Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Crump, Byron C.; Wojahn, John Michael Adrian; Tomàs, Fiona; Mueller, Robert F.

doi:10.3389/fmicb.2018.00388

Cited by 110 publications

(183 citation statements)

References 131 publications

(176 reference statements)

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“…Recent results (Cúcio et al, 2016) suggest that sympatric seagrass species (in this case Z. marina, Z. noltei, and Cymodocea nodosa) might share largely the same rhizosphere community. Similar results were very recently obtained by (Crump et al, 2018) for a comparison between sympatric Z. marina and Z. japonica in Oregon, USA using metatranscriptomics and 16S amplicon sequencing. The co-occuring Halophila ovalis, Halodule uninervis, and Cymodocea serrulata each showed unique root microbiomes, as light was experimentally reduced their root exudation was altered which reduced the abundance of microorganisms that are potentially beneficial to the seagrasses, but not the predicted function (Martin et al, 2018).…”

Section: A3 Marine Macrophyte Holobionts and Their Hologenomessupporting

confidence: 88%

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

et al. 2018

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Marine macrophytes are the foundation of algal forests and seagrass meadows-some of the most productive and diverse coastal marine ecosystems on the planet. These ecosystems provide nursery grounds and food for fish and invertebrates, coastline protection from erosion, carbon sequestration, and nutrient fixation. For marine macrophytes, temperature is generally the most important range limiting factor, and ocean warming is considered the most severe threat among global climate change factors. Ocean warming induced losses of dominant macrophytes along their equatorial range edges, as well as range extensions into polar regions, are predicted and already documented. While adaptive evolution based on genetic change is considered too slow to keep pace with the increasing rate of anthropogenic environmental changes, rapid adaptation may come about through a set of non-genetic mechanisms involving the functional composition of the associated microbiome, as well as epigenetic modification of the genome and its regulatory effect on gene expression and the activity of transposable elements. While research in terrestrial plants demonstrates that the integration of non-genetic mechanisms provide a more holistic picture of a species' evolutionary potential, research in marine systems is lagging behind. Here, we aim to review the potential of marine macrophytes to acclimatize and adapt to major climate change effects via intraspecific variation at the genetic, epigenetic, and microbiome levels. All three levels create phenotypic variation that may either enhance fitness within individuals (plasticity) or be subject to selection and ultimately, adaptation. We

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Section: A3 Marine Macrophyte Holobionts and Their Hologenomessupporting

confidence: 88%

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

et al. 2018

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“…The observation of consistently distinct microbial communities between compartments of Z. marina is in line with studies describing the structure of seagrass microbiomes from field-collected samples, where large differences are observed between plant microbial communities and those in the surrounding environment (15, 18, 19, 36–39). In the study by Cúcio et al (15) where the rhizosphere compartment was specifically analyzed, significant differences were found between communities of bulk and rhizosphere sediments.…”

Section: Discussionsupporting

confidence: 88%

“…Seagrasses are marine vascular plants that form key ecosystems on coastal areas worldwide, where they provide numerous ecosystem services (17). Recent evidence suggests that members of the seagrass microbiome may modulate host growth and response to environmental stresses (15, 18, 19). In addition to fixing nitrogen and producing phytohormones (20, 21), the seagrass microbiome is proposed to mitigate the toxic effects of hydrogen sulfide in sediments, which have been linked to declines in seagrass health and localized die-back events (22–24).…”

Section: Introductionmentioning

confidence: 99%

Recovery and Community Succession of theZostera marinaRhizobiome After Transplantation

