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

Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere

Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows

Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.

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.

Microbiomes of Thalassia testudinum throughout the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico are influenced by site and region while maintaining a core microbiome

Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones

BACKGROUND

Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.

RESULTS

Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.

CONCLUSIONS

Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.

Plant growth and development of tropical seagrass determined rhizodeposition and its related microbial community

In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.

Organic enrichment reduces sediment bacterial and archaeal diversity, composition, and functional profile independent of bioturbator activity

Eutrophication is a worldwide issue that can disrupt ecosystem processes in sediments. Studies have shown that macrofauna influences sediment processes by engineering environments that constrain microbial communities. Here, we explored the effect of different sizes of the Sydney cockle (Anadara trapezia), on bacterial and archaeal communities in natural and experimentally enriched sediments. A mesocosm experiment was conducted with two enrichment conditions (natural or enriched) and 5 cockle treatments (small, medium, large, mixed sizes and a control). This study was unable to detect A. trapezia effects on microbial communities irrespective of body size. However, a substantial decrease of bacterial richness, diversity, and structural and functional shifts, were seen with organic enrichment of sediments. Archaea were similarly changed although the magnitude of effect was less than for bacteria. Overall, we found evidence to suggest that A. trapezia had limited capacity to affect sediment microbial communities and mitigate the effects of organic enrichment.

Use of a wastewater recovery product (struvite) to enhance subtropical seagrass restoration

Seagrasses are in decline worldwide, and their restoration is relatively expensive and unsuccessful compared to other coastal systems. Fertilization can improve seagrass growth in restoration but can also release nutrients and pollute the surrounding ecosystem. A slow-release fertilizer may reduce excessive nutrient discharge while still providing resources to the seagrass's rhizosphere. In this study, struvite (magnesium ammonium phosphate), a relatively insoluble, sustainable compound harvested in wastewater treatment plants, was compared to Osmocote™(14:14:14 Nitrogen: Phosphorus: Potassium, N:P:K), a popular polymer coated controlled release fertilizer commonly used in seagrass restoration. Two experiments compared the effectiveness of both fertilizers in a subtropical flow-through mesocosm setup. In the first experiment, single 0.5 mg of P per g dry weight (DW) doses of Osmocote™and struvite fertilizers were added to seagrass plots. Seagrass shoot counts were significantly higher in plots fertilized with struvite than both the Osmocote™and unfertilized controls (p< 0.0001). A significant difference in total P concentration was observed in porewater samples of Osmocote™vs struvite and controls (p< 0.0001), with struvite fertilized plots emitting more than controls (p ≤ 0.0001), but less than 2% of the total dissolved P (TDP) of Osmocote™fertilized plots (100+ mg/L versus x > 5 mg/L). A subsequent experiment, using smaller doses (0.01 and 0.025 mg of P per gram DW added), also found that the struvite treatments performed better than Osmocote™, with 16-114% more aboveground biomass (10-60% higher total biomass) while releasing less N and P. These results indicate the relatively rapid dissolution of Osmocote™may pose problems to restoration efforts, especially in concentrated doses and possibly leading to seagrass stress. In contrast, struvite may function as a slow-release fertilizer applicable in seagrass and other coastal restoration efforts.

Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific

Predicting outcomes of marine disease outbreaks presents a challenge in the face of both global and local stressors. Host-associated microbiomes may play important roles in disease dynamics but remain understudied in marine ecosystems. Host-pathogen-microbiome interactions can vary across host ranges, gradients of disease, and temperature; studying these relationships may aid our ability to forecast disease dynamics. Eelgrass, Zostera marina, is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae. We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We detected effects of geography (11%) and smaller, but distinct, effects of temperature (30-day max sea surface temperature, 4%) and disease (lesion prevalence, 3%) on microbiome composition. Declines in alpha diversity on asymptomatic tissue occurred with rising wasting disease prevalence within meadows. However, no change in microbiome variability (dispersion) was detected between asymptomatic and symptomatic tissues. Further, we identified members of Cellvibrionaceae, Colwelliaceae, and Granulosicoccaceae on asymptomatic tissue that are predictive of wasting disease prevalence across the geographic range (3,100 kilometers). Functional roles of Colwelliaceae and Granulosicoccaceae are not known. Cellvibrionaceae, degraders of plant cellulose, were also enriched in lesions and adjacent green tissue relative to nonlesioned leaves. Cellvibrionaceae may play important roles in disease progression by degrading host tissues or overwhelming plant immune responses. Thus, inclusion of microbiomes in wasting disease studies may improve our ability to understand variable rates of infection, disease progression, and plant survival. IMPORTANCE The roles of marine microbiomes in disease remain poorly understood due, in part, to the challenging nature of sampling at appropriate spatiotemporal scales and across natural gradients of disease throughout host ranges. This is especially true for marine vascular plants like eelgrass (Zostera marina) that are vital for ecosystem function and biodiversity but are susceptible to rapid decline and die-off from pathogens like eukaryotic slime-mold Labyrinthula zosterae (wasting disease). We link bacterial members of phyllosphere tissues to the prevalence of wasting disease across the broadest geographic range to date for a marine plant microbiome-disease study (3,100 km). We identify Cellvibrionaceae, plant cell wall degraders, enriched (up to 61% relative abundance) within lesion tissue, which suggests this group may be playing important roles in disease progression. These findings suggest inclusion of microbiomes in marine disease studies will improve our ability to predict ecological outcomes of infection across variable landscapes spanning thousands of kilometers.

Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes)

Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Background: Seagrasses (Alismatales) are the only fully marine angiosperms.  Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass  Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.  

Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. 

Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. 

Conclusions: As an important marine angiosperm, the improved  Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces

Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.

Diversity and abundance of diazotrophic communities of seagrass Halophila ovalis based on genomic and transcript level in Daya Bay, South China Sea

Seagrass ecosystems are among the most productive marine ecosystems, and diazotrophic communities play a crucial role in sustaining the productivity and stability of such ecosystems by introducing fixed nitrogen. However, information concerning both total and active diazotrophic groups existing in different compartments of seagrass is lacking. This study comprehensively investigated the diversity, structure, and abundance of diazotrophic communities in different parts of the seagrass Halophila ovalis at the DNA and RNA level from clone libraries and real-time quantitative PCR. Our results indicated that nearly one-third of existing nitrogen-fixing bacteria were active, and their abundance might be controlled by nitrogen to phosphorus ratio (N:P). Deltaproteobacteria and Gammaproteobacteria were dominant groups among the total and active diazotrophic communities in all samples. These two groups accounted for 82.21% and 70.96% at the DNA and RNA levels, respectively. The genus Pseudomonas and sulfate-reducing bacteria (genera: Desulfosarcina, Desulfobulbus, Desulfocapsa, and Desulfopila) constituted the significant fraction of nitrogen-fixing bacteria in the seagrass ecosystem, playing an additional role in denitrification and sulfate reduction, respectively. Moreover, the abundance of the nitrogenase gene, nifH, was highest in seawater and lowest in rhizosphere sediments from all samples. This study highlighted the role of diazotropic communities in the subtropical seagrass ecosystem.

Global Diversity and Biogeography of the Zostera marina Mycobiome

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses.

IMPORTANCE Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass Zostera marina across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.

Recovery and Community Succession of the Zostera marina Rhizobiome after Transplantation

Seagrasses can form mutualisms with their microbiomes that facilitate the exchange of energy sources, nutrients, and hormones and ultimately impact plant stress resistance. Little is known about community succession within the belowground seagrass microbiome after disturbance and its potential role in the plant's recovery after transplantation. We transplanted Zostera marina shoots with and without an intact rhizosphere and cultivated plants for 4 weeks while characterizing microbiome recovery and effects on plant traits. Rhizosphere and root microbiomes were compositionally distinct, likely representing discrete microbial niches. Furthermore, microbiomes of washed transplants were initially different from those of sod transplants and recovered to resemble an undisturbed state within 14 days. Conspicuously, changes in the microbial communities of washed transplants corresponded with changes in the rhizosphere sediment mass and root biomass, highlighting the strength and responsive nature of the relationship between plants, their microbiome, and the environment. Potential mutualistic microbes that were enriched over time include those that function in the cycling and turnover of sulfur, nitrogen, and plant-derived carbon in the rhizosphere environment. These findings highlight the importance and resilience of the seagrass microbiome after disturbance. Consideration of the microbiome will have meaningful implications for habitat restoration practices.IMPORTANCE Seagrasses are important coastal species that are declining globally, and transplantation can be used to combat these declines. However, the bacterial communities associated with seagrass rhizospheres and roots (the microbiome) are often disturbed or removed completely prior to transplantation. The seagrass microbiome benefits seagrasses through metabolite, nutrient, and phytohormone exchange and contributes to the ecosystem services of seagrass meadows by cycling sulfur, nitrogen, and carbon. This experiment aimed to characterize the importance and resilience of the seagrass belowground microbiome by transplanting Zostera marina with and without intact rhizospheres and tracking microbiome and plant morphological recovery over 4 weeks. We found the seagrass microbiome to be resilient to transplantation disturbance, recovering after 14 days. Additionally, microbiome recovery was linked with seagrass morphology, coinciding with increases in the rhizosphere sediment mass and root biomass. The results of this study can be used to include microbiome responses in informing future restoration work.