Skip to main content

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant

Applied Microbiology and Biotechnology volume 102, pages 4025–4037 (2018)Cite this article

Abstract

Microbial population dynamics associated with corn silage, with and without Lactobacillus plantarum treatment, was studied. Whole crop corn was ensiled using laboratory silos and sampled at different times, up to 3 months. The dominant bacteria, before ensiling, were Acinetobacter (38.5%) and Klebsiella (16.3%), while the dominant fungi were Meyerozyma (53.5%) and Candida (27.7%). During ensiling, the microbial population shifted considerably, and Lactobacillus (> 94%) and Candida (> 74%) became the most dominant microbial genera in both treated and untreated silages. Yet, lactic acid content was higher in the treated silage, while the microbial diversity was lower than in the untreated silage. Upon aerobic exposure, spoilage occurred more rapidly in the treated silage, possibly due to the higher abundance of lactic acid-assimilating fungi, such as Candida. Our study is the first to describe microbial population dynamics during whole-crop corn ensiling and the results indicate that microbial diversity may be an indicator of aerobic stability.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  • Arasu MV, Jung M-W, Kim DH, Ilavenil S, Jane M, Park HS, Al-Dhabi NA, Jeon BT, Choi KC (2014) Enhancing nutritional quality of silage by fermentation with Lactobacillus plantarum. Indian J Microbiol 54(4):396–402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bao W, Mi Z, Xu H, Zheng Y, Kwok LY, Zhang H, Zhang W (2016) Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters. Sci Rep 6:28358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barker BS, Summerson WH (1941) The colorimetric determination of lactic acid in biological material. J Biol Chem 138:535–554

    CAS  Google Scholar 

  • Bokulich NA, Mills DA (2012) Next-generation approaches to the microbial ecology of food fermentations. BMB Rep 45(7):377–389

    Article  CAS  PubMed  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108:4516–4522

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Weinberg ZG (2014) The effect of relocation of whole-crop wheat and corn silages on their quality. J Dairy Sci 97:406–410

    Article  CAS  PubMed  Google Scholar 

  • Cherney DJR, Cherney JH, Cox WJ (2004) Fermentation characteristics of corn forage ensiled in mini-silos. J Dairy Sci 87:4238–4246

    Article  CAS  PubMed  Google Scholar 

  • Dolci P, Tabacco E, Cocolin L, Borreani G (2011) Microbial dynamics during aerobic exposure of corn silage stored under oxygen barrier or polyethylene films. Appl Environ Microbiol 77:7499–7507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Driehuis F, Oude Elferink SJWH (2000) The impact of the quality of silage on animal health and food safety: a review. Vet Q 22:212–217

    Article  CAS  PubMed  Google Scholar 

  • Dunière L, Sindou J, Chaucheyras-Durand F, Chevallier I, Thévenot-Sergentet D (2013) Silage processing and strategies to prevent persistence of undesirable microorganisms. Anim Feed Sci Technol 182:1–15

    Article  Google Scholar 

  • Duniere L, Xu S, Long J, Elekwachi C, Wang Y, Turkington K, Forster R, McAllister TA (2017) Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage. BMC Microbiol 17:50

    Article  PubMed  PubMed Central  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A (2013) Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling. J Biotechnol 167:334–343

    Article  CAS  PubMed  Google Scholar 

  • Garon D, Richard E, Sage L, Bouchart V, Pottier D, Lebailly P (2006) Mycoflora and multimycotoxin detection in corn silage: experimental study. J Agric Food Chem 54:3479–3484

    Article  CAS  PubMed  Google Scholar 

  • Green SJ, Venkatramanan R, Naqib A (2015) Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PLoS One 10(5):e0128122

    Article  PubMed  PubMed Central  Google Scholar 

  • Inglis GD, Yanke LJ, Kawchuk LM, McAllister TA (1999) The influence of bacterial inoculants on the microbial ecology of aerobic spoilage of barley silage. Can J Microbiol 45:77–87

