Files and links (1)
CC BY V4.0, Open Access
Journal article
Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database
Frontiers in microbiology, Vol.12, 682886
2021
PMID: 34349739
Abstract
High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
Details
- Title
- Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database
- Authors/Creators
- Briony Jones - Bangor UniversityTim Goodall - UK Centre for Ecology & HydrologyPaul B. L. George - , , , , , , , ,Hyun S. Gweon - University of ReadingJeremy Puissant - UK Centre for Ecology & HydrologyDaniel S. Read - UK Centre for Ecology & HydrologyBridget A. Emmett - UK Centre for Ecology & HydrologyDavid A. Robinson - UK Centre for Ecology & HydrologyDavey L. Jones - , , , , , , , ,Robert I. Griffiths - , , , , , , , ,
- Publication Details
- Frontiers in microbiology, Vol.12, 682886
- Publisher
- Frontiers Media S.A
- Identifiers
- 991005560441107891
- Copyright
- © 2021 Jones et al.
- Murdoch Affiliation
- Centre for Sustainable Farming Systems
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
41 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.45 Soil Science
- 3.45.112 Soil Carbon Dynamics
- Web Of Science research areas
- Microbiology
- ESI research areas
- Microbiology