Zahn G, Amend AS. Foliar fungi alter reproductive timing and allocation in Arabidopsis under normal and water-stressed conditions. Fungal Ecol. 2019;41:101–6.
Arnold AE, Engelbrecht BMJ. Fungal endophytes nearly double minimum leaf conductance in seedlings of a neotropical tree species. J Trop Ecol. 2007;23:369–72.
Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, et al. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol. 2009;75:748–57.
Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K. Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiol Ecol. 2017;93:fix050. https://doi.org/10.1093/femsec/fix050.
Choudoir MJ, Barberan A, Menninger HL, Dunn RR, Fierer N. Variation in range size and dispersal capabilities of microbial taxa. Ecology. 2017;99:322–34.
Klironomos JN. Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature. 2002;417:67–70.
Dini-Andreote F, Raaijmakers JM. Embracing community ecology in plant microbiome research. Trends Plant Sci. 2018;23:467–9.
Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions. Plant J Cell Mol Biol. 2019;97:164–81.
Peay KG, Kennedy PG, Talbot JM. Dimensions of biodiversity in the Earth mycobiome. Nat Rev Microbiol. 2016;14:434–47.
Wang J, Soininen J, He J, Shen J. Phylogenetic clustering increases with elevation for microbes. Environ Microbiol Rep. 2012;4:217–26.
Zimmerman NB, Vitousek PM. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proc Natl Acad Sci USA. 2012;109:13022–7.
Yang Y, Gao Y, Wang S, Xu D, Yu H, Wu L, et al. The microbial gene diversity along an elevation gradient of the Tibetan grassland. ISME J. 2014;8:430–40.
Shen C, Ni Y, Liang W, Wang J, Chu H. Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra. Front Microbiol. 2015;6:582.
Yao F, Yang S, Wang Z, Wang X, Ye J, Wang X, et al. Microbial taxa distribution is associated with ecological trophic cascades along an elevation gradient. Front Microbiol. 2017;8:2071.
Na X, Xu TT, Li M, Ma F, Kardol P. Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients. J Soils Sediment. 2017;17:122–32.
Jangid K, Williams MA, Franzluebbers AJ, Schmidt TM, Coleman DC, Whitman WB. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties. Soil Biol Biochem. 2011;43:2184–93.
Talbot JM, Bruns TD, Taylor JW, Smith DP, Branco S, Glassman SI, et al. Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci USA. 2014;111:6341–6.
Oono R, Rasmussen A, Lefèvre E. Distance decay relationships in foliar fungal endophytes are driven by rare taxa: distance decay in fungal endophytes. Environ Microbiol. 2017;19:2794–805.
Amend AS, Cobian GM, Laruson AJ, Remple K, Tucker SJ, Poff KE, et al. Phytobiomes are compositionally nested from the ground up. PeerJ. 2019;7:e6609.
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci USA. 2018;115:E1157–65.
Bálint M, Tiffin P, Hallström B, O’Hara RB, Olson MS, Fankhauser JD, et al. Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera). PLoS ONE. 2013;8:e53987.
Bálint M, Bartha L, O’Hara RB, Olson MS, Otte J, Pfenninger M, et al. Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Mol Ecol. 2015;24:235–48.
Coleman‐Derr D, Desgarennes D, Fonseca‐Garcia C, Gross S, Clingenpeel S, Woyke T, et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. N. Phytol. 2016;209:798–811.
Lindow SE, Brandl MT. Microbiology of the phyllosphere. Appl Environ Microbiol. 2003;69:1875–83.
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol. 2010;12:2885–93.
Leff JW, Del Tredici P, Friedman WE, Fierer N. Spatial structuring of bacterial communities within individual Ginkgo biloba trees. Environ Microbiol. 2015;17:2352–61.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–63.
de Souza RSC, Okura VK, Armanhi JSL, Jorrín B, Lozano N, da Silva MJ, et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci Rep. 2016;6:28774.
Wearn JA, Sutton BC, Morley NJ, Gange AC. Species and organ specificity of fungal endophytes in herbaceous grassland plants. J Ecol. 2012;100:1085–92.
Beckers B, Op De Beeck M, Weyens N, Boerjan W, Vangronsveld J. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome. 2017;5:25.
Desgarennes D, Garrido E, Torres-Gomez MJ, Peña-Cabriales JJ, Partida-Martinez LP. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species. FEMS Microbiol Ecol. 2014;90:844–57.
Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe SG, Partida-Martínez LP. The cacti microbiome: interplay between habitat-filtering and host-specificity. Front Microbiol. 2016;7:150.
