Is there a possibility of ranking benthic quality assessment indices to select the most responsive to different human pressures?

Borja, Ángel; Marín, Sandra L.; Muxika, Iñigo; Pino, Loreto; Rodríguez, José Germán

doi:10.1016/j.marpolbul.2015.06.030

Cited by 110 publications

(40 citation statements)

References 46 publications

(60 reference statements)

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“…These organisms are considered a good indicator of ecosystem health and have demonstrated a rapid response to a range of natural and anthropogenic pressures (Johnston and Roberts, 2009). As a result, the macroinvertebrate community has been largely used to develop biotic indices (Diaz et al, 2004;Pinto et al, 2009;Borja et al, 2015), such as the AZTI's Marine Biotic Index (AMBI; Borja et al, 2000), used worldwide to assess the marine benthic status (Borja et al, 2015). Nevertheless, biomonitoring based upon benthic organisms has limitations because species identification requires extensive taxonomic expertise and it is time-consuming, expensive, and laborious (Yu et al, 2012;Wood et al, 2013;Aylagas et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

2016

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Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

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Section: Introductionmentioning

confidence: 99%

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

2016

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“…The rapid response of benthic organisms to a range of natural and anthropogenic pressures makes this community a suitable ecological component for marine biomonitoring (Johnston and Roberts, 2009). Above all, macroinvertebrates are widely used to assess environmental quality through the calculation of benthic indices (Diaz et al, 2004;Borja et al, 2015). Yet, the fast environmental degradation and the necessity of cost-effective methods for biodiversity assessment urge the need of new tools that allow species identification in a much faster way compared to morphological methodologies .…”

Section: Introductionmentioning

confidence: 99%

Marine Sediment Sample Pre-processing for Macroinvertebrates Metabarcoding: Mechanical Enrichment and Homogenization

et al. 2016

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Metabarcoding is an accurate and cost-effective technique that allows for simultaneous taxonomic identification of multiple environmental samples. Application of this technique to marine benthic macroinvertebrate biodiversity assessment for biomonitoring purposes requires standardization of laboratory and data analysis procedures. In this context, protocols for creation and sequencing of amplicon libraries and their related bioinformatics analysis have been recently published. However, a standardized protocol describing all previous steps (i.e., processing and manipulation of environmental samples for macroinvertebrate community characterization) is lacking. Here, we provide detailed procedures for benthic environmental sample collection, processing, enrichment for macroinvertebrates, homogenization, and subsequent DNA extraction for metabarcoding analysis. Since this is the first protocol of this kind, it should be of use to any researcher in this field, having the potential for improvement.

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“…Bremner et al, 2006;Bremner, 2008), as opposed to the use of mostly structural approaches (e.g. taxonomic-based indices, see Borja et al, 2015). Indeed, increasing evidence suggests that a species ability to deal with environmental disturbance is at least partly driven by its traits (Pearson and Rosenberg, 1978;Bremner et al, 2003;Culhane et al, 2014).…”

Section: Introductionmentioning

confidence: 99%