Wang

English

Tomàs

et al. 2020

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18Seagrasses can form mutualisms with their microbiomes that facilitate the exchange of 19 energy sources, nutrients, and hormones, and ultimately impact plant stress resistance. Little is 20 known about community succession within the belowground seagrass microbiome after 21 disturbance and its potential role in the plant's recovery after transplantation. We transplanted 22 Zostera marina shoots with and without an intact rhizosphere and cultivated plants for four 23 weeks while characterizing microbiome recovery and effects on plant traits. Rhizosphere and 24 root microbiomes were compositionally distinct, likely representing discrete microbial niches. 25 Furthermore, microbiomes of washed transplants were initially different from those of sod 26 transplants, and recovered to resemble an undisturbed state within fourteen days. Conspicuously, 27 changes in microbial communities of washed transplants corresponded with changes in 28 rhizosphere sediment mass and root biomass, highlighting the strength and responsive nature of 29 the relationship between plants, their microbiome, and the environment. Potential mutualistic 30 microbes that were enriched over time include those that function in the cycling and turnover of 31 sulfur, nitrogen, and plant-derived carbon in the rhizosphere environment. These findings 32 highlight the importance and resiliency of the seagrass microbiome after disturbance. 33 Consideration of the microbiome will have meaningful implications on habitat restoration 34 practices. 35Importance 37 Seagrasses are important coastal species that are declining globally, and transplantation 38 can be used to combat these declines. However, the bacterial communities associated with 39 seagrass rhizospheres and roots (the microbiome) are often disturbed or removed completely 40 prior to transplantation. The seagrass microbiome benefits seagrasses through metabolite, 41 nutrient, and phytohormone exchange, and contributes to the ecosystem services of seagrass 42 meadows by cycling sulfur, nitrogen, and carbon. This experiment aimed to characterize the 43 importance and resilience of the seagrass belowground microbiome by transplanting Zostera 44 marina with and without intact rhizospheres and tracking microbiome and plant morphological 45 recovery over four weeks. We found the seagrass microbiome to be resilient to transplantation 46 disturbance, recovering after fourteen days. Additionally, microbiome recovery was linked with 47 seagrass morphology, coinciding with increases in rhizosphere sediment mass and root biomass. 48Results of this study can be used to include microbiome responses in informing future restoration 49 work. 52The rhizobiome has long been recognized to have important impacts on plant growth and 53 health (1). The microbes of the rhizobiome, which directly interact with and are influenced by 54 the roots (2), can benefit their plant hosts through recycling and producing bioavailable nutrients 55 (3-5), increasing disease resistance through competition with or in...

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“…Several studies demonstrated close relationships between individual seagrass species and their microbial communities. Most of these focused on species from North America, Europe, China and the Red Sea, including Z. marina, Z. japonica, Cymodocea nodosa and T. hemprichii (Crump et al 2018;Cucio et al 2016;Yu-Feng Jiang et al 2015;Ettinger et al 2017;. However, little is known about these associations between microbiomes and seagrasses species occurring in Kenya.…”

Section: Discussionmentioning

confidence: 99%

Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum

Kaimenyi

Villiers

Ngoi

et al. 2018

Preprint

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Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs and mangrove forests with little direct action taken to conserve seagrass meadows. Pollution, over-exploitation of marine resources and minimal efforts towards enforcement of conservation laws of marine environments, have caused degradation and defoliation of seagrass habitats. Little is known about the microbes associated with seagrass species in Kenya and this study aimed to characterize the genetic diversity of the microbiomes of two prominent seagrass species, Enhalus acoroides and Thallasodendron ciliatum, which are the most commonly occurring species. Methods. Replicate microbiome samples were collected from leaves, roots, sediment and water columns associated with the two seagrass species from two sites on the Kenyan coast. The microbial communities of the samples were characterized and compared using 16S ribosomal RNA gene PCR and sequencing. Microbiome features including diversity and taxonomic composition were used to compare within and between sample types and sites. Results. Leaf samples from both E. acoroides and T. ciliatum had significantly different microbial communities comparted to root and sediment samples, revealing a diversity gradient with lowest diversity in water samples and highest in sediment. There were no significant variation in seagrass microbial composition associated with leaf and rhizosphere microbiomes of either E. acoroides or T. ciliatum. However, we did see a difference between water samples associated with each seagrass species. Discussion. This study of the microbiomes associated with the sediments, roots, leaves and surrounding water of E. acoroides and T. ciliatum, included a limited number of samples from a small geographic area, providing a valuable first assessment of the microbial diversity of seagrass beds on the Kenyan coast. We found no significant differences between the plant-associated bacterial communities of the two-seagrass species investigated. Significant differences however, were observed amongst leaf-, root-, sediment- and water-associated bacterial communities. This work will contribute to understanding the dynamic environment of seagrass beds and will contribute to helping conserving and re-establishing seagrass beds degraded by due to anthropogenic activities.

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Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Cited by 110 publications

References 131 publications

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential

Recovery and Community Succession of theZostera marinaRhizobiome After Transplantation

Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum

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