scholarly journals BBI: an R package for the computation of Benthic Biotic Indices from composition data

2018 ◽  
Vol 2 ◽  
pp. e25649 ◽  
Author(s):  
Tristan Cordier ◽  
Jan Pawlowski
Keyword(s):  
Deep Sea ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
R Package ◽  
Biotic Indices ◽  
Oil Drilling ◽  
Composition Data ◽  
Ecological Quality Status ◽  
Custom Script ◽  
Quality Status

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.

The ecological quality status of the Elbe estuary. A comparative approach on different benthic biotic indices applied to a highly modified estuary

2012 ◽  
Vol 19 ◽  
pp. 118-129 ◽  
Author(s):  
Markus A. Wetzel ◽  
Peter C. von der Ohe ◽  
Werner Manz ◽  
Jochen H.E. Koop ◽  
Dierk-Steffen Wahrendorf
Keyword(s):  
Comparative Approach ◽  
Ecological Quality ◽  
Biotic Indices ◽  
Elbe Estuary ◽  
Ecological Quality Status ◽  
Quality Status

Assessing the ecological quality status of a temperate urban estuary by means of benthic biotic indices

2015 ◽  
Vol 91 (2) ◽  
pp. 441-453 ◽  
Author(s):  
M. Hutton ◽  
N. Venturini ◽  
F. García-Rodríguez ◽  
E. Brugnoli ◽  
P. Muniz
Keyword(s):  
Ecological Quality ◽  
Biotic Indices ◽  
Urban Estuary ◽  
Ecological Quality Status ◽  
Quality Status

scholarly journals Assessment of Benthic Ecological Quality Status Using Multi-Biotic Indices Based on Macrofaunal Assemblages in a Semi-Enclosed Bay

2021 ◽  
Vol 8 ◽  
Author(s):  
Xin Lu ◽  
Jing Xu ◽  
Zhaodong Xu ◽  
Xiaoshou Liu
Keyword(s):  
Environmental Assessment ◽  
Ecological Quality ◽  
Biotic Indices ◽  
Wiener Diversity Index ◽  
Ecological Quality Status ◽  
Benthic Environment ◽  
Enclosed Bay ◽  
Unassigned Species ◽  
Quality Status ◽  
Better Than

Semi-enclosed bays have physical and chemical characteristics influenced by both land and sea systems and the quality of the benthic environment is always of great concern. Macrofauna are considered good indicators for evaluating the benthic ecological quality status owing to their biological characteristics. In this study, six biotic indices, namely the Shannon–Wiener diversity index (H′), Abundance-Biomass Comparison (ABC) curve, AZTI’s Marine Biotic Index (AMBI), multivariate-AMBI (M-AMBI), BOPA index, and BENTIX index, were used to evaluate the adaptability of different biological indices in the bioassessment of the benthic environment in a semi-enclosed bay. In the annual environmental assessment of the study area, the average values of the six indices (H′, ABC curve, AMBI, M-AMBI, BOPA, and BENTIX) were 4.494, 0.182, 2.433, 0.791, 0.033, and 3.813, respectively; accordingly, H′, M-AMBI, and BOPA met the high standards whereas the other indices met the good standards, indicating that the whole study bay was slightly disturbed and had good ecological quality. From the perspective of spatial variation, the benthic environment in the middle of the bay was better than that in the north; the environmental problems in the northeast were particularly noteworthy. In terms of temporal patterns, the benthic environment in winter and summer was significantly better than that in spring and autumn, with obvious seasonal differences. The present results indicate that the H′ and ABC curve based on benthic abundance and biomass should be avoided for environmental assessment in mariculture areas. AMBI and M-AMBI should be used with caution when the percentage of unassigned species is high, in which case H′ is the appropriate choice. When there are few unassigned species, M-AMBI is more conducive for accurate evaluation of the benthic environment than AMBI and H′.

scholarly journals The ecological quality status of the Bay of Seine and the Seine estuary: Use of biotic indices

2007 ◽  
Vol 55 (1-6) ◽  
pp. 241-257 ◽  
Author(s):  
Jean-Claude Dauvin ◽  
Thierry Ruellet ◽  
Nicolas Desroy ◽  
Anne-Laure Janson
Keyword(s):  
Ecological Quality ◽  
Biotic Indices ◽  
Seine Estuary ◽  
Ecological Quality Status ◽  
Quality Status

scholarly journals Assessment of the environmental health status of the Marchica lagoon (Morocco, Mediterranean) using Cymodocea nodosa meadows and its associated macrofauna: preliminary results

2015 ◽  
Author(s):  
Reda El Kamcha ◽  
Oussama Bououarour ◽  
Loubna Boutahar ◽  
Zineb El Fatouani ◽  
Ayoub El Adnani ◽  
...  
Keyword(s):  
Ecological Status ◽  
Complex Mixture ◽  
Benthic Macrofauna ◽  
Leaf Biomass ◽  
Ecological Quality ◽  
Biotic Indices ◽  
Cymodocea Nodosa ◽  
Preliminary Results ◽  
Ecological Quality Status ◽  
Quality Status

