Effects of chemical preservation on bulk and amino acid isotope ratios of zooplankton, fish, and squid tissues

Lipid extraction alters amino acid composition and bulk, but not amino acid, carbon and nitrogen isotope values

RATIONALE

Concerns exist over observed shifts in value and variance of nitrogen isotopes following physicochemical extraction of lipids from organic matter. The mechanisms behind these apparent changes in bulk tissue δ15N values are not fully understood yet have major implications for analytical costs and integrity of data interpretations.

METHODS

Changes in proximate analysis, amino acid composition, C:N ratios, bulk tissue and amino acid δ13C and δ15N values, and resulting isotope-based food web metrics were compared between lipid-intact and lipid-extracted muscle tissue of fishes spanning <1% to >20% muscle fat content to identify mechanisms of nitrogen isotope fractionation associated with physicochemical lipid extraction.

RESULTS

Bulk δ13C and δ15N values increased and %N, C:N ratios and crude protein content decreased following lipid extraction. Resulting bulk isotope niche spacing and overlap varied significantly between lipid-intact and lipid-extracted tissues. While amino acid composition significantly changed during lipid extraction, particularly for lipid-associated amino acids (e.g., Glu, Lys, Ser), individual amino acid δ13C and δ15N values, and their associated compound-specific isotope analysis of amino acids (CSIA-AA)-based food web metrics, did not.

CONCLUSIONS

Physicochemical lipid extraction caused significant tissue composition changes (e.g., leaching of amino acids and 15N-deplete nitrogenous waste) that affected δ13C and δ15N values and tissue %C and %N beyond simply removing lipids. However, lipid extraction did not alter individual amino acid δ13C or δ15N values or their associated CSIA-AA-based food web metrics.

Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics

Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. In this article, we explore the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common currency interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at local to continental scales. Challenges including the analysis of sparse samples, a lack of information about baseline isotopic composition, and the effects of preservation remain, but none of these challenges is insurmountable. The proposed research framework interfaces with existing databases and observatories to provide benchmarks for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, reference points for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.

Can preserved museum specimens be used to reconstruct fish mercury burden and sources through time?

To evaluate the utility of preserved fishes for reconstructing historical and spatial patterns of mercury (Hg) exposure, we experimentally tested the stability of Hg concentrations and Hg stable isotope ratios under standard museum practices of specimen preservation. We found that loss of unidentified constituents during preservation increased Hg concentrations in fish muscle. Low-Hg fish reared in the laboratory were susceptible to exogenous contamination with inorganic mercury (iHg) when preservative fluids were intentionally spiked or iHg leached passively from contaminated wild fishes in the same container. This contamination impacted Hg isotope values of total Hg, but the conservative nature of methylmercury allows us to quantitatively correct for iHg contamination. Our findings validate the potential to use fishes from the world's museums to generate spatiotemporal baselines for the Minamata Convention on Mercury, but we recommend a set of precautions to maximize inference strength. Selecting the largest specimens of a target species helps dilute any iHg contamination. Specimens should be drawn from lots that were not comingled with fishes from other collections to minimize risk of iHg transfer among fish with different contamination histories. Finally, focusing on low-lipid species will enhance the comparability of Hg concentrations between historical and contemporary collections.

Temporal dynamics in zooplankton δ13C and δ15N isoscapes for the North Atlantic Ocean: Decadal cycles, seasonality, and implications for predator ecology

The limited amount of ecological data covering offshore parts of the ocean impedes our ability to understand and anticipate the impact of anthropogenic stressors on pelagic marine ecosystems. Isoscapes, i.e., spatial models of the distribution of stable isotope ratios, have been employed in the recent years to investigate spatio-temporal patterns in biogeochemical process and ecological responses. Development of isoscapes on the scale of ocean basins is hampered by access to suitable reference samples. Here we draw on archived material from long-running plankton survey initiatives, to build temporally explicit isoscape models for the North Atlantic Ocean (&gt; 40°N). A total of 570 zooplankton samples were retrieved from Continuous Plankton Recorder archives and analysed for δ13C and δ15N values. Bayesian generalised additive models were developed to (1) model the relations between isotopic values and a set of predictors and (2) predict isotopic values for the whole of the study area. We produced yearly and seasonal isoscape models for the period 1998–2020. These are the first observation-based time-resolved C and N isoscapes developed at the scale of the North Atlantic Ocean. Drawing on the Stable Isotope Trajectory Analysis framework, we identify five isotopically distinct regions. We discuss the hydro-biogeochemical processes that likely explain theses modes, the differences in temporal dynamics (stability and cycles) and compare our results with previous bioregionalization efforts. Finally, we lay down the basis for using the isoscapes as a tool to define predator distributions and their interactions with the trophic environment. The isoscapes developed in this study have the potential to update our knowledge of marine predator ecology and therefore our capacity to improve their conservation in the future.

