A hands-on overview of tissue preservation methods for molecular genetic analyses

New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales)

Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.

Tegumental topography and molecular characterisation of two trematodes (Platyhelminthes: Digenea) from Clarias gariepinus (Burchell, 1822) in Kenya

The discoveries of new taxonomic features of digenean species through the application of contemporary techniques, such as scanning electron microscopy (SEM) and molecular analysis are still growing. Two species of trematodes Glossidium pedatum and Tylodelphys mashonensis from the intestine and vitreous humour of Clarias gariepinus were recovered from Lake Ol'Bolossat, Kenya. The two endo-helminths were prepared for morphological examination using SEM and molecular characterisation. Additional morphological features were observed for G. pedatum such as domed papillae in the anterior extremity and a protruding cirrus which was unarmed, laterally folded and with a blunt tip as the first such observation for the genus and led to additional characteristics of the diagnosis of the genus. Tylodelphys mashonensis was characterised by a round oral sucker and tribocytic organ rounded with rows of papillae symmetrically arranged. The molecular analyses using ribosomal marker 28S large subunit (LSU) rDNA and mitochondrial (mtDNA) cytochrome c oxidase subunit 1 (cox1) for both G. pedatum and T. mashonensis confirmed the identity of the species and their phylogenetic relationship within the subclass Digenea. This study provides the first mitochondrial (mt)DNA sequence for G. pedatum and also extends the geographical record of two parasites to Kenya.

Assessing the feasibility of free DNA for disaster victim identification and forensic applications

In tropical disaster victim identification (DVI) scenarios, challenging environmental conditions lead to accelerated DNA degradation in remains. To further enhance the utilization of leached DNA from tissue in the preservative solution (termed "free DNA") as an alternative source, we incorporated new results by assessing its integrity in postmortem and decomposing cadavers preserved in DNA/RNA Shield™ and modified TENT, with silica-based purification (QIAquick®) for faster processing. The psoas muscle tissues of one decomposed and ten cadavers were preserved in each solution at 25 °C and 35 °C for 3 months. Free DNA efficiency was compared with individual reference samples for reliable results in quantity, quality, and STR profiles. The findings revealed that DNA/RNA Shield™ effectively preserves free DNA integrity for extended storage, while modified TENT is more suitable for short-term storage due to higher degradation levels. Moreover, the use of free DNA samples with massive parallel sequencing displays potential for forensic DNA analysis. Successful amplification of the mtDNA control region enables variant calling and heteroplasmy analysis while also serving as quality control using ACTB and enabling differentiation within the 16S rRNA region for microbiome analysis. The simplicity of handling free DNA for PCR-based forensic analysis adds to its potential for various applications, including DVI and field-based analysis of biological evidence.

Canine urothelial carcinoma: a pilot study of microRNA detection in formalin-fixed, paraffin-embedded tissue samples and in normal urine

We assessed the effects of fixation time in formalin and inclusion of surrounding tissue on microRNA (miRNA) cycle quantification (Cq) values in formalin-fixed, paraffin-embedded (FFPE) urothelial carcinoma (UC) tissue (n = 3), and the effect of conditions on miRNAs in urine from 1 healthy dog. MiRNAs were extracted using commercial kits and quantified using miRNA-specific fluorometry in normal bladder tissue scrolls, UC tissue cores, and bladder muscularis tissue cores from 4 FFPE bladder sections (3 UCs, 1 normal), plus 1 UC stored in formalin for 1, 8, 15, and 22 d before paraffin-embedding. Urine was collected from a healthy dog on 4 occasions; 1-mL aliquots were stored at 20, 4, -20, and -80°C for 4, 8, 24, and 48 h, and 1 and 2 wk. For both FFPE tissue and urine, we used reverse-transcription quantitative real-time PCR (RT-qPCR) to quantify miR-143, miR-152, miR-181a, miR-214, miR-1842, and RNU6B in each tissue or sample, using miR-39 as an exogenous control gene. The Cq values were compared with ANOVA and t-tests. The time of tissue-fixation in formalin did not alter miRNA Cq values; inclusion of the muscularis layer resulted in a statistically different miRNA Cq profile for miR-152, miR-181a, and RNU6B in bladder tissue. MiRNAs in acellular urine were stable for up to 2 wk regardless of the storage temperature. Our findings support using stored FFPE and urine samples for miRNA detection; we recommend measuring miRNA only in the tissue of interest in FFPE sections.

