Abstract
Aims
The pea seeds (Pisum sativum) hosts a complex microbial community that is exposed to environmental constraints modulated by biotic, abiotic and anthropogenic factors. The aim of this study was to explore the effect of geographical origins on the composition of the microbial communities associated with pea seeds from storage locations in different countries. These seeds are used by Roquette Frères® as source proteins for human food after industrial extraction process of their proteins.
Methods
The high-throughput sequencing of two phylogenetic markers (V3-V4 regions of the 16S rRNA gene and ITS2 region) was used to evaluate the structure of the microbial community associated with pea seeds. The pea seeds were harvested by different suppliers from three countries (France, Sweden and Canada) with different climates and stored in six cooperatives. Representative microbial strains of dominant species were isolated and characterized using phenotypic methods.
Results
Although the pea seed microbiota shared a dominant core microbiota at the genus level, seeds showed a species-specific, highly unique microbial signature with variable abundances according to origin. Origin was identified as the main driver of the composition of the pea seed microbiota.
Conclusions
These results provide an initial insight into the broad factors such as country and cooperative that may determine the assembly of the pea microbiota before processing.
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Abbreviations
- BHI:
-
Brain Heart Infusion Broth
- DNA:
-
Deoxyribonucleic acid
- EDTA:
-
Ethylenediaminetetraacetic acid
- ITS:
-
Internal Transcribed Spacer
- LAB:
-
Lactic Acid Bacteria
- MRS:
-
De Man, Rogosa and Sharpe
- OTUs:
-
Operational Taxonomic Units
- RNA:
-
Ribonucleic Acid
- TTC:
-
Tetrazolium chloride
- YEGC:
-
Yeast Extract Glucose Chloramphenicol
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We thank the INRAE MIGALE bioinformatics platform (https://migale.inrae.fr/) for providing computational resources and support.
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Supplementary Information
ESM 1
Figure S1 Clustering of 49 bacterial strains isolated from pea samples by metabolic properties based on API 50 CH and API ZYM. Dark black indicates carbon sources and enzyme activities with a positive reaction in the API50 and APIZYM panels; white indicates a negative reaction. The bacterial strains were clustered by an Ascending Hierarchical Classification and color-coded by cluster. The 15 species detected by metabarcoding analysis were noticed in red. Fig. S2 Total viable count of microorganisms in pea seeds from six cooperatives (A, B, C, D, E and F) located in three different countries (France, Sweden and Canada), over five days of soaking on different isolation media. The MRS (De Man, Rogosa and Sharpe), BHI (Brain Heart Infusion) and YEGC (Yeast Extract Glucose Chloramphenicol) agar media are suitable for lactic acid bacteria, mesophilic aerobic bacteria (medium BHI) and fungi (molds and yeasts), respectively. Only the averages of triplicates are given with the standard errors of the mean (SEM) (PDF 144 kb)
ESM 2
Figure S3 Rarefaction curves of V3/V4 Miseq sequencing reads of the bacterial 16S rRNA gene from 16 samples (a) and the ribosomal internal transcribed spacer 2 (ITS2) region for fungi from 17 samples (b) of soaked pea seeds from different cooperatives (A, B, C, D, E and F) located in three different countries (France, Canada and Sweden) (PDF 48 kb)
ESM 3
Table S1 The specific meteorological data (temperature, precipitation, humidity, sunshine and winds) of the countries (France, Sweden and Canada) of cultivation and cooperatives (A, B, C, D, E and F) in 2017. Data were taken from the NASA website (https://power.larc.nasa.gov/data-access-viewer/) (XLSX 10 kb)
ESM 4
Table S2 List of 101 microorganisms isolated from pea seeds from six cooperatives (A, B, C, D, E and F) located in three different countries (France, Canada and Sweden). Origin (country and cooperative) and culture conditions (agar medium, temperature and anaerobic and aerobic conditions) are indicated. The identification of bacteria was determined by comparison of the 16S rRNA gene sequences to the EZ Biocloud database, and the identification of the yeasts was determined by comparison of the 26S rRNA gene sequences (D1D2 region) to the Genbank database using the Basic Local Alignment Search Tool (BLAST) (XLSX 23 kb)
ESM 5
Table S3 Metabolic properties of the three fungal strains isolated from pea seeds based on the API Candida and API ZYM galleries. Dark black indicates carbon sources and enzyme activities with a positive reaction in the API Candida and API ZYM panels; white indicates a negative reaction (XLSX 11 kb)
ESM 6
Table S4 Summary of information regarding the runs performed with the MiSeq sequencing platform and bio-informatics analysis. The number of paired-reads, quality sequences, operational taxonomic units (OTUs), abundant OTUs (aOTUs representing at least 0.005% of the library size) and abundant quality sequences are indicated for each seed sample and in each column. In the column, % of sequences belonging to contaminating OTUs, a represents the sequences occurring in contaminating OTUs other than Cellulosimicrobium, and b represents the sequences belonging to the OTU of Cellulosimicrobium. * Samples with less than 1000 sequences were eliminated from the analysis. (XLSX 14 kb)
ESM 7
Table S5 Differentially abundant microbial OTUs between Canadian and French peas. The 7 bacterial and 13 fungal species were represented by more than 0.5% of all reads. The log2FoldChange is the difference in cluster detection between the two origins (Canada to France). When it is positive, the cluster is more abundant in French peas than in Canadian peas, and the higher it is, the higher the difference in detection is. When negative, the cluster is more abundant in Canadian peas than in French peas. Padj = p value adjusted by the Benjamini-Hochberg method proposed within the DESeq2 package. Only OTUs with a padj <0.05 were considered as differentially abundant between sample groups. * Species belonging to core microbiome. (XLSX 14 kb)
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Chartrel, V., Dugat-Bony, E., Sarthou, AS. et al. The microbial community associated with pea seeds (Pisum sativum) of different geographical origins. Plant Soil 462, 405–427 (2021). https://doi.org/10.1007/s11104-021-04856-6
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DOI: https://doi.org/10.1007/s11104-021-04856-6