the shell was closed, and FRD, CAT, and SOD were activated. At this point, Manila clams responded to H₂S stress through the anaerobic metabolism and antioxidant defense systems. However, high temperatures (≥28 °C) altered the defense strategy of Manila clams. With co-exposure to high temperatures and high H₂S concentrations (≥20 μmol/L), the Manila clams immediately closed their shells and changed from aerobic respiration to anaerobic metabolism while immediately activating antioxidant defense systems. Nevertheless, this defense strategy was short lived. In addition to this, apparent damage to tissue and cell structures, including mitochondrial ridge dissolution and many vacuoles, was observed in Manila clams exposed to high temperatures and high H₂S concentrations. Thus, prolonged exposure to high temperature and H₂S damages the tissue structure of Manila clams, affecting their behavioral capacity and future survival. In summary, profiling Manila clams' physiological response strategies to H₂S exposure provided ecological behavioral support for our current understanding of H₂S detrimental toxicity on marine bivalves.

Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient

Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO₂ conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.

Sand supplementation favors tropical seagrass Thalassia hemprichii in eutrophic bay: implications for seagrass restoration and management

BACKGROUND

Sediment is crucial for the unique marine angiosperm seagrass growth and successful restoration. Sediment modification induced by eutrophication also exacerbates seagrass decline and reduces plantation and transplantation survival rates. However, we lack information regarding the influence of sediment on seagrass photosynthesis and the metabolics, especially regarding the key secondary metabolic flavone. Meanwhile, sulfation of flavonoids in seagrass may mitigate sulfide intrusion, but limited evidence is available.

RESULTS

We cultured the seagrass Thalassia hemprichii under controlled laboratory conditions in three sediment types by combining different ratios of in-situ eutrophic sediment and coarse beach sand. We examined the effects of beach sand mixed with natural eutrophic sediments on seagrass using photobiology, metabolomics and isotope labelling approaches. Seagrasses grown in eutrophic sediments mixed with beach sand exhibited significantly higher photosynthetic activity, with a larger relative maximum electron transport rate and minimum saturating irradiance. Simultaneously, considerably greater belowground amino acid and flavonoid concentrations were observed to counteract anoxic stress in eutrophic sediments without mixed beach sand. This led to more positive belowground stable sulfur isotope ratios in eutrophic sediments with a lower Eh.

CONCLUSIONS

These results indicated that coarse beach sand indirectly enhanced photosynthesis in T. hemprichii by reducing sulfide intrusion with lower amino acid and flavonoid concentrations. This could explain why T. hemprichii often grows better on coarse sand substrates. Therefore, it is imperative to consider adding beach sand to sediments to improve the environmental conditions for seagrass and restore seagrass in eutrophic ecosystems.

An assessment of hydrogen sulfide intrusion in the seagrass Halodule wrightii

Hydrogen sulfide (H2S, “sulfide”) is a naturally occurring component of the marine sediment. Eutrophication of coastal waters, however, can lead to an excess of sulfide production that can prove toxic to seagrasses. We used stable sulfur isotope ratio (δ34S) measurements to assess sulfide intrusion in the seagrass Halodule wrightii, a semi-tropical species found throughout the Gulf of Mexico, Caribbean Sea, and both western and eastern Atlantic coasts. We found a gradient in δ34S values (−5.58 ± 0.54‰+13.58 ± 0.30‰) from roots to leaves, in accordance with prior observations and those from other species. The results may also represent the first values reported for H. wrightii rhizome tissue. The presence of sulfide-derived sulfur in varying proportions (15–55%) among leaf, rhizome, and root tissues suggests H. wrightii is able to assimilate sedimentary H2S into non-toxic forms that constitute a significant portion of the plant’s total sulfur content.

Calcification-driven CO2 emissions exceed "Blue Carbon" sequestration in a carbonate seagrass meadow

Long-term “Blue Carbon” burial in seagrass meadows is complicated by other carbon and alkalinity exchanges that shape net carbon sequestration. We measured a suite of such processes, including denitrification, sulfur, and inorganic carbon cycling, and assessed their impact on air-water CO₂ exchange in a typical seagrass meadow underlain by carbonate sediments. Eddy covariance measurements reveal a consistent source of CO₂ to the atmosphere at an average rate of 610 ± 990 μmol m⁻² hour⁻¹ during our study and 700 ± 660 μmol m⁻² hour⁻¹ (6.1 mol m⁻² year⁻¹) over an annual cycle. Net alkalinity consumption by ecosystem calcification explains >95% of the observed CO₂ emissions, far exceeding organic carbon burial and anaerobic alkalinity generation. We argue that the net carbon sequestration potential of seagrass meadows may be overestimated if calcification-induced CO₂ emissions are not accounted for, especially in regions where calcification rates exceed net primary production and burial.

Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution

The global seagrass bed ecosystem acts as a natural ecological barrier in the littoral coastal zone. In recent years, this ecosystem has suffered from serious eutrophication and destruction caused by the continuous expansion of aquaculture. However, our understanding of the influence of aquaculture on the bacterial community remains limited. In this study, we used 16S amplicon sequencing to evaluate the impact of aquaculture feed extract solution on the composition and function of bacterial epiphytes and endophyte communities of the core seagrass from the seagrass bed ecosystem in Hainan, Thalassia hemprichii. The feed extract solution was the main factor that significantly affected the bacterial epiphyte and endophyte community structure of seagrass leaves but had no marked effect on alpha diversity was observed. Additionally, the bacterial epiphyte and endophyte community of the T. hemprichii leaves alleviated the effects of organic matter, sulfide, and nutrients caused by aquaculture wastewater. The feed extract solution promoted the proliferation of Bacteroidales, Vibrio, Desulfobulbaceae, Desulfobacteraceae, Pseudoalteromonas, Paludibacter, Marinomonas, and Pseudomonas in the leaves and root of T. hemprichii, which can effectively improve the digestibility of eutrophication. In fact, Desulfobacteraceae and Desulfobulbaceae can reduce sulfate to sulfide and oxidize sulfide to sulfur within seagrass, indicating that the increase in Desulfobulbaceae and Desulfobacteraceae facilitated the accumulation of sulfide with the treatment of feed extract solution, which may be the reason for the degradation of seagrass caused by aquaculture wastewater containing high concentrations of organic pollutants. These results suggest that although seagrass beds can withstand low concentrations of aquaculture pollutants, sulfide emissions should be minimized.

Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan

Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.

Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes

Seagrasses are vital coastal ecosystem engineers, which are mutualistically associated with microbial communities that contribute to the ecosystem services provided by meadows. The seagrass microbiome and sediment microbiota play vital roles in belowground biogeochemical and carbon cycling. These activities are influenced by nutrient, carbon and oxygen availability, all of which are modulated by environmental factors and plant physiology. Seagrass meadows are increasingly threatened by nutrient pollution, and it is unknown how the seagrass microbiome will respond to this stressor. We investigated the effects of fertilization on the physiology, morphology and microbiome of eelgrass (Zostera marina) cultivated over 4 weeks in mesocosms. We analyzed the community structure associated with eelgrass leaf, root and rhizosphere microbiomes, and of communities from water column and bulk sediment using 16S rRNA amplicon sequencing. Fertilization led to a higher number of leaves compared with that of eelgrass kept under ambient conditions. Additionally, fertilization led to enrichment of sulfur and nitrogen bacteria in belowground communities. These results suggest nutrient enrichment can stimulate belowground biogeochemical cycling, potentially exacerbating sulfide toxicity in sediments and decreasing future carbon sequestration stocks.

Imaging O2 dynamics and microenvironments in the seagrass leaf phyllosphere with magnetic optical sensor nanoparticles

Eutrophication leads to epiphyte blooms on seagrass leaves that strongly affect plant health, yet the actual mechanisms of such epiphyte-induced plant stress remain poorly understood. We used magnetic optical sensor nanoparticles in combination with luminescence lifetime imaging to map the O₂ concentration and dynamics in the heterogeneous seagrass phyllosphere under changing light conditions. By incorporating magnetite into the sensor nanoparticles, it was possible to image the spatial O₂ distribution under flow over seagrass leaf segments in the presence of a strong magnetic field. Local microniches with low leaf surface O₂ concentrations were found under thick epiphytic biofilms, often leading to anoxic microhabitats in darkness. High irradiance led to O₂ supersaturation across most of the seagrass phyllosphere, whereas leaf microenvironments with reduced O₂ conditions were found under epiphytic biofilms at low irradiance, probably driven by self-shading. Horizontal micro-profiles extracted from the O₂ images revealed pronounced heterogeneities in local O₂ concentration over the base of the epiphytic biofilm, with up to 52% reduction in O₂ concentrations in areas with relatively thick (>2 mm), compared with thin (≤1 mm), epiphyte layers in darkness. We also present evidence of enhanced relative internal O₂ transport within leaves with epiphyte overgrowth, compared with bare seagrass leaves, in light as a result of limited mass transfer across thick outward diffusion pathways. The local availability of O₂ was still markedly reduced in the epiphyte-covered leaves, however. The leaf phyllosphere is thus characterized by a complex microlandscape of O₂ availability that strongly affects microbial processes occurring within the epiphytic biofilm, which may have implications for seagrass health, as anoxic microhabitats have been shown to promote the microbiological production of reduced toxic compounds, such as nitric oxide.

Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host these sulphur-oxidising Ca. Thiodiazotropha that could aid their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidising Ca. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescence in situ hybridisation to visually confirm the presence of Ca. Thiodiazotropha on roots of Halophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence that Ca. Thiodiazotropha are commonly present on seagrass roots, providing another mechanism for seagrasses to alleviate sulphide stress globally.

Root microbiomes as indicators of seagrass health

The development of early warning indicators that identify ecosystem stress is a priority for improving ecosystem management. As microbial communities respond rapidly to environmental disturbance, monitoring their composition could prove one such early indicator of environmental stress. We combined 16S rRNA gene sequencing of the seagrass root microbiome of Halophila ovalis with seagrass health metrics (biomass, productivity and Fsulphide) to develop microbial indicators for seagrass condition across the Swan-Canning Estuary and the Leschenault Estuary (south-west Western Australia); the former had experienced an unseasonal rainfall event leading to declines in seagrass health. Microbial indicators detected sites of potential stress that other seagrass health metrics failed to detect. Genera that were more abundant in 'healthy' seagrasses included putative methylotrophic bacteria (e.g. Methylotenera and Methylophaga), iron cycling bacteria (e.g. Deferrisoma and Geothermobacter) and N2 fixing bacteria (e.g. Rhizobium). Conversely, genera that were more abundant in 'stressed' seagrasses were dominated by putative sulphur-cycling bacteria, both sulphide-oxidising (e.g. Candidatus Thiodiazotropha and Candidatus Electrothrix) and sulphate-reducing (e.g. SEEP-SRB1, Desulfomonile and Desulfonema). The sensitivity of the microbial indicators developed here highlights their potential to be further developed for use in adaptive seagrass management, and emphasises their capacity to be effective early warning indicators of stress.

Ecological risk assessment of trace metals and comprehensive contamination indicators in the coastal waters of Macao, South China Sea

Few systematic and scientific assessments have been conducted on marine environmental quality in the coastal waters of Macao, a major city in the Pearl River Delta, China. In this study, we investigated the spatial distribution of trace metals (TMs) and comprehensive contamination indicators of marine water in Macao and evaluated their ecological risks. The total amount of typical TMs (∑TMs) in surface water ranged from 2.71 μg/L to 201 μg/L. ∑TMs (Hg, As, and Cd) in sediments ranged from 0.34 mg/kg to 54.8 mg/kg. TM contamination in surface water was influenced by spatial position and tidal current direction. The spatial distribution and correlation analysis of TMs and comprehensive contamination indicators were assessed, and ecological risk assessment indicated that the surface water and sediments in coastal waters of Macao are of relatively good quality, although high sulfide levels could be detected in surface water.

Ecosystem engineering creates a new path to resilience in plants with contrasting growth strategies

Plant species can be characterized by different growth strategies related to their inherent growth and recovery rates, which shape their responses to stress and disturbance. Ecosystem engineering, however, offers an alternative way to cope with stress: modifying the environment may reduce stress levels. Using an experimental study on two seagrass species with contrasting traits, the slow-growing Zostera marina vs. the fast-growing Zostera japonica, we explored how growth strategies versus ecosystem engineering may affect their resistance to stress (i.e. addition of organic material) and recovery from disturbance (i.e. removal of above-ground biomass). Ecosystem engineering was assessed by measuring sulphide levels in the sediment porewater, as seagrass plants can keep sulphide levels low by aerating the rhizosphere. Consistent with predictions, we observed that the fast-growing species had a high capacity to recover from disturbance. It was also more resistant to stress and still able to maintain high standing stock with increasing stress levels because of its ecosystem engineering capacity. The slow-growing species was not able to maintain its standing stock under stress, which we ascribe to a weak capacity for ecosystem engineering regarding this particular stress. Overall, our study suggests that the combination of low-cost investment in tissues with ecosystem engineering to alleviate stress creates a new path in the growth trade-off between investment in strong tissues or fast growth. It does so by being both fast in recovery and more resistant. As such low-cost ecosystem engineering may occur in more species, we argue that it should be considered in assessing plant resilience.