Optimizing immunostaining of archival fish samples to enhance museum collection potential

Immunohistochemistry (IHC) is a powerful biochemical technique that uses antibodies to specifically label and visualize proteins of interests within biological samples. However, fluid-preserved specimens within natural history collection often use fixatives and protocols that induce high background signal (autofluorescence), which hampers IHC as it produces low signal-to-noise ratio. Here, we explored techniques to reduce autofluorescence using sodium borohydride (SBH), citrate buffer, and their combination on fish tissue preserved with paraformaldehyde, formaldehyde, ethanol, and glutaraldehyde. We found SBH was the most effective quenching technique, and applied this pretreatment to the gill or skin of 10 different archival fishes - including specimens that had been preserved in formaldehyde or ethanol for up to 65 and 37 years, respectively. The enzyme Na⁺/K⁺-ATPase (NKA) was successfully immunostained and imaged using confocal fluorescence microscopy, allowing for the identification and characterization of NKA-rich ionocytes essential for fish ionic and acid-base homeostasis. Altogether, our SBH-based method facilitates the use of IHC on archival samples, and unlocks the historical record on fish biological responses to environmental factors (such as climate change) using specimens from natural history collections that were preserved decades to centuries ago.

No evidence for effects of mill-grinding on δ13 C, δ15 N and δ34 S values in different marine taxa

RATIONALE

The analysis of natural variation in light stable isotopes such as carbon (δ¹³ C), nitrogen (δ¹⁵ N) and sulfur (δ³⁴ S) plays an important role in deepening our understanding of ecosystems. To avoid misinterpretation, robust results are required, where pre-treatment steps such as sample homogenization are crucial to guarantee representative samples. The grinding of samples using stainless steel balls in polypropylene tubes (e.g., laboratory bead-beater) has been identified as a potential source of bias.

METHODS

We tested possible effects of mill-grinding (e.g., contamination) of samples of coastal marine taxa including primary producers, primary consumers and higher trophic level fish. We compared potential impacts of homogenization by mill-grinding with hand-grinding over an extended time on δ¹³ C, δ¹⁵ N and δ³⁴ S values.

RESULTS

One-way Welch's analysis of variance (ANOVA) showed that there were no statistical differences between methods for all the studied taxa. Also, repeated measures ANOVA showed no evidence of effects of grinding for extended times (from 30 to 120 seconds) for δ¹³ C, δ¹⁵ N and δ³⁴ S values.

CONCLUSIONS

We found no evidence that grinding samples in polypropylene tubes in a bead-beater resulted in any marked alteration of the isotopic composition on the studied samples, e.g., through contamination by plastic. As such, we consider mill-grinding as an appropriate method for the homogenization of samples from a range of different marine taxa, which under controlled conditions did not affect δ¹³ C, δ¹⁵ N and δ³⁴ S analysis.

Regional patterns of δ 13C and δ 15N for European common cuttlefish (Sepia officinalis) throughout the Northeast Atlantic Ocean and Mediterranean Sea

Stable isotope compositions of carbon and nitrogen (expressed as δ 13C and δ 15N) from the European common cuttlefish (Sepia officinalis) were measured in order to evaluate the utility of using these natural tracers throughout the Northeast Atlantic Ocean and Mediterranean Sea (NEAO-MS). Mantle tissue was obtained from S. officinalis collected from 11 sampling locations spanning a wide geographical coverage in the NEAO-MS. Significant differences of both δ 13C and δ 15N values were found among S. officinalis samples relative to sampling location. δ 13C values did not show any discernable spatial trends; however, a distinct pattern of lower δ 15N values in the Mediterranean Sea relative to the NEAO existed. Mean δ 15N values of S. officinalis in the Mediterranean Sea averaged 2.5‰ lower than conspecifics collected in the NEAO and showed a decreasing eastward trend within the Mediterranean Sea with the lowest values in the most eastern sampling locations. Results suggest δ 15N may serve as a useful natural tracer for studies on the population structure of S. officinalis as well as other marine organisms throughout the NEAO-MS.

