Host-Generalist Fungal Pathogens of Seedlings May Maintain Forest
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1 Supporting Information 2 Article title: : Host-generalist fungal pathogens of seedlings may maintain forest diversity via 3 host-specific impacts and differential susceptibility among tree species 4 Authors: Erin R. Spear and Kirk D. Broders 5 6 The following Supporting Information is available for this article: 7 Fig. S1 Examples of disease symptoms in the forests of Panama. 8 Fig. S2 Details of shadehouse-based inoculation experiments. 9 Fig. S3 Rank abundance plot and OTU accumulation curve. 10 Fig. S4 Overlap in fungal OTUs among sampling years, methods used to obtain symptomatic 11 seedlings, isolation media, and tissue sampled. 12 Fig. S5 Correlation between OTU host range and isolation frequency. 13 Table S1 Taxonomic assignments, traits, sampling effort, and observed OTUs for tree species 14 evaluated in our survey and experimental approaches. 15 Table S2 Methodological details pertaining to the multi-year collection of symptomatic 16 seedlings, and microbial isolation and sequencing. 17 Table S3 Average light levels, air temperatures, and relative humidities of the shadehouses 18 used for inoculation experiments versus ambient conditions. 19 Table S4 Estimated taxonomic placement, isolation frequency, number of observed hosts, 20 estimated host specialization, and phylogenetic pattern of host use of the OTUs. 21 Table S5 Overlap in seedling-associated OTUs among tree species. 22 Table S6 Results of the beta-binomial generalized linear regression with the proportion of 23 diseased seedlings as a function of seed size and shade tolerance. 24 Table S7 Average estimates based on the best-ranked beta-binomial generalized linear 1 25 regressions with the proportion of diseased seedlings as a function of seed size and spatial 26 distribution relative to annual rainfall. 27 Methods S1 Methods used to estimate the taxonomic placement of the 66 OTUs and assign 28 nomenclature. 2 29 30 Fig. S1 Disease symptoms on the (a,g-j,m,o,p-t,v) stems, (b-f,k,l,n,o) leaves, and (u) root of 31 seedlings in the forests of Panama. In some panels, arrows direct the viewer’s attention to 32 disease. 3 33 34 Fig. S2 (a) Inoculation experiments were conducted in Smithsonian Tropical Research Institute 35 shadehouses in Gamboa, Panama. (b) Surface-sterilized seeds were germinated in flats of 36 autoclave-sterilized commercial soil. (c,f) Seedlings were transplanted to individual pots 37 containing autoclaved commercial soil and (d,e) either rice visibly colonized by one of the 38 fungal isolates or inoculum-free, autoclave-sterilized rice. Disease symptoms were documented 39 every three days and were categorized as seedling mortality, (g-o) stem damage, (p,q) wilted 40 tissue, and (r,s) stunted seedling growth. 4 41 42 Fig. S3 (a) The 66 observed OTUs, defined by 99% ITS sequence similarity, are ranked from most 43 to least abundant on the horizontal axis, with the total number of isolates per OTU plotted on 44 the vertical axis (full dataset: n = 211 isolates) (BiodiversityR package; Kindt & Coe, 2005). Most 45 of the OTUs are rare (50% singletons), indicated by the steep shape of the curve. The four 46 common OTUs (observed ≥10 times and comprising 35% of the isolates) are named. (b) Non- 47 asymptotic accumulation of OTUs isolated from 124 symptomatic seedlings (vegan package; 48 Oksanen et al., 2019). The curve, derived from the observed richness and representing the 49 mean accumulation of OTUs over 999 randomizations of seedling order, indicates incomplete 50 sampling and a diverse community. 5 51 References: 52 Kindt R, Coe R. 2005. Tree diversity analysis. A manual and software for common statistical 53 methods for ecological and biodiversity studies. Nairobi, Kenya: World Agroforestry 54 Centre (ICRAF). 55 Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, 56 Simpson GL, Solymos P et al. 2019. vegan: Community Ecology Package. R package 57 version 2.5-6. [WWW document] URL https://CRAN.R-project.org/package=vegan 58 [accessed 2 June 2020]. 