Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

Abstract

The use of culture-dependent methods in studying bacterial community has been proven to be inadequate, and often give misleading results. In this work, metagenomic analysis targeting the 16S ribosomal RNA genes was used to study the diversity and community structure of bacteria associated with postharvest Irvingia fruits. Results showed that Simpson's diversity indices and number of Operational Taxonomic Units were dependent on the storage period (days after harvest, DAH) of fruits. Fresh fruits assessed on the day of harvest (DAH = 0) had a Simpson's diversity index of 0.82, while fruits assessed on the 3 rd and 6 th DAH had diversity indices of 0.69 and 0.72, respectively. Whilst fruits assessed on the day of harvest had 64 OTUs spanning across 7 phyla, 11 Classes, 32 genera with total reads of 23,776, fruits assessed on the 3 rd and 6 th days after harvest had 58 OTUs spanning across 6 phyla, 9 Classes, 30 genera with 20,949 reads and 66 OTUs spanning across 4 phyla, 6 Classes, 33 genera with 30,722 reads, respectively. Results further showed that majority of the OTUs belonged to two phyla -Proteobacteria and Firmicutes, mostly represented by members of Alphaproteobacteria and Bacilli subdivisions respectively. Predominant among these OTUs were sequences belonging to Acetobacter ghanensis (11.94%), A. okinawensis (15.36%), Lactobacillus species (14.90%), L. collinoides (12.35%), L. plantarum (7.11%) and L. vaccinostercus (2.89%). The relative abundance of these microorganisms indicates that fleshy pericarp of Irvingia fruits hitherto treated as wastes could potentially be used as a substrate in food and pharmaceutical industries.

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“…However, whilst sequences belonging to members of Bacteroidetes were amplified from Treatment 1 and 2 soils, not a single 16S rRNA partial gene sequence belonging to any member of Bacteroidetes was amplified from Treatment 3 soil. A very recent work on bacteria associated with postharvest Irvingia fruit wastes showed the presence of members of this bacterial Phylum irrespective of the stage of decay; albeit in relatively low proportions (Etebu et al, 2018). Studying the effect of postharvest Irvingia fruit wastes on members of Bacteroidetes would therefore make an interesting investigation.…”

“…Interestingly, extracts from postharvest Irvingia fruits undergoing decay have been reported to potentially inhibit bacterial growth (Etebu and Tungbulu, 2015). Similarly, a recently published article on the metagenomics of bacterial community associated with postharvest Irvingia fruits showed a decrease in number of bacterial taxonomic Phyla and Classes as postharvest period increased (Etebu et al, 2018), whilst preferentially accommodating the growth of specific Genera of bacteria. These findings apparently suggest that extracts of postharvest Irvingia fruit would significantly influence soil microbial structure and diversity.…”

“…In contrast, the application of metagenomics in the assessment of microorganisms in their natural environments, without recourse to culture of individual species, have greatly enhanced the study of microbial communities (Pinto et al, 2014). Although metagenomics of bacterial community associated with postharvest Irvingia fruits have recently been studied (Etebu et al, 2018); the approach is yet to be extended to study the microbial community structure and diversity of soil amended with postharvest Irvingia fruit waste.…”

Effects of postharvest Irvingia fruit wastes on soil microbial diversity and physico-chemical properties

“…This suggests that the topsoil used in this work, in its original un-amended form had no Streptococcus pneumoniae. Also, there has been no indication in earlier works that this bacterium is associated with postharvest Irvingia fruit wastes (Etebu and Tungbulu, 2015, Etebu, 2012, 2013Etebu et al, 2018). It is therefore difficult to unreservedly explain the source of this bacterium in Treatment 3 soil.…”

“…Norcadioides species whose 16S rRNA partial gene sequence was amplified from Treatment 3 soils could be antibody producing type, which probably depended on postharvest Irvingia fruit wastes as a substrate for growth, and in the process produced antimicrobial substances inimical to the growth of other bacteria. The potential production of antimicrobials by microbes, whilst feeding on Irvingia fruit waste extract, has often been suggested (Etebu and Tungbulu, 2015;Etebu et al, 2018). Similar to Nocardioides species, one sequence read amounting to 6.25% of total bacterial sequence reads amplified from Treatment 3 soil was identified as belonging to Pseudomonas syringae (Table 3).…”