    Article  CAS  PubMed  Google Scholar 

  • Jatkauskas J, Vrotniakiene V, Ohlsson C, Lund B (2013) The effects of three silage inoculants on aerobic stability in grass, clovergrass, lucerne and maize silages. Agric Food Sci 22:137–144

    CAS  Google Scholar 

  • Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiß M, Larsson K-H (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277

    Article  PubMed  Google Scholar 

  • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kraut-Cohen J, Tripathi V, Chen Y, Gatica J, Volchinski V, Sela S, Weinberg Z, Cytryn E (2016) Temporal and spatial assessment of microbial communities in commercial silages from bunker silos. Appl Microbiol Biotechnol 100(15):6827–6835

    Article  CAS  PubMed  Google Scholar 

  • Lianhua L, Yongming S, Zhenhong Y, Xiaoying K, Yao W, Ligui Y, Yi Z, Dong L (2015) Effect of microalgae supplementation on the silage quality and anaerobic digestion performance of Manyflower silvergrass. Bioresour Technol 189:334–340

    Article  Google Scholar 

  • Lozupone C, Hamady M, Knight R (2006) UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371

    Article  PubMed  PubMed Central  Google Scholar 

  • May LA, Smiley B, Schmidt MG (2001) Comparative denaturing gradient gel electrophoresis analysis of fungal communities associated with whole plant corn silage. Can J Microbiol 47(9):829–841

    Article  CAS  PubMed  Google Scholar 

  • McGarvey JA, Franco RB, Palumbo JD, Hnasko R, Stanker L, Mitloehner FM (2013) Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air. J Appl Microbiol 114(6):1661–1670

    Article  CAS  PubMed  Google Scholar 

  • Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P (2016) Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability. Grass Forage Sci 72:281–289

    Article  Google Scholar 

  • Moon NJ, Ely LO (1979) Identification and properties of yeasts associated with the aerobic deterioration of wheat and alfalfa silages. Mycopathologia 69:153–156

    Article  Google Scholar 

  • Moon NJ, Ely LO, Sudweeks EM (1980) Aerobic deterioration of wheat, lucerne and maize silages prepared with Lactobacillus acidophilus and a Candida spp. J Appl Bacteriol 49:75–87

    Article  CAS  Google Scholar 

  • Ni K, Minh TT, Tu TT, Tsuruta T, Pang H, Nishino N (2017) Comparative microbiota assessment of wilted Italian ryegrass, whole crop corn, and wilted alfalfa silage using denaturing gradient gel electrophoresis and next-generation sequencing. Appl Microbiol Biotechnol 101:1385–1394

    Article  CAS  PubMed  Google Scholar 

  • Pahlow G, Muck RE, Driehuis F, Oude Elferink SJWH, Spoelstra SF (2003) Microbiology of ensiling. In: Buxton DR, Muck RE, Harrison JH (eds) Silage science and technology, American Society of Agronomy, Madison, pp 31–93

  • Parvin S, Nishino N (2010) Succession of lactic acid bacteria in wilted rhodes grass silage assessed by plate culture and denaturing gradient gel electrophoresis. Grassl Sci 56:51–55

    Article  CAS  Google Scholar 

  • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007) SILVA, a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Richard E, Heutte N, Sage L, Pottier D, Bouchart V, Lebailly P, Garon D (2007) Toxigenic fungi and mycotoxins in mature corn silage. Food Chem Toxicol 45:2420–2425

    Article  CAS  PubMed  Google Scholar 

  • Romero JJ, Zhao Y, Balseca-Paredes MA, Tiezzi F, Gutierrez-Rodriguez E, Castillo MS (2017) Laboratory silo type and inoculation effects on nutritional composition, fermentation, and bacterial and fungal communities of oat silage. J Dairy Sci 100(3):1812–1828

    Article  CAS  PubMed  Google Scholar 

  • Santos MC, Golt C, Joerger RD, Mechor GD, Mourão GB, Kung L (2017) Identification of the major yeasts isolated from high moisture corn and corn silages in the United States using genetic and biochemical methods. J Dairy Sci 100(2):1151–1160

