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Corresponding author: Tristan Cordier ( tristan.cordier@gmail.com ) Academic editor: Dirk Steinke
© 2018 Tristan Cordier, Jan Pawlowski.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Cordier T, Pawlowski J (2018) BBI: an R package for the computation of Benthic Biotic Indices from composition data. Metabarcoding and Metagenomics 2: e25649. https://doi.org/10.3897/mbmg.2.25649
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The monitoring of impacts of anthropic activities in marine environments, such as aquaculture, oil-drilling platforms or deep-sea mining, relies on Benthic Biotic Indices (BBI). Several indices have been formalised to reduce the multivariate composition data into a single continuous value that is ascribed to a discrete ecological quality status. Such composition data is traditionally obtained from macrofaunal inventories, which is time-consuming and expertise-demanding. Important efforts are ongoing towards using High-Throughput Sequencing of environmental DNA (eDNA metabarcoding) to replace or complement morpho-taxonomic surveys for routine biomonitoring. The computation of BBI from such composition data is usually being undertaken by practitioners with excel spreadsheets or through custom script. Hence, the updating of reference morpho-taxonomic tables and cross studies comparison could be hampered. Here we introduce the R package BBI for the computation of BBI from composition data, either obtained from traditional morpho-taxonomic inventories or from metabarcoding data. Its aim is to provide an open-source, transparent and centralised method to compute BBI for routine biomonitoring.
Biotic indices, biomonitoring, R package, benthos, composition data
Biodiversity monitoring is the standard approach for the environmental impact assessment of anthropogenic activities. In marine environments, impact assessments are carried out through benthic macro-invertebrates surveys, which involve the sorting and the morpho-taxonomic identification of numerous specimens for a single site (
High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) offers a fast and cost-effective method to describe biological communities (
Some of these BBI can be calculated with user-friendly software (AMBI from AZTI, available at: http://ambi.azti.es), including R packages in the case of freshwaters (see the ‘biotic’ package, Briers 2016) or marine ecosystems (see the ‘BEQI2’ package, van Loon et al. 2015). However, none of these packages included the NSI, ISI, NQI1, Bentix or nEQR indices and required the development of custom script in order to use the published reference ecological weights database (
Here we introduce the R package BBI for the computation of BBI from composition data, either obtained from traditional morpho-taxonomic inventories or from metabarcoding data. It provides an open-source tool for transparent BBI computation and aims to centralise available tools for BBI in various aquatic ecosystems.
The R package BBI (version 0.2.0) is available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/BBI/index.html. It can be installed within the R environment, on any operating system (Linux, macOS or Windows), by using the command install.packages(“BBI”). All instructions for installation of current release or development versions can be consulted on the GitHub repository page (https://github.com/trtcrd/BBI). The package requires the package “vegan” (
A reference dataset is included in the package, containing 7822 metazoan taxonomic entries, covering ecological weights and groups for five BBI (Table
BBI | Entries | Reference |
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AMBI | 6750 |
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NSI | 585 |
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ITI | 1506 | Maurer et al. 1999 |
ISI2012 | 585 |
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Bentix | 359 |
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We introduced the R package BBI for the computation of Benthic Biotic Indices from composition data. It provides two simple R functions to automate the search for matches between the taxonomic assignments and the reference morpho-taxonomic database of 5 BBI (Table
The BBI package will be kept up-to-date for new entries in morpho-taxonomic reference databases for the 5 BBI included here. Hence, the package aims to provide biomonitoring practitioners with a reliable, up-to-date and open-source tool for the computation of BBI from composition data, either obtained from morpho-taxonomic inventories or by eDNA metabarcoding.
Title: BBI: an R package for the computation of Benthic Biotic Indices from composition data
Study area description: Microscopy, Metabarcoding, Biomonitoring, Biotic Indices
Download page: https://cran.r-project.org/web/packages/BBI/index.html
Programming language: R
Licence: GNU Affero General Public Licence v3
Conceived and designed the study: TC; Wrote the R package: TC; Analysed the data: TC; Wrote the paper: TC, JP
The R package was developed in the context of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219). TC and JP were supported by the Norwegian Seafood Research Fund (FHF project number 901092), by the Swiss Network for International Studies and by the Swiss National Science Foundation (grants 316030_150817 and 31003A_159709).