Search

Fish stocking occurs in aquatic systems for conservation purposes, to create or enhance recreational fisheries and to enhance wild-catch commercial fisheries. Identifying and quantifying the contribution of stocking efforts to wild populations is crucial to informing these management objectives. Provenance determination methods trade off accuracy, replicability, and cost-effectiveness at fishery-relevant scales. We present and assess multiple methods for provenance determination using a case study of barramundi (Lates calcarifer) in the Dry Tropics region of northern Australia. A novel application of near-infrared spectroscopy (NIRS) is compared to two established methods for fish provenance, otolith microchemistry and genetic parentage analysis using microsatellites. The otolith microchemistry method was able to provide extremely high provenance resolution (>99% accuracy). The microsatellite parentage analysis method had a slightly lower overall accuracy (95%), likely as a result of genetic introgression in this region. Provenance determination using otolith NIRS had the lowest overall accuracy (76%). Once limitations regarding spectral noise, image resolution, and sample size are addressed, NIRS may have potential for cost-effectively determining provenance in fish.

Researchers from Queensland’s Department of Agriculture and Fisheries, James Cook University, and the University of Western Australia tested a range of otolith-based and genetic methods to identify hatchery-born from wild-born Barramundi. The project took place in the Dry Tropics region, where extensive historical and ongoing impoundment stocking (release of hatchery-born Barramundi into freshwater bodies) may be contributing to the downstream wild-capture marine and estuarine fishery. Fish samples were collected from the commercial and recreational wild-capture marine and estuarine fishery in 2019 and 2020, following the major Townsville floods in February 2019. The team identified a cost-effective means of using trace elements in fish otoliths to reliably distinguish hatchery-origin from wild-origin fish, measure the contribution of stocked fish to the wild population, and assess the sustainability of the wild-capture fishery.

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminif

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

Emiliania huxleyi cells were grown in artificial seawater of different Li and Ca concentrations and coccolith Li/Ca ratios determined. Coccolith Li/Ca ratios were positively correlated to seawater Li/Ca ratios only if the seawater Li concentration was changed, not if the seawater Ca concentration was changed. This Li partitioning pattern of E. huxleyi was previously also observed in the benthic foraminifer Amphistegina lessonii and inorganically precipitated calcite. We argue that Li partitioning in both E. huxleyi and A. lessonii is dominated by a coupled transmembrane transport of Li and Ca from seawater to the site of calcification. We present a refined version of a recently proposed transmembrane transport model for Li and Ca. The model assumes that Li and Ca enter the cell via Ca channels, the Li flux being dependent on the Ca flux. While the original model features a linear function to describe the experimental data, our refined version uses a power function, changing the stoichiometry of Li and Ca. The version presented here accurately predicts the observed dependence of DLi on seawater Li/Ca ratios. Our data demonstrate that minor element partitioning in calcifying organisms is partly mediated by biological processes even if the partitioning behavior of the calcifying organism is indistinguishable from that of inorganically precipitated calcium carbonate.

Mediterranean Outflow Water (MOW) actsas a net source of salt and heat into North Atlantic intermediate depths that ultimately contributes to the Atlantic Meridional Overturning Circulation, and it has been hypothesised that MOW variability might influence global climate. Although several studies have documented major glacial-interglacial changes in deep- and intermediate Mediterranean circulation patterns, littleisknown about associated impacts on MOW properties, in particular its residence time and geochemical signature. Using cold-water coral sets from along the pre- and MOW-path from the Alboran Seato the northern Galician Bank weaimto identify changes in both the ventilation state of the watermasses flowing out of the Mediterranean and the distribution of coral growth through paired Uranium-series and AMS radiocarbon ages complemented by trace element measurements in benthic foraminifera. Our results show a particular spatio-temporal coral distribution with glacial presence only at the deepest sites of the Gulf of Cadiz (~1000m), followed by ~300m Western Mediterranean (WMed) coral appearance across the deglaciation/mid Holocene (14-4kyr), to end with a proliferation at the Strait of Gibraltar and Galicia Bank from ~6kyr towards the present. We hypothesise 1) that ~300m WMed area might have been bathed in Atlantic waters inflow during the glacial due tosea-level drop, returning to Levantine Intermediate Water influence over the deglaciation, and 2) that MOW reached deeper areas outside of the Mediterranean Seain the Gulf of Cadiz during the glacial. Regarding the reservoir age, a little ~300yr change is observed at the WMedat 150-450m when corals appear at the Bølling-Allerød, but in synchrony with significant changes in hydrographical parameters. Overall, our results suggest a watermass reorganization at the surface-intermediate layer of the WMed during the deglaciation/early Holocene, that need to be further explored through Nd isotope analysis and trace elem

