Storage and shipping of tissue samples for DNA analyses: A case study on earthworms

Bacterial communities associated with Acrobeles complexus nematodes recovered from tomato crops in South Africa

The productivity of agricultural ecosystems is heavily influenced by soil-dwelling organisms. To optimize agricultural practices and management, it is critical to know the composition, abundance, and interactions of soil microorganisms. Our study focused on Acrobeles complexus nematodes collected from tomato fields in South Africa and analyzed their associated bacterial communities utilizing metabarcoding analysis. Our findings revealed that A. complexus forms associations with a wide range of bacterial species. Among the most abundant species identified, we found Dechloromonas sp., a bacterial species commonly found in aquatic sediments, Acidovorax temperans, a bacterial species commonly found in activated sludge, and Lactobacillus ruminis, a commensal motile lactic acid bacterium that inhabits the intestinal tracts of humans and animals. Through principal component analysis (PCA), we found that the abundance of A. complexus in the soil is negatively correlated with clay content (r = -0.990) and soil phosphate levels (r = -0.969) and positively correlated with soil sand content (r = 0.763). This study sheds light on the bacterial species associated to free-living nematodes in tomato crops in South Africa and highlights the occurrence of various potentially damaging and beneficial nematode-associated bacteria, which can in turn, impact soil health and tomato production.

Eye and hair color prediction of human DNA recovered from Lucilia sericata larvae

Forensic entomological evidence is employed to estimate minimum postmortem interval (PMImin), location, and identification of fly samples or human remains. Traditional forensic DNA analysis (i.e., STR, mitochondrial DNA) has been used for human identification from the larval gut contents. Forensic DNA phenotyping (FDP), predicting human appearance from DNA-based crime scene evidence, has become an established approach in forensic genetics in the past years. In this study, we aimed to recover human DNA from Lucilia sericata (Meigen 1826) (Diptera: Calliphoridae) gut contents and predict the eye and hair color of individuals using the HIrisPlex system. Lucilia sericata larvae and reference blood samples were collected from 30 human volunteers who were under maggot debridement therapy. The human DNA was extracted from the crop contents and quantified. HIrisPlex multiplex analysis was performed using the SNaPshot minisequencing procedure. The HIrisPlex online tool was used to assess the prediction of the eye and hair color of the larval and reference samples. We successfully genotyped 25 out of 30 larval samples, and the most SNP genotypes (87.13%) matched those of reference samples, though some alleles were dropped out, producing partial profiles. The prediction of the eye colors was accurate in 17 out of 25 larval samples, and only one sample was misclassified. Fourteen out of 25 larval samples were correctly predicted for hair color, and eight were misclassified. This study shows that SNP analysis of L. sericata gut contents can be used to predict eye and hair color of a corpse.

Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study

Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at - 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.

Role of TaqMan array card in determining causative organisms of acute febrile illness in hospitalized patients

BACKGROUND

Acute febrile illness (AFI) is a prevalent disease in developing countries that is difficult to diagnose due to the diversity of infectious organisms and the poor quality of clinical diagnosis. TaqMan array card (TAC) can detect up to 35 AFI-associated organisms in 1.5 h, addressing diagnostic demands. In this study, we aimed to evaluate the role of TAC in determining the causative organisms in hospitalized AFI patients.

METHODS

The study had a cross-sectional design and enrolled 120 admitted patients with persistent fever for three or more days from the medicine ward of Chittagong Medical College Hospital (CMCH) and Bangladesh Institute of Tropical and Infectious Diseases Hospital (BITID). Blood samples were collected and then subjected to automated BacT/Alert blood culture, microbial culture, TAC assay, and typhoid/paratyphoid test.

RESULTS

The total number of study participants was 120, among them 48 (40%) samples showed a positive result in TAC card, 29 (24.16%) were TP positive and nine (7.51%) were culture positive. The number of organisms detected by the TAC card was 13 bacteria, three viruses, one protozoan, and one fungus. The sensitivity and specificity of the TAC assay for different bacterial pathogen compared to blood culture was 44.44%, and 90.99%, respectively. In contrast, the TP test had a sensitivity and specificity of 100% and 80%, respectively, compared to the blood culture test.