Origin determination of the Eastern oyster (Crassostrea virginica) using a combination of whole-body compound-specific isotope analysis and heavy metal analysis

Various samples of the Eastern oyster, Crassostrea virginica, were collected from five harvest bay areas in the Gulf of Mexico coastal waters of Florida (FL), Louisiana (LA) and Texas (TX). Cadmium and lead concentrations from the extracted whole-body soft tissues were analyzed by inductively coupled plasma-mass spectrometry (ICP-MS), and bulk δ13C and δ15N isotope ratios and amino-acid-specific δ13C values were analyzed via isotope ratio mass-spectrometry (IRMS). The combined data was subjected to multivariate statistical analysis to assess whether oysters could be linked to their harvest area. Results indicate that discriminant analysis using the δ13C values of five amino acids-serine, glycine, valine, lysine and phenylalanine-could discriminate oysters from two adjacent harvesting in Florida with 90% success rate, using leave-one-out cross validation. The combination of trace elements and isotope ratios could also predict geographic provenance of oysters with a success rate superior to the isolated use of each technique. The combinatory approach proposed in this study is a proof-of-concept that compound specific stable isotope analysis is a potential tool for oyster fisheries managers, wildlife, and food safety enforcement officers, as well as to forensics and ecology research areas, although significantly more work would need to be completed to fully validate the approach and achieve more reliable statistical results.

Effects of long-term ethanol storage on muscle architecture

Muscle excursion and force potential can be estimated from architectural variables, including mass, volume, fascicle length, and density. These have been collected from fresh specimens, preserved specimens, and sometimes mixed samples of both. However, preservation alters the gross morphology of muscles. This study aims to quantify the effects of long-term storage on myological properties across a sample of fresh and ethanol preserved Mus musculus specimens ranging in storage time from 16 to 130 years. Masses, volumes, and densities of biceps femoris, quadriceps femoris, and triceps surae were measured, and histological cross-sections of some specimens were used to evaluate the microscale effects of long-term fluid preservation. For the remainder of the sample, chemically dissected fascicle lengths were measured to evaluate the fixation effects on the linear dimensions of muscle architecture. Relative muscle mass, volume, fascicle length, average fiber area, and density, and percent fiber area were regressed against years stored in ethanol. Muscle size dropped steeply between fresh and stored samples, ultimately decreasing by 62 and 60%, respectively. These losses correlate with histologically measured shrinking of average muscle fiber area. Density of stored specimens plateaued 5% below that of fresh ones. Although muscles lost mass and volume during ethanol storage, fascicle lengths did not shorten significantly (presumably because they were preserved attached on either end to bone). This study demonstrates that muscle mass, volume, and density of specimens stored long-term in ethanol should be corrected by factors of 2.64, 2.49, and 1.054 respectively for comparability to fresh specimens.

Land-use change erodes trophic redundancy in tropical forest streams: Evidence from amino acid stable isotope analysis

Studies have shown that food chain length is governed by interactions between species richness, ecosystem size and resource availability. While redundant trophic links may buffer impacts of species loss on food chain length, higher extinction risks associated with predators may result in bottom-heavy food webs with shorter food chains. The lack of consensus in earlier empirical studies relating species richness and food chain length reflects the need to account robustly for the factors described above. In response to this, we conducted an empirical study to elucidate impacts of land-use change on food chain length in tropical forest streams of Southeast Asia. Despite species losses associated with forest loss at our study areas, results from amino acid isotope analyses showed that food chain length was not linked to land use, ecosystem size or resource availability. Correspondingly, species losses did not have a significant effect on occurrence likelihoods of all trophic guilds except herbivores. Impacts of species losses were likely buffered by initial high levels of trophic redundancy, which declined with canopy cover. Declines in trophic redundancy were most drastic amongst invertivorous fishes. Declines in redundancy across trophic guilds were also more pronounced in wider and more resource-rich streams. While our study found limited evidence for immediate land-use impacts on stream food chains, the potential loss of trophic redundancy in the longer term implies increasing vulnerability of streams to future perturbations, as long as land conversion continues unabated.

