Free-living Species Research Articles

Identification of Factors Affecting Environmental Contamination Represented by Post-Hatching Eggshells of a Common Colonial Waterbird with Usage of Artificial Neural Networks.

Artificial Neural Networks are used to find the influence of habitat types on the quality of the environment expressed by the concentrations of toxic and harmful elements in avian tissue. The main habitat types were described according to the Corine Land Cover CLC2012 model. Eggs of free-living species of a colonial waterbird, the grey heron Ardea cinerea, were used as a biological data storing media for biomonitoring. For modeling purposes, pollution indices expressing the sum of the concentration of harmful and toxic elements (multi-contamination rank index) and indices for single elements were created. In the case of all the examined indices apart from Cd, the generated topologies were a multi-layer perceptron (MLP) with 1 hidden layer. Interestingly, in the case of Cd, the generated optimal topology was a network with a radial basis function (RBF). The data analysis showed that the increase in environmental pollution was mainly influenced by human industrial activity. The increase in Hg, Cd, and Pb content correlated mainly with the increase in the areas characterized by human activity (industrial, commercial, and transport units) in the vicinity of a grey heron breeding colony. The decrease in the above elements was conditioned by relative areas of farmland and inland waters. Pollution with Fe, Mn, Zn, and As was associated mainly with areas affected by industrial activities. As the location variable did not affect the quality of the obtained networks, it was removed from the models making them more universal.

Free-living Trichomonads are Unexpectedly Diverse

The vast majority of the more than 450 described species of Parabasalia are intestinal symbionts or parasites of animals. This endobiotic life-history is presumably ancestral although the root of Parabasalia still needs to be robustly established. The half-dozen putatively free-living species thus far described are likely independently derived from endobiotic ancestors and represent the most neglected ecological group of parabasalids. Thus, we isolated and cultivated 45 free-living strains of Parabasalia obtained from a wide variety of anoxic sediments to conduct detailed morphological and SSU rRNA gene phylogenetic analyses. Sixteen species of trichomonads were recovered. Among them, we described seven new species, three new genera, two new families, and one new order. Most of the newly described species were more or less closely related to members of already described genera. However, we uncovered a new deep-branching lineage without affinity to any currently known group of Parabasalia. The newly discovered free-living parabasalids will be key taxa in comparative analyses aimed at rooting the entire lineage and deciphering the evolutionary innovations involved in transitioning between endobiotic and free-living habitats.

Entomopathogens from agricultural soil and their pathogenicity against the potato leaf miner, Liriomyza huidobrensis (Diptera: Agromyzidae)

ABSTRACT The potato leaf miner, Liriomyza huidobrensis (Diptera: Agromyzidae), is an important economic pest of potatoes across the world, causing substantial damage in most potato-growing areas. The use of local entomopathogens for the control of insect pests has been widely encouraged, coupled with several environmental advantages being contrasted to the effects achieved using chemical pesticides. The current study surveyed potato field soil to determine the presence of entomopathogenic nematode (EPN) and entomopathogenic fungi (EPF) species in the Sandveld region of the Western Cape province. Susceptibility of L. huidobrensis larvae and pupae to the isolated pathogens and other locally sourced isolates was evaluated. The results of the survey indicated the presence of an unknown free-living bacteria feeding insect-associated nematode species of the genus Acrobeloides, the EPN Heterorhabditis zealandica and two EPF species, Metarhizium robertsii and M. majus. All L. huidobrensis pupal (45–57%) and larval stages (52–72%) of the potato leaf miner showed susceptibility to the EPN species tested. Laboratory bioassays showed that the pupal and larval stages was the most susceptible (>72% infection) to Heterorhabditis baujardi. Liriomyza huidobrensis pupal stage showed high pathogenicity to isolates of M. robertsii (10C). Overall, all isolates of M. robertsii showed pupal pathogenicity ranging between 80% and 91%. Metarhizium robertsii outperformed Beauveria bassiana as a biocontrol agent against L. huidobrensis pupae in the laboratory. Results from this study indicate the potential of biologicals as future biocontrol agents in an integrated pest management system for potato production.

Prevalent association with the bacterial cell envelope of prokaryotic expansins revealed by bioinformatics analysis.

Expansins are a group of proteins from diverse organisms from bacteria to plants. Although expansins show structural conservation, their biological roles seem to differ among kingdoms. In plants, these proteins remodel the cell wall during plant growth and other processes. Contrarily, determination of bacterial expansin activity has proven difficult, although genetic evidence of bacterial mutants indicates that expansins participate in bacteria-plant interactions. Nevertheless, a large proportion of expansin genes are found in the genomes of free-living bacteria, suggesting roles that are independent of the interaction with living plants. Here, we analyzed all available sequences of prokaryotic expansins for correlations between surface electric charge, extra protein modules, and sequence motifs for association with the bacteria exterior after export. Additionally, information on the fate of protein after translocation across the membrane also points to bacterial cell association of expansins through six different mechanisms, such as attachment of a lipid molecule for membrane anchoring in diderm species or covalent linking to the peptidoglycan layer in monoderms such as the Bacilliales. Our results have implications for expansin function in the context of bacteria-plant interactions and also for free-living species in which expansins might affect cell-cell or cell-substrate interaction properties and indicate the need to re-examine the roles currently considered for these proteins.

Life history and reproductive traits of the East Atlantic deep-sea quill worm Hyalinoecia robusta Southward, 1977 (Annelida: Onuphidae)

Polychaetes or bristle worms (Annelida) are one of the best represented invertebrate groups in marine environments worldwide. Although the reproductive biology and life histories of polychaetes from many marine and estuarine habitats are well documented, our knowledge of the reproduction and life cycles of deep-sea polychaetes is still far from comprehensive. Hyalinoeciinae, a subfamily of Onuphidae, one of the most dominant and successful tubicolous deep-sea polychaete families, are characterised by their peculiar lifestyle as free-living epibenthic species, as they protrude from their tubes in a caterpillar-like fashion known as epibenthic crawling. The reproductive biology, sexual strategies and developmental modes of Hyalinoecia spp. are largely unknown. We have studied quarterly samples of the East Atlantic deep-sea quill worm Hyalinoecia robusta Southward, 1977, collected during 2012–2013, from the adjacent slope of the Avilés submarine Canyons System (Bay of Biscay) at 1500 m depth. Here we report on the annual cycle, revealing that H. robusta is iteroparous, reproducing annually during a breeding season from early spring to summer. The performed histological study revealed that the species is a simultaneous hermaphrodite with a previous adolescent male phase. This is the first evidence of the occurrence of hermaphroditism in the subfamily Hyalinoeciinae. Mature sperm was of the ent-aquasperm type and was stored in modified nephridial chambers that develop into external papillae that may detach from the worm and act as spermatophores at the time of reproduction. In H. robusta, the egg fertilisation seems to occur within intersegmental dorsal openings of the worm body wall or inside the worm tube. This hypothesis is consistent with the finding of fertilised eggs and developing embryos attached to the body wall and/or inside the worm tube in some specimens. The herein reported H. robusta reproductive traits do not support their conspecificity with populations from outside North Atlantic Ocean. Thus, the name H. robusta may be hiding other deep-water Hyalinoecia species.

Ecological indices and factors influencing communities of ectoparasitic laelapid mites (Acari, Mesostigmata, Laelapidae) of small mammals in Lithuania.