It has long since been noted that minor element (Me) partitioning into biogenic carbonates is sometimes different from Me partitioning into inorganically precipitated carbonates. The prime example is the partitioning coefficient, which might be lower or even higher than the one of inorganically precipitated carbonate. Such a difference is usually termed “vital effect” and is seen as indicative of a biologically modified minor element partitioning. Over the last three decades interest in conceptual biomineralization models compatible with minor element and isotope fractionation has been steadily increasing. However, inferring features of a biomineralization mechanism from Me partitioning is complicated, because not all partitioning coefficients show vital effects in every calcium carbonate producing organism. Moreover, the partitioning coefficient is not the only aspect of Me partitioning. Other aspects include polymorph specificity and rate dependence. Patellogastropod limpets are ideally suited for analysing Me partitioning in terms of biomineralization models, because they feature both aragonitic and calcitic shell parts, so that polymorph specificity can be tested. In this study, polymorph-specific partitioning of the minor elements Mg, Li, B, Sr, and U into shells of the patellogastropod limpet Patella caerulea from within and outside a CO2 vent site at Ischia (Italy) was investigated by means of LA-ICP-MS. The partitioning coefficients of U, B, Mg, and Sr (in aragonite) differed from the respective inorganic ones, while the partitioning coefficients of Li and Sr (in calcite) fell within the range of published values for inorganically precipitated carbonates. Polymorph specificity of Me partitioning was explicable in terms of inorganic precipitation in the case of Sr and Mg, but not Li and B. Seawater carbon chemistry did not have the effect on B partitioning that was expected on the basis of data on inorganic precipitates and foraminifera. Carbon chemistry did

The shallow water benthic foraminifer Amphistegina lessonii was grown in seawater of variable Li and Ca concentration and shell Li/Ca was determined by means of LA-ICPMS. Shell Li/Ca is positively correlated to seawater Li/Ca only when the Li concentration of seawater is changed. If the seawater Ca concentration is changed, shell Li/Ca remains constant. This indicates that Li does not compete with Ca for incorporation in the shell of A. lessonii. A recently proposed calcification model can be applied to divalent cations (e.g., Mg and Sr), which compete for binding sites of ion transporters and positions in the calcite lattice. By contrast, the transport pathway of monovalent cations such as Li is probably diffusion based (e.g., ion-channels), and monovalent cations do not compete with Ca for a position in the calcite lattice. Here we present a new model for Li partitioning into foraminiferal calcite which predicts our experimental results and should also be applicable to other alkali metals.

The Sr/Ca ratio of coral aragonite is used to reconstruct past sea surface temperature (SST). Twenty-one laboratories took part in an interlaboratory study of coral Sr/Ca measurements. Results show interlaboratory bias can be significant, and in the extreme case could result in a range in SST estimates of 7°C. However, most of the data fall within a narrower range and the Porites coral reference material JCp-1 is now characterized well enough to have a certified Sr/Ca value of 8.838 mmol/mol with an expanded uncertainty of 0.089 mmol/mol following International Association of Geoanalysts (IAG) guidelines. This uncertainty, at the 95% confidence level, equates to 1.5°C for SST estimates using Porites, so is approaching fitness for purpose. The comparable median within laboratory error is <0.5°C. This difference in uncertainties illustrates the interlaboratory bias component that should be reduced through the use of reference materials like the JCp-1. There are many potential sources contributing to biases in comparative methods but traces of Sr in Ca standards and uncertainties in reference solution composition can account for half of the combined uncertainty. Consensus values that fulfil the requirements to be certified values were also obtained for Mg/Ca in JCp-1 and for Sr/Ca and Mg/Ca ratios in the JCt-1 giant clam reference material. Reference values with variable fitness for purpose have also been obtained for Li/Ca, B/Ca, Ba/Ca, and U/Ca in both reference materials. In future, studies reporting coral element/Ca data should also report the average value obtained for a reference material such as the JCp-1.

The advent of new microanalytical techniques such as electron microprobe mapping (EMP) and laser ablation microsamplers coupled to mass spectrometers (LA-ICP-MS) provides a new array of possibilities to explore in great detail the trace elements distribution in foraminiferal carbonates. Here we apply these techniques to characterize diagenetic phases present in foraminiferal shells from Ocean Drilling Program Site 1240 in the Panama Basin, a region characterized by the presence of manganese-rich minerals in the sediments. The combined application of these techniques allows us to characterize the elemental and spatial distribution on the surface and across the foraminiferal shells. Results illustrate the presence of at least two different Mn-rich contaminant phases in the foraminiferal carbonates: Mn-rich carbonates and ferromanganese oxides. Elemental maps also highlight the relevance of the foraminifera shell texture and porosity in the distribution and formation of these contaminant phases. In the case of Neogloboquadrina dutertrei, Mn phases form a continuous thin layer in the inner part of the chambers, whereas for Globigerinoides ruber, Mn phases have a rather patchy distribution and are usually found within the pores. Significant high magnesium concentrations are always associated with these Mn-rich phases. These new findings support the need of removing these Mn-rich contaminant phases in order to measure accurately the Mg/Ca ratios in the foraminifera shell and therefore obtain reliable Mg/Ca paleotemperature reconstructions.