Fluid-preserved fishes are one solution for assessing historical change in fish trophic level

There are few resources available for assessing historical change in fish trophic dynamics, but specimens held in natural history collections could serve as this resource. In contemporary trophic ecology studies, trophic and source information can be obtained from compound-specific stable isotope analysis of amino acids of nitrogen (CSIA-AA-N).We subjected whole Sebastes ruberrimus and Clupea pallasii to formalin fixation and 70% ethanol preservation. We extracted tissue samples from each fish pre-fixation, after each chemical change, and then in doubling time for 32-64 days once placed in the final preservative. All samples were subjected to CSIA-AA-N, and their glutamic acid and phenylalanine profiles and associated trophic position were examined for differences over time by species.Glutamic acid and phenylalanine values were inconsistent in direction and magnitude, particularly during formalin fixation, but stabilized similarly (in 70% ethanol) among conspecifics. In some cases, the amino acid values of our final samples were significantly different than our initial pre-preservation samples. Nonetheless, significant differences in glutamic acid, phenylalanine, and estimated trophic position were not detected among samples that were in 70% ethanol for >24 hr.Our results suggest that the relative trophic position of fluid-preserved specimens can be estimated using CSIA-AA-N, and CSIA-AA-N estimates for fluid-preserved specimens should only be reported as relative differences. Timelines of trophic position change can be developed by comparing specimens collected at different points in time, revealing trophic information of the past and cryptic ecosystem responses.

Effects of fixatives on stable isotopes of fish muscle tissue: implications for trophic studies on preserved specimens

Isotopic ecology has been widely used to understand spatial connectivity and trophic interactions in marine systems. However, its potential for monitoring an ecosystem's health and function has been hampered by the lack of consistent sample storage and long-term studies. Preserved specimens from museum collections are a valuable source of tissue for analyses from ancient and pre-modern times, but isotopic signatures are known to be affected by commonly used fixatives. The aim of the present study was to understand the effects of fixatives on isotopic signatures of bulk tissue (δ¹³ C_m and δ¹⁵ N_m ) and amino acids (δ¹³ C_AA and δ¹⁵ N_AA ) of fish muscle and to provide correction equations for the isotopic shifts. Two specimens of each: blue cod (Parapercis colias), blue warehou (Seriolella brama), and king salmon (Oncorhynchus tschawytscha) were sampled at five locations along their dorsal musculature, at four time periods: (1) fresh, (2) after 1 month preserved in formalin, and after (3) 3 and (4) 12 months fixed in either ethanol or isopropanol. Lipid content was positively correlated with C:N ratio (r² = 0.83) and had a significant effect on δ¹³ C after treatments, but not on δ¹⁵ N. C:N ratio (for δ¹³ C_m ) and percent N (for δ¹⁵ N_m ) from preserved specimens contributed to the most parsimonious mixed models, which explained 79% of the variation due to fixation and preservation for δ¹³ C and 81% for δ¹⁵ N. δ¹³ C_AA were generally not affected by fixatives and preservatives, while most δ¹⁵ N_AA showed different signatures between treatments. δ¹⁵ N_AA variations did not affect the magnitude of differences between amino acids, allowing scientists to retrieve ecological information (e.g., trophic level) independently of time under preservation. Corrections were applied to the raw data of the experiment, highlighting the importance of δ¹³ C_m and δ¹⁵ N_m correction when fish muscle tissues from wet collections are compared to fresh samples. Our results make it possible to retrieve δ¹³ C_m , δ¹⁵ N_m , δ¹³ C_AA , and δ¹⁵ N_AA from museum specimens and can be applied to some of the fundamental questions in ecology, such as trophic baseline shifts and changes in community's food web structure through time.