Amyl acetate: an alternative technique to dry mount Chalcidoidea (Hymenoptera) from alcohol, faster and inexpensively

Ethanol (EtOH) 70% is commonly used in collections to preserve and store many unprepared soft-bodied Chalcidoidea. Specimens air-dried directly from alcohol, however, often suffer from collapse of some body parts, making subsequent observation of their morphology difficult or even impossible. We propose an inexpensive method for processing and dry-mounting specimens of Chalcidoidea, using a chemical process including amyl acetate. Four treatments using amyl acetate at different concentrations and exposure times were evaluated for specimens of Eulophidae, Mymaridae, Encyrtidae, Aphelinidae, Pteromalidae, and Trichogrammatidae. Treatment with amyl acetate resulted in specimens of consistently higher quality. Based on our results, treatment of specimens for 1 h with 50:50 amyl acetate and ethanol mixture, followed by treatment for 1 h with 100% amyl acetate, yielded specimens adequate for morphological observations for most of the families. Further experiments are required, however, to optimize this approach for Trichogrammatidae and Eulophidae. This method is a relatively simple, inexpensive, and safe alternative to other methods commonly used for restoring Chalcidoidea preserved in alcohol.

A Comparative Study on the Effect of Euthanasia Methods and Sample Storage Conditions on RNA Yield and Quality in Porcine Tissues

Animals used in research often have to be euthanised, especially when tissue sampling is essential. Recently, a euthanasia method, utilizing an inhalant anaesthetic 'nitrogen gas in foam' in an anoxia box (ANOXIA^TM), has gained considerable interest as it claimed to be more animal-friendly. However, it is not clear whether the use of this euthanasia method has an influence on RNA measurements. Moreover, there are no studies on the interaction effect of different euthanasia methods on the tissue sample storage conditions. The current study compared RNA measurements from two euthanasia methods (ANOXIA^TM vs. T-61^® injection) and two storage conditions (RNAlater™ vs. snap freezing) in 12 male piglets. The nitrogen anoxia method had a significantly higher RNA yield (p < 0.01) compared to the T-61^® method. However, no effect of the euthanasia methods on the A260/230 ratio and RIN value was observed. Tissues stored in RNAlater™ had significantly higher RIN values (p < 0.001) compared to snap frozen samples. The present study could not find a significant difference between the two euthanasia methods in piglets, with regard to RNA quality measurements. Hence, the nitrogen anoxia technique (ANOXIA^TM) might be considered as a suitable alternative to T-61^® for euthanasia of piglets used in research.

Greater than pH 8: The pH dependence of EDTA as a preservative of high molecular weight DNA in biological samples

Ethylenediaminetetraacetic acid (EDTA) is a divalent cation chelator and chemical preservative that has been shown to be the active ingredient of the popular DNA preservative DESS. EDTA may act to reduce DNA degradation during tissue storage by sequestering divalent cations that are required by nucleases naturally occurring in animal tissues. Although EDTA is typically used between pH 7.5 and 8 in preservative preparations, the capacity of EDTA to chelate divalent cations is known to increase with increasing pH. Therefore, increasing the pH of EDTA-containing preservative solutions may improve their effectiveness as DNA preservatives. To test this hypothesis, we stored tissues from five aquatic species in 0.25 M EDTA adjusted to pH 8, 9, and 10 for 12 months at room temperature before DNA isolation. For comparison, tissues from the same specimens were also stored in 95% ethanol. DNA extractions performed on tissues preserved in EDTA pH 9 or 10 resulted in as great or greater percent recovery of high molecular weight DNA than did extractions from tissues stored at pH 8. In all cases examined, percent recovery of high molecular weight DNA from tissues preserved in EDTA pH 10 was significantly better than that observed from tissues preserved in 95% ethanol. Our results support the conclusion that EDTA contributes to DNA preservation in tissues by chelating divalent cations and suggest that preservative performance can be improved by increasing the pH of EDTA-containing DNA preservative solutions.

