Addison S, Armstrong C, Wigley K, Hartley R, Wakelin S. What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata. Environ Microbiome. 2023;18(1):45.
Anderson MJ. A new method for non-parametric multivariate analysis of variance: non-parametric manova for ecology. Austral Ecol. 2001;26(1):32–46.
Arnold AE, Mejía LC, Kyllo D, Rojas EI, Maynard Z, Robbins N, et al. Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci U S A. 2003;100(26):15649–54.
Baldrian P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol Rev. 2017;41(2):109–30.
BBMap. 2022. SourceForge. July 15, 2022. https://sourceforge.net/projects/bbmap/.
Berlemont R, Martiny AC. Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol. 2013;79(5):1545–54.
Bizjak T, Sellstedt A, Gratz R, Nordin A. Presence and activity of nitrogen-fixing bacteria in Scots pine needles in a boreal forest: a nitrogen-addition experiment. Tree Physiol. 2023;43(8):1354–64.
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8(1):209.
Bobay LM, Ochman H. 2017. Biological species are universal across life’s domains. Genome Biol Evol. 2017. https://academic.oup.com/gbe/article/9/3/491/2982379.
Bograd A, Oppenheimer-Shaanan Y, Levy A. Plasmids, prophages, and defense systems are depleted from plant microbiota genomes. Genome Biol. 2025;26(1):163.
Bonan GB. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science. 2008;320(5882):1444–9.
Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, et al. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics. 2015;16(1):856.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35(8):725–31.
Bowers RM, Sullivan AP, Costello EK, Collett JL, Knight R, Fierer N. Sources of bacteria in outdoor air across cities in the Midwestern United States. Appl Environ Microbiol. 2011;77(18):6350–6.
Bringel F, Couée I. Pivotal Roles of Phyllosphere Microorganisms at the Interface between Plant Functioning and Atmospheric Trace Gas Dynamics. Front Microbiol. 2015;6(May):486.
Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B, et al. Identification of mobile genetic elements with geNomad. Nat Biotechnol. 2023. https://doi.org/10.1038/s41587-023-01953-y.
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. EggNOG-Mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825–9.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972.
Caro-Quintero A, Konstantinidis KT. Inter-Phylum HGT Has Shaped the Metabolism of Many Mesophilic and Anaerobic Bacteria. ISME J. 2015;9(4):958–67.
Carper DL, Lawrence TJ, Quiroz D, Kueppers LM, Frank AC. Needle Bacterial Community Structure across the Species Range of Limber Pine. ISME Commun. 2024;4(1):ycae062.
Carrell AA, Carper DL, Frank AC. Subalpine Conifers in Different Geographical Locations Host Highly Similar Foliar Bacterial Endophyte Communities. FEMS Microbiol Ecol. 2016;92(8). https://doi.org/10.1093/femsec/fiw124.
Carroll G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology. 1988;69(1):2–9.
Chan PP, Lowe TM. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. In Gene Prediction: Methods and Protocols, edited by Martin Kollmar, 2019:1–14. New York, NY: Springer New York.
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2020;36(6):1925–7.
Chen IMA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 2021;49(D1):D751–63.
Chen IMA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, et al. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res. 2023;51(D1):D723–32.
Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023;20(8):1203–12.
Clarke KR. Non-parametric multivariate analyses of changes in community structure. Aust J Ecol. 1993;18(1):117–43.
Cui J, Zhang M, Chen L, Zhang S, Luo Y, Cao W, et al. Methanotrophs Contribute to Nitrogen Fixation in Emergent Macrophytes. Front Microbiol. 2022;13(April):851424.
Cuthbertson L, Nodwell JR. The TetR Family of Regulators. Microbiol Mol Biol Rev. 2013;77(3):440–75.
Delgado LF, Andersson AF. Evaluating metagenomic assembly approaches for biome-specific gene catalogues. Microbiome. 2022;10(1):72.
Díaz-Muñoz SL. “Viral Coinfection Is Shaped by Host Ecology and Virus-Virus Interactions across Diverse Microbial Taxa and Environments.” Virus Evol. 2017;3(1):vex011.
Dove NC, Carrell AA, Engle NL, Klingeman DM, Rodriguez M, Wahl T, Tschaplinski TJ, Muchero W, Schadt CW, Cregger MA. Relationships between Sphaerulina musiva infection and the Populus microbiome and metabolome. mSystems. 2022;7(4):e0012022.
Dudareva N, Pichersky E, Gershenzon J. Biochemistry of plant volatiles. Plant Physiol. 2004;135(4):1893–902.
Emms DM, Kelly S. Orthofinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16(1):157.
Erill I, Campoy S, Mazon G, Barbé J. Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. Nucleic Acids Res. 2006;34(1):66–77.
Ewers FW, Schmid R. Longevity of needle fascicles of Pinus longaeva (bristlecone pine) and other North American pines. Oecologia. 1981;51(1):107–15.
Faiola CL, Buchholz A, Kari E, Yli-Pirilä P, Holopainen JK, Kivimäenpää M, et al. Terpene Composition Complexity Controls Secondary Organic Aerosol Yields from Scots Pine Volatile Emissions. Sci Rep. 2018;8(1):1–13.
Fanin N, Lin D, Freschet GT, Keiser AD, Augusto L, Wardle DA, et al. “Home-Field Advantage of Litter Decomposition: From the Phyllosphere to the Soil.” New Phytol. 2021;231(4):1353–8.
Frasz SL, Walker AK, Nsiama TK, Adams GW, Miller JD. “Distribution of the Foliar Fungal Endophyte Phialocephala Scopiformis and Its Toxin in the Crown of a Mature White Spruce Tree as Revealed by Chemical and qPCR Analyses.” Can J Forest Res. 2014;44(9):1138–43.
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3(9):722–32.
Garzoli S, Masci VL, Caradonna V, Tiezzi A, Giacomello P, Ovidi E. Liquid and vapor phase of four conifer-derived essential oils: comparison of chemical compositions and antimicrobial and antioxidant properties. Pharmaceuticals (Basel, Switzerland). 2021;14(2):134.
George PBL, Leclerc S, Turgeon N, Veillette M, Duchaine C. “Conifer Needle Phyllosphere as a Potential Passive Monitor of Bioaerosolised Antibiotic Resistance Genes.” Antibiotics. 2022;11(7):907.
Guerrieri R, Cáliz J, Mattana S, Barceló A, Candela M, Elustondo D, et al. Substantial contribution of tree canopy nitrifiers to nitrogen fluxes in European forests. Nat Geosci. 2024;17(2):130–6.
Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9(1):37.
Hakola H, Tarvainen V, Laurila T, Hiltunen V, Hellén H, Keronen P. “Seasonal Variation of VOC Concentrations above a Boreal Coniferous Forest.” Atmos Environ. 2003;37(12):1623–34.
Heijden MGAVD, Martin FM, Selosse M-A, Sanders IR. “Mycorrhizal Ecology and Evolution: The Past, the Present, and the Future.” New Phytol. 2015;205(4):1406–23.
Heil JA, Simler-Williamson A, Striluk ML, Trawick D, Capezza R, DeFehr C, et al. Weather and leaf age separately contribute to temporal shifts in phyllosphere fungal community structure in sagebrush. Ecosphere. 2025;16(6):e70295.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFboot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518–22.
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, et al. Terabase-scale metagenome coassembly with MetaHipMer. Sci Rep. 2020;10(1). https://doi.org/10.1038/s41598-020-67416-5.
Howe A, Stopnisek N, Dooley SK, Yang F, Grady KL, Shade A. Seasonal activities of the phyllosphere microbiome of perennial crops. Nat Commun. 2023;14(1):1039.
Huang X-R, Neilson R, Yang L-Y, Deng J-J, Shu-Yi-Dan Zhou Hu, Li Y-G, et al. Urban Greenspace Types Influence the Microbial Community Assembly and Antibiotic Resistome More in the Phyllosphere than in the Soil. Chemosphere. 2023;338(139533):139533.
Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. “Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification.” BMC Bioinformatics. 2010;11(March):119.
Innerebner G, Knief C, Vorholt JA. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microbiol. 2011;77(10):3202–10.
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.
Jean M, Holland-Moritz H, Melvin AM, Johnstone JF, Mack MC. “Experimental Assessment of Tree Canopy and Leaf Litter Controls on the Microbiome and Nitrogen Fixation Rates of Two Boreal Mosses.” New Phytol. 2020;227(5):1335–49.
Jia Z, Davies PL. Antifreeze proteins: an unusual receptor-ligand interaction. Trends Biochem Sci. 2002;27(2):101–6.
Joshi K, Kumar P, Kataria R. “Microbial Carotenoid Production and Their Potential Applications as Antioxidants: A Current Update.” Process Biochemistry (Barking, London, England). 2023;128(May):190–205.
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. “MetaBAT 2: An Adaptive Binning Algorithm for Robust and Efficient Genome Reconstruction from Metagenome Assemblies.” PeerJ. 2019;7(July):e7359.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772.
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 U S A. 2014;111(38):13715–20.
Kopaczyk JM, Warguła J, Jelonek T. The Variability of Terpenes in Conifers under Developmental and Environmental Stimuli. Environ Exp Bot. 2020;180(104197):104197.
Koskella B, Meaden S. Understanding bacteriophage specificity in natural microbial communities. Viruses. 2013;5(3):806–23.
Kurtti TJ, Felsheim RF, Burkhardt NY, Oliver JD, Heu CC, Munderloh UG. “Rickettsia Buchneri Sp. Nov., a Rickettsial Endosymbiont of the Blacklegged Tick Ixodes Scapularis.” Int J Syst Evol Microbiol. 2015;65(Pt 3):965–70.
Ku Y-S, Wang Z, Duan S, Lam H-M. Rhizospheric communication through mobile genetic element transfers for the regulation of microbe-plant interactions. Biology. 2021;10(6):477.
Laforest-Lapointe I, Messier C, Kembel SW. “Host Species Identity, Site and Time Drive Temperate Tree Phyllosphere Bacterial Community Structure.” Microbiome. 2016;4(1):1–10.
Lawley TD, Klimke WA, Gubbins MJ, Frost LS. F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett. 2003;224(1):1–15.
Lee K-Y, Morgan XC, Dunfield PF, Tamas I, McDonald IR, Stott MB. Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. ISME J. 2014;8(7):1522–33.
Le S, He X, Tan Y, Huang G, Zhang L, Lux R, et al. Mapping the tail fiber as the receptor binding protein responsible for differential host specificity of Pseudomonas aeruginosa bacteriophages PaP1 and JG004. PLoS ONE. 2013;8(7):e68562.
Leveau JH, Lindow SE. “Appetite of an Epiphyte: Quantitative Monitoring of Bacterial Sugar Consumption in the Phyllosphere.” Proc Natl Acad Sci U S A. 2001;98(6):3446–53.
Levy A, Gonzalez Salas I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2017;50(1):138–50.
Li F, Zi H, Sonne C, Li X. “Microbiome Sustains Forest Ecosystem Functions across Hierarchical Scales.” Eco-Environment & Health. 2023;2(1):24–31.
Li H. BFC: correcting Illumina sequencing errors. Bioinformatics. 2015;31(17):2885–7.
Li M, Hong L, Ye W, Wang Z, Shen H. Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest. Environ Microbiome. 2022;17(1):29.
Lindow SE, Brandl MT. Microbiology of the phyllosphere. Appl Environ Microbiol. 2003;69(4):1875.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The Carbohydrate-Active Enzymes Database (CAZy) in 2013. Nucleic Acids Res. 2014;42(Database issue):D490–95.
Lomsadze A, Gemayel K, Tang S, Borodovsky M. Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes. Genome Res. 2018;28(7):1079–89.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Low WW, Wong JLC, Beltran LC, Seddon C, David S, Kwong H-S, et al. Mating pair stabilization mediates bacterial conjugation species specificity. Nat Microbiol. 2022;7(7):1016–27.