CONCLUSION

TAC can be a handful tool for detecting multiple organisms in AFI with high specificity which can facilitate early diagnosis of different pathogens contributing to AFI.

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.

First Report of Aphelenchoides Bicaudatus (Imamura, 1931) Filipjev and Schuurmans Stekhoven, 1941 Associated with Grass in South Africa

Aphelenchoides bicaudatus associated with grass in South Africa was identified morphologically and molecularly. This population is characterized by a body length of 409 - 529 μm, a stylet length of 9.5 - 13 μm, a post-vulval uterine sac of 45 - 50 μm, and the characteristic tail bifurcated at the end with one prong longer than the other. Molecular analyses based on the 18S and ITS rDNA data confirmed the primary morphological identification of the A. bicaudatus species. The obtained phylogenetic trees revealed a close positioning of the South African population to other representatives of A. bicaudatus with the maximum (1.00) posterior probability value. Principal component analysis (PCA) also indicated a variation within the populations of A. bicaudatus. This is the first report of A. bicaudatus from South Africa.

Molecular Character of Mylonchulus hawaiiensis and Morphometric Differentiation of Six Mylonchulus (Nematoda; Order: Mononchida; Family: Mylonchulidae) Species Using Multivariate Analysis

Mononchida members are predatory nematodes with the potential to reduce the number of plant-parasitic nematodes in the soil. During a survey on Mononchida in Iran, several populations of Mylonchulus were recovered from various localities. A population of M. hawaiiensis was studied using 18S rDNA. The phylogenetic analysis using Bayesian inference placed the sequenced M. hawiinesis (OP210758) together with other M. hawaiiensis from Japan (AB361438-AB361442) with a 1.00 posterior probability support. In addition, morphological differences between six Mylonchulus (Nematoda; order: Mononchida; Family: Mylonchulidae) populations were investigated in Iran using discriminant analyses (DA), PERMANOVA, and principal coordinate analysis (PCoA). The purpose was to evaluate the efficacy of PCoA and DA in separating the Mylonchulus species, namely M. sigmaturus, M. paitensis, M. lacustris, M. brachyuris, M. kermaninesis, and M. hawaiiensis. To achieve this, 16 morphometric measurements (body length, a, b, c, c′, V, G1, G2, buccal cavity length, buccal cavity width, dorsal tooth apex, dorsal tooth length, neck length, amphid from anterior end, rectum, and tail length) were made on 160 specimens. The analysis of variance showed that all features were significantly different among the species, except a, b, and the amphid position from the anterior end and tail length. The stepwise discriminant analysis revealed that body length, tail length, neck length, and c′ value were the four most discriminating variables useful to distinguish clearly the six species of Mylonchulus. The variables with strong discriminatory power correctly classified 98.87% of individuals from Iran’s sample of known Mylonchulus species. The results provide a morphometric basis for effectively distinguishing Mylonchulus species.

A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic

Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l^-1) followed by the canyon head (1,065 μg l^-1) and lowest at the canyon flank (494 μg l^-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.

Observation on Hemicriconemoides Brachyurus () Chitwood & Birchfield, 1957 Associated with Grass in South Africa

Hemicriconemoides brachyurus was identified morphologically, using body annuli number (103105), stylet length (49-52 μm), tail conical with small rounded lobe, spermatheca with round sperm, and VL/VB (1.3). Molecular analysis was also undertaken, based on the 18S rDNA region, and the obtained DNA sequence data confirmed the present population from South Africa as Hemicriconemoides. Phylogenetic analysis using the Bayesian inference method places this population close to H. fujianensis from China (MH444620-21; MH444626-28). To the best of our knowledge, this is the first report of the 18S rDNA sequence for H. brachyurus.