Family Laelapidae is an ecologically diverse group that includes free-living species and parasites of vertebrates and invertebrates. At least seven genera in this family are associated with small mammals. In this study, ectoparasitic laelapid mites of rodents and shrews were investigated in Lithuania. In total, 2,274 small mammal specimens of 12 species were trapped and 6,089 laelapid mites were collected. The updated list of ectoparasitic mites in Lithuania included 21 mite species. Seven mite species were identified as highly specific for a host species or genus, one species was moderately specific, and four mite species were assigned to generalist parasites. All host species had one or two superdominant mite species. The prevalence and mean intensity varied significantly depending on host species and habitat. We analyzed the influence of the host (species, sex, age) and environmental factors (landscape morphology type, habitat, anthropogenic effect) on the abundance of the mite community and most numerous mite species, as well as the impact of the host community (Shannon's diversity index, species richness, host abundance) on mean abundance of the mite community. Only particular host species (Apodemus flavicollis, Microtus agrestis, and Microtus arvalis) and habitats (pastures, mixed forests) influenced the abundance of mites.

Parasite infection influences the biomarker response and locomotor activity of Gammarus fossarum exposed to conventionally-treated wastewater

Modern wastewater treatment plants cannot completely remove pollutants. Often, effluents entering the aquatic environment still contain micropollutants such as pharmaceuticals or pesticides, which may impose adverse effects on aquatic biota. At the same time, a large proportion of free-living aquatic species are known to be infected with parasites, which raises the question of interactions between environmental stressors (such as micropollutants) and parasite infection. We chose the freshwater amphipod Gammarus fossarum (Koch, 1835) as a test organism to investigate potential pollutant-parasite interactions. This gammarid is frequently used in ecotoxicological tests and is also commonly infected with larvae of the acanthocephalan parasite species Polymorphus minutus (Zeder, 1800) Lühe, 1911. We exposed infected and uninfected specimens of G. fossarum to conventionally-treated wastewater and river water in a 22-day flow channel experiment. The test organisms’ response was measured as mortality rates, concentrations or activities of five biomarkers, and overall locomotor activity. No significant differences were found between mortality rates of different exposure conditions. Contrastingly, three biomarkers (phenoloxidase activity, glycogen, and lipid concentrations) showed a significant increase in infected gammarids, while the effect of the water type was insignificant. Infected gammarids also showed a significantly higher locomotor activity in both water types. Our results suggest that the response of G. fossarum during the exposure experiments was mainly driven by parasite infection. This implies that parasites may act as additional biotic stressors in multiple stressor scenarios, and therefore, might play an important role when measuring the response of organisms to chemical stressors. Future ecotoxicological studies and assessments thus should consider parasite infection as an additional test parameter.

Parasite communities in English Sole (Parophrys vetulus) have changed in composition but not richness in the Salish Sea, Washington, USA since 1930.

AbstractEarth is rapidly losing free-living species. Is the same true for parasitic species? To reveal temporal trends in biodiversity, historical data are needed, but often such data do not exist for parasites. Here, parasite communities of the past were reconstructed by identifying parasites in fluid-preserved specimens held in natural history collections. Approximately 2500 macroparasites were counted from 109 English Sole (Parophrys vetulus) collected between 1930 and 2019 in the Salish Sea, Washington, USA. Alpha and beta diversity were measured to determine if and how diversity changed over time. Species richness of parasite infracommunities and community dispersion did not vary over time, but community composition of decadal component communities varied significantly over the study period. Community dissimilarity also varied: prior to the mid-20th century, parasites shifted in abundance in a seemingly stochastic manner and, after this time period, a canalization of community change was observed, where species' abundances began to shift in consistent directions. Further work is needed to elucidate potential drivers of these changes and to determine if these patterns are present in the parasite communities of other fishes of the Salish Sea.

First mitochondrial genomes of Chrysopetalidae (Annelida) from shallow-water and deep-sea chemosynthetic environments.