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith DP, Peay KG (2014) Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 9(2):e90234

    Article  PubMed  PubMed Central  Google Scholar 

  • Spadaro D, Bustos-Lopez MP, Gullino ML, Piano S, Tabacco E, Borreani G (2015) Evolution of fungal populations in corn silage conserved under polyethylene or biodegradable films. J Appl Microbiol 119(2):510–520

    Article  CAS  PubMed  Google Scholar 

  • Stevenson DM, Muck RE, Shinners K, Weimer PJ (2006) Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover. Appl Microbiol Biotechnol 71:329–338

    Article  CAS  PubMed  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang YS, Shi W, Huang LT, Ding CL, Dai CC (2016) The effect of lactic acid bacterial starter culture and chemical additives on wilted rice straw silage. Anim Sci J 87(4):525–535

    Article  CAS  PubMed  Google Scholar 

  • Weinberg ZG, Ashbell G (2003) Engineering aspects of ensiling. Biochem Eng J 13:181–188

    Article  Google Scholar 

  • Weinberg ZG, Chen Y (2013) Effects of storage period on the composition of whole crop wheat and corn silages. Anim Feed Sci Technol 185:196–200

    Article  CAS  Google Scholar 

  • Weinberg ZG, Chen Y, Solomon R (2009) The quality of commercial wheat silages in Israel. J Dairy Sci 92(2):638–644

    Article  CAS  PubMed  Google Scholar 

  • Wilkinson JM, Bolsen KK, Lin CJ (2003) History of silage. In: Buxton DR, Muck RE, Harrison JH (eds) Silage science and technology, American Society of Agronomy, Madison, pp 1–30

  • Woolford MK (1990) The detrimental effects of air on silage. J Appl Bacteriol 68:101–116

    Article  CAS  PubMed  Google Scholar 

  • Woolford MK, Pahlow G (1998) The silage fermentation. In: Wood BJB (ed) Microbiology of fermented foods. Springer, Boston, pp 73–102

    Chapter  Google Scholar 

  • Zhao Y, Yu J, Liu J, Yang H, Gao L, Yuan X, Cui ZJ, Wang X (2016) Material and microbial changes during corn stalk silage and their effects on methane fermentation. Bioresour Technol 222:89–99

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Contribution from the Agricultural Research Organization (ARO), The Volcani Center, No. 798/17. This study was partially supported by BARD (United States-Israel Binational Agricultural Research and Development Fund), Project IS-4704-14. SSS was a member of the EU COST Action FA1202 (CGAFA1202): A European Network for Mitigating Bacterial Colonisation and Persistence on Foods and Food Processing Environments (http://www.bacfoodnet.org/) and acknowledge this action. JK was supported by ARO Postdoctoral Fellowship Fund (2015-2017) under the Indo-Israeli Research and Development Programme.

Author information

Authors and Affiliations

  1. Microbial Food-Safety Research Unit, Department of Food Quality and Safety, The Volcani Center, Agriculture Research Organization, Institute for Postharvest and Food Sciences, Derech HaMaccabim Road 68, POB 15159, 7528809, Rishon-LeZion, Israel

    Jitendra Keshri, Yaira Chen, Riky Pinto, Yulia Kroupitski, Zwi G. Weinberg & Shlomo Sela (Saldinger)

Authors
  1. Jitendra Keshri
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yaira Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Riky Pinto
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yulia Kroupitski
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zwi G. Weinberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shlomo Sela (Saldinger)
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shlomo Sela (Saldinger).

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Electronic supplementary material

ESM 1

(PDF 416 kb).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Keshri, J., Chen, Y., Pinto, R. et al. Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant. Appl Microbiol Biotechnol 102, 4025–4037 (2018). https://doi.org/10.1007/s00253-018-8903-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-018-8903-y

Keywords

  • Bacterial diversity
  • Fungal diversity
  • Silage
  • Feed
  • Aerobic stability