The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and appropriately accounting for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a ‘Mutationathon,’ a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a twofold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria, and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

Bacterial communities associated with Zeldia punctata, a bacterivorous soil-borne nematode

Soil inhabiting organisms are important determinants of agroecosystem productivity. Understanding the composition, the abundance, and the type of interactions established by soil microorganisms is therefore crucial to design strategies to improve agricultural practices and agroecosystem management. In this study, we collected Zeldia punctata nematodes in maize fields in South Africa and profiled their associated bacterial communities using next-generation sequencing. We observed that Z. punctata nematodes establish associations with ecologically diverse bacterial species. The most abundant species observed are Pseudomonas syringae, a phytopathogenic bacterial complex; Lactobacillus paraplantarum, a broadly distributed bacterial species that is present in soils, water bodies, and animal intestinal tracts and has certain probiotic and antimicrobial properties; and Melissococcus plutonius, a serious pathogenic bacterial species that causes brood disease in honeybees. Our study contributes to a better understanding of the soil bacterial communities associated with nematodes in maize agricultural soils in South Africa and unravels the presence of diverse detrimental and beneficial nematode-associated bacteria.

A Practical Approach to Identifying Processed White Meat of Guinea Fowl, Rabbit, and Selected Fish Species Using End-Point PCR

Among the foodstuff, most often adulterated are white meat and meat products as well as fish and fish products. For this reason, we evaluated in practice the possibilities of identifying selected species of white meat, i.e., guinea fowl and rabbit as well as four fish species, namely, pollock, hake, sole, and panga, in thermally treated samples. The aim was to check whether the previously published in the scientific literature species-specific primers allows for the identification of processed meat using the end-point PCR technique. To identify the six species, the short sequence fragments (from 130 to 255 bp) of 12S rRNA, COX3, mitochondrial ATP synthase Fo subunit 6 (ATP6) gene, pantophysin (Pan I) gene, 5S rRNA gene, and microsatellite markers (locus: Phy01-KUL) were selected. Stability and specificity of the six pair primers were evaluated on cooked and autoclaved meat, and commercially processed food samples such as rabbit and guinea pâtés, ready-made baby food, and breaded, fried, and deep-frozen fish products. The method proved to be useful for the authentication of severely processed food products against fraudulent species substitution and mislabelling and this approach may be an alternative to more advanced and more expensive PCR techniques.

Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil

Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.

First report of Bitylenchus ventrosignatus () associated with wild grass in Botswana

During a survey on the biodiversity of plant-parasitic nematodes of natural areas in Botswana, Bitylenchus ventrosignatus was discovered around the rhizosphere of wild grass. The nematodes were extracted using the tray method and then fixed according to the available protocols. The morphological characters fit well with the description of B. ventrosignatus. In addition, molecular analysis using 18 S and 28 S rDNA indicated 98% (KJ461617) and 95% (KJ461567) similarity with the Spanish population of B. ventrosignatus. The phylogenetic analysis of 18 S and 28 S rDNA placed the examined population with other populations of B. ventrosignatus in a group with a posterior probability support value of 100. According to published literature, this is the first report of B. ventrosignatus from Botswana.

A practical, low-cost, short-term storage method for genomic DNA

The aim of this study was to assess the DNA preservation capability of cellulose paper towel and blotting paper as low-cost alternatives to commercial DNA preservation products. Chicken blood was applied as DNA source to each paper towel, blotting paper, FTA^® cards and DNA/RNA Shield™. All samples were stored at room temperature for 130 days. DNA extraction from dried blood spots was performed after various time periods using Tris-EDTA and NaOH protocols. PCR activity and the mean amount of DNA isolated from paper towels were reliable. The results of this study demonstrated that cellulose-based blotting paper and especially paper towel had considerable DNA binding and preservation capacity for at least 130 days at room temperature without DNA degradation.

