biotic indices
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2022 ◽  
Vol 465 ◽  
pp. 109859
Author(s):  
M.M. Nicolosi Gelis ◽  
M.B. Sathicq ◽  
J. Jupke ◽  
J. Cochero
Keyword(s):  

Water ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 2821
Author(s):  
Antoine Dubois ◽  
Christine Barras ◽  
Jean-Charles Pavard ◽  
Annick Donnay ◽  
Melvin Béatrix ◽  
...  

Corsican marine aquaculture is one of the highest contributors of fish production in France, which may result in environmental perturbations caused by organic matter (OM) accumulation under fish farms and impacting natural communities. This study aimed to (1) characterise the environmental conditions at two different fish farms, (2) monitor the response of benthic foraminiferal species to this activity, and (3) assess the accuracy of existing foraminiferal biotic indices. In 2017, sea floor sediment was sampled in transects from two Corsican fish farms for living foraminiferal and sedimentary analyses. Four indices were calculated and compared: exp(H′bc), Foram-AMBI, Foram Stress Index and TSI-Med. A significant increase in total organic carbon (TOC) has been shown, mainly below the fish cages. Communities were characterized by a shift from high density, opportunistic and tolerant species under the cages to lower densities and more sensitive species further away. According to their distribution patterns along the TOC gradient, we propose to update the ecological group classification of seven species to improve Foram-AMBI’s accuracy and sensitivity: Triloculina oblonga and Quinqueloculina lamarckiana to Ecological Group (EG) I; Rosalina bradyi to EGIII; and Bolivina dilatata, Bulimina aculeata and Quinqueloculina stalkeri to EGIV. We recommend prioritising the use of TSI-Med and Foram-AMBI with the updated list to assess ecological quality in coastal waters of the Mediterranean Sea.


2021 ◽  
Vol 8 ◽  
Author(s):  
Xin Lu ◽  
Jing Xu ◽  
Zhaodong Xu ◽  
Xiaoshou Liu

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′.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sigamani Sivaraj ◽  
Durga Prasad Behera ◽  
Kolandhasamy Prabhu

Macrobenthic community being used as marine health indictor vis-à-vis to anthropogenic disturbance since their characteristic of life cycle (reproductive mode, sedentary, energy transfer, sensitive-resistance species, indicator organism etc.). Therefore, the present study was chosen in Vizag port waters have been subject to a variety of anthropogenic pressure in the last two decades. The purpose of this study was to assess the ecological status of the port environment through biotic indices like AZTI 's Marine Biotic Index (AMBI) and Multivariate-AMBI Index (M-AMBI) which have been successfully validated geographically and anthropogenically stressed habitats. The result revealed that the inner harbor (IHC, Iron ore Q1 & Iron ore Q7) stations are heavily disturbed while the outer harbor fall between undisturbed and moderately disturbed status. It was observed that the reduced tidal action inside the harbor determines the health status indicating that the Iron ore transporting areas are at high risk with respect to benthic population.


Author(s):  
Eva Aylagas ◽  
Javier Atalah ◽  
Pablo Sánchez‐Jerez ◽  
John Pearman ◽  
Nuria Casado ◽  
...  

2021 ◽  
Author(s):  
Maria Mercedes Nicolosi Gelis ◽  
Maria Belen Sathicq ◽  
Jonathan Jupke ◽  
Joaquin Cochero

1- Diatoms are widely used to detect changes in water quality due to their specific sensibility to a variety of environmental conditions. Among the different diatom-based tools to measure water quality, the biotic indices, ecological and morphological traits are the most commonly used. 2- DiaThor, contains 19 functions that provide morphological data of the samples (number and shape of chloroplasts, total biovolume), ecological data (species richness, evenness, diversity, size classes, ecological guilds, ecological preferences) and biotic indices (Descy Index, EPID Index, Indice Diatomique Artois-Picardie, Swiss Diatom Index, Pampean Diatom Index, ILM index, Specific Pollution sensitivity Index, Lobo Index, Sladecek index, SPEAR(herbicides) index and the Trophic index). A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment. 3- The structure of the package, how it functions and the structure of the input and output data are explained. To demonstrate the most common use of DiaThor, an example of the package performance is also provided. 4- The DiaThor package aims to contribute to the water quality assessment based on diatom assemblages, while also providing researchers with an open platform to suggest new statistics and functionalities to be integrated into future builds.


2021 ◽  
Author(s):  
Nawfel Mosbahi ◽  
Jean-Philippe Pezy ◽  
Lassad Neifar ◽  
Jean-Claude Dauvin

Abstract This study from January to December 2018 was the first initiative of a Port Baseline Survey (PBS) aimed at assessing the impact of biological invasions in harbours of the Gulf of Gabès (GG). A total of 12 fishing and industrial harbours were seasonally prospected during 2018. A total of 174 macrobenthos taxa were recorded, belonging to eight zoological groups, with a dominance of crustaceans (32%), molluscs (31%) and polychaetes (20%). Among these taxa, 57 were Non-Indigenous Species (NIS) for Tunisian waters, while 27 species were recorded for the first time in GG harbours and three decapods ( Dyspanopeus sayi, Hippolyte prideauxiana and Pilumnus minutus ) and one amphipod ( Hamimaera hamigera ) were newly recorded from Tunisian waters. Two main categories of harbours are distinguished according to their macrobenthic communities and environmental features (essentially edaphic factors). The industrial harbours yield higher numbers of species and abundance of NIS than the fishing ports. The ALEX metric is used to evaluate the biological invasion status of the Gulf of Gabès harbours, showing that their status ranges from unaffected in fishing harbours to extremely affected in industrial harbours. Three biotic indices (AMBI, BO2A and BENTIX) are applied to assess the ecological status of harbours, which varies from moderate to good. ALEX and the other biotic indices are significantly correlated with harbour characteristics, maritime traffic and edaphic factors (organic matter and chemical contamination). The present study gives an overview of all available benthic data, the impact of biological invasions and the ecological quality status of harbours in the Gulf of Gabès. The results could be considered as providing important baseline data for the implementation of environmental policies and management plans in the future.


2021 ◽  
Vol 4 ◽  
Author(s):  
Anders Lanzén ◽  
Jon Thomassen Hestetun ◽  
Andrea Bagi ◽  
Thomas Dahlgren

Routine biological monitoring of the areas affected by offshore oil drilling and extraction is critical for ensuring proper environmental management. In addition to sufficient knowledge of the ecosystem affected, formalised e.g. as biotic indices of indicator species, adequate temporal and spatial resolution is also required, to provide accurate information. As already demonstrated in several types of environments, environmental DNA (eDNA) metabarcoding offers an attractive alternative to current morphology-based assessments, including for impacts of oil extraction or spills. We have recently studied the influence of different experimental strategies on the accuracy of marine sediment metabarcoding, suggesting minimum criteria for technical and spatial replication (Hestetun et al. 2020). Here, we aim to evaluate the predictive power of this strategy, through agreement with assessments based on physicochemical measurements and current bioindicators. To this end, we targeted the metazoan, and total eukaryotic benthic communities, using COI and 18S V1-V2 markers, respectively. Sampled sites ranged from high to low impacts. The studied areas were located near active production installations and reference sites on the Norwegian continental shelf, in the North Sea and Barents Sea. As a proxy for accumulated impact, we developed a simple physicochemical pressure index (PI) based on total hydrocarbons, PAH16, barium and copper, all of which agreed well with impact reported from recent routine monitoring. Alpha diversity of both molecular datasets, as well as of morphology data, correlated strongly with this PI. However, the correlation was stronger yet with the macroinvertebrate-based Norwegian Sensitivity Index (NSI) derived from COI metabarcoding data, which also agreed well with NSI values derived from morphology-based monitoring. We also identified a set of bioindicator taxa from each of the two metabarcoding datasets, used to develop two novel metabarcoding-based biotic indeces. Using cross-validation, we demonstrated that predictions based on these indeces agreed well with PI. Predictive performance was better, and similar to NSI, for the COI-based index, but also high for the 18S-based version. In conclusion, this study demonstrates how de novo biotic indices can be developed, that perform comparably to existing biotic indices. We are confident that, using a larger set of samples, performance can be improved beyond that of current monitoring practices. Thanks to the reduced costs of eDNA analysis in comparison to morphological identifiation, this would also pave the way for improved spatial and temporal resolution employed in routine environmental monitoring. In doing so, it can also provide valuable raw data for improving our understanding of benthic ecology, biodiversity and its sensitivity to anthropogenic pressures.