Cutting corners: The impact of storage and DNA extraction on quality and quantity of DNA in honeybee (Apis mellifera) spermatheca

The purpose of our study was to investigate methods of short-term storage that allow preservation, transport and retrieval of genetic information contained in honeybee queen's spermatheca. Genotyping of the honeybee colony requires well ahead planned sample collection, depending on the type of data to be acquired. Sampling and genotyping of spermatheca's content instead of individual offspring is timesaving, allowing answers to the questions related to patriline composition immediately after mating. Such procedure is also cheaper and less error prone. For preservation either Allprotect Tissue Reagent (Qiagen) or absolute ethanol were used. Conditions during transportation were simulated by keeping samples 6-8 days at room temperature. Six different storing conditions of spermathecas were tested, complemented with two DNA extraction methods. We have analysed the concentration of DNA, RNA, and proteins in DNA extracts. We also analysed how strongly the DNA is subjected to fragmentation (through amplification of genetic markers ANT2 and tRNA^leu-COX2) and whether the quality of the extracted DNA is suitable for microsatellite (MS) analysis. Then, we tested the usage of spermatheca as a source of patriline composition in an experiment with three instrumentally inseminated virgin queens and performed MS analysis of the extracted DNA from each spermatheca, as well as queens' and drones' tissue. Our results show that median DNA concentration from spermathecas excised prior the storage, regardless of the storing condition and DNA extraction method, were generally lower than median DNA concentration obtained from spermathecas dissected from the whole queens after the storage. Despite the differences in DNA yield from the samples subjected to different storing conditions there was no significant effect of storage method or the DNA extraction method on the amplification success, although fewer samples stored in EtOH amplified successfully in comparison to ATR storing reagent. However, we recommend EtOH as a storing reagent due to its availability, low price, simplicity in usage in the field and in the laboratory, and capability of good preservation of the samples for DNA analysis during transport at room temperature.

Comparing preservation substrates under field conditions for efficient DNA recovery in bone

Often bones are the only biological material left for the identification of human remains. As situations may occur where samples need to be stored for an extended period without access to cooling, appropriate storage of the bone samples is necessary for maintaining the integrity of DNA for profiling. To simulate DNA preservation under field conditions, pig rib bones were used to evaluate the effects of bone cleaning, buffer composition, storage temperature, and time on DNA recovery from bone samples. Bones were stored in three different buffers: TENT, solid sodium chloride, and ethanol-EDTA, at 20 °C and 35 °C for 10, 20, and 30 days. Bones were subsequently dried and ground to powder. DNA was extracted and quantified. Results show that temperature and storage time have no significant influence on DNA yield. DNA recovery from bones stored in solid sodium chloride or ethanol-EDTA was significantly higher compared to bones stored in TENT, and grinding of bones was facilitated by the extent of dehydration in solid sodium chloride and ethanol-EDTA compared to TENT. Overall, solid sodium chloride was found to be superior over ethanol-EDTA; when it comes to transportation, dry material such as salt eliminates the risk of leaking; it is non-toxic and in contrast to ethanol not classified as dangerous goods. Based on this study's results, we recommend NaCl as a storage substrate for forensic samples in cases where no cooling/freezing conditions are available.

Sampling and curation of rove beetles (Insecta, Coleoptera, Staphylinidae) for comprehensive and DNA-grade collections to enhance biodiversity exploration in Northern Eurasia

Staphylinidae beetles form a major portion of terrestrial biodiversity globally and, in particular, in Northern Eurasia, a large area with a historically better known north temperate, subarctic and arctic biota. However, even here, rove beetles remain amongst the so-called "dark taxa" with a high fraction of taxonomically unknown lineage diversity. The propagation of DNA-based technologies in systematic entomology in recent decades has brought new opportunities for biodiversity exploration, true also for Staphylinidae. Simultaneously, new methods have revealed limitations of specimens sampled and curated by traditional practices, as existing legacy collections, whether institutional or private, unfortunately do not always qualify as a source of DNA-grade material. In addition, both legacy and newly-collected DNA-grade material of Staphylinidae remain highly biased towards Central Europe, a region with a traditionally well-developed scientific infrastructure and long-established culture for the maintenance of entomological collections. To increase the degree of biodiversity knowledge for our target organismal group across the globe, efficient sampling of DNA-grade material and, in particular, the development of comprehensive local collections in under-studied regions is highly desirable. To facilitate that, here we provide a practical guide for collecting and curation of Staphylinidae with a focus on capacity building for DNA-grade collections in Siberia and elsewhere in Northern Eurasia.

