Comparing the efficacy of MALDI-TOF MS and sequencing identification techniques to monitor the microbial community of irrigation water

In order to intensify agricultural productivity and to help feed the world's rapidly growing population, irrigation increasingly depends on poorly characterized sources of water. This phenomenon leads to an increase of occurrence of foodborne diseases. Therefore, analyzing the microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF MS identification to 16S rRNA gene sequencing of waterborne microbes. Furthermore, the whole microbial community of irrigation water was analyzed using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene sequencing were almost identical at species level (66.7%; 64.3%). Among cultivated genera, Acinetobacter spp., Enterobacter spp., Pseudomonas spp. and Brevundimonas spp. were the most abundant ones. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to monitor the microbiological quality of irrigation water.