Morphological and molecular characters of Scutellonema brachyurus () from South Africa

During a survey on plant-parasitic nematodes from South Africa, Scutellonema brachyurus was recovered from soil samples collected around the rhizosphere of wild grass in the North West and Limpopo provinces. This species characterized by a hemispherical lip region with four to six annuli, basal lip's annuli with longitudinal incisures, body length 696-904 µm (a = 25.1-33.5; b = 5.0-7.2; c = 48.9-75.3; c' = 0.5-0.9; V = 55-60), stylet 21-27 µm length, tail rounded with 10-19 µm length and spermatheca nonfunctional and male absent. The nblast analysis based on the D2-D3 segment of 28 S rDNA placed South African populations of S. brachyurus with 98% similarity to Greece (KU059494) and 99% similarity to South African (JX472052) S. brachyurus. Besides, nblast of COI of mtDNA showed 98% similarity of the test species with South African populations of S. brachyurus (JX472096; JX472097). The phylogenetic analysis put the South African populations of S. brachyurus together with other S. brachyurus with a 100 posterior probability support. Besides, the measurements, line illustration, and scanning electron microscopy photographs are provided for S. brachyurus from South Africa.

First report of Mesocriconema sphaerocephalum (Taylor, 1936) Loof, 1989 associated with wild grass in Botswana

During a survey on the biodiversity of plant-parasitic nematodes of natural areas in Botswana, Mesocriconema sphaerocephalum was discovered around the rhizosphere of the wild grass. The nematodes were extracted using the tray method and then fixed according to the available protocols. The morphological characters fit well with the M. sphaerocephalum. Besides, molecular aspects using 18S and 28S rDNA were studied. The phylogenetic analysis of 18S and 28S rDNA placed the examined population with other populations of M. sphaerocephalum in a group. According to the knowledge, this is the first report of M. spaherocephalum from Botswana.

Antarctic coastal nanoplankton dynamics revealed by metabarcoding of desalination plant filters: Detection of short-term events and implications for routine monitoring

One of the main requirements of any sound biological monitoring is the availability of long term and, possibly, temporal data with a high resolution. This is often difficult to be achieved, especially in Antarctica, due to a variety of logistic constraints, which make continuous sampling and monitoring activities generally unfeasible. Here we focus on the 5 μm filters used in the desalination plant of the Italian research base "Mario Zucchelli" in the Terra Nova Bay area (Ross Sea, Antarctica) to evaluate intra-annual coastal nanoplankton dynamics. These filters, together with others of larger mesh sizes, are used to decrease the amount of organisms and debris in the input seawater before the desalination processes take place, hence automatically collect the plankton present in the water column around the desalination system intake. We have used a DNA metabarcoding approach to characterize the communities retained by filters' sets collected in January 2012 and 2013. Intra-annual dynamics were disclosed with an unprecedented detail, that would not have been possible by using standard sampling approaches, and highlighted the importance of extreme, stochastic events such as katabatic wind pulses, which triggered dramatic, short-term shifts in coastal nanoplankton composition. This method, by combining a cost-effective sampling and molecular techniques, may represent a viable solution for long-term monitoring programs focusing on Antarctic coastal communities.

First Report of Xiphinema Diffusum from Pakistan

The population of Xiphinema americanum species group was detected from the soil surronding the roots of peach (Prunus persica) during a survey of plant-parasitic nematodes in Gilgit-Baltistan, Pakistan. From the results of the morphological study, the species was identified as X. diffusum. Morphometrics of X. diffusum generally agree with those of the type species and the topotype specimens. Molecular analysis of 18S rDNA of X. diffusum from Pakistan indicated two nucleotide differences and 99 % similarity with the Chinese (AM086669) and the Australian (AM086685) population of X. diffusum. Phylogenetic analysis of 18S rDNA placed the Pakistanis population close to X. diffusum from China and Australia. This species is reported for the first time from Pakistan

Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

Storage of soil samples prior to metagenomic analysis presents a problem. If field sites are remote or if samples are collected by third parties, transport to analytical laboratories may take several days or even weeks. The bulk of such samples and requirement for later homogenisation precludes the convenient use of a stabilisation buffer, so samples are usually cooled or frozen during transit. There has been limited testing of the most appropriate storage methods for later study of soil organisms by eDNA approaches. Here we tested a range of storage methods on two contrasting soils, comparing these methods to the control of freezing at -80 °C, followed by freeze-drying. To our knowledge, this is the first study to examine the effect of storage conditions on eukaryote DNA in soil, including both viable organisms (fungi) and DNA contained within dying/dead tissues (plants). For fungi, the best storage regimes (closest to the control) were storage at 4 °C (for up to 14 d) or active air-drying at room temperature. The worst treatments involved initial freezing, followed by thawing which led to significant later spoilage. The key spoilage organisms were identified as Metarhizium carneum and Mortierella spp., with a general increase in saprotrophic fungi and reduced abundances of mycorrhizal/biotrophic fungi. Plant data showed a similar pattern, but with greater variability in community structure, especially in the freeze-thaw treatments, probably due to stochastic variation in substrates for fungal decomposition, algal proliferation and some seed germination. In the absence of freeze drying facilities, samples should be shipped refrigerated, but not frozen if there is any risk of thawing.

New data on known species of Hirschmanniella and Pratylenchus (Rhabditida, Pratylenchidae) from Iran and South Africa

Hirschmanniella anchoryzae from Iran and Pratylenchus hippeastri from South Africa were recovered during a survey of plant-parasitic nematodes belonging to the family Pratylenchidae. Both species were studied using morphological and molecular techniques. Hirschmanniella anchoryzae is identified based on the flattened head, short stylet (19–22 µm), excretory pore position (anterior to pharyngo-intestinal junction), spicule length (27–30 µm), and existence of an axial mucro at the tail end. Phylogenetic analysis using 28S rDNA showed monophyly of Hirschmanniella which Iranian H. anchoryzae placed close to H. halophila (EU620464; EU620465). This result was supported by the principal component analysis of Hirschmanniella species. SEM observation of the South African population of P. hippeastri showed the presence of two annuli in the lip region. Morphometric characters resembled those of specimens earlier reported from South Africa. Hierarchal cluster using morphometrical criteria showed that the Floridian (USA) and South African populations form a group. However, the principal component analysis showed variation within this species. The molecular study of P. hippeastri populations using 18S, ITS, 28S rDNA, and COI of mtDNA showed that all P. hippeastri cluster in one group and confirmed the identification of the species using both morphological and molecular techniques. In addition, the results indicated that South African populations group close to the USA populations. Illustrations of both species including light and scanning electron microscopy observations for P. hippeastri are provided.

High prevalence of Trichomonas gallinae in wild columbids across western and southern Europe

Background

Avian trichomonosis is known as a widespread disease in columbids and passerines, and recent findings have highlighted the pathogenic character of some lineages found in wild birds. Trichomonosis can affect wild bird populations including endangered species, as has been shown for Mauritian pink pigeons Nesoenas mayeri in Mauritius and suggested for European turtle doves Streptopelia turtur in the UK. However, the disease trichomonosis is caused only by pathogenic lineages of the parasite Trichomonas gallinae. Therefore, understanding the prevalence and distribution of both potentially pathogenic and non-pathogenic T. gallinae lineages in turtle doves and other columbids across Europe is relevant to estimate the potential impact of the disease on a continental scale.

Results

We examined 281 samples from four wild columbid species for Trichomonas infection and determined the genetic lineages. The overall prevalence was 74%. There were significant differences between the species (P = 0.007). The highest prevalence was found in stock doves Columba oenas (86%, n = 79) followed by wood pigeons Columba palumbus (70%, n = 61) and turtle doves (67%, n = 65), while three of five collared doves Streptopelia decaocto (60%) were infected. We found seven different lineages, including four lineages present in columbids in the UK, one lineage already described from Spain and three new lineages, one of those found in a single turtle dove migrating through Italy and another one found in a breeding stock dove. Stock doves from Germany and collared doves from Malta were infected with a potentially pathogenic lineage (lineage A/B), which is known to cause lesions and mortality in columbids, raptors and finches.

Conclusions

Generally, turtle doves showed high prevalence of Trichomonas infection. Furthermore, the potentially pathogenic lineage A/B (or genotype B according to previous literature) was found in a recovering stock dove population. Both findings are worrying for these columbid species due to the occasional epidemic character of trichomonosis, which can have severe negative effects on populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2170-0) contains supplementary material, which is available to authorized users.

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.