Among Annelida, Chrysopetalidae is an ecologically and morphologically diverse group, which includes shallow-water, deep-sea, free-living, and symbiotic species. Here, the four first mitochondrial genomes of this group are presented and described. One of the free-living shallow-water species Chrysopetalum debile (Chrysopetalinae), one of the yet undescribed free-living deep-sea species Boudemos sp., and those of the two deep-sea bivalve endosymbionts Craseoschema thyasiricola and Iheyomytilidicola lauensis (Calamyzinae). An updated phylogeny of Chrysopetalidae is performed, which supports previous phylogenetic hypotheses within Chrysopetalinae and indicates a complex ecological evolution within Calamyzinae. Additionally, analyses of natural selection pressure in the four mitochondrial genomes and additional genes from the two shallow-water species Bhawania goodei and Arichlidon gathofi were performed. Relaxed selection pressure in the mitochondrion of deep-sea and symbiotic species was found, with many sites under selection identified in the COX3 gene of deep-sea species.

The response of Naegleria gruberi to oxidative stress.

Aerobic organisms require oxygen for respiration but must simultaneously cope with oxidative damages inherently linked with this molecule. Unicellular amoeboflagellates of the genus Naegleria, containing both free-living species and opportunistic parasites, thrive in aerobic environments. However, they are also known to maintain typical features of anaerobic organisms. Here, we describe the mechanisms of oxidative damage mitigation in Naegleria gruberi and focus on the molecular characteristics of three noncanonical proteins interacting with oxygen and its derived reactive forms. We show that this protist expresses hemerythrin, protoglobin, and an aerobic-type rubrerythrin, with spectral properties characteristic of the cofactors they bind. We provide evidence that protoglobin and hemerythrin interact with oxygen in vitro and confirm the mitochondrial localization of rubrerythrin by immunolabeling. Our proteomic analysis and immunoblotting following heavy metal treatment revealed upregulation of hemerythrin, while rotenone treatment resulted in an increase in rubrerythrin protein levels together with a vast upregulation of alternative oxidase. Our study provided new insights into the mechanisms employed by N. gruberi to cope with different types of oxidative stress and allowed us to propose specific roles for three unique and understudied proteins: hemerythrin, protoglobin, and rubrerythrin.

Histopathology of Endocrine Organs of Miranda's White-Lipped Frogs (Leptodactylus macrosternum) from Cultivated and Non-Cultivated Regions in Semi-Arid Northeastern Brazil

Endocrine disruption defines the influence of environmental contaminants on the control of behaviour, growth and reproduction of free-living species. Amphibians are considered as bioindicators of environmental balance in aquatic and terrestrial systems and of physiological and immunological sensitivity to environmental stressors. In the Caatinga Domain of northeastern Brazil, the Lower Jaguaribe River (LJR) region is outstanding for the conservation of anurans and has considerable species diversity. However, the use of pesticides and chemical fertilisers is of increasing concern because of consequent risks to environmental, human and animal health. Miranda's white-lipped frogs (Leptodactylus macrosternum) are abundant and well-adapted in this region and, therefore, are considered to be a suitable bioindicator. The objective of this work was to evaluate the morphology of endocrine organs of this species for evidence of potential impacts of agrosystems. We found significantly smaller females and parathyroid cytolysis in frogs collected from cultivated areas, compared with those from non-cultivated regions. Interrenal degeneration was found in both sample populations. Chemical analysis detected pesticides and potentially toxic elements in tissues of Miranda's white-lipped frog tissues from the LJR region (data not shown). These findings suggest that the parathyroid gland acts as a biomarker of environmental toxicity in cultivated areas in the LJR region. In this study, the other examined endocrine organs did not show significant potential for use in biomonitoring the impact of toxic chemicals.

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Significance The results provide strong evidence of extensive SARS-CoV-2 infection of white-tailed deer, a free-living wild animal species with widespread distribution across North, Central, and South America. The analysis shows infection of deer resulted from multiple spillovers from humans, followed by efficient deer-to-deer transmission. The discovery of widespread infection of white-tailed deer indicates their establishment as potential reservoir hosts for SARS-CoV-2, a finding with important implications for the ecology, long-term persistence, and evolution of the virus, including the potential for spillback to humans.

Balamuthia spinosa n. sp. (Amoebozoa, Discosea) from the brackish-water sediments of Nivå Bay (Baltic Sea, The Sound)-a novel potential vector of Legionella pneumophila in the environment.

We have found a new free-living amoeba species named Balamuthia spinosa n. sp. (Amoebozoa, Discosea) in the bottom sediments of the brackish-water Nivå Bay (Baltic Sea, The Sound). This species resembles members of the genus Stygamoeba morphologically and was (mis)identified as belonging to this genus during the initial investigation. However, SSU rRNA gene data show that it robustly groups with Balamuthia mandrillaris sequence among Acanthopodida and represents a new species of the genus Balamuthia. Fragments of Legionella pneumophila genome were found among the NGS contigs obtained from B. spinosa n. sp., suggesting that this species may be a vector of Legionella in the environment. We discuss a remarkable morphological and ultrastructural similarity between the genus Balamuthia and the genus Stygamoeba. In addition, our phylogenetic analysis based on the SSU rRNA gene sequences revealed a close relationship between the genera Stygamoeba and Vermistella. It is one more confirmation of the order Stygamoebida, which was formed basing on the morphological evidence. The position of these branches close to Thecamoebida clade is congruent with current phylogenomic data.

Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria.

ABSTRACTSialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role.IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.

A Global Review of Causes of Morbidity and Mortality in Free-Living Vultures.

Vulture species worldwide play a key role in ecosystems as obligate scavengers, and several populations have had precipitous declines. Research on vulture health is critical to conservation efforts including free-living vultures and captive breeding programs, but is limited to date. In this systematic review, we determined the reported causes of free-living vulture species morbidity and mortality worldwide. The most commonly reported cause of mortality was from toxins (60%), especially lead and pesticides, followed by traumatic injury (49%), including collisions with urban infrastructure and gunshot. Neglected areas of research in free-living vulture health include infectious diseases (16%), endocrine and nutritional disorders (6%), and neoplasia (< 1%). Almost half of the studies included in the review were conducted in either Spain or the USA, with a paucity of studies conducted in South America and sub-Saharan Africa. The highest number of studies was on Griffon (Gyps fulvus) (24%) and Egyptian vultures (Neophron percnopterus) (19%), while half of all vulture species had five or fewer studies. Future investigations on free-living vulture health should focus on neglected areas of research, such as infectious diseases, and areas with gaps in the current literature, such as South America, sub-Saharan Africa, and under-studied vulture species.

Жесткокрылые (Coleoptera) в гнездах мухоловки-пеструшки Ficedula hypoleuca (Pallas, 1764) на юго-востоке Приладожья (Республика Карелия)

Invertebrates collected in the Republic of Karelia in 2016 from nests of the pied flycatcher Ficedula hypoleuca (Pallas, 1764) are analyzed and 516 specimens of invertebrates are identified. The vast majority of these invertebrates are Hymenoptera (ants of the genus Camponotus) – 46.6% and various beetles (Coleoptera) – 46.37%. An annotated list of 38 species of beetle from 22 families is presented. The beetle fauna of the studied European pied flycatcher nests is mixed and includes both nidicolous species and free-living species that are not directly related to nest microcenoses. The rare beetles species Melandrya dubia (Schaller, 1783) and Otho sphondyloides (Germar, 1818), were found.

Exploration of the homology among the muscles associated with the female genitalia of the three suborders of Psocodea (Insecta)

By using μCT technology, we reconstructed 3D models of the female genital structures and associated muscles of seven species from three suborders of Psocodea (free-living species only, formerly known as independent insect order “Psocoptera”). The homology of the female genital structures and associated muscles of different species is discussed. A total of 21 muscle groups were observed, and except for one muscle, all were homologized throughout the order. Moreover, some of the homologous muscles could be identified confidently in holometabolan insects. Using the muscles as landmarks, we discuss the homology of the ovipositor valves between Psocodea and other neopteran insects. Most importantly, the ovipositor of the suborder Trogiomorpha was identified to consist of the well-developed external valve (V3) plus a remnant of the dorsal valve (V2). We also examined the phylogenetic information included in the female genital muscles and found that certain muscles provide useful information and support deeper nodes (e.g., monophyly of the suborder Psocomorpha). The present study of female genital muscles not only helps us to better understand the phylogeny of Psocodea but also provides a solid foundation for research on muscle evolution.

Vitamin B12 and predatory behavior in nematodes.

The round worms or nematodes are the largest phylum of animals with an estimated species number of more than one million. Nematodes have invaded all ecosystems and are known from all continents including Antarctica. Parasitic species infest plants, animals and humans often with high host-specificity. Free-living species are known from marine, fresh water and soil systems, the latter of which contain many culturable species. This includes Caenorhabditis elegans, a species that was developed as one of the most prominent model systems in modern biology since the 1960ies. Pristionchus pacificus is a second nematode model organism that can easily be cultured in the laboratory. This species shows a number of complex traits including omnivorous feeding and the capability of predation on other nematodes. Predation depends on the formation of teeth-like denticles in the mouth of P. pacificus, structures unknown from C. elegans and most other nematodes. Here, we review the current knowledge about the role of vitamin B12 for the predatory behavior in P. pacificus and correlate its role with that on the physiology and development in C. elegans.

Radiographic evaluation of cardiac size in the white stork (Ciconia ciconia)

Physical examination of the cardiovascular system in birds is quite difficult compared to other animals. As in humans and mammalian animals, radiography is a reliable diagnostic tool to identify cardiovascular disorders in birds. However, cardiovascular radiography studies for birds are very limited and reference information is lacking. In this study the aim was to determine the reference values of cardiac radiographic measurements that can be used especially in the diagnosis of cardiomegaly in storks, which is a free-living bird species. For this purpose, 26 white storks without cardiovascular disorders were used in the study. Radiographs were taken in lateral and ventrodorsal projections. Five measurements: heart length (61.70 ± 6.69 mm), heart width (51.65 ± 4.84), carina length (139.80 ± 10.05), thoracic width (87.45 ± 6.58), and coracoid width (10.24 ± 1.20) were performed. The ratio of the heart width to thoracic width was 59.16%. The ratio of heart length to carina length was 44.28%. Heart width correlates significantly and positively with the thoracic width (R: 0.556, R2: 0.310, P: 0.003). The heart width can be estimated by using the thoracic width values with the regressionbased formula in the results of this study. Clinically, it can be determined whether an individual case falls between the minimum or maximum reference values for heart width or length. The results presented in this study may provide clinicians with reference information regarding cardiomegaly.

Host specificity and the reproductive strategies of parasites.

Environmental stability can have profound impacts on life history trait evolution in organisms, especially with respect to development and reproduction. In theory, free-living species, when subjected to relatively stable and predictable conditions over many generations, should evolve narrow niche breadths and become more specialized. In parasitic organisms, this level of specialization is reflected by their host specificity. Here, we tested how host specificity impacts the reproductive strategies of parasites, a subject seldomly addressed for this group. Through an extensive review of the literature, we collated a worldwide dataset to predict, through Bayesian multilevel modelling, the effect of host specificity on the reproductive strategies of parasitic copepods of fishes or corals. We found that copepods of fishes with low host specificity (generalists) invest more into reproductive output with larger clutch sizes, whereas generalist copepods of corals invest less into reproductive output with smaller clutch sizes. The differences in host turnover rates through an evolutionary timescale could explain the contrasting strategies across species observed here, which should still favour the odds of parasites encountering and infecting a host. Ultimately, the differences found in this study reflect the unique evolutionary history that parasites share both intrinsically and extrinsically with their hosts.