@article{fdi:010086001,
  title = {{T}he impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western {B}urkina {F}aso},
  author = {{B}arro, {M}. and {W}onni, {I}. and {S}imonin, {M}arie and {K}assankogno, {A}. {I}. and {K}lonowska, {A}gnieszka and {M}oulin, {L}ionel and {B}{\'e}na, {G}illes and {S}omda, {I}. and {B}runel, {C}aroline and {T}ollenaere, {C}harlotte},
  editor = {},
  language = {{ENG}},
  abstract = {{D}ue to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. {H}ere, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in {B}urkina {F}aso, using an amplicon metabarcoding approach of the 16{S} r{RNA} gene (prokaryotes, three plant samples per field) and {ITS} (fungi, one sample per field). {I}n addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. {I}n irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). {C}ore taxa were different between the two systems, and indicator species were identified: mostly within {B}acillaceae in rainfed lowlands, and within {B}urkholderiaceae and {M}oraxellaceae in irrigated areas. {F}inally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). {O}ur results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications. {I}rrigated rice and rainfed lowlands harbor contrasted root-associated microbiomes in small farmer's fields from {B}urkina {F}aso, with contrasted richness, and peculiar indicator taxa in each system.},
  keywords = {irrigated rice ; rainfed lowlands ; root associated microorganisms ; metabarcoding ; {O}ryza sativa ; rice production system ; {W}est {A}frica ; {AFRIQUE} {DE} {L}'{OUEST} ; {BURKINA} {FASO}},
  booktitle = {},
  journal = {{FEMS} {M}icrobiology {E}cology},
  volume = {98},
  numero = {9},
  pages = {fiac085 [17 ]},
  ISSN = {0168-6496},
  year = {2022},
  DOI = {10.1093/femsec/fiac085},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086001},
}