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Opportunistic feeding habits of two African freshwater clupeid fishes: DNA metabarcoding unravels spatial differences in diet and microbiome, and identifies new prey taxa
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The African Lake Tanganyika clupeids play an important role in the lake's ecosystem and have a high regional economic and nutritional value. Using DNA metabarcoding, we analysed the prey item composition and microbiome of these two clupeid species, Stolothrissa tanganicae and Limnothrissa miodon. We sequenced the mitochondrial COI region of the gut content for prey analysis and the 16S rRNA region of the hindgut content for microbiome analysis of 140 fish sampled at five locations across Lake Tanganyika. Our research confirmed previously reported prey items and discovered prey items that were not reported before, including the jellyfish Limnocnida tanganjicae. The hindgut of the fish harboured 15 bacterial phyla, with the most common being Firmicutes and Proteobacteria. The two clupeid species differed in diet, but not in microbiome. Further, the diet of S. tanganicae, but not its microbiome, varied on a spatial scale, whereas the microbiome, but not the diet, of L. miodon showed spatial variation. Our findings suggest that the Lake Tanganyika clupeids are opportunists, with a diet reflecting the local zooplankton community's composition. These results can serve as a useful reference for monitoring the health status of economically important fish stocks.
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RBINS Staff Publications 2023
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A 1500-year record of North Atlantic storm flooding from lacustrine sediments, Shetland Islands (UK)
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Severe storm flooding poses a major hazard to the coasts of north-western Europe. However, the long-term recurrence patterns of extreme coastal flooding and their governing factors are poorly understood. Therefore, high-resolution sedimentary records of past North Atlantic storm flooding are required. This multi-proxy study reconstructs storm-induced overwash processes from coastal lake sediments on the Shetland Islands using grain-size and geochemical data, and the re-analysis of historical data. The chronostratigraphy is based on Bayesian age–depth modelling using accelerator mass spectrometry 14C and 137Cs data. A high XRF-based Si/Ti ratio and the unimodal grain-size distribution link the sand layers to the beach and thus storm-induced overwash events. Periods with more frequent storm flooding occurred 980–1050, 1150–1300, 1450–1550, 1820–1900 and 1950–2000 ce, which is largely consistent with a positive North Atlantic Oscillation mode. The Little Ice Age (1400–1850 ce) shows a gap of major sand layers suggesting a southward shift of storm tracks and a seasonal variance with more storm floods in spring and autumn. Warmer phases shifted winter storm tracks towards the north-east Atlantic, indicating a possible trend for future storm-track changes and increased storm flooding in the northern North Sea region.
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RBINS Staff Publications 2023
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No difference between critical and sprint swimming speeds for two galaxiid species
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Researchers have used laboratory experiments to examine how fish might be affected by anthropogenic alterations and conclude how best to adjust fish passage and culvert remediation designs in response. A common way to document swimming performance for this purpose is measuring fish critical swimming speed (Ucrit). Nonetheless, the Ucrit protocol as defined by Brett [(1964) Journal of the Fisheries Research Board of Canada, 21, 1183–1226] may be inappropriate for studying swimming performance and determining how it relates to upstream migration in benthic fish, as they may not actively swim throughout the entire Ucrit test. An alternative method to estimate swimming performance is sprint swimming speed (Usprint), which is suggested to be a measure of the burst speed of fish rather than maximum sustained swimming speed. The authors conducted comparative swimming performance experiments to evaluate whether Usprint can be used to compare swimming performance of benthic species to that of pelagic, actively swimming species. They measured individual swimming speeds of īnanga (Galaxias maculatus), an actively swimming pelagic species, and banded kōkopu (Galaxias fasciatus), a fish that exhibits benthic station-holding behaviour, using both the Usprint and Ucrit test. Experiments revealed that no significant statistical difference between swimming speeds was estimated using the Ucrit and Usprint test protocols for both G. maculatus and G. fasciatus. The result of this study suggests that fish swimming speeds obtained using these two methods are comparable for the species used in this study. By using Usprint for benthic-associated fish and Ucrit for pelagic fish, we may be able to compare a broader range of species' swimming abilities for use in a fish passage context.
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RBINS Staff Publications 2023
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Sedimentary evidence of the Late Holocene tsunami in the Shetland Islands (UK) at Loch Flugarth, northern Mainland
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Tsunami deposits around the North Sea basin are needed to assess the long-term hazard of tsunamis. Here, we present sedimentary evidence of the youngest tsunami on the Shetland Islands from Loch Flugarth, a coastal lake on northern Mainland. Three gravity cores show organic-rich background sedimentation with many sub-centimetre-scale sand layers, reflecting recurring storm overwash and a sediment source limited to the active beach and uppermost subtidal zone. A basal 13-cm-thick sand layer, dated to 426–787 cal. a CE based on 14C, 137Cs and Bayesian age–depth modelling, was found in all cores. High-resolution grain-size analysis identified four normally graded or massive sublayers with inversely graded traction carpets at the base of two sublayers. A thin organic-rich ‘mud’ drape and a ‘mud’ cap cover the two uppermost sublayers, which also contain small rip-up clasts. Grain-size distributions show a difference between the basal sand layer and the coarser and better sorted storm layers above. Multivariate statistical analysis of X-ray fluorescence core scanning data also distinguishes both sand units: Zr, Fe and Ti dominate the thick basal sand, while the thin storm layers are high in K and Si. Enriched Zr and Ti in the basal sand layer, in combination with increased magnetic susceptibility, may be related to higher heavy mineral content reflecting an additional marine sediment source below the storm-wave base that is activated by a tsunami. Based on reinterpretation of chronological data from two different published sites and the chronostratigraphy of the present study, the tsunami seems to date to c. 1400 cal. a BP. Although the source of the tsunami remains unclear, the lack of evidence for this event outside of the Shetland Islands suggests that it had a local source and was smaller than the older Storegga tsunami (8.15 cal. ka BP), which affected most of the North Sea basin.