Lindström ES, Langenheder S. Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep. 2012;2012:1–9.
Kembel SW, O’Connor TK, Arnold HK, Hubbell SP, Wright SJ, Green JL. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci USA. 2014;111:13715–20.
Frank AC, Saldierna Guzmán JP, Shay JE. Transmission of bacterial endophytes. Microorganisms. 2017;5:70.
Wu Z, Raven PH, Hong D. Hibiscus tiliaceus. eFloras. St. Louis, MO: Missouri Botanical Garden & Cambridge, MA: Harvard University Herbaria; 2019. p. 287–8.
Motooka P, Castro L, Nelson D, Nagai G, Ching L. Weeds of Hawaiʻi’s pastures and natural areas: an identification and management guide. Honolulu: University of Hawaiʻi Press; 2014.
Quesada T, Hughes J, Smith K, Shin K, James P, Smith J. A low-cost spore trap allows collection and real-time PCR quantification of airborne Fusarium circinatum spores. Forests. 2018;9:586.
Smith DP, Peay KG. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE. 2014;9:e90234.
Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, et al. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems. 2016;1:e00009–15.
Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 2010;10:189.
Rivers AR, Weber KC, Gardner TG, Liu S, Armstrong SD. ITSxpress: software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Research. 2018;7:1418.
Hannon GJ. FASTX-Toolkit: FASTQ/A short-reads pre-processing tools. 2010. http://hannonlab.cshl.edu/fastx_toolkit/.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43.
Gdanetz K, Benucci GMN, Vande Pol N, Bonito G. CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. BMC Bioinforma. 2017;18:538.
Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R, Brunbjerg AK, Pietroni C, et al. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nat Commun. 2017;8:1188.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6:226.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
Giambelluca TW, Shuai X, Barnes ML, Alliss RJ, Longman RJ, Miura T, et al. Evapotranspiration of Hawai’i. 2014. Final report submitted to the U.S. Army Corps of Engineers—Honolulu District, and the Commission on Water Resource Management, State of Hawai’i.
Hijmans RJ. raster: geographic data analysis and modeling. R package v 2.9-5. 2019. https://CRAN.R-project.org/package=raster.
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: community ecology package. R package v 2.5-5. 2019. https://CRAN.R-project.org/package=vegan.
Guillot G, Rousset F. Dismantling the Mantel tests. Methods Ecol Evol. 2013;4:336–44.
Dormann CF, Gruber B, Fruend J. Introducing the bipartite package: analysing ecological networks. R N. 2008;8:8–11.
Dormann CF, Fründ J, Blüthgen N, Gruber B. Indices, graphs and null models: analyzing bipartite ecological networks. Open Ecol J. 2009;2:7–24.
Atmar W, Patterson BD. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia. 1993;96:373–82.
Almeida‐Neto M, Guimarães P, Guimarães PR, Loyola RD, Ulrich W. A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos. 2008;117:1227–39.
Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, et al. The soil microbiome influences grapevine-associated microbiota. mBio. 2015;6:e02527–14. https://mbio.asm.org/content/6/2/e02527-14.
Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DBM, et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE. 2011;6:e24570.
Matthew W, Fraser DBG, Pauline F, Grierson BL, Kendrick GaryA. Metagenomic evidence of microbial community responsiveness to phosphorus and salinity gradients in seagrass sediments. Front Microbiol. 2018;9:1703.
Peay KG, Schubert MG, Nguyen NH, Bruns TD. Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules. Mol Ecol. 2012;21:4122–36.
Massoni J, Bortfeld-Miller M, Jardillier L, Salazar G, Sunagawa S, Vorholt JA. Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. ISME J. 2020;14:245–58.
Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL. Evolutionary histories of soil fungi are reflected in their large-scale biogeography. Ecol Lett. 2014;17:1086–93.
Nguyen HDT, Chabot D, Hirooka Y, Roberson RW, Seifert KA. Basidioascus undulatus: genome, origins, and sexuality. IMA Fungus. 2015;6:215–31.
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, et al. Rokubacteria: genomic giants among the uncultured bacterial phyla. Front Microbiol. 2017;8:2264.
Meiser A, Bálint M, Schmitt I. Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. N Phytol. 2014;201:623–35.
Crowther TW, Maynard DS, Crowther TR, Peccia J, Smith JR, Bradford MA. Untangling the fungal niche: the trait-based approach. Front Microbiol. 2014;5:579.
Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, et al. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS ONE. 2013;8:e76382.
Source: Ecology - nature.com