Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome

Abstract

Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri , within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify “core microbiome” members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with “core” taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified “core” microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.

Characterization of the mycobiome of the seagrass,Zostera marina, reveals putative associations with marine chytrids

“…Post-hoc Dunn tests identified that the alpha diversity for bulk root and rhizome tissues was consistently lower than the alpha diversity of the sediment ( p < 0.05, Table S6). This is consistent with previous sequence-based studies of seagrass associated fungi (Hurtado-McCormick et al, 2019). The alpha diversity of the Z. marina mycobiome was found to be much lower than that previously seen for the bacterial communities associated with Z. marina (Ettinger et al, 2017).…”

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina

“…Members of the Sordariomycetes and Dothideomycetes have been found to be the predominant members of land plant fungal endophyte communities [89], while Eurotiomycetes have been found to be the dominant members of freshwater plant communities [90]. Dark septate endophytes (DSE), particularly members of the Pleosporales within the Dothideomycetes (Fig 6), have been observed to form associations with several seagrass species [33,42,44,71,72,[91][92][93]. DSE are a morphological, not phylogenetic (e.g.…”

“…Culture-based studies have found fungi associated with leaves, roots and rhizomes of seagrasses, but there is little agreement between studies about the taxonomic composition of these communities within and between seagrass species [26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42]. Recently cultureindependent studies of seagrass-associated fungi have more thoroughly investigated the diversity of these microorganisms and highlighted a need to further understand factors affecting their biogeography and community dynamics [43][44][45][46]. However, these studies were severely hampered by a lack of representation of fungal sequences from the marine environment in public databases and found that taxonomic assignments could not be made for many fungal sequences associated with seagrasses.…”

All small things considered: the diversity of fungi, bacteria and oomycota isolated from the seagrass, Zostera marina

“…Dark septate endophytes (DSE), particularly members of the Pleosporales within the Dothideomycetes (Figure 6), have been observed to form associations with several seagrass species (Panno et al, 2013;Gnavi et al, 2014;Vohník et al, 2015Vohník et al, , 2016Vohník et al, , 2017Vohník et al, , 2019Borovec & Vohník, 2018;Hurtado-McCormick et al, 2019). DSE are a morphological, not phylogenetic (e.g.…”

“…Culture-based studies have found fungi associated with leaves, roots and rhizomes of seagrasses, but there is little agreement between studies about the taxonomic composition of these communities within and between seagrass species (Newell, 1981;Kuo, 1984;Cuomo et al, 1985;Devarajan & Suryanarayanan, 2002;Sakayaroj et al, 2010;Mata & Cebrián, 2013;Shoemaker & Wyllie-Echeverria, 2013;Supaphon et al, 2013Supaphon et al, , 2014Supaphon et al, , 2017Panno et al, 2013;Kirichuk & Pivkin, 2015;Venkatachalam, 2015;Venkatachalam et al, 2015;Torta et al, 2015;Ling et al, 2015;Vohník et al, 2016). Recently culture-independent studies of seagrassassociated fungi have more thoroughly investigated the diversity of these microorganisms and highlighted a need to further understand factors affecting their biogeography and community dynamics (Wainwright et al, 2018(Wainwright et al, , 2019Hurtado-McCormick et al, 2019;Ettinger & Eisen, 2019). However, these studies were severely hampered by a lack of representation of fungal sequences from the marine environment in public databases and found that taxonomic assignments could not be made for many fungal sequences associated with seagrasses.…”