Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches

none14sìMercury (Hg) is a highly toxic element for living organisms and is known to bioaccumulate and biomagnify. Here, we analyze the response of benthic foraminifera communities cultured in mesocosm and exposed to different concentrations of Hg. Standard morphological analyses and environmental DNA metabarcoding show evidence that Hg pollution has detrimental effects on benthic foraminifera. The molecular analysis provides a more complete view of foraminiferal communities including the soft-walled single-chambered monothalamiids and small-sized hard-shelled rotaliids and textulariids than the morphological one. Among these taxa that are typically overlooked in morphological studies we found potential bioindicators of Hg pollution. The mesocosm approach proves to be an effective method to study benthic foraminiferal responses to various types and concentrations of pollutants over time. This study further supports foraminiferal metabarcoding as a complementary and/or alternative method to standard biomonitoring program based on the morphological identification of species communities.openFrontalini, Fabrizio; Greco, Mattia; Di Bella, Letizia; Lejzerowicz, Franck; Reo, Emanuela; Caruso, Antonio; Cosentino, Claudia; Maccotta, Antonella; Scopelliti, Giovanna; Nardelli, Maria Pia; Losada, Maria Teresa; Armynot du Châtelet, Eric; Coccioni, Rodolfo; Pawlowski, JanFrontalini, Fabrizio; Greco, Mattia; Di Bella, Letizia; Lejzerowicz, Franck; Reo, Emanuela; Caruso, Antonio; Cosentino, Claudia; Maccotta, Antonella; Scopelliti, Giovanna; Nardelli, Maria Pia; Losada, Maria Teresa; Armynot du Châtelet, Eric; Coccioni, Rodolfo; Pawlowski, Ja

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

The study was supported by Swiss National Science Foundation grants 31003A-140766 and 313003A-159709 and by the DFG Research Centre/Cluster of Excellence “The Ocean in the Earth System”.Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.Publisher PDFPeer reviewe

A New Integrated Approach to Taxonomy: The Fusion of Molecular and Morphological Systematics with Type Material in Benthic Foraminifera

This work was supported by NERC grant NE4/G018502/1 and NE/G020310/1 (Website: http://www.nerc.ac.uk). The authors also thank the following for their support the Carnegie Trust for the Universities of Scotland (Website: http://www.carnegie-trust.org) and the Estuarine Coastal and Shelf Science Association (Website: http://www.ecsanews.org). M.S. was also supported by the Swiss National Science Foundation (SNSF), fellowships for advanced researchers PA00P2_126226 and PA00P2_142065 (Website: http://www.snf.ch/en/Pages/default.aspx).A robust and consistent taxonomy underpins the use of fossil material in palaeoenvironmental research and long-term assessment of biodiversity. This study presents a new integrated taxonomic protocol for benthic foraminifera by unequivocally reconciling the traditional taxonomic name to a specific genetic type. To implement this protocol, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene is used in combination with 16 quantitative morphometric variables to fully characterise the benthic foraminiferal species concept of Elphidium williamsoni Haynes, 1973. A combination of live contemporary topotypic specimens, original type specimens and specimens of genetic outliers were utilised in this study. Through a series of multivariate statistical tests we illustrate that genetically characterised topotype specimens are morphologically congruent with both the holotype and paratype specimens of E. williamsoni Haynes, 1973. We present the first clear link between morphologically characterised type material and the unique SSU rRNA genetic type of E. williamsoni. This example provides a standard framework for the benthic foraminifera which bridges the current discontinuity between molecular and morphological lines of evidence, allowing integration with the traditional Linnaean roots of nomenclature to offer a new prospect for taxonomic stability.Publisher PDFPeer reviewe

Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium

International audienceRecent palaeogenetic studies have demonstrated the occurrence of preserved ancient DNA (aDNA) in various types of fossilised material. Environmental aDNA sequences assigned to modern species have been recovered from marine sediments dating to the Pleistocene. However, the match between the aDNA and the fossil record still needs to be evaluated for the environmental DNA approaches to be fully exploited. Here, we focus on foraminifera in sediments up to one thousand years old retrieved from the Hornsund fjord (Svalbard). We compared the diversity of foraminiferal microfossil assemblages with the diversity of aDNA sequenced from subsurface sediment samples using both cloning and high-throughput sequencing (HTS). Our study shows that 57% of the species archived in the fossil record were also detected in the aDNA data. However, the relative abundance of aDNA sequence reads and fossil specimens differed considerably. We also found a limited match between the stratigraphic occurrence of some fossil species and their aDNA sequences, especially in the case of rare taxa. The aDNA data comprised a high proportion of non-fossilised monothalamous species, which are known to dominate in modern foraminiferal communities of the Svalbard region. Our results confirm the relevance of HTS for studying past micro-eukaryotic diversity and provide insight into its ability to reflect fossil assemblages. Palaeogenetic studies including aDNA analyses of non-fossilised groups expand the range of palaeoceanographical proxies and therefore may increase the accuracy of palaeoenvironmental reconstructions

Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test

Environmental (e)DNA metabarcoding holds great promise for biomonitoring and ecotoxicological applications. However, few studies have compared the performance of eDNA versus eRNA metabarcoding in assessing organismal response to marine pollution, in experimental conditions. Here, we performed a chromium (Cr)-spiked mesocosm experimental test on benthic foraminiferal community to investigate the effects on species diversity by analysing both eDNA and eRNA metabarcoding data across different Cr concentrations in the sediment. Foraminiferal diversity in the eRNA data showed a significant negative correlation with the Cr concentration in the sediment, while a positive response was observed in the eDNA data. The foraminiferal OTUs exhibited a higher turnover rate in eRNA than in the eDNA-derived community. Furthermore, in the eRNA samples, OTUs abundance was significantly affected by the Cr gradient in the sediment (Pseudo-R2 = 0.28, p = 0.05), while no significant trend was observed in the eDNA samples. The correlation between Cr concentration and foraminiferal diversity in eRNA datasets was stronger when the less abundant OTUs (&lt;100 reads) were removed and the analyses were conducted exclusively on OTUs shared between eRNA and eDNA datasets. This indicates the importance of metabarcoding data filtering to capture ecological impacts, in addition to using the putatively active organisms in the eRNA dataset. The comparative analyses on foraminiferal diversity revealed that eRNA-based metabarcoding can better assess the response to heavy metal exposure in presence of subtle concentrations of the pollutant. Furthermore, our results suggest that to unlock the full potential for ecosystem assessment, eDNA and eRNA should be studied in parallel to control for potential sequence artifacts in routine ecosystem surveys

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

International audienceAssessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities

Assessing the effect of mercury pollution on cultured benthic foraminifera using DNA metabarcoding and morphological approaches

Heavy metals such as mercury (Hg) occur in ecosystems from both natural sources and human activities, with large variations in concentrations and pose a significant health hazard through bioaccumulation and biomagnification. The aim of this experimental study is to assess the impact of different concentrations of Hg through time on the diversity of cultured benthic foraminifera. Tanks with concentrations of Hg up to 100 ppm were considered. Mesocosms containing 1-cm-thick sediment from each tank were subsampled at pre-established time intervals for geochemical (Hg content), morphological and molecular analyses. Morphological analyses were based on both Rose Bengal and the CellTracker Green (CTG) techniques. Molecular analyses comprised high-throughput sequencing (HTS) of foraminiferal DNA. A total of 6 datasets were generated: two from Rose Bengal morphological analysis (fraction> 63 μm and fraction >125 μm), one from CTG morphological analysis (fraction>125 μm), three from HTS run (one for each considered filter: Filter1, Filter10, Filter100). Species richness, Shannon and Fisher α alpha indices were all negatively correlated with the Hg concentrations both in water and sediment regardless the considered datasets. Since the strongest correlations were observed among diversity indices and normalized fourth-root transformed HTS data (Filter1), the multivariate analyses (nMDS and Cluster Analysis) were based on this dataset only. The nMDS highlights the negative effect of Hg pollution on the benthic foraminiferal assemblages at the highest concentrations, namely 10 ppm after three weeks and 100 ppm after two weeks of treatment. This experiment demonstrates the huge potential of metabarcoding for unraveling the impact of pollution on benthic foraminiferal assemblages

(Supplement 1) Detailed information on environmental samples and sequence data

Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (<10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies