{"entity": "researcher", "timestamp": "2026-07-22T16:37:51.989Z", "family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "affiliations": ["Universit\u00e9 Bourgogne Franche-Comt\u00e9, INRAE, AgroSup Dijon, Agro\u00e9cologie, Dijon, France. Laurent.philippot@inrae.fr."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c"}}, "publications": [{"entity": "publication", "iuid": "23d7ef3496e949c7b6f354ee8b433bbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc"}}, "title": "Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A"}, {"family": "Banerjee", "given": "Samiran", "initials": "S"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "M"}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Chabbi", "given": "Abad", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S"}, {"family": "van der Heijden", "given": "Marcel G A", "initials": "MGA"}, {"family": "Saghai", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "issn-l": null, "volume": "17", "issue": "1", "pages": "1"}, "abstract": "Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.\r\n\r\nWe showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.\r\n\r\nOur findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.", "doi": "10.1186/s40793-021-00396-9", "pmid": "34991714", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40793-021-00396-9"}, {"db": "pmc", "key": "PMC8740439"}], "notes": [], "created": "2022-03-29T13:48:27.073Z", "modified": "2022-08-19T08:54:32.507Z"}, {"entity": "publication", "iuid": "9582fbb5d0864897a3b6e0fd249a194b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b"}}, "title": "Unraveling negative biotic interactions determining soil microbial community assembly and functioning.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A", "orcid": "0000-0002-4707-9559", "researcher": {"href": "https://publications.scilifelab.se/researcher/38996366bf744d2e89398d9f5195c0c1.json"}}, {"family": "Aubert", "given": "Julie", "initials": "J", "orcid": "0000-0001-5203-5748", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ebb159d634b4e52bc684668009ce33c.json"}}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "MC"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Mounier", "given": "Arnaud", "initials": "A"}, {"family": "Ouadah", "given": "Sarah", "initials": "S"}, {"family": "Tsiknia", "given": "Myrto", "initials": "M", "orcid": "0000-0002-0924-4509", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab7fd9f77f824b3196b57cc1d86d0636.json"}}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2021-07-28", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362"}, "abstract": "Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.", "doi": "10.1038/s41396-021-01076-9", "pmid": "34321619", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-021-01076-9"}], "notes": [], "created": "2021-10-01T09:03:46.208Z", "modified": "2021-12-06T13:48:07.440Z"}]}