Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?
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 attem...
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doaj-f9b4c6d49d774449ab3bc089bfa3cab32021-01-13T00:05:27ZengMDPI AGApplied Sciences2076-34172021-01-011168868810.3390/app11020688Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?Chakriya Sansupa0Sara Fareed Mohamed Fareed Mohamed Wahdan1Shakhawat Hossen2Terd Disayathanoowat3Tesfaye Wubet4Witoon Purahong5Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, ThailandDepartment of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, 06120 Halle (Saale), GermanyDepartment of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, 06120 Halle (Saale), GermanyDepartment of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, ThailandDepartment of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, 06120 Halle (Saale), GermanyDepartment of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, 06120 Halle (Saale), GermanyFAPROTAX 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 (<i>p</i> > 0.05). There were strong and significant correlations (σ = 0.90–0.95, <i>p</i> < 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.https://www.mdpi.com/2076-3417/11/2/688soilFAPROTAXfunctional annotationbacterial function |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chakriya Sansupa Sara Fareed Mohamed Fareed Mohamed Wahdan Shakhawat Hossen Terd Disayathanoowat Tesfaye Wubet Witoon Purahong |
spellingShingle |
Chakriya Sansupa Sara Fareed Mohamed Fareed Mohamed Wahdan Shakhawat Hossen Terd Disayathanoowat Tesfaye Wubet Witoon Purahong Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? Applied Sciences soil FAPROTAX functional annotation bacterial function |
author_facet |
Chakriya Sansupa Sara Fareed Mohamed Fareed Mohamed Wahdan Shakhawat Hossen Terd Disayathanoowat Tesfaye Wubet Witoon Purahong |
author_sort |
Chakriya Sansupa |
title |
Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? |
title_short |
Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? |
title_full |
Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? |
title_fullStr |
Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? |
title_full_unstemmed |
Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria? |
title_sort |
can we use functional annotation of prokaryotic taxa (faprotax) to assign the ecological functions of soil bacteria? |
publisher |
MDPI AG |
series |
Applied Sciences |
issn |
2076-3417 |
publishDate |
2021-01-01 |
description |
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 (<i>p</i> > 0.05). There were strong and significant correlations (σ = 0.90–0.95, <i>p</i> < 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. |
topic |
soil FAPROTAX functional annotation bacterial function |
url |
https://www.mdpi.com/2076-3417/11/2/688 |
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