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

Abstract

42Seagrasses are globally distributed marine flowering plants that are foundation species in coastal 43 ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling and 44 in protecting the coastline from erosion. Although many studies have focused on seagrass 45 ecology, only a limited number have investigated their associated fungi. In terrestrial systems, 46 fungi can have beneficial and detrimental effects on plant fitness. However, not much is known 47 about marine fungi and even less is known about seagrass associated fungi. Here we used 48 culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to 49 characterize the taxonomic diversity of fungi associated with the seagrass, Zostera marina. We 50 sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal 51 diversity within and between plants. Our results indicate that there are many fungal taxa for 52 which a taxonomic assignment cannot be made living on and inside Z. marina leaves, roots and 53 rhizomes and that these plant tissues harbor distinct fungal communities. The most prevalent ITS 54 amplicon sequence variant (ASV) associated with Z. marina leaves was classified as fungal, but 55 could not initially be assigned to a fungal phylum. We then used PCR with a primer targeting 56 unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA 57 gene to amplify part of the 28S rRNA gene region and link it to this ASV. Sequencing and 58 phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this 59 ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum 60 Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is 61 possible this chytrid is directly infecting Z. marina leaf tissues. This work highlights a need for 62 further studies focusing on marine fungi and the potential importance of these understudied 63 communities to the larger seagrass ecosystem.64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 109 110In contrast to their apparent lack of mycorrhizal associations, some studies of seagrasses have 111 observed associations with novel fungal endophytes similar to dark septate endophytes (DSE) 112 common in land plants (Borovec and Vohník, 2018; Torta et al., 2015; Vohník et al., 2015 Vohník et al., , 2016 Vohník et al., , 113 2017 Vohník et al., , 2019). DSE are a morphology based type and not a phylogenetic group, and are largely 114 uncharacterized. In some cases, DSEs have been shown to transfer nitrogen and receive carbon 115 from plants as well as increase overall plant nutrient content and growth (Porras-Alfaro and 116 Bayman, 2011; Usuki and Narisawa, 2007). DSEs are not the only fungi that have been observed 117to form associations with seagrasses. Additional culture based studies have found fungi 118 associated with the leaves, roots and rhizomes of different seagrasses; however, many of these 119...

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

“…Chytridiomycota were found to be prevalent members of the Z. marina leaf microbiome in Ettinger & Eisen (2019), however, no chytrids were cultured in this study. This is likely because the isolation methods used here favor cultivation of Dikarya.…”

“…are drivers of the positive relationship observed previously between the number of tissue types and number of media types a fungal genus was isolated from ( Figure S2). Ettinger & Eisen (2019) We compared the diversity of the fungi isolated here to high throughput sequencing data associated with Z. marina from the same location (as previously analysed in Ettinger & Eisen (2019). We found that the fungal genera isolated in this study were generally also detected in the sequencing data (Table 1).…”

“…Individual Zostera marina plants and associated sediment were collected opportunistically from Westside Point (GPS: 38°19'10.67"N, 123° 3'13.71"W) in Bodega Bay, CA during several sampling trips between summer 2017 and summer 2018 using a 2.375 inch diameter modified PVC pipe as described in Ettinger & Eisen (2019). Bulk leaf tissue was also collected during these trips using gloves and placed in sterile plastic bags.…”

“…Comparisons to ITS amplicon data from Ettinger & Eisen (2019) To compare to high throughput sequencing data associated with Z. marina from the same location (Westside Point, Bodega Bay, CA), we utilized an amplicon sequence variant (ASV) dataset previously analysed in Ettinger & Eisen (2019). Specifically, we are using the subset ASV table that was used to investigate differences between bulk sample types.…”

“…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.…”