Interactive effects of global warming and eutrophication on a fast-growing Mediterranean seagrass

Coastal ecosystems, such as seagrasses, are subjected to local (e.g. eutrophication) and global (e.g. warming) stressors. While the separate effects of warming and eutrophication on seagrasses are relatively well known, their joint effects remain largely unstudied. In order to fill this gap, and using Cymodocea nodosa as a model species, we assessed the joint effects of warming (three temperatures, 20 °C, 30 °C and 35 °C) with two potential outcomes of eutrophication: (i) increase in nutrients concentration in the water column (30 and 300 μM), and (ii) organic enrichment in the sediment). Our results confirm that temperature in isolation clearly affects plant performance; while plants exposed to 30 °C performed better than control plants, plants exposed to 35 °C showed clear symptoms of deterioration (e.g. decline of photosynthetic capacity, increase of incidence of necrotic tissue). Plants were unaffected by high ammonium concentrations; however, organic enrichment of sediment had deleterious effects on plant function (photosynthesis, growth, demographic balance). Interestingly, these negative effects were exacerbated by increased temperature. Our findings indicate that in addition to the possibility of the persistence of C. nodosa being directly jeopardized by temperature increase, the joint effects of warming and eutrophication may further curtail its survival. This should be taken into consideration in both predictions of climate change consequences and in local planning.

The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites

Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassiatestudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.

Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan

Nitrous oxide (N₂O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N₂O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N₂O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N₂O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N₂O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N₂O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N₂O only. Collectively, these results suggest that the N₂O-reducing microbiome in eelgrass meadows is largely responsible for coastal N₂O mitigation.

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea

Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.

Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada

Eelgrass (Zostera marina) has been designated an Ecologically Significant Species in Atlantic Canada. The development and rapid expansion of netpen finfish aquaculture into sensitive coastal habitats has raised concerns about the impacts of finfish aquaculture on eelgrass habitats. To date, no studies have been done in Atlantic Canada to examine these impacts or to identify potential monitoring variables that would aid in the development of specific conservation and management objectives. As a first step in addressing this gap, we examined differences in environmental variables, eelgrass bed structure and macroinfauna communities at increasing distances from a finfish farm in Port Mouton Bay, a reference site in adjacent Port Joli Bay, and published survey results from other sites without finfish farms along the Atlantic Coast of Nova Scotia. Drawing on research done elsewhere and our results, we then identified possible metrics for assessing and monitoring local impacts of finfish aquaculture on eelgrass habitats. Our results suggest some nutrient and organic enrichment, higher epiphyte loads, lower eelgrass cover and biomass, and lower macroinfauna biomass closer to the farm. Moreover, community structure significantly differed between sites with some species increasing and others decreasing closer to the farm. Changes in the macroinfauna community could be linked to observed differences in environmental and eelgrass bed variables. These results provide new insights into the potential impacts of finfish aquaculture on eelgrass habitats in Atlantic Canada. We recommend a suite of measures for assessment and monitoring that take into account response time to disturbance and account for different levels of eelgrass organizational response (from physiological to community).

Shading and simulated grazing increase the sulphide pool and methane emission in a tropical seagrass meadow

Though seagrass meadows are among the most productive habitats in the world, contributing substantially to long-term carbon storage, studies of the effects of critical disturbances on the fate of carbon sequestered in the sediment and biomass of these meadows are scarce. In a manipulative in situ experiment, we studied the effects of successive loss of seagrass biomass as a result of shading and simulated grazing at two intensity levels on sulphide (H₂S) content and methane (CH₄) emission in a tropical seagrass meadow in Zanzibar (Tanzania). In all disturbed treatments, we found a several-fold increase in both the sulphide concentration of the sediment pore-water and the methane emissions from the sediment surface (except for CH₄ emissions in the low-shading treatment). This could be due to the ongoing degradation of belowground biomass shed by the seagrass plants, supporting the production of both sulphate-reducing bacteria and methanogens, possibly exacerbated by the loss of downwards oxygen transport via seagrass plants. The worldwide rapid loss of seagrass areas due to anthropogenic activities may therefore have significant effects on carbon sink-source relationships within coastal seas.

