The core seed mycobiome ofPseudotsuga menziesiivar.menziesiiacross provenances of the Pacific Northwest, USA

Abstract

Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. "Core" taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of Coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: 1) Seed mycobiome composition differed among seed provenances. 2) Despite spatial variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp., Hormonema macrosporum, Mucor plumbeus and Talaromyces rugulosus.Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival and competition.

Different Airway Inflammatory Phenotypes Correlate with Specific Fungal and Bacterial Microbiota in Asthma and Chronic Obstructive Pulmonary Disease

“…For bacteria, PCR amplification of the 16S rRNA genes was performed using the forward primer 27F (5′-AGAGTTTGA TCMTGGCTCAG-3′) and the reverse primer 1492R (5′-ACCTTGTTACGACTT-3′) [5,14]. Fungal ITS genes were performed using primers ITS1F (5′-CTTGGTCATTTAGA GGAAGTAA-3 ′ ) and LR3 (5 ′ -CCGTGTTTCAAGAC GGG-3 ′ ) [15][16][17]. The nearly full-length sequencing of 16S rRNA and ITS genes was carried out according to PacBio Sequel Systems powered by Single Molecule, Real-Time (SMRT) sequencing technology.…”

A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds

“…b matured seed disperse and becomes colonized from sources such as air (suggested in Gandolfi et al, 2013), water (Crocker et al, 2016), animals (Correia et al, 2019;Lash et al, 2020), soil (Fort et al, 2021), and other seeds in storage (suggested in Bergmann and Busby, 2021). Seed dormancy and germination are likely to represent a very active period of such horizontal transmission, as soil microbes interact with seed exudates and pre-existing microorganisms on and within the seed (Nelson, 1990;Ofek et al, 2011).…”

“…Several studies have shown that seed microbial communities differ significantly across geographic locations, i.e., at the macroscale, for example in B. napus (Morales Moreira et al, 2021), Elymus nutans (Guo et al, 2020), Phelipanche ramosa (Huet et al, 2020) and Pseudotsuga menziesii (Bergmann and Busby, 2021). For most of these studies, the abiotic factors that are important for structuring these seed microbial communities remain to be identified.…”

“…Previous work on seed microbiota has primarily taken a pattern-based approach to studying assembly processes (e.g., Rezki et al, 2018). Such an approach uses culturing (Ganley and Newcombe, 2006;U'Ren et al, 2009;Heitmann et al, 2021) and/or next-generation sequencing (e.g., Barret et al, 2015;Rezki et al, 2018;Prado et al, 2020;Bergmann and Busby, 2021;Fort et al, 2021) to compare, contrast, and correlate patterns in microbial community composition, diversity, and species co-occurrences. Typically, however, these community data provide limited (i.e., mostly indirect) insights into processes such as dispersal, microbe-plant interactions, and microbemicrobe interactions.…”

“…This emphasis on multiple scales and heterogeneity can help explain the main drivers of community assembly and patterns of biodiversity and co-occurrence (Leibold and Chase, 2018). Plant-associated microbial communities vary widely across environmental gradients (Barge et al, 2019) and host genetics (Wagner et al, 2016) from the levels of tissues (Cregger et al, 2018) to populations (Bergmann and Busby, 2021). As such, treating individual plants as heterogeneous habitats for microorganisms that are embedded in a larger, heterogeneous landscape of multiple plants representing different species provides a new approach to observing, testing, and modeling drivers of microbial community variation (Figure 1).…”