Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

Chakriya Sansupa,Witoon Purahong,Terd Disayathanoowat,Tesfaye Wubet,Sara Fareed Mohamed Wahdan,Shakhawat Hossen

doi:10.3390/app11020688

Abstract

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.

Highlights

Microbes are known as engines of an ecosystem as their growth and metabolisms drive various biogeochemical cycles and mediate many ecological processes such as decomposing organic compounds, solubilizing mineral substances and promoting plant performance [1]
Keeping possible biases inherent to molecular technique and next-generation sequencing (NGS) in mind [9] (i.e., PCR, short-read sequences, pan-genome concept of bacterial evolution), many works demonstrated that NGS can be successfully used to improve our understanding of bacterial taxonomic structure and functional profile across aquatic [9,17,18,19,20,21] and terrestrial ecosystems [22,23,24,25]
We demonstrated that FAPROTAX was able to assign functions to prokaryotic taxa derived from both aquatic and terrestrial sources, especially soils

Summary

Introduction

Microbes are known as engines of an ecosystem as their growth and metabolisms drive various biogeochemical cycles and mediate many ecological processes such as decomposing organic compounds, solubilizing mineral substances and promoting plant performance [1]. Various tools have been developed for the prediction of ecological functions of microbial taxa derived from amplicon-based next-generation sequencing data These tools allow us to investigate both community and functional composition of microbes. FUNGuild is a typical functional prediction tool for fungi, providing guild characteristics of the detected taxa, such as saprotroph, pathogen, decomposer or lichenivorous fungi, based on their taxonomic identity [10] Other tools such as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) [11,12], pathway prediction by phylogenetic placement (PAPRICA) [13], predicting functional profiles from metagenomic 16S rRNA data (Tax4Fun) [8] and functional annotation of prokaryotic taxa (FAPROTAX) [9] were developed to predict bacterial and archaeal functions. FAPROTAX may be more preferable for functional prediction of the biogeochemical cycle of environmental samples [9,14,15]

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