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Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

  • 1.

    Mauchamp, L., Mouly, A., Badot, P.-M. & Gillet, F. Impact of nitrogen inputs on multiple facets of plant biodiversity in mountain grasslands: Does nutrient source matter?. Appl. Veg. Sci. 19, 206–217 (2016).

    Article 

    Google Scholar 

  • 2.

    Mesbahi, G., Michelot-Antalik, A., Goulnik, J. & Plantureux, S. Permanent grassland classifications predict agronomic and environmental characteristics well, but not ecological characteristics. Ecol. Indic. 110, 105956 (2020).

    Article 

    Google Scholar 

  • 3.

    Karimi, B. et al. Biogeography of soil microbial habitats across France. Glob. Ecol. Biogeogr. 29, 1399–1411 (2020).

    Article 

    Google Scholar 

  • 4.

    Mahaut, L., Fort, F., Violle, C. & Freschet, G. T. Multiple facets of diversity effects on plant productivity: Species richness, functional diversity, species identity and intraspecific competition. Funct. Ecol. 34, 287–298 (2020).

    Article 

    Google Scholar 

  • 5.

    Tilman, D. The ecological consequences of changes in biodiversity: A search for general principles. Ecology 80, 1455–1474 (1999).

    Google Scholar 

  • 6.

    van der Heijden, M. G. A., Bardgett, R. D. & van Straalen, N. M. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 11, 296–310 (2008).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 7.

    Tardy, V. et al. Stability of soil microbial structure and activity depends on microbial diversity: Linking microbial diversity and stability. Environ. Microbiol. Rep. 6, 173–183 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 8.

    Philippot, L. et al. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 7, 1609–1619 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 9.

    Fierer, N., Barberan, A. & Laughlin, D. C. Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities. Front. Microbiol. 5, 614 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 10.

    Loreau, M. Linking biodiversity and ecosystems: Towards a unifying ecological theory. Philos. Trans. R. Soc. B 365, 49–60 (2010).

    Article 

    Google Scholar 

  • 11.

    Buchin, S., Martin, B., Dupont, D., Bornard, A. & Achilleos, C. Influence of the composition of Alpine highland pasture on the chemical, rheological and sensory properties of cheese. J. Dairy Res. 66, 579–588 (1999).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 12.

    Bugaud, C., Buchin, S., Hauwy, A. & Coulon, J.-B. Flavour and texture of cheeses according to grazing type: The Abundance cheese. INRA Prod. Anim. 15, 31–36 (2002).

    Article 

    Google Scholar 

  • 13.

    Monnet, J. C., Berodier, F. & Badot, P. M. Characterization and localization of a cheese georegion using edaphic criteria (Jura Mountains, France). J. Dairy Sci. 83, 1692–1704 (2000).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Mariotte, P., Vandenberghe, C., Kardol, P., Hagedorn, F. & Buttler, A. Subordinate plant species enhance community resistance against drought in semi-natural grasslands. J. Ecol. 101, 763–773 (2013).

    Article 

    Google Scholar 

  • 15.

    Montel, M.-C. et al. Traditional cheeses: Rich and diverse microbiota with associated benefits. Int. J. Food Microbiol. 177, 136–154 (2014).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Bouton, Y., Guyot, P., Berthier, F., & Beuvier, E. Investigation of bacterial community development from raw milk and starter to curd and mature Comte cheese. in Cheese ripening and technology: abstracts of IDF symposium held in Banff, Canada, March 2000 (ed. International Dairy Federation) 85 (Brussel, Belgium, 2000).

  • 17.

    Demarigny, Y., Beuvier, E., Buchin, S., Pochet, S. & Grappin, R. Influence of raw milk microflora on the characteristics of Swiss-type cheese. Lait 77, 151–167 (1997).

    CAS 
    Article 

    Google Scholar 

  • 18.

    Bouton, Y., Buchin, S., Duboz, G., Pochet, S. & Beuvier, E. Effect of mesophilic lactobacilli and enterococci adjunct cultures on the final characteristics of a microfiltered milk Swiss-type cheese. Food Microbiol. 26, 183–191 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 19.

    Vacheyrou, M. et al. Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms. Int. J. Food Microbiol. 146, 253–262 (2011).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 20.

    Verdier-Metz, I. et al. Cow teat skin, a potential source of diverse microbial populations for cheese production. Appl. Environ. Microbiol. 78, 326–333 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Doyle, C. J., Gleeson, D., O’Toole, P. W. & Cotter, P. D. Impacts of seasonal housing and teat preparation on raw milk microbiota: A high-throughput sequencing study. Appl. Environ. Microbiol. 83(e02694–16), e02694-e2716 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 22.

    Frétin, M. et al. Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems. Sci. Rep. 8, 200 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 23.

    Falentin, H. et al. Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis. Front. Microbiol. 7, 480 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 24.

    Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

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

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 26.

    Dequiedt, S. et al. Biogeographical patterns of soil bacterial communities. Environ. Microbiol. Rep. 1, 251–255 (2009).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 27.

    Sadet-Bourgeteau, S. et al. Lasting effect of repeated application of organic waste products on microbial communities in arable soils. Appl. Soil Ecol. 125, 278–287 (2018).

    Article 

    Google Scholar 

  • 28.

    Nacke, H. et al. Pyrosequencing-based assessment of bacterial community structure along different management types in german forest and grassland soils. PLoS ONE 6, e17000 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Coolon, J. D., Jones, K. L., Todd, T. C., Blair, J. M. & Herman, M. A. Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in Tallgrass Prairie. PLoS ONE 8, e67884 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Toyota, K. & Kuninaga, S. Comparison of soil microbial community between soils amended with or without farmyard manure. Appl. Soil Ecol. 33, 39–48 (2006).

    Article 

    Google Scholar 

  • 31.

    Garnier, E. & Navas, M.-L. A trait-based approach to comparative functional plant ecology: Concepts, methods and applications for agroecology: A review. Agron. Sustain. Dev. 32, 365–399 (2012).

    Article 

    Google Scholar 

  • 32.

    Mauchamp, L., Mouly, A., Badot, P.-M. & Gillet, F. Impact of management type and intensity on multiple facets of grassland biodiversity in the French Jura Mountains. Appl. Veg. Sci. 17, 645–657 (2014).

    Article 

    Google Scholar 

  • 33.

    Chytrý, M. et al. European map of alien plant invasions based on the quantitative assessment across habitats. Divers. Distrib. 15, 98–107 (2009).

    Article 

    Google Scholar 

  • 34.

    Klaudisová, M., Hejcman, M. & Pavlů, V. Long-term residual effect of short-term fertilizer application on Ca, N and P concentrations in grasses Nardus stricta L. and Avenella flexuosa L. Nutr. Cycl. Agroecosyst. 85, 187–193 (2009).

    Article 
    CAS 

    Google Scholar 

  • 35.

    Terrat, S. et al. Mapping and predictive variations of soil bacterial richness across France. PLoS ONE 12, e0186766 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 36.

    Terrat, S. et al. Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding. Heredity 114, 468–475 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 37.

    Navrátilová, D. et al. Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiy208 (2018).

    Article 

    Google Scholar 

  • 38.

    Zhang, Q. et al. Niche differentiation in the composition, predicted function, and co-occurrence networks in bacterial communities associated with antarctic vascular plants. Front. Microbiol. 11, 1036 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Falardeau, J., Keeney, K., Trmčić, A., Kitts, D. & Wang, S. Farm-to-fork profiling of bacterial communities associated with an artisan cheese production facility. Food Microbiol. 83, 48–58 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 40.

    Plassart, P. et al. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Sci. Rep. 9, 605 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 41.

    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).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 42.

    Andrews, T., Neher, D. A., Weicht, T. R. & Barlow, J. W. Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status. PLoS ONE 14, e0225001 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 43.

    Karimi, B. et al. Biogeography of soil bacteria and archaea across France. Sci. Adv. 4, 1808 (2018).

    ADS 
    Article 

    Google Scholar 

  • 44.