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RBINS Staff Publications 2023
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Microbiomes of aquatic animals
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RBINS Staff Publications 2023
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Automated curve fitting and unsupervised clustering of manganese oxide Raman responses
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Natural manganese oxides characterization represents a challenge due to the broad variety of their structures and geochemical compositions along with a frequent poor crystallinity. This characterization requires the ability to conduct both a phase separation and a phase association operation. In this paper, the Raman spectra acquired on a selection of natural manganese oxide minerals are first processed with an automated curve-fitting model called MnOx. The adjustment of convolution envelope is realized, thanks to the Levenberg–Marquardt algorithm applied on a set of randomly generated seed pseudo-Voigt curves. The application conditions of the automated curve-fitting and, in particular, the number of seed curves are investigated with regards to the risk of overfitting. The MnOx model outputs are in a second step treated by data mining techniques and in particular by unsupervised clustering methods. This data processing shows promising results in terms of phase separation when the number of clusters is equivalent to the number of phases. By contrast, the decrease of number of clusters leads to a phase association which reflects spectral affinities between phases. This result shows the existence of 6 to 7 vibrational bands in Mn oxides Raman spectra, with contrasting behaviours between clustering. Thereby, vibrational bands located in the low wave number domain (<510 cm−1) are more mobile and therefore more sensitive to structural modifications, while bands with higher wave number are less affected by structural changes. Besides these results, Raman responses collected during this study provide new refinement regarding the spectral content of some Mn oxides in particular todorokite, nsutite, and chalcophanite.
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RBINS Staff Publications 2017
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Publishing data to support the fight against human vector-borne diseases
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Vector-borne diseases are responsible for more than 17% of human cases of infectious diseases. In most situations, effective control of debilitating and deadly vector-bone diseases (VBDs), such as malaria, dengue, chikungunya, yellow fever, Zika and Chagas requires up to-date, robust and comprehensive information on the presence, diversity, ecology, bionomics and geographic spread of the organisms that carry and transmit the infectious agents. Huge gaps exist in the information related to these vectors, creating an essential need for campaigns to mobilise and share data. The publication of data papers is an effective tool for overcoming this challenge. These peer-reviewed articles provide scholarly credit for researchers whose vital work of assembling and publishing well-described, properly formatted datasets often fails to receive appropriate recognition. To address this, GigaScience’s sister journal GigaByte partnered with the Global Biodiversity Information Facility (GBIF) to publish a series of data papers, with support from the Special Programme for Research and Training in Tropical Diseases (TDR), hosted by the World Health Organisation (WHO). Here we outline the initial results of this targeted approach to sharing data and describe its importance for controlling VBDs and improving public health.
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RBINS Staff Publications 2022
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Where are we now with European forest multi-taxon biodiversity and where can we head to?
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The European biodiversity and forest strategies rely on forest sustainable management (SFM) to conserve forest biodiversity. However, current sustainability assessments hardly account for direct biodiversity indicators. We focused on forest multi-taxon biodiversity to: i) gather and map the existing information; ii) identify knowledge and research gaps; iii) discuss its research potential. We established a research network to fit data on species, standing trees, lying deadwood and sampling unit description from 34 local datasets across 3591 sampling units. A total of 8724 species were represented, with the share of common and rare species varying across taxonomic classes: some included many species with several rare ones (e.g., Insecta); others (e.g., Bryopsida) were repre sented by few common species. Tree-related structural attributes were sampled in a subset of sampling units (2889; 2356; 2309 and 1388 respectively for diameter, height, deadwood and microhabitats). Overall, multi taxon studies are biased towards mature forests and may underrepresent the species related to other developmental phases. European forest compositional categories were all represented, but beech forests were over represented as compared to thermophilous and boreal forests. Most sampling units (94%) were referred to a habitat type of conservation concern. Existing information may support European conservation and SFM strategies in: (i) methodological harmonization and coordinated monitoring; (ii) definition and testing of SFM indicators and thresholds; (iii) data-driven assessment of the effects of environmental and management drivers on multi-taxon forest biological and functional diversity, (iv) multi-scale forest monitoring integrating in-situ and remotely sensed information.
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RBINS Staff Publications 2023
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Taphonomy of marine vertebrates of the Pisco Formation (Miocene, Peru): Insights into the origin of an outstanding Fossil-Lagerstätte
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RBINS Staff Publications 2021
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Collagen stable isotopes provide insights into the end of the mammoth steppe in the central East European plains during the Epigravettian
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Higher δ15N values in bone collagen of mammoth (Mammuthus primigenius) compared with coeval large herbivores is a classic trait of the mammoth steppe. An exception applies to the Epigravettian site of Mezhyrich (ca. 18–17.4 ka cal BP) in the central East European plains, where mammoth bones have δ15N values equivalent to or in a lower range than those of horse specimens (Equus sp.). We expanded our preliminary dataset to a larger sampling size of mammoth, other large herbivores, and carnivores from contemporaneous and nearby sites of Buzhanka 2, Eliseevichi, and Yudinovo. The unusual low mammoth δ15N values were confirmed at Buzhanka 2 and for some specimens from Eliseevichi, while most individuals from Yudinovo displayed the expected high δ15N values, meaning similar to those of the large canids. The possibility of a contrast in migration pattern is not supported since the δ34S values, a marker of mobility, do not correlate with the δ15N values of mammoth bone collagen. No clear chronological tendency could be revealed, at least not at the scale of radiocarbon dating. The low range in δ15N values is likely to reflect a change in the specific niche of the mammoth in the southern part of its distribution.
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RBINS Staff Publications 2018
