in

Seasonal activities of the phyllosphere microbiome of perennial crops

  • Robertson, G. P. et al. Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes. Sci. (80-.) 356, 1–9 (2017).

    Article 

    Google Scholar 

  • Ma, L. et al. The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus. Phytobiomes J. 5, 51–59 (2021).

    Article 

    Google Scholar 

  • Hestrin, R., Lee, M. R., Whitaker, B. K. & Pett-Ridge, J. The switchgrass microbiome: a review of structure, function, and taxonomic distribution. Phytobiomes J. 5, 14–28 (2021).

    Article 

    Google Scholar 

  • Heaton, E. A., Dohleman, F. G. & Long, S. P. Meeting US biofuel goals with less land: The potential of Miscanthus. Glob. Chang. Biol. 14, 2000–2014 (2008).

    Article 
    ADS 

    Google Scholar 

  • Langholtz, M., Stokes, B. & Eaton, L. 2016 billion-ton report: Advancing domestic resources for a thriving bioeconomy (Executive Summary). Ind. Biotechnol. 12, 282–289 (2016).

    Article 

    Google Scholar 

  • Roley, S. S. et al. Associative nitrogen fixation (ANF) across a nitrogen input gradient. PLoS One 13, 1–19 (2018).

    Article 

    Google Scholar 

  • Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).

    Article 
    PubMed 

    Google Scholar 

  • Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, 1–14 (2017).

    Article 

    Google Scholar 

  • Wang, N. R. & Haney, C. H. Harnessing the genetic potential of the plant microbiome. Biochem. (Lond.) 42, 20–25 (2020).

    Article 
    CAS 

    Google Scholar 

  • Haskett, T. L., Tkacz, A. & Poole, P. S. Engineering rhizobacteria for sustainable agriculture. ISME J. 15, 949–964 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hacquard, S. et al. Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17, 603–616 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gopal, M. & Gupta, A. Microbiome selection could spur next-generation plant breeding strategies. Front. Microbiol. 7, 1971 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hardoim, P. R. et al. The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Andrews, J. H. & Harris, R. F. The ecology and biogeography of microorganisms on plant surfaces. Annu. Rev. Phytopathol. 38, 145–180 (2000).

    Article 
    PubMed 

    Google Scholar 

  • Bulgarelli, D., Schlaeppi, K., Spaepen, S., van Themaat, E. V. L. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Müller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The Plant Microbiota: Systems-Level Insights and Perspectives. Annu. Rev. Genet. 50, 120215–034952 (2016).

    Article 

    Google Scholar 

  • Kuzyakov, Y. & Razavi, B. S. Rhizosphere size and shape: Temporal dynamics and spatial stationarity. Soil Biol. Biochem. 135, 343–360 (2019).

    Article 
    CAS 

    Google Scholar 

  • Bell, T. H. et al. Manipulating wild and tamed phytobiomes: Challenges and opportunities. Phytobiomes J. 3, 3–21 (2019).

    Article 

    Google Scholar 

  • Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Koskella, B. The phyllosphere. Curr. Biol. 30, R1143–R1146 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bringel, F. & Couée, I. Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front. Microbiol. 6, 486 (2015).

  • Dorokhov, Y. L., Sheshukova, E. V. & Komarova, T. V. Methanol in plant life. Front. Plant Sci. 871, 1–6 (2018).

    Google Scholar 

  • Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Peñuelas, J. & Terradas, J. The foliar microbiome. Trends Plant Sci. 19, 278–280 (2014).

    Article 
    PubMed 

    Google Scholar 

  • Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA. 112, E911–E920 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl Acad. Sci. 115, E4284–E4293 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shade, A. & Stopnisek, N. Abundance-occupancy distributions to prioritize plant core microbiome membership. Curr. Opin. Microbiol. 49, 50–58 (2019).

    Article 
    PubMed 

    Google Scholar 

  • Stopnisek, N. & Shade, A. Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. ISME J. 15, 2708–2722 (2021).

  • Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. & Shade, A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat. Commun. 10, 4135 (2019).

  • Singer, E., Bonnette, J., Kenaley, S. C., Woyke, T. & Juenger, T. E. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. Environ. Microbiol. Rep. 11, 185–195 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Bahulikar, R. A., Torres-Jerez, I., Worley, E., Craven, K. & Udvardi, M. K. Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of Northern Oklahoma. Appl. Environ. Microbiol. 80, 5636–5643 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Roley, S. S., Xue, C., Hamilton, S. K., Tiedje, J. M. & Robertson, G. P. Isotopic evidence for episodic nitrogen fixation in switchgrass (Panicum virgatum L.). Soil Biol. Biochem. 129, 90–98 (2019).

    Article 
    CAS 

    Google Scholar 

  • Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yoon, S. H., Ha, S. M., Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van. Leeuwenhoek, Int. J. Gen. Mol. Microbiol. 110, 1281–1286 (2017).

    Article 
    CAS 

    Google Scholar 

  • Julsing, M. K., Rijpkema, M., Woerdenbag, H. J., Quax, W. J. & Kayser, O. Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis. Appl. Microbiol. Biotechnol. 75, 1377–1384 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Laskowska, E. & Kuczyńska-Wiśnik, D. New insight into the mechanisms protecting bacteria during desiccation. Curr. Genet. 66, 313–318 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zou, H. et al. The metabolism and biotechnological application of betaine in microorganism. Appl. Microbiol. Biotechnol. 100, 3865–3876 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Rastogi, G., Coaker, G. L. & Leveau, J. H. J. New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol. Lett. 348, 1–10 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Urrejola, C. et al. Genomic features for desiccation tolerance and sugar biosynthesis in the extremophile gloeocapsopsis sp. UTEX B3054. Front. Microbiol. 10, 1–11 (2019).

    Article 

    Google Scholar 

  • Lacerda-Júnior, G. V. et al. Land use and seasonal effects on the soil microbiome of a Brazilian dry forest. Front. Microbiol. 10, 1–14 (2019).

    Article 

    Google Scholar 

  • Dai, J. et al. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci. Rep. 5, 1–9 (2015).

    Article 

    Google Scholar 

  • Harty, C. E. et al. Ethanol stimulates trehalose production through a SpoT-DksA-AlgU-dependent pathway in Pseudomonas aeruginosa. J. Bacteriol. 201, 1–21 (2019).

  • Kimmerer, T. W. & MacDonald, R. C. Acetaldehyde and ethanol biosynthesis in leaves of plants. Plant Physiol. 84, 1204–1209 (1987).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ferner, E., Rennenberg, H. & Kreuzwieser, J. Effect of flooding on C metabolism of flood-tolerant (Quercus robur) and non-tolerant (Fagus sylvatica) tree species. Tree Physiol. 32, 135–145 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kimmerer, T. W. & Kozlowski, T. T. Ethylene, ethane, acetaldehyde, and ethanol production by plants under stress. Plant Physiol. 69, 840–847 (1982).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, Y. et al. Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters. Biotechnol. Biofuels 8, 1–18 (2015).

    Article 

    Google Scholar 

  • Wingler, A. et al. Trehalose 6-phosphate is required for the onset of leaf senescence associated with high carbon availability. Plant Physiol. 158, 1241–1251 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gottschlich, L., Geiser, P., Bortfeld-Miller, M., Field, C. M. & Vorholt, J. A. Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses. Sci. Rep. 9, 1–13 (2019).

    Article 
    CAS 

    Google Scholar 

  • Chen, C., Li, S., McKeever, D. R. & Beattie, G. A. The widespread plant-colonizing bacterial species Pseudomonas syringae detects and exploits an extracellular pool of choline in hosts. Plant J. 75, 891–902 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Valenzuela-Soto, E. M. & Figueroa-Soto, C. G. Biosynthesis and degradation of glycine betaine and its potential to control plant growth and development. in Osmoprotectant-Mediated Abiotic Stress Tolerance in Plants (eds. Anwar Hossain, M., Kumar, V., Burritt, D. J., Fujita, M. & Makela, P. S. A.) 241–256 (Springer, 2019). https://doi.org/10.1007/978-3-030-27423-8_5.

  • Kerchev, P., De Smet, B., Waszczak, C., Messens, J. & Van Breusegem, F. Redox strategies for crop improvement. Antioxid. Redox Signal 23, 1186–1205 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Considine, M. J. & Foyer, C. H. Redox regulation of plant development. Antioxid. Redox Signal. 21, 1305–1326 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Spaepen, S., Vanderleyden, J. & Remans, R. Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol. Rev. 31, 425–448 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Egamberdieva, D., Wirth, S. J., Alqarawi, A. A., Abd-Allah, E. F. & Hashem, A. Phytohormones and beneficial microbes: Essential components for plants to balance stress and fitness. Front. Microbiol. 8, 1–14 (2017).

    Article 

    Google Scholar 

  • Lajoie, G., Maglione, R. & Kembel, S. W. Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. Microbiome 8, 1–10 (2020).

    Article 

    Google Scholar 

  • McGenity, T. J., Crombie, A. T. & Murrell, J. C. Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth. ISME J. 12, 931–941 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sharkey, T. D., Wiberley, A. E. & Donohue, A. R. Isoprene emission from plants: Why and how. Ann. Bot. 101, 5–18 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Zuo, Z. et al. Isoprene acts as a signaling molecule in gene networks important for stress responses and plant growth. Plant Physiol. 180, 124–152 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sharkey, T. D. & Yeh, S. Isoprene emission from plants. Plant Mol. Biol. 52, 407–436 (2001).

    CAS 

    Google Scholar 

  • Sharkey, T. D., Loreto, F. & Delwiche, C. High carbon dioxide and sun/shade effects on isoprene emission from oak and aspen tree leaves. Plant, Cell Environ. 14, 333–338 (1991).

    Article 
    CAS 

    Google Scholar 

  • Eller, A. S. D. et al. Volatile organic compound emissions from switchgrass cultivars used as biofuel crops. Atmos. Environ. 45, 3333–3337 (2011).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Morrison, E. C., Drewer, J. & Heal, M. R. A comparison of isoprene and monoterpene emission rates from the perennial bioenergy crops short-rotation coppice willow and Miscanthus and the annual arable crops wheat and oilseed rape. GCB Bioenergy 8, 211–225 (2016).

    Article 
    CAS 

    Google Scholar 

  • Sivy, T. L., Shirk, M. C. & Fall, R. Isoprene synthase activity parallels fluctuations of isoprene release during growth of Bacillus subtilis. Biochem. Biophys. Res. Commun. 294, 71–75 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Crombie, A. T. et al. Poplar phyllosphere harbors disparate isoprene-degrading bacteria. Proc. Natl Acad. Sci. USA. 115, 13081–13086 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • El Khawand, M. et al. Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing. Environ. Microbiol. 18, 2743–2753 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nowicka, B. & Kruk, J. Occurrence, biosynthesis and function of isoprenoid quinones. Biochim. Biophys. Acta – Bioenerg. 1797, 1587–1605 (2010).

    Article 
    CAS 

    Google Scholar 

  • Kałużna, M. et al. Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry. Syst. Appl. Microbiol. 39, 370–377 (2016).

    Article 
    PubMed 

    Google Scholar 

  • El-Tarabily, K. A., Nassar, A. H., Hardy, G. E. S. J. & Sivasithamparam, K. Plant growth promotion and biological control of Pythium aphanidermatum, a pathogen of cucumber, by endophytic actinomycetes. J. Appl. Microbiol 106, 13–26 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Javed, Z., Tripathi, G. D., Mishra, M. & Dashora, K. Actinomycetes – the microbial machinery for the organic-cycling, plant growth, and sustainable soil health. Biocatal. Agric. Biotechnol. 31, 101893 (2021).

    Article 
    CAS 

    Google Scholar 

  • Anwar, S., Ali, B. & Sajid, I. Screening of rhizospheric actinomycetes for various in-vitro and in-vivo plant growth promoting (PGP) traits and for agroactive compounds. Front. Microbiol. 7, 1–11 (2016).

    Article 

    Google Scholar 

  • Bao, L. et al. Microbial community overlap between the phyllosphere and rhizosphere of three plants from Yongxing Island, South China Sea. Microbiologyopen 9, 1–18 (2020).

    Article 

    Google Scholar 

  • Remus-Emsermann, M. N. P. & Schlechter, R. O. Phyllosphere microbiology: at the interface between microbial individuals and the plant host. N. Phytol. 218, 1327–1333 (2018).

    Article 

    Google Scholar 

  • Beilsmith, K. et al. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host–microbe interactions. Plant J. 97, 164–181 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Levy, A., Conway, J. M., Dangl, J. L. & Woyke, T. Elucidating bacterial gene functions in the plant microbiome. Cell Host Microbe 24, 475–485 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Choi, H. et al. Identification of viruses and viroids infecting tomato and pepper plants in vietnam by metatranscriptomics. Int. J. Mol. Sci. 21, 1–16 (2020).

    Article 
    ADS 

    Google Scholar 

  • Marzano, S. Y. L. & Domier, L. L. Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Res 213, 332–342 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Chao S, et al. Metatranscriptomic sequencing suggests the presence of novel RNA viruses in rice rransmitted by brown planthopper. Viruses. 13, 2464 (2021).

  • Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl Acad. Sci. 106, 16428–16433 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Suzuki, Y., Makino, A. & Mae, T. An efficient method for extraction of RNA from rice leaves at different ages using benzyl chloride. J. Exp. Bot. 52, 1575–1579 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. 108, 4516–4522 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Druzhinina, I. S. et al. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet. 14, e1007322 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Haridas, S. et al. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud. Mycol. 96, 141–153 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gostinčar, C. et al. Genome sequencing of four Aureobasidium pullulans varieties: Biotechnological potential, stress tolerance, and description of new species. BMC Genomics 15, 549 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gill, U. S. et al. Draft genome sequence resource of switchgrass rust pathogen, puccinia novopanici isolate ard-01. Phytopathology 109, 1513–1515 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Bowsher, A. W., Benucci, G. M. N., Bonito, G. & Shade, A. Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria. Phytobiomes J. 5, 60–68 (2021).

  • Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kang, D. D. et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 2019, 1–13 (2019).

    Google Scholar 

  • Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Swan, B. K. et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl Acad. Sci. USA. 110, 11463–11468 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for’omics data. PeerJ. 2015, 1–29 (2015).

    Google Scholar 

  • Lee, M. D. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35, 4162–4164 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Blin, K. et al. AntiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–W35 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Navarro-Muñoz, J. C. et al. A computational framework to explore large-scale biosynthetic diversity. Nat. Chem. Biol. 16, 60–68 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Zimmermann, J., Kaleta, C. & Waschina, S. Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol. 22, 1–35 (2021).

    Article 

    Google Scholar 

  • Tseng, T. T., Tyler, B. M. & Setubal, J. C. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol 9, 1–9 (2009).

    Article 

    Google Scholar 

  • Lucke, M., Correa, M. G. & Levy, A. The role of secretion systems, effectors, and secondary metabolites of beneficial rhizobia in interactions with plants and microbes. Front. Plant Sci. 11, 589416 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Palmer, J. L., Hilton, S., Picot, E., Bending, G. D. & Schäfer, H. Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria. Environ. Microbiol. 23, 6309–6327 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Bay, S. K. et al. Trace gas oxidizers are widespread and active members of soil microbial communities. Nat. Microbiol. 6, 246–256 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 


  • Source: Ecology - nature.com

    Rethinking river water temperature in a changing, human-dominated world

    Improving health outcomes by targeting climate and air pollution simultaneously