6 59 60 Fig. S4 Venn diagrams depicting the overlap in non-singleton fungal operational taxonomic 61 units (OTUs; based on 99% sequence similarity) among the five sampling years, three methods 62 used to obtain seedlings with disease symptoms, four media used for isolation, and three 63 tissues sampled (data subset A: n = 178 isolates, from 110 seedlings). (a) Fungi, and two 64 oomycetes, were isolated from symptomatic seedlings in Panama over five years (2007, 2010- 65 2012, 2019). (b) Symptomatic seedlings were obtained in three ways: (i) opportunistic 66 collection of naturally occurring seedlings, (ii) seedlings germinated in a shadehouse and then 67 transplanted to forest sites, and (iii) surface-sterilized seeds planted directly in forest sites. (c, 7 68 d) The advancing margin(s) of diseased area(s) was/were excised, and the excised tissue 69 piece(s) (leaf, stem, and/or root) was/were surface sterilized (Gilbert & Webb, 2007) and plated 70 on (i) Water agar, (ii) Pimaricin, Ampicillin, Rifampicin, and Pentachloronitrobenzene (PARP); 71 and/or Malt Extract Agar (MEA) amended with antibiotic to prevent bacterial growth, either (iii) 72 chloramphenicol or (iv) rifampicin. See Table S2 and Spear (2007) for additional methodological 73 details. (a) Of the 33 non-singleton OTUs, 19 were observed in more than one year. While no 74 OTUs were observed across all five years, three OTUs were observed across four of the 75 sampling years. The greatest number of unique, non-singleton OTUs were observed in 2019, 76 the year we collected the greatest number of seedlings. (b) Eighteen non-singleton OTUs were 77 isolated from seedlings obtained using more than one method. Four non-singleton OTUs were 78 isolated from seedlings obtained using all three methods. We isolated the greatest number of 79 unique, non-singleton OTUs from naturally occurring seedlings, the most common sampling 80 method. (c) Nineteen non-singleton OTUs were isolated on multiple media. One non-singleton 81 OTU was isolated from tissue pieces plated on all four media. We isolated the greatest number 82 of unique, non-singleton OTUs on MEA + rifampicin, the media used for the greatest number of 83 seedlings and tissue pieces. (d) Twenty-two non-singleton OTUs were isolated from multiple 84 tissues. Four non-singleton OTUs were isolated from all three tissues. We isolated the greatest 85 number of unique, non-singleton OTUs from leaves, the best-sampled tissue. 86 References: 87 Gilbert GS, Webb CO. 2007. Phylogenetic signal in plant pathogen-host range. Proceedings of 88 the National Academy of Sciences, USA 104: 4979-4983. 89 Spear ER. 2017. Phylogenetic relationships and spatial distributions of putative fungal 90 pathogens of seedlings across a rainfall gradient in Panama. Fungal Ecology 26: 65-73 8 91 92 Fig. S5 The observed host range of an OTU is positively correlated with isolation frequency 93 (survey-based assessment of host range: blue points, one-tailed Spearman's rank correlation 94 rho = 0.963, P < 0.001; host range observed during the inoculation experiments: green points, 95 one-tailed Spearman's rank correlation rho = 0.721, P = 0.053), suggesting that host-generalized 96 fungi may be more common in this system. 9 97 Table S1 Tree species from which putative pathogens were isolated (original host = OH, 26 tree species) and/or for which 98 vulnerability to pathogens was assessed (target = T, 35 tree species) via inoculation experiments. For each tree species, the following 99 is listed: a two- or three-letter code (for Fig. 3 and Tables 1, S2, and S5), taxonomic assignments, and the number of seedlings 100 collected, sites from which seedlings were collected, unique isolates observed, and OTUs observed. Average seed dry mass (mg), 101 shade tolerance, and spatial distribution relative to annual rainfall are listed for the tree species used to explore the relationship 102 between disease susceptibility and plant life history traits. The imperfect match between original hosts and targets was driven by 103 limited seed availability, long seed dormancy periods, and space and time constraints. Additionally, several tree species that were 104 not original hosts were included in the inoculation experiments as phytometers (measures of the pathogenicity of the isolates) 105 because of their previously observed disease susceptibility (e.g., L. seemannii, Augspurger & Wilkinson, 2007). Role Species Code Family Order Seed Shade Dist.3 Seedlings Sites Isolates OTUs mass tol.2 collected (mg)1 OH, T Anacardium excelsum ANE Anacardiaceae Sapindales 1507 dry 20 5 41 24 OH, T Dalbergia retusa DR Fabaceae Fabales 130 tol dry 18 2 20 10 OH Pouteria reticulata PR Sapotaceae Ericales 11 1 30 18 OH, T Virola surinamensis VS Myristicaceae Magnoliales 11 3 15 11 OH Faramea occidentalis FO Rubiaceae Gentianales 7 1 13 7 OH Protium panamense PP Burseraceae Sapindales 7 1 18 11 OH Protium tenuifolium PT Burseraceae Sapindales 6 2 10 9 OH, T Calophyllum longifolium CL Calophyllaceae Malpighiales 5 1 14 9 OH, T Castilla elastica CE Moraceae Rosales 203.4 dry 5 2 6 4 OH, T Hymenaea courbaril HC Fabaceae Fabales 5 3 6 5 OH Cassia moschata CAM Fabaceae Fabales 4 3 5 4 OH, T Lacmellea panamensis LAP Apocynaceae Gentianales 237.4 tol wet 4 3 7 5 OH Nectandra cuspidata NC Lauraceae Laurales 4 2 5 5 OH, T Cochlospermum vitifolium CV Bixaceae Malvales 26 intol 3 1 4 4 OH Swietenia macrophylla SWM Meliaceae Sapindales 2 1 2 2 OH, T Trichilia tuberculata TT Meliaceae Sapindales 151 tol 2 2 2 2 OH, T Brosimum utile