Seagrass leaf element content: A global overview

Knowledge on the role of seagrass leaf elements and in particular micronutrients and their ranges is limited. We present a global database, consisting of 1126 unique leaf values for ten elements, obtained from literature and unpublished data, spanning 25 different seagrass species from 28 countries. The overall order of average element values in seagrass leaves was Na>K>Ca>Mg>S>Fe>Al>Si>Mn>Zn. Although we observed differences in leaf element content between seagrass families, high intraspecific variation indicated that leaf element content was more strongly determined by environmental factors than by evolutionary history. Early successional species had high leaf Al and Fe content. In addition, seagrass leaf element content also showed correlations with macronutrients (N and P), indicating that productivity also depends on other elements. Expected genomes of additional seagrass species in combination with experiments manipulating (micro)nutrients and environmental drivers might enable us to unravel the importance of various elements to sustain productive and flourishing meadows.

Losing a winner: thermal stress and local pressures outweigh the positive effects of ocean acidification for tropical seagrasses

Seagrasses are globally important coastal habitat-forming species, yet it is unknown how seagrasses respond to the combined pressures of ocean acidification and warming of sea surface temperature. We exposed three tropical species of seagrass (Cymodocea serrulata, Halodule uninervis, and Zostera muelleri) to increasing temperature (21, 25, 30, and 35°C) and pCO₂ (401, 1014, and 1949 μatm) for 7 wk in mesocosms using a controlled factorial design. Shoot density and leaf extension rates were recorded, and plant productivity and respiration were measured at increasing light levels (photosynthesis-irradiance curves) using oxygen optodes. Shoot density, growth, photosynthetic rates, and plant-scale net productivity occurred at 25°C or 30°C under saturating light levels. High pCO₂ enhanced maximum net productivity for Z. muelleri, but not in other species. Z. muelleri was the most thermally tolerant as it maintained positive net production to 35°C, yet for the other species there was a sharp decline in productivity, growth, and shoot density at 35°C, which was exacerbated by pCO₂ . These results suggest that thermal stress will not be offset by ocean acidification during future extreme heat events and challenges the current hypothesis that tropical seagrass will be a 'winner' under future climate change conditions.

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe-plant mutualisms support the health and growth of aquatic plants.

Species-specific response to sulfide intrusion in native and exotic Mediterranean seagrasses under stress

We explored the sulfur dynamics and the relationships between sediment sulfur and nutrient pools, seagrass structural and physiological variables and sulfide intrusion in native (Posidonia oceanica, Cymodocea nodosa) and exotic (Halophila stipulacea) Mediterranean seagrasses at six sites affected by cumulative anthropogenic pressures to understand the factors controlling sulfide intrusion in seagrass. Sensitive indicators of seagrass stress (leaf TN, δ¹⁵N, TS, F_sulfide) were increased at several sites, implying that seagrasses are under pressure. Sulfide intrusion was not related to sediment TOC but it was negatively related to shoot size and below-ground biomass. Sulfide intrusion in seagrass tissue was high in P. oceanica (12-17%) and considerably higher in C. nodosa (27-35%). Intrusion was particularly high in H. stipulacea (30-50%), suggesting that its possible biogeographical expansion due to warming of the Mediterranean may result in accumulation of sulfides in the sediments and hypoxia/anoxia with further implications in ecosystem function.

The Seagrass Holobiont and Its Microbiome

Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H₂S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome.

