publication . Article . 2014

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

Eva Aylagas; Ángel Borja; Naiara Rodríguez-Ezpeleta;
  • Published: 06 Mar 2014
  • Publisher: Public Library of Science (PLoS)
Abstract
Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology, Ecology, Ecological Environments, Marine Environments, Environmental Protection, Marine Ecology, Marine Biology, Marine Conservation, Marine Monitoring, Marine Technology, Earth Sciences, Marine and Aquatic Sciences, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Genetics, Species diversity, Biodiversity, DNA barcoding, Ecosystem health, Marine ecosystem, Biotic index
Funded by
EC| DEVOTES
Project
DEVOTES
DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status
  • Funder: European Commission (EC)
  • Project Code: 308392
  • Funding stream: FP7 | SP1 | ENV
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49 references, page 1 of 4

1 Halpern BS, Longo C, Hardy D, McLeod KL, Samhouri JF, et al (2012) An inde x to assess the health and benefits of the global ocean. Nature 488: 615–620.22895186 [PubMed]

2 Claudet J, Fraschetti S (2010) Human-driven impacts on marine habitats: a regional meta-analysis in the Mediterranean Sea. Biological Conservation 143: 2195–2206. [OpenAIRE]

3 UNCLOS (1982) United Nations Convention on the Law of the Sea, signed at Montego Bay, Jamaica, on 10 December. 1982: 202 www.un.org/Depts/los/index.htm.

4 CBD (2000) Ecosystem Approach. Fifth Conference of the Parties to the Convention on Biodiversity. Nairobi, Kenya, May.

5 Borja A, Dauer DM (2008) Assessing the environmental quality status in estuarine and coastal systems: Comparing methodologies and indices. Ecological Indicators 8: 6.

6 De Jonge VN, Elliott M, Brauer VS (2006) Marine monitoring: its shortcomings and mismatch with the EU Water Framework Directive's objectives. Marine Pollution Bulletin 53: 5–19.16426645 [PubMed]

7 Borja A, Bald J, Franco J, Larreta J, Muxika I, et al (2009) Using multiple ecosystem components, in assessing ecological status in Spanish (Basque Country) Atlantic marine waters Marine Pollution Bulletin. 59: 54–64.

8 BorjaÁ, Galparsoro I, Irigoien X, Iriondo A, Menchaca I, et al (2011) Implementation of the European Marine Strategy Framework Directive: A methodological approach for the assessment of environmental status, from the Basque Country (Bay of Biscay). Marine Pollution Bulletin 62: 889–904.21507430 [OpenAIRE] [PubMed]

9 Ranasinghe JA, Stein ED, Miller PE, Weisberg SB (2012) Performance of Two Southern California Benthic Community Condition Indices Using Species Abundance and Presence-Only Data: Relevance to DNA Barcoding PLoS one 7..

10 Diaz RJ, Solan M, Valente RM (2004) A review of approaches for classifying benthic habitats and evaluating habitat quality. Journal of Environmental Management 73: 165–181.15474734 [OpenAIRE] [PubMed]

11 Pinto R, Patricio J, Baeta A, Fath B, Neto J, et al (2009) Review and evaluation of estuarine biotic indices to assess benthic condition. Ecological Indicators 9: 1–25.

12 Borja A, Franco J, Perez V (2000) A Marine Biotic Index to Establish the Ecological Quality of Soft-Bottom Benthos Within European Estuarine and Coastal Environments. Marine Pollution Bulletin 40: 12.

13 Borja A, Miles A, Occhipinti-Ambrogi A, Berg T (2009) Current status of macroinvertebrate methods used for assessing the quality of European marine waters: implementing the Water Framework Directive. Hydrobiologia 633: 181–196.

