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Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

The ISME Journalvolume 12pages10611071 (2018) | Download Citation


Changes in frequency and amplitude of rain events, that is, precipitation patterns, result in different water conditions with soil depth, and likely affect plant growth and shape plant and soil microbial activity. Here, we used 18O stable isotope probing (SIP) to investigate bacterial and fungal communities that actively grew or not upon rewetting, at three different depths in soil mesocosms previously subjected to frequent or infrequent watering for 12 weeks (equal total water input). Phylogenetic marker genes for bacteria and fungi were sequenced after rewetting, and plant-soil microbial coupling documented by plant 13C-CO2 labeling. Soil depth, rather than precipitation pattern, was most influential in shaping microbial response to rewetting, and had differential effects on active and inactive bacterial and fungal communities. After rewetting, active bacterial communities were less rich, more even and phylogenetically related than the inactive, and reactivated throughout the soil profile. Active fungal communities after rewetting were less abundant and rich than the inactive. The coupling between plants and soil microbes decreased under infrequent watering in the top soil layer. We suggest that differences in fungal and bacterial abundance and relative activity could result in large effects on subsequent soil biogeochemical cycling.

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These authors contributed equally: Ilonka C. Engelhardt, Amy Welty.


  1. 1.

    IPCC. Climate change 2007: impacts, adaptation and vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, UK: Cambridge University Press; 2007.

  2. 2.

    Sowerby A, Emmett BA, Tietema A, Beier C. Contrasting effects of repeated summer drought on soil carbon efflux in hydric and mesic heathland soils. Glob Change Biol. 2008;14:2388–404.

  3. 3.

    Ruehr NK, Offerman C, Gessler A, Winkler BJ, Ferrio JP, Buchmann N, et al. Effects of drought on allocation of recent carbon: from beech leaves to soil respiration. New Phytol. 2009;184:950–61.

  4. 4.

    Bloor JMG, Bardgett RD. Stability of above-ground and below-ground processes to extreme drought in model grassland ecosystems: interactions with plant species diversity and soil nitrogen availability. Perspect Plant Ecol Evol Syst. 2012;14:193–204.

  5. 5.

    Hartmann AA, Niklaus PA. Effects of simulated drought and nitrogen fertilizer on plant productivity and nitrous oxide (N2O) emissions of two pastures. Plant Soil. 2012;361:411–26.

  6. 6.

    Bimüller C, Dannenmann M, Tejedor J, von Lützow M, Buegger F, Meier R, et al. Prolonged summer droughts retard soil N processing and stabilization in organo-mineral fractions. Soil Biol Biochem. 2014;68:241–51.

  7. 7.

    Fuchslueger L, Bahn M, Hasibeder R, Kienzl S, Fritz K, Schmitt M, et al. Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event. J Ecol. 2016;104:1453–65.

  8. 8.

    Hoover DL, Knapp AK, Smith MD. The immediate and prolonged effects of climate extremes on soil respiration in a mesic grassland. J Geophys Res Biogeosci. 2016;121:1034–44.

  9. 9.

    Canarini A, Dijkstra FA. Dry-rewetting cycles regulate wheat carbon rhizodeposition, stabilization and nitrogen cycling. Soil Biol Biochem. 2015;81:195–203.

  10. 10.

    Chou WW, Silver WL, Jackson RD, Thompson AW, Allen-Diaz B. The sensitivity of annual grassland carbon cycling to the quantity and timing of rainfall. Glob Change Biol. 2008;14:1382–94.

  11. 11.

    Nielsen UN, Ball BA. Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems. Glob Chang Biol. 2015;21:1407–21.

  12. 12.

    Placella SA, Brodie EL, Firestone MK. Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc Natl Acad Sci USA. 2012;109:10931–6.

  13. 13.

    Barnard RL, Osborne CA, Firestone MK. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME J. 2013;7:2229–41.

  14. 14.

    de Vries FT, Shade A. Controls on soil microbial community stability under climate change. Front Microbiol. 2013;4:265.

  15. 15.

    Landesman WJ, Dighton J. Shifts in microbial biomass and the bacteria: fungi ratio occur under field conditions within 3 h after rainfall. Microb Ecol. 2011;62:228–36.

  16. 16.

    Barnard RL, Osborne CA, Firestone MK. Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate. ISME J. 2015;9:947–57.

  17. 17.

    de Boer W, Folman LB, Summerbell RC, Boddy L. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev. 2005;29:795–811.

  18. 18.