Toxicity of sulfide to early life stages of wild rice (Zizania palustris)

The sensitivity of wild rice (Zizania palustris) to sulfide is not well understood. Because sulfate in surface waters is reduced to sulfide by anaerobic bacteria in sediments and historical information indicated that 10 mg/L sulfate in Minnesota (USA) surface water reduced Z. palustris abundance, the Minnesota Pollution Control Agency established 10 mg/L sulfate as a water quality criterion in 1973. A 21-d daily-renewal hydroponic study was conducted to evaluate sulfide toxicity to wild rice and the potential mitigation of sulfide toxicity by iron (Fe). The hydroponic design used hypoxic test media for seed and root exposure and aerobic headspace for the vegetative portion of the plant. Test concentrations were 0.3, 1.6, 3.1, 7.8, and 12.5 mg/L sulfide in test media with 0.8, 2.8, and 10.8 mg/L total Fe used to evaluate the impact of iron on sulfide toxicity. Visual assessments (i.e., no plants harvested) of seed activation, mesocotyl emergence, seedling survival, and phytoxicity were conducted 10 d after dark-phase exposure. Each treatment was also evaluated for time to 30% emergence (ET30), total plant biomass, root and shoot lengths, and signs of phytotoxicity at study conclusion (21 d). The results indicate that exposure of developing wild rice to sulfide at ≥3.1 mg sulfide/L in the presence of 0.8 mg/L Fe reduced mesocotyl emergence. Sulfide toxicity was mitigated by the addition of Fe at 2.8 mg/L and 10.8 mg/L relative to the control value of 0.8 mg Fe/L, demonstrating the importance of iron in mitigating sulfide toxicity to wild rice. Ultimately, determination of site-specific sulfate criteria taking into account factors that alter toxicity, including sediment Fe and organic carbon, are necessary. Environ Toxicol Chem 2017;36:2217-2226. © 2017 SETAC.

Global-Scale Structure of the Eelgrass Microbiome

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments.

IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina, or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host.

Sediment Resuspension and Deposition on Seagrass Leaves Impedes Internal Plant Aeration and Promotes Phytotoxic H2S Intrusion

HIGHLIGHTS: Sedimentation of fine sediment particles onto seagrass leaves severely hampers the plants' performance in both light and darkness, due to inadequate internal plant aeration and intrusion of phytotoxic H₂S. Anthropogenic activities leading to sediment re-suspension can have adverse effects on adjacent seagrass meadows, owing to reduced light availability and the settling of suspended particles onto seagrass leaves potentially impeding gas exchange with the surrounding water. We used microsensors to determine O₂ fluxes and diffusive boundary layer (DBL) thickness on leaves of the seagrass Zostera muelleri with and without fine sediment particles, and combined these laboratory measurements with in situ microsensor measurements of tissue O₂ and H₂S concentrations. Net photosynthesis rates in leaves with fine sediment particles were down to ~20% of controls without particles, and the compensation photon irradiance increased from a span of 20-53 to 109-145 μmol photons m^-2 s^-1. An ~2.5-fold thicker DBL around leaves with fine sediment particles impeded O₂ influx into the leaves during darkness. In situ leaf meristematic O₂ concentrations of plants exposed to fine sediment particles were lower than in control plants and exhibited long time periods of complete meristematic anoxia during night-time. Insufficient internal aeration resulted in H₂S intrusion into the leaf meristematic tissues when exposed to sediment resuspension even at relatively high night-time water-column O₂ concentrations. Fine sediment particles that settle on seagrass leaves thus negatively affect internal tissue aeration and thereby the plants' resilience against H₂S intrusion.

Metabolomics Reveals Cryptic Interactive Effects of Species Interactions and Environmental Stress on Nitrogen and Sulfur Metabolism in Seagrass

Eutrophication of estuaries and coastal seas is accelerating, increasing light stress on subtidal marine plants and changing their interactions with other species. To date, we have limited understanding of how such variations in environmental and biological stress modify the impact of interactions among foundational species and eventually affect ecosystem health. Here, we used metabolomics to assess the impact of light reductions on interactions between the seagrass Zostera marina, an important habitat-forming marine plant, and the abundant and commercially important blue mussel Mytilus edulis. Plant performance varied with light availability but was unaffected by the presence of mussels. Metabolomic analysis, on the other hand, revealed an interaction between light availability and presence of M. edulis on seagrass metabolism. Under high light, mussels stimulated seagrass nitrogen and energy metabolism. Conversely, in low light mussels impeded nitrogen and energy metabolism, and enhanced responses against sulfide toxicity, causing inhibited oxidative energy metabolism and tissue degradation. Metabolomic analysis thereby revealed cryptic changes to seagrass condition that could not be detected by traditional approaches. Our findings suggest that coastal eutrophication and associated reductions in light may shift seagrass-bivalve interactions from mutualistic to antagonistic, which is important for conservation management of seagrass meadows.

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific

Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.

Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea

Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species' capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.