The Marchica lagoon is the single lagoon on the Mediterranean coast of Morocco. Beside its ecological and socio-economic values, the lagoon is under pressure of a complex mixture of human-mediated stressors (urbanization, pollution, overfishing, tourism, etc.). Nowadays, many institutional efforts have been undertaken to establish a sustainable management plan of the lagoon in the context of an Integrated Coastal Zone Management (ICZM) approach. Thus, understanding how these stressors impact upon ecological status and ecosystem services is a sound step for any efficient integral management. Based on sampling performed on June 2014, the present work aimed at assessing the ecological quality status (ES) of the northern part of the lagoon using Cymodocea nodosa (Ucria) Ascherson meadows and benthic macrofauna. 16 stations (11 with C. nodosa and 5 on bare sediment) were sampled using a Van Veen grab. Preliminary results showed differences between stations. Shoots biomass fluctuated between 8.02 and 61.2 g dw m-2 while the roots-rhizomes biomass oscillated between 10.8 and 235.5 g dw m-2. The root-rhizome and leaf biomass ratio revealed high values (up to 10.8) in the central sector suggesting a potential nutrient enrichment.Benthic macrofauna revealed the presence of 90 species belonging to six zoological groups and dominated by crustaceans, molluscs and polychaetes. The assessment of the ecological quality status, based on benthic macrofauna, was evaluated using Biotic Indices (AMBI, M-AMBI, Benthix, BITS). The results showed partial agreement between single index-derived ES and underlined the dependency of these biotic indices on the habitat characteristics, on the one hand, and the necessity to define specific reference conditions to the Marchica lagoon.

scholarly journals Foraminiferal-based biotic indices to assess the ecological quality status of the Gulf of Gabes (Tunisia): Present limitations and future perspectives

2020 ◽  
Vol 111 ◽  
pp. 105962 ◽  
Author(s):  
Akram El Kateb ◽  
Claudio Stalder ◽  
Michael Martínez-Colón ◽  
Guillem Mateu-Vicens ◽  
Fabio Francescangeli ◽  
...  
Keyword(s):  
Ecological Quality ◽  
Biotic Indices ◽  
Future Perspectives ◽  
Gulf Of Gabes ◽  
Gulf Of Gabès ◽  
Ecological Quality Status ◽  
Quality Status

scholarly journals Assessment of the environmental health status of the Marchica lagoon (Morocco, Mediterranean) using Cymodocea nodosa meadows and its associated macrofauna: preliminary results

2015 ◽  
Author(s):  
Reda El Kamcha ◽  
Oussama Bououarour ◽  
Loubna Boutahar ◽  
Zineb El Fatouani ◽  
Ayoub El Adnani ◽  
...  
Keyword(s):  
Ecological Status ◽  
Complex Mixture ◽  
Benthic Macrofauna ◽  
Leaf Biomass ◽  
Ecological Quality ◽  
Biotic Indices ◽  
Cymodocea Nodosa ◽  
Preliminary Results ◽  
Ecological Quality Status ◽  
Quality Status

The Marchica lagoon is the single lagoon on the Mediterranean coast of Morocco. Beside its ecological and socio-economic values, the lagoon is under pressure of a complex mixture of human-mediated stressors (urbanization, pollution, overfishing, tourism, etc.). Nowadays, many institutional efforts have been undertaken to establish a sustainable management plan of the lagoon in the context of an Integrated Coastal Zone Management (ICZM) approach. Thus, understanding how these stressors impact upon ecological status and ecosystem services is a sound step for any efficient integral management. Based on sampling performed on June 2014, the present work aimed at assessing the ecological quality status (ES) of the northern part of the lagoon using Cymodocea nodosa (Ucria) Ascherson meadows and benthic macrofauna. 16 stations (11 with C. nodosa and 5 on bare sediment) were sampled using a Van Veen grab. Preliminary results showed differences between stations. Shoots biomass fluctuated between 8.02 and 61.2 g dw m-2 while the roots-rhizomes biomass oscillated between 10.8 and 235.5 g dw m-2. The root-rhizome and leaf biomass ratio revealed high values (up to 10.8) in the central sector suggesting a potential nutrient enrichment.Benthic macrofauna revealed the presence of 90 species belonging to six zoological groups and dominated by crustaceans, molluscs and polychaetes. The assessment of the ecological quality status, based on benthic macrofauna, was evaluated using Biotic Indices (AMBI, M-AMBI, Benthix, BITS). The results showed partial agreement between single index-derived ES and underlined the dependency of these biotic indices on the habitat characteristics, on the one hand, and the necessity to define specific reference conditions to the Marchica lagoon.

Sign in / Sign up

Export Citation Format

Share Document