14 Valenca AP, Santos PJ (2012) Macrobenthic community for assessment of estuarine health in tropical areas (Northeast, Brazil): review of macrofauna classification in ecological groups and application of AZTI Marine Biotic Index. Mar Pollut Bull 64: 1809–1820.22748505 [OpenAIRE] [PubMed]

15 Warwick RM, Clarke KR, Somerfield PJ (2010) Exploring the marine biotic index (AMBI): variations on a theme by Angel Borja. Mar Pollut Bull 60: 554–559.20005531 [PubMed]

49 references, page 1 of 4
Abstract
Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology, Ecology, Ecological Environments, Marine Environments, Environmental Protection, Marine Ecology, Marine Biology, Marine Conservation, Marine Monitoring, Marine Technology, Earth Sciences, Marine and Aquatic Sciences, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Genetics, Species diversity, Biodiversity, DNA barcoding, Ecosystem health, Marine ecosystem, Biotic index
Funded by
EC| DEVOTES
Project
DEVOTES
DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status
  • Funder: European Commission (EC)
  • Project Code: 308392
  • Funding stream: FP7 | SP1 | ENV
Download fromView all 5 versions
PLoS ONE
Article . 2014
ZENODO
Article . 2014
Provider: ZENODO
PLoS ONE
Article . 2014
Provider: Crossref
49 references, page 1 of 4

1 Halpern BS, Longo C, Hardy D, McLeod KL, Samhouri JF, et al (2012) An inde x to assess the health and benefits of the global ocean. Nature 488: 615–620.22895186 [PubMed]

2 Claudet J, Fraschetti S (2010) Human-driven impacts on marine habitats: a regional meta-analysis in the Mediterranean Sea. Biological Conservation 143: 2195–2206. [OpenAIRE]

3 UNCLOS (1982) United Nations Convention on the Law of the Sea, signed at Montego Bay, Jamaica, on 10 December. 1982: 202 www.un.org/Depts/los/index.htm.

4 CBD (2000) Ecosystem Approach. Fifth Conference of the Parties to the Convention on Biodiversity. Nairobi, Kenya, May.

5 Borja A, Dauer DM (2008) Assessing the environmental quality status in estuarine and coastal systems: Comparing methodologies and indices. Ecological Indicators 8: 6.

6 De Jonge VN, Elliott M, Brauer VS (2006) Marine monitoring: its shortcomings and mismatch with the EU Water Framework Directive's objectives. Marine Pollution Bulletin 53: 5–19.16426645 [PubMed]

7 Borja A, Bald J, Franco J, Larreta J, Muxika I, et al (2009) Using multiple ecosystem components, in assessing ecological status in Spanish (Basque Country) Atlantic marine waters Marine Pollution Bulletin. 59: 54–64.

8 BorjaÁ, Galparsoro I, Irigoien X, Iriondo A, Menchaca I, et al (2011) Implementation of the European Marine Strategy Framework Directive: A methodological approach for the assessment of environmental status, from the Basque Country (Bay of Biscay). Marine Pollution Bulletin 62: 889–904.21507430 [OpenAIRE] [PubMed]

9 Ranasinghe JA, Stein ED, Miller PE, Weisberg SB (2012) Performance of Two Southern California Benthic Community Condition Indices Using Species Abundance and Presence-Only Data: Relevance to DNA Barcoding PLoS one 7..

10 Diaz RJ, Solan M, Valente RM (2004) A review of approaches for classifying benthic habitats and evaluating habitat quality. Journal of Environmental Management 73: 165–181.15474734 [OpenAIRE] [PubMed]

11 Pinto R, Patricio J, Baeta A, Fath B, Neto J, et al (2009) Review and evaluation of estuarine biotic indices to assess benthic condition. Ecological Indicators 9: 1–25.

12 Borja A, Franco J, Perez V (2000) A Marine Biotic Index to Establish the Ecological Quality of Soft-Bottom Benthos Within European Estuarine and Coastal Environments. Marine Pollution Bulletin 40: 12.

13 Borja A, Miles A, Occhipinti-Ambrogi A, Berg T (2009) Current status of macroinvertebrate methods used for assessing the quality of European marine waters: implementing the Water Framework Directive. Hydrobiologia 633: 181–196.

14 Valenca AP, Santos PJ (2012) Macrobenthic community for assessment of estuarine health in tropical areas (Northeast, Brazil): review of macrofauna classification in ecological groups and application of AZTI Marine Biotic Index. Mar Pollut Bull 64: 1809–1820.22748505 [OpenAIRE] [PubMed]

15 Warwick RM, Clarke KR, Somerfield PJ (2010) Exploring the marine biotic index (AMBI): variations on a theme by Angel Borja. Mar Pollut Bull 60: 554–559.20005531 [PubMed]

49 references, page 1 of 4
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