FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbiological references. This study, however, has attempted to access the application of FAPROTAX in soil environments. We hypothesized that FAPROTAX was compatible with terrestrial ecosystems. The potential use of FAPROTAX to assign ecological functions of soil bacteria was investigated using meta-analysis and our newly designed experiments. Soil samples from two major terrestrial ecosystems, including agricultural land and forest, were collected. Bacterial taxonomy was analyzed using Illumina sequencing of the 16S rRNA gene and ecological functions of the soil bacteria were assigned by FAPROTAX. The presence of all functionally assigned OTUs (Operation Taxonomic Units) in soil were manually checked using peer-reviewed articles as well as standard microbiology books. Overall, we showed that sample source was not a predominant factor that limited the application of FAPROTAX, but poor taxonomic identification was. The proportion of assigned taxa between aquatic and non-aquatic ecosystems was not significantly different (p > 0.05). There were strong and significant correlations (σ = 0.90–0.95, p < 0.01) between the number of OTUs assigned to genus or order level and the number of functionally assigned OTUs. After manual verification, we found that more than 97% of the FAPROTAX assigned OTUs have previously been detected and potentially performed functions in agricultural and forest soils. We further provided information regarding taxa capable of N-fixation, P and K solubilization, which are three main important elements in soil systems and can be integrated with FAPROTAX to increase the proportion of functionally assigned OTUs. Consequently, we concluded that FAPROTAX can be used for a fast-functional screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases.

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This study investigated both bacterial and fungal communities in corbicular pollen and hive-stored bee bread of two commercial honey bees, Apis mellifera and Apis cerana, in China. Although both honey bees favor different main floral sources, the dynamics of each microbial community is similar. During pH reduction in hive-stored bee bread, results from conventional culturable methods and next-generation sequencing showed a declining bacterial population but a stable fungal population. Different honey bee species and floral sources might not affect the core microbial community structure but could change the number of bacteria. Corbicular pollen was colonized by the Enterobacteriaceae bacterium (Escherichia-Shiga, Panteoa, Pseudomonas) group; however, the number of bacteria significantly decreased in hive-stored bee bread in less than 72 h. In contrast, Acinetobacter was highly abundant and could utilize protein sources. In terms of the fungal community, the genus Cladosporium remained abundant in both corbicular pollen and hive-stored bee bread. This filamentous fungus might encourage honey bees to reserve pollen by releasing organic acids. Furthermore, several filamentous fungi had the potential to inhibit both commensal/contaminant bacteria and the growth of pathogens. Filamentous fungi, in particular, the genus Cladosporium, could support pollen preservation of both honey bee species.

This study investigated bacterial community structures in the midguts of Apis mellifera and Apis cerana in Thailand to understand how bacterial communities develop in Apis species. The bacterial species present in replicate colonies from different locations and life stages were analysed. PCR amplification of bacterial 16S rRNA gene fragments and terminal restriction fragment length polymorphism analyses revealed a total of 16 distinct terminal restriction fragments (T-RFs), 12 of which were shared between A. mellifera and A. cerana populations. The T-RFs were affiliated to Beta- and Gammaproteobacteria, Firmicutes and Actinomycetes. The Gammaproteobacteria were found to be common in all stages of honey bee, but in addition, the Firmicutes group was found to be present in the worker bees. Bacterial community structure showed no difference amongst the replicate colonies, but was affected to some degree by geographical location, life stage and species of honey bees.