A comparison of drying methods on the quality for bryophyte molecular specimens collected in the field

A major challenge in extracting high-quality DNA from bryophytes is the treatment of bryophyte material in the field. The existing and commonly used treatment methods in the field have several shortcomings. Natural drying methods can lead to DNA breaks. In addition, it is highly cumbersome to carry large quantities of silica gel in the field due to its weight and high risk of contamination among samples. In this study, we explored more convenient drying methods to treat bryophyte specimens and promote more efficient DNA recovery. The quantity and quality of genomic DNA extracted from every bryophyte species using different drying methods, including hot-air drying methods (150°C, 80°C, and 40°C), natural drying method, and silica gel drying method, were measured. Spectrophotometry, electrophoresis, and PCR amplification were performed to assess the effects of different drying methods. The results of total DNA purity, total DNA concentration, PCR success, and OD 260/230 ratios suggested that the hot-air drying (40-80°C) was the best method. The morphological comparison revealed that hot-air drying at 40°C and 80°C exerted no significant adverse effects on plant morphology and taxonomic studies. Thus, this method prevents rapid DNA degradation and silica gel pollution and saves the workforce from carrying large amounts of silica gel to the field. Several inexpensive devices, such as portable hairdryers, fan heaters, and electric blankets, are available that can be easily carried to the field for drying molecular specimens.

Effect of different fixatives on yield of DNA from human fecal samples

Fixation and transportation of human fecal samples is often difficult in geographically remote locations due to unavailability of options for immediate freezing. In this study effectiveness of five different chemical fixatives were evaluated on human fecal samples including for supernatant using RNAprotect Bacteria Reagent (Qiagen), 95% ethanol, acetone, TRIzol and a mixture of all these fixatives, in addition to immediate freezing. DNA was extracted from the fecal samples using QIAamp Fast Stool DNA Minikit as well as quality and yield of extracted DNA was monitored for a period of 30 days. It was found that except TRIzol, all other preservatives showed good DNA quality and yield for a period of one month based on agarose gel electrophoresis, Nanodrop and Qubit measurements. It was also found that supernatant of fecal sample fixed with RNAprotect Bacteria Reagent gave reliable DNA yield in comparison to other various fixatives. The study also revealed that quality and yield of DNA from fecal samples fixed in acetone were very promising since it is a cost-effective fixative. Overall, the study shows future applicability for downstream DNA analyses of the RNAprotect Bacteria Reagent, 95% ethanol, acetone, and a mixture of all these fixatives for fixing human fecal samples to be collected from geographically remote locations or in regions where available resources are largely limited.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis

Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage methods on the microbial composition of the organism is unknown. Using crayfish and dragonfly nymphs collected from a natural pond and crayfish maintained in an aquarium, the effects of two common storage methods, preserving in 95% ethanol and freezing at −20 °C, on the invertebrate bacterial microbiome was evaluated. We found that the bacterial community was conserved for two sample types (gut and exoskeleton) of field-collected crayfish stored either in ethanol or frozen, as was the gut microbiome of aquarium crayfish. However, there were significant differences between the bacterial communities found on the exoskeleton of aquarium crayfish stored in ethanol compared to those that were frozen. Dragonfly nymphs showed significant differences in gut microbial composition between species, but the microbiome was conserved between storage methods. These results demonstrate that preserving field-collected specimens of aquatic invertebrates in 95% ethanol is likely to be a simple and effective sample preservation method for subsequent gut microbiome analysis but is less reliable for the external microbiome.

DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana

Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.

Seroprevalence and detection of Trypanosoma cruzi in dogs living in a non-endemic area for Chagas disease in the legal Amazon region, Brazil

Trypanosoma cruzi, the etiological agent for Chagas disease, is widely distributed in the Americas. Its hosts are humans and wild and domestic mammals, and its vectors are triatomine insects. Studies have indicated that domestic dogs are sentinel animals in the epidemiology of Chagas disease in endemic regions, including states in the Legal Amazon region of Brazil. In São Luís, the capital of Maranhão, a non-endemic state, the existence of a domestic cycle involving domestic rats has been proven, along with a wild cycle maintained by didelphids. However, no studies on T. cruzi infection in domestic animals in this locality have been conducted. The aim of this study was to investigate occurrence of T. cruzi in dogs living in the Itaqui Bacanga district of São Luís, Maranhão, by means of serological and molecular tests. Blood samples were obtained from 330 dogs and structured epidemiological questionnaires were applied to their keepers. These samples were used in the indirect immunofluorescent antibody test (IFAT), enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). Fisher's exact test was used for statistical calculations with the aim of identifying risk factors. Out of the 330 animals, 105 (31.8%) were reactive in IFAT, 46 (13.0%) in ELISA and 20 (6.0%) in both serological tests. The results were not significant (p > 0.05) when submitted to statistical analysis for the studied variables. From PCR, 58 samples (17.5%) were found to be positive and, of these, one (0.3%) showed similarity to T. cruzi after sequencing. These data demonstrate that dogs were exposed to and infected by T. cruzi. Thus, they can be considered sentinel animals for Chagas disease in the locality studied, which signals that there is a need for epidemiological surveillance actions.

