A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle

Here we compared microbial results for the same Phosphorus (P) biogeochemical cycle genes from a GeoChip microarray and PICRUSt functional predictions from 16S rRNA data for 20 samples in the four spatially separated Gotjawal forests on Jeju Island in South Korea. The high homogeneity of microbial communities detected at each site allows sites to act as environmental replicates for comparing the two different functional analysis methods. We found that while both methods capture the homogeneity of the system, both differed greatly in the total abundance of genes detected, as well as the diversity of taxa detected. Additionally, we introduce a more comprehensive functional assay that again captures the homogeneity of the system but also captures more extensive community gene and taxonomic information and depth. While both methods have their advantages and limitations, PICRUSt appears better suited to asking questions specifically related to microbial community P as we did here. This comparison of methods makes important distinctions between both the results and the capabilities of each method and can help select the best tool for answering different scientific questions. Sanghoon Kang ( ) Corresponding author: [email protected] : Conceptualization, Data Curation, Formal Analysis, Methodology, Software, Validation, Visualization, Writing – Original Author roles: LeBrun ES Draft Preparation, Writing – Review & Editing; : Conceptualization, Data Curation, Project Administration, Supervision, Writing – Review & Kang S Editing No competing interests were disclosed. Competing interests: LeBrun ES and Kang S. How to cite this article: A comparison of computationally predicted functional metagenomes and microarray 2018, analysis for microbial P cycle genes in a unique basalt-soil forest [version 1; referees: awaiting peer review] F1000Research 7 :179 (doi: ) 10.12688/f1000research.13841.1 © 2018 LeBrun ES and Kang S. This is an open access article distributed under the terms of the Copyright: Creative Commons Attribution , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Licence The author(s) declared that no grants were involved in supporting this work. Grant information: 12 Feb 2018, :179 (doi: ) First published: 7 10.12688/f1000research.13841.1 Referee Status: AWAITING PEER REVIEW 12 Feb 2018, :179 (doi: ) First published: 7 10.12688/f1000research.13841.1 12 Feb 2018, :179 (doi: ) Latest published: 7 10.12688/f1000research.13841.1 v1 Page 1 of 6 F1000Research 2018, 7:179 Last updated: 12 FEB 2018