    Gordon H, Haygarth PM, Bardgett RD. Drying and rewetting effects on soil microbial community composition and nutrient leaching. Soil Biol Biochem. 2008;40:302–11.

  19. 19.

    Ebrahimi A, Or D. Hydration and diffusion processes shape microbial community organization and function in model soil aggregates. Water Resour Res. 2015;51:9804–27.

  20. 20.

    Tecon R, Or D. Bacterial flagellar motility on hydrated rough surfaces controlled by aqueous film thickness and connectedness. Sci Rep. 2016;6:19409.

  21. 21.

    Dechesne A, Wang G, Gülez G, Or D, Smets BF. Hydration-controlled bacterial motility and dispersal on surfaces. Proc Natl Acad Sci USA. 2010;107:14369–72.

  22. 22.

    Wang G, Or D. Hydration dynamics promote bacterial coexistence on rough surfaces. ISME J. 2013;7:395–404.

  23. 23.

    Volkmann TH, Haberer K, Gessler A, Weiler M. High-resolution isotope measurements resolve rapid ecohydrological dynamics at the soil-plant interface. New Phytol. 2016;210:839–49.

  24. 24.

    Hasibeder R, Fuchslueger L, Richter A, Bahn M. Summer drought alters carbon allocation to roots and root respiration in mountain grassland. New Phytol. 2015;205:1117–27.

  25. 25.

    von Rein I, Gessler A, Premke K, Keitel C, Ulrich A, Kayler ZE. Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum. Glob Chang Biol. 2016a;22:2861–74.

  26. 26.

    Vance ED, Brookes PC, Jenkinson DS. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem. 1987;19:703–7.

  27. 27.

    Lang SQ, Bernasconi SM, Früh-Green GL. Stable isotope analysis of organic carbon in small (μg C) samples and dissolved organic matter using a GasBench preparation device. Rapid Commun Mass Spectrom. 2012;6:9–16.

  28. 28.

    Blazewicz SJ, Schwartz E. Dynamics of 18O incorporation from H2 18O into soil microbial DNA. Microb Ecol. 2011;61:911–6.

  29. 29.

    Muyzer G, de Waal EC, Uitierlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59:695–700.

  30. 30.

    White TJ, Bruns T, Lee S, Taylor JW. PCR protocols: a guide to methods and applications. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. New York: Academic Press Inc.; 1990. p. 315–22.

  31. 31.

    Berry D, Ben Mahfoudh K, Wagner M, Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol. 2011;77:7846–9.

  32. 32.

    Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M. Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing. PLoS ONE. 2014;9:e105592.

  33. 33.

    Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.

  34. 34.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010b;7:335–6.

  35. 35.

    Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.

  36. 36.

    Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010a;26:266–7.

  37. 37.

    Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum-evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26:1641–50.

  38. 38.

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

  39. 39.

    McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.

  40. 40.

    Altschul SF, Gish W, Webb M, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.

  41. 41.

    Abarenkov K, Nilsson RH, Larsson KH, Alexander IJ, Eberhardt U, Erland S, et al. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist. 2010;186:281–5.

  42. 42.

    Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–35.

  43. 43.

    Webb CO. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am Nat. 2000;156:145–55.

  44. 44.

    Webb CO, Ackerly DD, M MA, Donoghue MJ. Phylogenies and community ecology. Annu Rev Ecol Syst. 2002;33:475–505.

  45. 45.

    Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26:1463–4.

  46. 46.

    R Core Team (2014). R: a language and environment for statistical computing. Vol. ISBN 3-900051-07-0: Vienna, Austria.

  47. 47.

    Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.

  48. 48.

    Strimmer K. fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics. 2008;24:1461–2.

  49. 49.

    Al Majou H, Bruand A, Duval O, Le Bas C, Vautier A. Prediction of soil water retention properties after stratification by combining texture, bulk density and the type of horizon. Soil Use Manag. 2008;24:383–91.

  50. 50.

    Fuchslueger L, Bahn M, Fritz K, Hasibeder R, Richter A. Experimental drought reduces the transfer of recently fixed plant carbon to soil microbes and alters the bacterial community composition in a mountain meadow. New Phytol. 2014;201:916–27.

  51. 51.

    Moyano FE, Manzoni S, Chenu C. Responses of soil heterotrophic respiration to moisture availability: an exploration of processes and models. Soil Biol Biochem. 2013;59:72–85.

  52. 52.

    von Rein I, Kayler ZE, Premke K, Gessler A. Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms. Plant Biol (Stuttg). 2016b;18:947–61.