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding

Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at - 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies.

Bone fragment or bone powder? ATR-FTIR spectroscopy-based comparison of chemical composition and DNA preservation of bones after 10 years in a freezer

Freezing bone samples to preserve their biomolecular properties for various analyses at a later time is a common practice. Storage temperature and freeze-thaw cycles are well-known factors affecting degradation of molecules in the bone, whereas less is known about the form in which the tissue is most stable. In general, as little intervention as possible is advised before storage. In the case of DNA analyses, homogenization of the bone shortly before DNA extraction is recommended. Because recent research on the DNA yield from frozen bone fragments and frozen bone powder indicates better DNA preservation in the latter, the aim of the study presented here was to investigate and compare the chemical composition of both types of samples (fragments versus powder) using ATR-FTIR spectroscopy. Pairs of bone fragments and bone powder originating from the same femur of 57 individuals from a Second World War mass grave, stored in a freezer at - 20 °C for 10 years, were analyzed. Prior to analysis, the stored fragments were ground into powder, whereas the stored powder was analyzed without any further preparation. Spectroscopic analysis was performed using ATR-FTIR spectroscopy. The spectra obtained were processed and analyzed to determine and compare the chemical composition of both types of samples. The results show that frozen powdered samples have significantly better-preserved organic matter and lower concentrations of B-type carbonates, but higher concentrations of A-type carbonates and stoichiometric apatite. In addition, there are more differences in the samples with a low DNA degradation index and less in the samples with a high DNA degradation index. Because the results are inconsistent with the current understanding of bone preservation, additional research into optimal preparation and long-term storage of bone samples is necessary.

Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing

The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.

Coping with Tissue Sampling in Suboptimal Conditions: Comparison of Different Tissue Preservation Methods for Histological and Molecular Analysis

A high quality of samples is crucial for the success of the analysis and diagnostic purposes, and therefore the right method of conservation is vitally important for an optimal preservation of tissues. Indeed, the time to deliver the sample to the laboratory could be remarkably long, especially under suboptimal conditions, and the use of specific fixatives or cold storage may not be possible. Moreover, the portability and cost of storage equipment, their toxicity, and their ease of use play a central role when choosing the correct preservation method. The aim of this study was the identification of a reliable and economic method for tissue preservation, to be used in "in-field" sampling, suitable for both histological and molecular analysis. Punch biopsies were collected from six cattle livers. Comparisons among methods of preservation using RNAlater, silica beads, and under-vacuum was carried out. These methods were tested through considering different times and temperatures, assuming three days as a maximum time interval from sampling to laboratory and choosing 4 °C and 24 °C as references for refrigeration temperature and room temperature, respectively. Histologically, the integrity of nucleus, cytoplasm, preservation of liver structure, and easiness of recognition of inflammatory infiltrate were evaluated. The integrity of the extracted DNA and RNA was evaluated through PCR and by means of an automated electrophoresis station, respectively. RNAlater and silica beads poorly preserved the histological parameters evaluated, independently from the temperature. Conversely, the vacuum-sealed samples showed a good grade of preservation until 48 h. DNA quality was acceptable for each sample. RNA integrity showed promising results only for samples preserved with silica beads.

The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies

Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90% made the insects more brittle, but for species with robust, thicker exoskeletons, this did not translate to an increased loss of appendages. Neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the retention of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry. We also found that DNA preserves less well at lower ethanol concentrations when stored at room temperature for an extended period. However, the magnitude of the effect varies among species; the concentrations at which the number of COI amplicon copies relative to the standard was significantly decreased compared to 95% ethanol ranged from 90% to as low as 50%. While higher ethanol concentrations positively affect long-term DNA preservation, there is a clear trade-off between preserving insects for morphological examination and genetic analysis. The optimal ethanol concentration for the latter is detrimental for the former, and vice versa. These trade-offs need to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of collected specimens.