Meyer KM, Porch R, Muscettola IE, Vasconcelos ALS, Sherman JK, Metcalf CJE, et al. Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. ISME J. 2022. https://doi.org/10.1038/s41396-021-01184-6.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013;41(12):e121.
Mohr KI, Moradi A, Glaeser SP, Kämpfer P, Gemperlein K, Nübel U, et al. Nannocystis konarekensis Sp. Nov., a novel myxobacterium from an Iranian desert. Int J Syst Evol Microbiol. 2018;68(3):721–9.
Moyes AB, Kueppers LM, Pett-Ridge J, Carper DL, Vandehey N, O’Neil J, Frank AC. Evidence for Foliar Endophytic Nitrogen Fixation in a Widely Distributed Subalpine Conifer. New Phytol. 2016;210(2). https://doi.org/10.1111/nph.13850.
Müller DB, Vogel C, Bai Y, Vorholt JA. The plant microbiota: systems-level insights and perspectives. Annu Rev Genet. 2016;50(1):211–34.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, et al. Rfam 12.0: Updates to the RNA Families Database. Nucleic Acids Res. 2015;43 (Database issue):D130.
Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29(22):2933.
Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes. Nat Biotechnol. 2020;39(5):578–85.
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Nies DH. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J Bacteriol. 1995;177(10):2707–12.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824–34. https://doi.org/10.1101/gr.213959.116. Epub 2017 Mar 15. PMID: 28298430; PMCID: PMC5411777.
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497(7451):579–84.
Oksanen J. Vegan : Community Ecology Package. 2010. http://vegan.r-Forge.r-Project.org/
, https://cir.nii.ac.jp/crid/1570291225091856896.
Oksanen J, Simpson GL, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, et al. Vegan: Community Ecology Package. 2025. https://CRAN.R-project.org/package=vegan.
Oliveira PH, Touchon M, Cury J, Rocha EPC. The chromosomal organization of horizontal gene transfer in bacteria. Nat Commun. 2017;8(1):841.
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. “Mash: Fast Genome and Metagenome Distance Estimation Using MinHash.” Genome Biol. 2016;17(1):1–14.
Pan Y, Birdsey RA, Fang J, Houghton R, Kauppi PE, Kurz WA, et al. A large and persistent carbon sink in the world’s forests. Science (New York, NY). 2011;333(6045):988–93.
Passel MWJV, Marri PR, Ochman H. The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput Biol. 2008;4(4):e1000059.
Pimentel D, Harvey C, Resosudarmo P, Sinclair K, Kurz D, McNair M, et al. “Environmental and Economic Costs of Soil Erosion and Conservation Benefits.” Science. 1995;267(5201):1117–23.
Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD. HMMER web server: 2018 update. Nucleic Acids Res. 2018;46(W1):W200-204.
Putkinen A, Siljanen HMP, Laihonen A, Paasisalo I, Porkka K, Tiirola M, et al. New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. New Phytol. 2021;231(2):524–36.
Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, et al. The TetR Family of Transcriptional Repressors. Microbiol Mol Biol Rev. 2005;69(2):326–56.
R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. 2024. https://www.R-project.org/.
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(11):2885–93.
Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, et al. Terabase-scale coassembly of a tropical soil microbiome. Microbiol Spectr. 2023;11(4):e00200–23. https://doi.org/10.1128/spectrum.00200-23.
Roberson EB, Firestone MK. Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp. Appl Environ Microbiol. 1992;58(4):1284–91.
Rodríguez-Rodríguez JC, Bergeron Y, Kembel SW, Fenton NJ. Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses. Environ Microbiol. 2022;24(8):3517–28.
Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B, Lejla Pašić T, Thingstad F, Rohwer F, et al. Explaining Microbial Population Genomics through Phage Predation. Nat Rev Microbiol. 2009;7(11):828–36.
Rousk K, Jones DL, DeLuca TH. Moss-Cyanobacteria Associations as Biogenic Sources of Nitrogen in Boreal Forest Ecosystems. Front Microbiol. 2013;4. https://doi.org/10.3389/fmicb.2013.00150.
Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, Nayfach S, Tritt A. iPHoP: An Integrated Machine-Learning Framework to Maximize Host Prediction for Metagenome-Assembled Virus Genomes. bioRxiv. 2022. https://doi.org/10.1101/2022.07.28.501908.
Roux S, Camargo AP, Coutinho FH, Dabdoub SM, Dutilh BE, Nayfach S, Tritt A. iPHoP: An Integrated Machine Learning Framework to Maximize Host Prediction for Metagenome-Derived Viruses of Archaea and Bacteria. PLoS Biol. 2023;21(4):e3002083.
Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev. 2020;44(5):606–30.
Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biol. 2020;21(1):244.
Saraiva JP, Bartholomäus A, Toscan RB, Baldrian P, da Rocha UN. “Recovery of 197 Eukaryotic Bins Reveals Major Challenges for Eukaryote Genome Reconstruction from Terrestrial Metagenomes.” Mol Ecol Resour. 2023;23(5):1066–76.
Seidl R, Thom D, Kautz M, Martin-Benito D, Peltoniemi M, Vacchiano G, et al. Forest disturbances under climate change. Nat Clim Change. 2017;7(6):395–402.
Seppey M, Manni M, Zdobnov EM. BUSCO: Assessing Genome Assembly and Annotation Completeness. In Methods in Molecular Biology, 2019;1962:227–45. Humana Press Inc.
Shaw J, Yu YW. Fast and robust metagenomic sequence comparison through sparse chaining with Skani. Nat Methods. 2023;20(11):1661–5.
Shkoporov AN, Hill C. Bacteriophages of the Human Gut: The ‘Known Unknown’ of the Microbiome. Cell Host Microbe. 2019;25(2):195–209.
Song W, Wemheuer B, Zhang S, Steensen K, Thomas T. MetaCHIP: Community-Level Horizontal Gene Transfer Identification through the Combination of Best-Match and Phylogenetic Approaches. Microbiome. 2019;7(1). https://doi.org/10.1186/s40168-019-0649-y.
Takeda K. Characteristics of a nitrogen-fixing methanotroph, Methylocystis T-1. Antonie Van Leeuwenhoek. 1988;54(6):521–34.
Tatum LA. “The Southern Corn Leaf Blight Epidemic: A New Race of the Fungus Helminthosporium Maydis Threatens Domestic Prices and Corn Reserves for Export.” Science. 1971;171(3976):1113–6.
Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. The Phyllosphere: Microbial Jungle at the Plant–climate Interface. Annu Rev Ecol Evol Syst. 2016;47(1):1–24.
Van Dongen S. “Graph Clustering Via a Discrete Uncoupling Process.” SIAM J Matrix Anal Appl. 2008;30(1):121–41.
Vorholt JA. “Microbial Life in the Phyllosphere.” Nat Rev Microbiol. 2012. https://doi.org/10.1038/nrmicro2910.
Wang W, Schalamun M, Morales-Suarez A, Kainer D, Schwessinger B, Lanfear R. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics. 2018;19(1):977.
Warner DF, Ndwandwe DE, Abrahams GL, Kana BD, Machowski EE, Venclovas C, et al. Essential Roles for imuA’- and imuB-Encoded Accessory Factors in DnaE2-Dependent Mutagenesis in Mycobacterium Tuberculosis. Proc Natl Acad Sci USA. 2010;107(29):13093–8.
West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res. 2018;28(4):569–80.
Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-Verlag; 2016.
Yamaguchi Y, Park J-H, Inouye M. Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet. 2011;45(1):61–79.
Yu G, Smith DK, Zhu H, Guan Yi, Lam T-Y. Ggtree : an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8(1):28–36. Edited by Greg McInerny.
Zheng J, Ge Q, Yan Y, Zhang X, Huang Le, Yin Y. “dbCAN3: Automated Carbohydrate-Active Enzyme and Substrate Annotation.” Nucleic Acids Res. 2023;51(W1):W115–21.