Organic Fertilization Enhances the Resistance and Resilience of Soil Microbial Communities Under Extreme Drought

Overview

Journal J Adv Res

Specialties General Medicine
Science

Date 2022 Jul 30

PMID 35907631

Authors

Yifei Sun

Chengyuan Tao

Xuhui Deng

Hongjun Liu

Zongzhuan Shen

Yaxuan Liu

Rong Li

Qirong Shen

Stefan Geisen

Affiliations

Soon will be listed here.

Abstract

Introduction: The soil bacterial microbiome plays a crucial role in ecosystem functioning. The composition and functioning of the microbiome are tightly controlled by the physicochemical surrounding. Therefore, the microbiome is responsive to management, such as fertilization, and to climate change, such as extreme drought. It remains a challenge to retain microbiome functioning under drought.

Objectives: This work aims to reveal if fertilization with organic fertilizer, can enhance resistance and resilience of bacterial communities and their function in extreme drought and subsequent rewetting compared with conventional fertilizers.

Methods: In soil mesocosms, we induced a long-term drought for 80 days with subsequent rewetting for 170 days to follow bacterial community dynamics in organic (NOF) and chemical (NCF) fertilization regimes.

Results: Our results showed that bacterial diversity was higher with NOF than with NCF during drought. In particular, the ecological resilience and recovery of bacterial communities under NOF were higher than in NCF. We found these bacterial community features to enhance pathogen-inhibiting functions in NOF compared to NCF during late recovery. The other soil ecology functional analyses revealed that bacterial biomass recovered in the early stage after rewetting, while soil respiration increased continuously following prolonged time after rewetting.

Conclusion: Together, our study indicates that organic fertilization can enhance the stability of the soil microbiome and ensures that specific bacterial-driven ecosystem functions recover after rewetting. This may provide the basis for more sustainable agricultural practices to counterbalance negative climate change-induced effects on soil functioning.

Citing Articles

Co-application of sheep manure and commercial organic fertilizer enhances plant productivity and soil quality in alpine mining areas.

Yu Z, Yao X, Yang M, Hu S, An X, Li C Front Microbiol. 2024; 15:1488121.

PMID: 39664060 PMC: 11632135. DOI: 10.3389/fmicb.2024.1488121.

Reducing drought vulnerability of forest soils using Xanthan gum-based soil conditioners.

Smolar J, Fortuna B, Logar J, Sorze A, Valentini F, Macek M Heliyon. 2024; 10(21):e39974.

PMID: 39568826 PMC: 11577230. DOI: 10.1016/j.heliyon.2024.e39974.

Abundance, diversity, and composition of root-associated microbial communities varied with tall fescue cultivars under water deficit.

Hu J, Miller G, Shi W Front Microbiol. 2023; 13:1078836.

PMID: 36713160 PMC: 9878326. DOI: 10.3389/fmicb.2022.1078836.

Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances.

Sun Y, Deng X, Tao C, Liu H, Shen Z, Liu Y mSystems. 2022; 7(5):e0055922.

PMID: 36121168 PMC: 9600180. DOI: 10.1128/msystems.00559-22.

References

de Vries F, Shade A . Controls on soil microbial community stability under climate change. Front Microbiol. 2013; 4:265. PMC: 3768296. DOI: 10.3389/fmicb.2013.00265. View

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

Rivett D, Bell T . Abundance determines the functional role of bacterial phylotypes in complex communities. Nat Microbiol. 2018; 3(7):767-772. PMC: 6065991. DOI: 10.1038/s41564-018-0180-0. View

Yergeau E, Kowalchuk G . Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency. Environ Microbiol. 2008; 10(9):2223-35. DOI: 10.1111/j.1462-2920.2008.01644.x. View

Bardgett R, van der Putten W . Belowground biodiversity and ecosystem functioning. Nature. 2014; 515(7528):505-11. DOI: 10.1038/nature13855. View

Wittwer R, Bender S, Hartman K, Hydbom S, Lima R, Loaiza V . Organic and conservation agriculture promote ecosystem multifunctionality. Sci Adv. 2021; 7(34). PMC: 8378818. DOI: 10.1126/sciadv.abg6995. View

Tao C, Li R, Xiong W, Shen Z, Liu S, Wang B . Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression. Microbiome. 2020; 8(1):137. PMC: 7510105. DOI: 10.1186/s40168-020-00892-z. View

Guo S, Tao C, Jousset A, Xiong W, Wang Z, Shen Z . Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. ISME J. 2022; 16(8):1932-1943. PMC: 9296445. DOI: 10.1038/s41396-022-01244-5. View

Evans S, Wallenstein M, Burke I . Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought?. Ecology. 2014; 95(1):110-22. DOI: 10.1890/13-0500.1. View

10.

Gibbons S . Keystone taxa indispensable for microbiome recovery. Nat Microbiol. 2020; 5(9):1067-1068. DOI: 10.1038/s41564-020-0783-0. View

11.

Kozich J, Westcott S, Baxter N, Highlander S, Schloss P . Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013; 79(17):5112-20. PMC: 3753973. DOI: 10.1128/AEM.01043-13. View

12.

Nocker A, Fernandez P, Montijn R, Schuren F . Effect of air drying on bacterial viability: A multiparameter viability assessment. J Microbiol Methods. 2012; 90(2):86-95. DOI: 10.1016/j.mimet.2012.04.015. View

13.

Tkacz A, Cheema J, Chandra G, Grant A, Poole P . Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 2015; 9(11):2349-59. PMC: 4611498. DOI: 10.1038/ismej.2015.41. View

14.

Hillebrand H, Langenheder S, Lebret K, Lindstrom E, Ostman O, Striebel M . Decomposing multiple dimensions of stability in global change experiments. Ecol Lett. 2017; 21(1):21-30. DOI: 10.1111/ele.12867. View

15.

Malik A, Martiny J, Brodie E, Martiny A, Treseder K, Allison S . Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J. 2019; 14(1):1-9. PMC: 6908601. DOI: 10.1038/s41396-019-0510-0. View

16.

Szekely A, Langenheder S . Dispersal timing and drought history influence the response of bacterioplankton to drying-rewetting stress. ISME J. 2017; 11(8):1764-1776. PMC: 5520042. DOI: 10.1038/ismej.2017.55. View

17.

Chng K, Ghosh T, Tan Y, Nandi T, Lee I, Ng A . Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut. Nat Ecol Evol. 2020; 4(9):1256-1267. DOI: 10.1038/s41559-020-1236-0. View

18.

Stoddard S, Smith B, Hein R, Roller B, Schmidt T . rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 2014; 43(Database issue):D593-8. PMC: 4383981. DOI: 10.1093/nar/gku1201. View

19.

Deng X, Zhang N, Shen Z, Zhu C, Liu H, Xu Z . Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum. NPJ Biofilms Microbiomes. 2021; 7(1):33. PMC: 8041757. DOI: 10.1038/s41522-021-00204-9. View

20.

Bickel S, Or D . The chosen few-variations in common and rare soil bacteria across biomes. ISME J. 2021; 15(11):3315-3325. PMC: 8528968. DOI: 10.1038/s41396-021-00981-3. View