Application of propylene glycol in DNA-based studies of invertebrates

High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.

The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.

When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.

Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.

Functional modulation of gut microbiota in diabetic rats following dietary intervention with pistachio nuts (Pistacia vera L.)

BACKGROUND

Gut microbiota holds a key-role in numerous biological functions and has emerged as a driving force for the development of diabetes. Diet contributes to gut microbiota diversity and functionality providing a tool for the prevention and management of the disease. The study aimed to investigate the effect of a dietary intervention with pistachio nuts, a rich source of monounsaturated fatty acids, dietary fibers and phytochemicals on gut microbiota composition in the rat model of Type 1 Diabetes.

METHODS

Male Wistar rats were randomly assigned into four groups: healthy animals which received control diet (CD) or pistachio diet (PD), and diabetic animals which received control diet (DCD) or pistachio diet (DPD) for 4 weeks. Plasma biochemical parameters were determined and histological examination of liver and pancreas was performed at the end of the dietary intervention. Adherent intestinal microbiota populations in jejunum, ileum, caecum and colon were analyzed. Fecal microbiota populations at the beginning and the end of the study were determined by microbiological analysis and 16S rRNA sequencing.

RESULTS

Diabetic animals of both groups exhibited high plasma glucose and low insulin concentrations, as well as characteristic pancreatic lesions. Pistachio supplementation significantly increased lactobacilli and bifidobacteria populations in jejunum, ileum and caecum (p < 0.05) and normalized microbial flora in all examined intestinal regions of diabetic animals. After 4 weeks of supplementation, populations of bifidobacteria and lactobacilli were increased in feces of both healthy and diabetic animals, while enterococci levels were decreased (p < 0.05). Next Generation Sequencing of fecal samples revealed increased and decreased counts of Firmicutes and Bacteroidetes, respectively, in healthy animals that received the pistachio diet. Actinobacteria OTUs were higher in diabetic animals and increased over time in the pistachio treated groups, along with increased abundance of Bifidobacterium. Lactobacillus, Turicibacter and Romboutsia populations were elevated in healthy animals administered the pistachio nuts. Of note, relative abundance of Bacteroides was higher in healthy than in diabetic rats (p < 0.05).

CONCLUSION

Dietary pistachio restored normal flora and enhanced the presence of beneficial microbes in the rat model of streptozotocin-induced diabetes.

DESS deconstructed: Is EDTA solely responsible for protection of high molecular weight DNA in this common tissue preservative?

DESS is a formulation widely used to preserve DNA in biological tissue samples. Although it contains three ingredients, dimethyl sulfoxide (DMSO), ethylenediaminetetraacetic acid (EDTA) and sodium chloride (NaCl), it is frequently referred to as a DMSO-based preservative. The effectiveness of DESS has been confirmed for a variety of taxa and tissues, however, to our knowledge, the contributions of each component of DESS to DNA preservation have not been evaluated. To address this question, we stored tissues of three aquatic taxa, Mytilus edulis (blue mussel), Faxonius virilis (virile crayfish) and Alitta virens (clam worm) in DESS, each component of DESS individually and solutions containing all combinations of two components of DESS. After storage at room temperature for intervals ranging from one day to six months, we extracted DNA from each tissue and measured the percentage of high molecular weight (HMW) DNA recovered (%R) and normalized HMW DNA yield (nY). Here, HMW DNA is defined as fragments >10 kb. For comparison, we also measured the %R and nY of HMW DNA from extracts of fresh tissues and those stored in 95% EtOH over the same time intervals. We found that in cases where DESS performed most effectively (yielding ≥ 20%R of HMW DNA), all solutions containing EDTA were as or more effective than DESS. Conversely, in cases where DESS performed more poorly, none of the six DESS-variant storage solutions provided better protection of HMW DNA than DESS. Moreover, for all taxa and storage intervals longer than one day, tissues stored in solutions containing DMSO alone, NaCl alone or DMSO and NaCl in combination resulted in %R and nY of HMW DNA significantly lower than those of fresh tissues. These results indicate that for the taxa, solutions and time intervals examined, only EDTA contributed directly to preservation of high molecular weight DNA.