  53. 53.

    Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 2009;3:738–44.

  54. 54.

    Evans SE, Wallenstein MD. Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter? Biogeochemistry. 2012;109:101–16.

  55. 55.

    Slaughter LC, Weintraub MN, McCulley RL. Seasonal effects stronger than three-year climate manipulation on grassland soil microbial community. Soil Sci Soc Am J. 2015;79:1352.

  56. 56.

    Zeglin LH, Bottomley PJ, Jumpponen A, Rice CW, Arango M, Lindsley A, et al. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales. Ecology. 2013;94:2334–45.

  57. 57.

    Taketani RG, Lanconi MD, Kavamura VN, Durrer A, Andreote FD, Melo IS. Dry season constrains bacterial phylogenetic diversity in a semi-arid rhizosphere system. Microb Ecol. 2017;73:153–61.

  58. 58.

    Jumpponen A, Jones KL. Tallgrass prairie soil fungal communities are resilient to climate change. Fungal Ecol. 2014;10:44–57.

  59. 59.

    Bapiri A, Bååth E, Rousk J. Drying–rewetting cycles affect fungal and bacterial growth differently in an arable soil. Microb Ecol. 2010;60:419–28.

  60. 60.

    Yuste JC, Penuelas J, Estiarte M, Garcia-Mas J, Mattana S, Ogaya R, et al. Drought-resistant fungi control soil organic matter decomposition and its response to temperature. Glob Change Biol. 2011;17:1475–86.

  61. 61.

    de Vries FT, Liiri ME, Bjornlund L, Bowker MA, Christensen S, Setala HM, et al. Land use alters the resistance and resilience of soil food webs to drought. Nat Clim Change. 2012;2:276–80.

  62. 62.

    Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, et al. Phylogenetic organization of bacterial activity. ISME J. 2016;10:2336–40.

  63. 63.

    Angel R, Pasternak Z, Soares MI, Conrad R, Gillor O. Active and total prokaryotic communities in dryland soils. FEMS Microbiol Ecol. 2013;86:130–8.

  64. 64.

    Eilers KG, Debenport S, Anderson S, Fierer N. Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem. 2012;50:58–65.

  65. 65.

    Jumpponen A, Jones KL, Blair J. Vertical distribution of fungal communities in tallgrass prairie soil. Mycologia. 2010;102:1027–41.

  66. 66.

    Vargas-Gastelum L, Romero-Olivares AL, Escalante AE, Rocha-Olivares A, Brizuela C, Riquelme M. Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing. FEMS Microbiol Ecol. 2015;91:fiv044.

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This research was supported by funding from the ANR (project INCITE, ANR-13-JSV7-0004), the European Commission (Career Integration Grant FP7-MC-CIG #618010) and the Conseil Régional de Bourgogne to RB. IE was supported in part by an INRA Ph.D. fellowship (Département Environnement et Agronomie). AG acknowledges support by an SNF grant (31003A_159866). We thank François Nuge and Xavier Buisson for kindly letting us use their soil, Michel Laderach (Dijon Céréales) for providing the seeds, Karine Palavioux, Céline Bernard, Franck Zenk, Damien Gironde, and Noureddine El Mjiyad for help in the greenhouse, Jérôme Fromentin for the ultracentrifuge, Samuel Jacquiod for sharing on functional response groups, Livio Antonielli for bioinformatics discussions, Virginie Bourion for root scans, Florian Bizouard for grinding, Marielle Adrian and Marie-Claire Héloir for the Li-6400, Arnaud Coffin and Marjorie Ubertosi for soil retention data. Matthieu Barret kindly provided the bacterial mock community, assembled within the MetaBAR project funded by the INRA MEM Metaprogramme.

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Author notes

    • Amy Welty

    Present address: Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA


  1. Agroécologie, INRA, AgroSup Dijon, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France

    • Ilonka C. Engelhardt
    • , Amy Welty
    • , David Bru
    • , Nadine Rouard
    • , Marie-Christine Breuil
    • , Aymé Spor
    •  & Romain L. Barnard
  2. Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA

    • Steven J. Blazewicz
  3. Swiss Federal Research Institute WSL, Zuercherstr. 111, 8903, Birmensdorf, Switzerland

    • Arthur Gessler
    •  & Lucía Galiano
  4. Forest History, Physiology and Genetics Research Group, Universidad Politecnica de Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain

    • José Carlos Miranda


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The authors declare that they have no conflict of interest.

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Correspondence to Romain L. Barnard.

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