Laser ablation inductively coupled plasma-mass spectrometry microanalysis of fossil and live Globigerinoides ruber from the eastern Indian Ocean reveals large variations of Mg/Ca composition both within and between individual tests from core top or plankton pump samples. Although the extent of intertest and intratest compositional variability exceeds that attributable to calcification temperature, the pooled mean Mg/Ca molar values obtained for core top samples between the equator and >30°S form a strong exponential correlation with mean annual sea surface temperature (Mg/Ca mmol/mol = 0.52 exp0.076SST°C, r2 = 0.99). The intertest Mg/Ca variability within these deep-sea core top samples is a source of significant uncertainty in Mg/Ca seawater temperature estimates and is notable for being site specific. Our results indicate that widely assumed uncertainties in Mg/Ca thermometry may be underestimated. We show that statistical power analysis can be used to evaluate the number of tests needed to achieve a target level of uncertainty on a sample by sample case. A varying bias also arises from the presence and varying mix of two morphotypes (G. ruber ruber and G. ruber pyramidalis), which have different mean Mg/Ca values. Estimated calcification temperature differences between these morphotypes range up to 5°C and are notable for correlating with the seasonal range in seawater temperature at different sites.

The advent of new microanalytical techniques such as electron microprobe mapping (EMP) and laser ablation microsamplers coupled to mass spectrometers (LA-ICP-MS) provides a new array of possibilities to explore in great detail the trace elements distribution in foraminiferal carbonates. Here we apply these techniques to characterize diagenetic phases present in foraminiferal shells from Ocean Drilling Program Site 1240 in the Panama Basin, a region characterized by the presence of manganese-rich minerals in the sediments. The combined application of these techniques allows us to characterize the elemental and spatial distribution on the surface and across the foraminiferal shells. Results illustrate the presence of at least two different Mn-rich contaminant phases in the foraminiferal carbonates: Mn-rich carbonates and ferromanganese oxides. Elemental maps also highlight the relevance of the foraminifera shell texture and porosity in the distribution and formation of these contaminant phases. In the case of Neogloboquadrina dutertrei, Mn phases form a continuous thin layer in the inner part of the chambers, whereas for Globigerinoides ruber, Mn phases have a rather patchy distribution and are usually found within the pores. Significant high magnesium concentrations are always associated with these Mn-rich phases. These new findings support the need of removing these Mn-rich contaminant phases in order to measure accurately the Mg/Ca ratios in the foraminifera shell and therefore obtain reliable Mg/Ca paleotemperature reconstructions

The distribution of foraminifers and some macrofossils at the Coniacian/Santonian boundary in four selected sections, two on the Mangyshlak Peninsula (West Kazakhstan) and two on the Russian Platform, are compared in this paper. The first occurrence (FO)

The Mg/Ca composition of calcium carbonate tests (shells) secreted by planktonic foraminifera is increasingly being employed to estimate past seawater temperatures and reconstruct paleocean and climate records spanning hundreds of thousands of years. We show, using two high-resolution microanalysis techniques, that the final chamber of the planktonic foraminifera Orbulina universa typically comprises between three and six paired, low and high Mg, growth bands. The number and spacing of these bands is consistent with a diurnal origin, modulated by changing pH within the foraminiferal microenvironment due to the day-night, photosynthesis-respiration cycle of algal symbionts. The amplitude of Mg/Ca variation within individual tests and across many daily growth bands cannot be accounted for by seawater temperature in the shallow, euphotic zone habitat of O. universa. Our results indicate the Mg/Ca composition of calcite precipitated by O. universa in nature is strongly influenced by diurnal changes in the biological activity of algal symbionts and the host foraminifer. This brings into question the fundamental premise often made in applying Mg/Ca palaeoseawater thermometry, that the Mg/Ca composition of foraminiferal calcite is determined by seawater temperature, and whether the Mg/Ca composition of other planktonic species that are more widely used for palaeoseawater thermometry are subject to similar influences.

Planktonic foraminifera record oceanic conditions in their shell geochemistry. Many palaeoenvironmental studies have used fossil planktonic foraminifera to constrain past seawater properties by defining species based on their shell morphology. Recent genetic studies, however, have identified ecologically distinct genotypes within traditionally recognized morphospecies, signaling potential repercussions for palaeoclimate reconstructions. Here we demonstrate how the presence of Globigerina bulloides cryptic genotypes in the Arabian Sea may influence geochemical signals of living and fossil assemblages of these morphospecies. We have identified two distinct genotypes of G. bulloides with either cool water (type-II) or warm water (type-I) temperature preferences in the Western Arabian Sea. We accompany these genetic studies with analyses of Mg/Ca and stable oxygen isotope (δ18O) compositions of individual G. bulloides shells. Both Mg/Ca and δ18O values display bimodal distribution patterns. The distribution of Mg/Ca values cannot be simply explained by seawater parameters, and we attribute it to genotype-specific biological controls on the shell geochemistry. The wide range of δ18O values in the fossil assemblage also suggests that similar controls likely influence this proxy in addition to environmental parameters. However, the magnitude of this effect on the δ18O signals is not clear from our data set, and further work is needed to clarify this. We also discuss current evidence of potential genotype-specific geochemical signals in published data on G. bulloides geochemistry and other planktonic foraminiferal species. We conclude that significant caution should be taken when utilizing G. bulloides geochemistry for paleoclimate reconstruction in the regions with upwelling activity or oceanographic fronts.