@article{fdi:010087743,
  title = {{Q}uantification of diversity sampling bias resulting from rice root bacterial isolation on popular and nitrogen-free culture media using 16{S} amplicon barcoding},
  author = {{S}ondo, {M}. and {W}onni, {I}. and {K}lonowska, {A}gnieszka and {K}oita, {K}. and {M}oulin, {L}ionel},
  editor = {},
  language = {{ENG}},
  abstract = {{C}ulturing bacteria from plant material is well known to be conducive to strong bias compared to the actual diversity in the original samples. {T}his bias is related to the bacterial cultivability, chemical composition of the media and culture conditions. {R}ecovery bias is often observed but has never been quantified on different media using an amplicon barcoding approach whereby plant microbiota {DNA} extractions are compared to {DNA} extracted from serial dilutions of the same plant tissues grown on bacterial culture media. {I}n this study, we: i) quantified the bacterial culturing diversity bias using 16{S} amplicon barcode sequencing by comparing a culture-dependent approach ({CDA}) focused on rice roots on four commonly used bacterial media (10% and 50% {TSA}, plant-based medium with rice flour, nitrogen free medium {NGN} and {NF}b) versus a culture-independent approach ({CIA}) assessed with {DNA} extracted directly from root and rhizosphere samples; ii) assessed enriched and missing taxa detected on the different media; iii) used biostatistics functional predictions to highlight metabolic profiles that could potentially be enriched in the {CDA} and {CIA}. {A} comparative analysis of the two approaches revealed that among the 22 phyla present in microbiota of the studied rice root samples, only five were present in the {CDA} ({P}roteobacteria, {F}irmicutes, {B}acteroidetes, {A}ctinobacteria, {V}errucomicrobia). {T}he {P}roteobacteria phylum was the most abundant in all {CDA} samples, showing high gamma-{P}roteobacteria enrichment. {T}he diversity of the combined culture media represented about a third of the total microbiota diversity, and its genus diversity and frequency was documented. {T}he functional prediction tool ({PICRUS}t2) detected nitrogenase enzyme enrichment in bacterial taxa sampled from nitrogen-free media, thus validating its predictive capacity. {F}urther functional predictions also showed that the {CDA} mostly missed anaerobic, methylotrophic, methanotrophic and photosynthetic bacteria compared to the {CIA}, thereby generating valuable insight that could enable the design of ad-hoc culture media and conditions to increase the rice-associated microbiota cultivability.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {18},
  numero = {4},
  pages = {e0279049 [20 p.]},
  ISSN = {1932-6203},
  year = {2023},
  DOI = {10.1371/journal.pone.0279049},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087743},
}