    Lewin, G. R. et al. Evolution and ecology of Actinobacteria and their bioenergy applications. Annu. Rev. Microbiol. 70, 235–254 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 45.

    Li, N. et al. Variation in raw milk microbiota throughout 12 months and the impact of weather conditions. Sci. Rep. 8, 2371 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 46.

    Lavoie, K., Touchette, M., St-Gelais, D. & Labrie, S. Characterization of the fungal microflora in raw milk and specialty cheeses of the province of Quebec. Dairy Sci. Technol. 92, 455–468 (2012).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 47.

    Verdier-Metz, I. & Monsallier, F. Place des pâturages des bovins dans les flux microbiens laitiers. Fourrages 6, 1–10 (2012).

    Google Scholar 

  • 48.

    Laforest-Lapointe, I., Paquette, A., Messier, C. & Kembel, S. W. Leaf bacterial diversity mediates plant diversity and ecosystem function relationships. Nature 546, 145–147 (2017).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 49.

    Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 103, 626–631 (2006).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 50.

    Mallet, A. et al. Quantitative and qualitative microbial analysis of raw milk reveals substantial diversity influenced by herd management practices. Int. Dairy J. 27, 13–21 (2012).

    Article 

    Google Scholar 

  • 51.

    Kottek, M., Grieser, J., Beck, C., Rudolf, B. & Rubel, F. World Map of the Köppen-Geiger climate classification updated. Metz 15, 259–263 (2006).

    ADS 
    Article 

    Google Scholar 

  • 52.

    Beck, H. E. et al. Present and future Köppen-Geiger climate classification maps at 1-km resolution. Sci. Data 5, 180214 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 53.

    QGIS.org. QGIS Geographic Information System. QGIS Association. http://www.qgis.org (2021).

  • 54.

    Homburger, H. & Hofer, G. Diversity change of mountain hay meadows in the Swiss Alps. Basic Appl. Ecol. 13, 132–138 (2012).

    Article 

    Google Scholar 

  • 55.

    Gillet, F., Mauchamp, L., Badot, P.-M. & Mouly, A. Recent changes in mountain grasslands: a vegetation resampling study. Ecol. Evol. 6, 2333–2345 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 56.

    Maabel, E. Transformation of cover-abundance values in phytosociology and its effects on community similarity. Vegetatio 39, 97–114 (1979).

    Article 

    Google Scholar 

  • 57.

    Jost, L. The relation between evenness and diversity. Diversity 26, 207–230 (2010).

    Article 

    Google Scholar 

  • 58.

    ChemidlinPrévost-Bouré, N. et al. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS ONE 6, e24166 (2011).

    ADS 
    Article 
    CAS 

    Google Scholar 

  • 59.

    Djemiel, C. et al. BIOCOM-PIPE: A new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. BMC Bioinform. 21, 492. https://doi.org/10.1186/s12859-020-03829-3 (2020).

    CAS 
    Article 

    Google Scholar 

  • 60.

    Cole, J. R. et al. The ribosomal database project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141–D145 (2009).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 61.

    Bardou, P., Mariette, J., Escudié, F., Djemiel, C. & Klopp, C. jvenn: An interactive Venn diagram viewer. BMC Bioinform. 15, 293 (2014).

    Article 

    Google Scholar 

  • 62.

    Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–7. https://CRAN.R-project.org/package=vegan (2020).

  • 63.

    Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 64.

    Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, e1029. https://doi.org/10.7717/peerj.1029 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 65.

    Yekutieli, D. & Benjamini, Y. The control of the false discovery rate in multiple testing under dependency. Ann. Statist. 29, 1165–1188 (2001).

    MathSciNet 
    MATH 

    Google Scholar 

  • 66.

    Gysi, D. M., Voigt, A., Fragoso, T. M., Almaas, E. & Nowick, K. wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. BMC Bioinform. 19, 392 (2018).

    Article 

    Google Scholar 

  • 67.

    Kursa, M. B. & Rudnicki, W. R. Feature Selection with the Boruta Package. J. Stat. Soft. 36, 11 (2010).

    Article 

    Google Scholar 

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