2021 ◽  
Vol 4 ◽  
Author(s):  
Jan Pawlowski ◽  
Maria Kahlert

Traditionally, the biological quality of aquatic ecosystems is assessed using selected groups of organisms that can be identified morphologically. Recent advances in high-throughput genomic approaches offered new opportunities to monitor biodiversity and assess ecological status using DNA barcoding and metabarcoding. The DNA-based tools have been used in three different ways: (1) to replace morphological identification of biological quality elements in existing biotic indices, (2) to develop new molecular indices based on morphologically inconspicuous groups of potential environmental indicators, and (3) to predict biotic indices from environmental DNA datasets using machine learning methods (Pawlowski et al. 2018). The next steps need to take advantages and challenges of these different approaches into account in view of their future application in routine bioassessment.The Working Group 2 of DNAqua-Net, Biotic Indices & Metrics, has worked with several task forces tackling different organism groups (fish, macroinvertebrates, diatoms, bacteria, protists, meiofauna), because challenges have been shown to be quite different dependent on the target organisms Kahlert et al. 2019. For the fish the eDNA-metabarcoding methods are well developed and give very good results in terms of species detection. The important question is to see if the semi-quantitative data retrieved from the metabarcoding (proportion in eDNA sequences) could be translated to proportions in biomass/numbers that are now used in many indices. The fish researchers are trying to fit these data in, but some correction factors might be needed to correct for differences between molecular and conventional methodsRegarding the macroinvertebrates, much discussion regarding index development was focusing on the importance of abundance measurements, and it was tested how existing indices would perform if barcoding data would be used instead of morphological data. Still discussion is ongoing on several technical issues, including the use of preservative for DNA extraction from bulk samples, the choice of primers for PCR amplification and the incompleteness of reference databases which impedes the correct assignment of eDNA sequences. Also minimum standards for routine operation are still missing.The diatom group has worked much on practical issues, starting a large initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardization (Bailet et al. 2019, Keck et al. 2018, Vasselon et al. 2017). With diatoms, all three approaches to develop molecular indices have been tested and seem promising, i.e. using existing indices with taxa names derived by matching sequences with reference databases, developing new indices based on molecular data only with traditional fixed scores, and using machine-learning techniques (Bailet et al. 2020, Vasselon et al. 2018, Tapolczai et al. 2019, Keck et al. 2018) The micro- and meiobiota group has worked towards an inclusion of microorganisms into aquatic assessment, because the microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems (Sagova-Mareckova et al. 2021). Another focus was on how sediment DNA analysis can be integrated into stated goals of routine monitoring applications. It has been an interesting journey, and we WG2 coordinators would like to thank all the people for their engagement! Keep up the good work!


2021 ◽  
Vol 3 ◽  
Author(s):  
Helen F. Dallas

Benthic macroinvertebrates are commonly used to assess water quality and ecological condition of aquatic ecosystems and they form the basis of several biotic indices. Many of these biotic indices are based on rapid bioassessment protocols (RBP). The first RBP based on macroinvertebrates, developed in Africa in the early 1990s, was the South Africa Scoring System (SASS). Since then SASS has been widely used in southern Africa and beyond, and has formed the basis of several other RBPs developed in Africa. This paper explores the RBPs and associated biotic indices currently used in Africa, primarily those that are rapid, field-based with low taxonomy (mostly family level) and which rely on sensitivity weightings of individual taxa to generate three metrics for interpreting water quality and ecological condition of aquatic ecosystems. Recommendations for future regional adaptation of RBPs, including calibration, validation, and modification of RBPs and biotic indices for new regions are provided. To date, five RBPs have been developed in Africa, while some existing biotic indices have been used outside their intended regional range. Key to the efficacy of any RBP and associated biotic index is the ability to detect a water quality impact, or change in river health. Important considerations when adapting an index for a new region or country include evaluating the suitability of the sampling protocol to local river conditions, evaluating the distribution of aquatic macroinvertebrate taxa in the region, assigning sensitivity weightings to new taxa in the region, evaluating the ability of the biotic index to detect impacts, evaluating within-country spatial and temporal variability in macroinvertebrate assemblages, and developing appropriate data interpretation guidelines based on metric scores and reference conditions. Often several iterations of a biotic index are needed, with improvement in efficacy with each version, following spatially and temporally comprehensive sampling. Future RBPs developed for bioassessment of rivers in Africa will promote the protection, conservation, and management of African riverine ecosystems.


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