Long-term stability of microbiome diversity and composition in fecal samples stored in eNAT medium

Fecal samples collected for microbiome analyses are typically frozen to avoid postcollection changes in microbial composition. eNAT is a guanidine thiocyanate-based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating microorganisms. We collected fecal samples (n = 50) from children undergoing hematopoietic stem cell transplantation. We divided samples into three aliquots: (a) stored in RNAlater and immediately transferred to -80°C; (b) stored in eNAT medium and immediately transferred to -80°C; and (c) stored in eNAT medium at ambient temperature (~20°C) for 30 days prior to transfer to -80°C. Mean (standard deviation) Shannon diversity and Chao1 indices in sample aliquots were 2.05 (0.62) and 23.8 (16.6), respectively. Comparing samples frozen immediately in RNAlater to samples frozen immediately in eNAT, there were no differences in Shannon diversity (p = .51), Chao1 richness (p = .66), and overall microbiome composition (p = .99). Comparing eNAT samples frozen immediately to samples stored at ambient temperature, we identified no differences in Shannon diversity (p = .65), Chao1 richness (p = .87), and overall microbiome composition (p = .99). Storage of fecal samples in eNAT at ambient temperature for 30 days did not alter microbiome richness, diversity, or composition. eNAT may be a useful medium for fecal microbiome studies, particularly when cold chain storage is unavailable.

Bovine neosporosis in dairy cattle from the southern highlands of Ecuador

The aim of this study was to describe bovine neosporosis in dairy cattle from the Sierra region, Ecuador. A case-control study was performed on 841 dairy cattle from 5 dairy herds. The overall seroprevalence was 23.4% having significant association between abortion and seropositivity (p < .05). Additionally, 46 fetuses were recovered from a local slaughterhouse to evaluate the frequency of vertical transmission. Seventeen and 3 fetuses were positive by PCR and had compatible histopathological lesions, respectively. N. caninum infection must be considered as a relevant cause of reproductive losses in Ecuador.

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms

In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) – EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations.

A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation

Objective

We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel.

Results

Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4–337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1–9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.

Tissue preservation in extreme temperatures for rapid response to military deaths

Many deployable forensic capabilities, including those used by the Australian Defense Force (ADF), employ mobile battery-operated fridge/freezers for DNA sample preservation that are not suitable for rapid response application due to their size and weight. These fridge/freezers are expensive, require regular specialised maintenance, and have a set payload. A variety of transport media are successful preservatives for DNA samples, however, there is no research specifically targeted to their suitability for operational environments where temperatures exceed 50 °C. This research examined whether sodium chloride (NaCl), ethanol, and dimethyl sulfoxide (DMSO) could preserve muscle and bone samples (fresh and early decomposition) as effectively as refrigeration, when stored at 21 °C, 45 °C, 55 °C, and 65 °C for at least one week. A total of 78 muscle and 78 bone samples were collected from an unknown deceased individual. Half of each tissue type was stored at 30 °C for 48 h to induce early decomposition. Following this, samples were stored in the transport media for one week at the above temperatures, and a control set of samples were refrigerated (-4 °C) without any transport media. Preserved samples would need to provide DNA profiles comparable to the refrigerated samples for the transport media to be considered a successful replacement method. NaCl and 70% ethanol preserved muscle samples (fresh and decomposed) up to 65 °C, as well as 70% ethanol and 20% DMSO for fresh bone samples. These results were comparable with refrigeration and therefore, these preservatives could be used in rapid response operations by the military and for disaster victim identification. Conversely, under the conditions of this study, 20% DMSO and 70% ethanol failed to consistently produce full DNA profiles from decomposed bone, and NaCl performed poorly at preserving DNA from fresh and decomposed bone samples.

Practical considerations for large-scale gut microbiome studies

First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.

Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species

High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods. Experimental mixes used larval fish tissue from multiple “common” species spiked with varying proportions of tissue from an additional “rare” species. Pyrosequencing of genetic marker, COI (cytochrome c oxidase subunit I) and subsequent sequence data analysis provided experimental evidence of low-level detection of the target “rare” species at biomass percentages as low as 0.02% of total sample biomass. Limits to detection varied interspecifically and were susceptible to amplification bias. Moreover, results showed some data processing methods can skew sequence-based biodiversity measurements from corresponding relative biomass abundances and increase false absences. We suggest caution in interpreting presence/absence and relative abundance in larval fish assemblages until metabarcoding methods are optimized for accuracy and precision.

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.

A workflow to preserve genome-quality tissue samples from plants in botanical gardens and arboreta

PREMISE OF THE STUDY

Internationally, gardens hold diverse living collections that can be preserved for genomic research. Workflows have been developed for genomic tissue sampling in other taxa (e.g., vertebrates), but are inadequate for plants. We outline a workflow for tissue sampling intended for two audiences: botanists interested in genomics research and garden staff who plan to voucher living collections.

METHODS AND RESULTS

Standard herbarium methods are used to collect vouchers, label information and images are entered into a publicly accessible database, and leaf tissue is preserved in silica and liquid nitrogen. A five-step approach for genomic tissue sampling is presented for sampling from living collections according to current best practices.

CONCLUSIONS

Collecting genome-quality samples from gardens is an economical and rapid way to make available for scientific research tissue from the diversity of plants on Earth. The Global Genome Initiative will facilitate and lead this endeavor through international partnerships.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

Cooled Propylene Glycol as a Pragmatic Choice for Preservation of DNA From Remote Field-Collected Diptera for Next-Generation Sequence Analysis

Next-generation sequencing (NGS)-based methods can now be applied to large population-scale studies, but this demands very high-quality DNA. For specimens collected from remote field locations, DNA degradation can be a problem, requiring logistically challenging preservation techniques. Simpler preservation techniques are therefore required. Prior to collection of exotic fruit fly (Tephritidae) species, a number of readily available preservatives with storage at either 4°C or room temperature were trialed here to determine the DNA quality for three locally available Diptera species, Fannia canicularis (L.), Musca domestica L., and Lucilia sericata Meigen. Considerable variation was observed between the different preservatives, species, and temperatures, but several preservatives at 4°C were favored. Chilled propylene glycol was subsequently used for the storage and carriage of Australian field-collected Bactrocera fruit fly specimens to New Zealand. When processed up to 20 d later, DNA fragments of ∼10-20 kb were obtained for successful genotyping by sequencing analysis. This protocol is therefore recommended as a logistically simple and safe approach for distant collection of dipteran samples for NGS population genomic studies.

Preservation of and DNA Extraction from Muscle Tissue

As well as protecting DNA for subsequent analysis, tissue preservation methods ideally should be safe, readily available, and easy to transport at relatively low cost. Formalin (formaldehyde solution), used extensively to preserve medical and museum specimens, irreparably damages DNA. We have found four tissue preservatives (solid salt, salt-saturated dimethyl sulfoxide (DMSO)-EDTA solution, ethanol solution, and ethanol-EDTA solution) that preserved muscle tissue at 35 °C for up to 1 month: full short tandem repeat (STR) profiles were obtained after preservation. In addition, salt-saturated DMSO-EDTA solution yielded full STR profiles from aliquots of the liquid preservative surrounding muscle tissue.

Preservation Methods Alter Carbon and Nitrogen Stable Isotope Values in Crickets (Orthoptera: Grylloidea)

Stable isotope analysis (SIA) is an important tool for investigation of animal dietary habits for determination of feeding niche. Ideally, fresh samples should be used for isotopic analysis, but logistics frequently demands preservation of organisms for analysis at a later time. The goal of this study was to establish the best methodology for preserving forest litter-dwelling crickets for later SIA analysis without altering results. We collected two cricket species, Phoremia sp. and Mellopsis doucasae, from which we prepared 70 samples per species, divided among seven treatments: (i) freshly processed (control); preserved in fuel ethanol for (ii) 15 and (iii) 60 days; preserved in commercial ethanol for (iv) 15 and (v) 60 days; fresh material frozen for (vi) 15 and (vii) 60 days. After oven drying, samples were analyzed for δ¹⁵N, δ¹³C values, N(%), C(%) and C/N atomic values using continuous flow isotope ratio mass spectrometry. All preservation methods tested, significantly impacted δ¹³C and δ¹⁵N and C/N atomic values. Chemical preservatives caused δ¹³C enrichment as great as 1.5‰, and δ¹⁵N enrichment as great as 0.9‰; the one exception was M. doucasae stored in ethanol for 15 days, which had δ¹⁵N depletion up to 1.8‰. Freezing depleted δ¹³C and δ¹⁵N by up to 0.7 and 2.2‰, respectively. C/N atomic values decreased when stored in ethanol, and increased when frozen for 60 days for both cricket species. Our results indicate that all preservation methods tested in this study altered at least one of the tested isotope values when compared to fresh material (controls). We conclude that only freshly processed material provides adequate SIA results for litter-dwelling crickets.

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota

Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways.