Investigating the relationship between genome structure,composition, and ecology in prokaryotes

Our thesis is that the DNA composition and structure of genomes are selected in part by mutation bias (GC pressure) and in part by ecology. To illustrate this point, we compare and contrast the oligonucleotide composition and the mosaic structure in 36 complete genomes and in 27 long genomic sequences from archaea and eubacteria. We report the following findings (1) High-GC-content genomes show a large underrepresentation of short distances between G(n) and C(n) homopolymers with respect to distances between A(n) and T(n) homopolymers; we discuss selection versus mutation bias hypotheses. (2) The oligonucleotide compositions of the genomes of Neisseria (meningitidis and gonorrhoea), Helicobacter pylori and Rhodobacter capsulatus are more biased than the other sequenced genomes. (3) The genomes of free-living species or nonchronic pathogens show more mosaic-like structure than genomes of chronic pathogens or intracellular symbionts. (4) Genome mosaicity of intracellular parasites has a maximum corresponding to the average gene length; in the genomes of free-living and nonchronic pathogens the maximum occurs at larger length scales. This suggests that free-living species can incorporate large pieces of DNA from the environment, whereas for intracellular parasites there are recombination events between homologous genes. We discuss the consequences in terms of evolution of genome size. (5) Intracellular symbionts and obligate pathogens show small, but not zero, amount of chromosome mosaicity, suggesting that recombination events occur in these species.     

Focal palatine erosion in captive and free-living cheetahs (Acinonyx jubatus) and other felid species

We examined 1,092 skulls of captive and free-living individuals, representing 33 felid species, to determine the prevalence of focal palatine erosion (FPE). FPE was detected in 3.2% of cats evaluated, including cheetah (Acinonyx jubatus) and 14 other felid species. The prevalence of FPE between cheetah (9.4%; n = 64) and non-cheetah species (2.8%; n = 1,028) (χ(2) test; P = 0.004) and between captive (5.7%; n = 246) and free-living (2.4%; n = 824) individuals (χ(2) test; P = 0.010) were significantly different, with prevalence between captive (19%; n = 21) and free-living (2.9%; n = 34) cheetahs approaching significance (Fisher's exact test; P = 0.064). FPE was diagnosed with equal prevalence in skulls from individuals in which the lower molars did not meet the palatine bone (60.6%) and individuals in which it did (39.4%; n = 33) (χ(2) test; P = 0.139). In cheetahs with FPE, one was a captive animal in Germany, one a free-living cheetah from Mali, one captive cheetah from Kenya, and three captive cheetahs of unknown origin. Additionally, we evaluated the medical records of 49 captive cheetahs in Namibia. Of these cheetahs, 48 (98.0%) had clinical signs consistent with FPE, although only 16 of these 48 (39.6%) had perforation of the palatine bone. Based on physical examinations, FPE was diagnosed in two caracals (Caracal caracal) and one fishing cat (Prionailurus viverrinus) from a North American Zoo. Results from this study confirm FPE in cheetahs outside of Namibia, in a minimum of 15 felid species, and a higher FPE prevalence in captive individuals than free-living ones. Clinical implications of these findings and recommendations for future studies are provided.     

The Effect of Some External Factors on Nitrogenase Activity in the Free-Living and Endophytic Nostoc of the Liverwort Blasia pusilla

The effects of pH, light intensity, temperature, oxygen and dehydration on nitrogenase activity in the free-living and endophytic Nostoc sp. of Blasia are described. The endophyte exhibits greater nitrogenase activity at lower pH's than the free-living alga. Maximal activity in the free-living alga is attained at much lower light intensities than those required by the endophyte. Both algae have low activities below 10°C, the free-living alga showing high activity above 12°C and the endophyte above 17°C. Increasing pO₂ levels cause a decrease in activity in both algae. The free-living alga is more tolerant to dehydration than the endophyte, although both algae are protected by mucilage. The results are discussed and possible benefits resulting from the symbiosis, with respect to nitrogen fixation rates, considered.     

Free-living marine nematodes from San Julián Bay (Santa Cruz,Argentina)

The free-living marine nematodes of San Julián Bay dataset is based on sediment samples collected in January 2009 during the project PICT AGENCIA-FONCYT 2/33345-2005. A total of 36 samples have been taken at three locations in the San Julián Bay, Santa Cruz Province, Argentina on the coastal littoral at three tidal levels. This presents a unique and important collection for the nematode benthic biodiversity assessment as this area remains one of the least known regions in Patagonia. In total 10,030 specimens of free-living marine nematodes belonging to 2 classes, 9 orders, 35 families, 78 genera and 125 species were collected. The San Julián city site presented a very high species richness.     

Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences

Ultrastructural and molecular phylogenetic evidence indicate that the Parabasalia consists of seven main subgroups: the Trichomonadida, Honigbergiellida, Hypotrichomonadida, Tritrichomonadida, Cristamonadida, Spirotrichonymphida, and Trichonymphida. Only five species of free-living parabasalids are known: Monotrichomonas carabina, Ditrichomonas honigbergii, Honigbergiella sp., Tetratrichomonas undula, and Pseudotrichomonas keilini. Phylogenetic analyses show that free-living species do not form a clade and instead branch in several different positions within the context of their parasitic relatives. Because the diversity of free-living parabasalids is poorly understood, the systematics of these lineages is in a significant state of disarray. In order to better understand the phylogenetic distribution of free-living parabasalids, we sequenced the small subunit rDNA from three different strains reminiscent of P. keilini; the strains were isolated from different geographical locations: (1) mangrove sediments in Japan and (2) sediments in Cyprus. These data demonstrated that the free-living parabasalids P. keilini and Lacusteria cypriaca n. g., n. sp., form a paraphyletic assemblage near the origin of a clade consisting mostly of parasitic trichomonadids (e.g. Trichomonas vaginalis). This paraphyletic distribution of similar morphotypes indicates that free-living trichomonadids represent a compelling example of morphostasis that provides insight into the suite of features present in the most recent free-living ancestor of their parasitic relatives.     

The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

New parasites and predators follow the introduction of two fish species to a subarctic lake: implications for food-web structure and functioning

Introduced species can alter the topology of food webs. For instance, an introduction can aid the arrival of free-living consumers using the new species as a resource, while new parasites may also arrive with the introduced species. Food-web responses to species additions can thus be far more complex than anticipated. In a subarctic pelagic food web with free-living and parasitic species, two fish species (arctic charr Salvelinus alpinus and three-spined stickleback Gasterosteus aculeatus) have known histories as deliberate introductions. The effects of these introductions on the food web were explored by comparing the current pelagic web with a heuristic reconstruction of the pre-introduction web. Extinctions caused by these introductions could not be evaluated by this approach. The introduced fish species have become important hubs in the trophic network, interacting with numerous parasites, predators and prey. In particular, five parasite species and four predatory bird species depend on the two introduced species as obligate trophic resources in the pelagic web and could therefore not have been present in the pre-introduction network. The presence of the two introduced fish species and the arrival of their associated parasites and predators increased biodiversity, mean trophic level, linkage density, and nestedness; altering both the network structure and functioning of the pelagic web. Parasites, in particular trophically transmitted species, had a prominent role in the network alterations that followed the introductions.     

Distribution Pattern of Serotoninergic Neurons in Trematode Cercariae

The review summarizes data on the number, size and localization of serotoninergic neurons in cercariae of 16 trematode species, referring to 11 families. Presented diagrams show distribution patterns of serotoninergic neurons in cercariae of trematodes from different taxonomic, biological and morphological groups. Data analysis indicates that the number, disposition and size of these neurons vary in cercariae of different species. The data are discussed in relation with a functional significance of serotonin as a neurotransmitter in free-living larvae—trematode cercariae.     

The free-living inland aquatic nematodes of Africa — a review

During the past three decades, much attention has been given to free-living nematodes and, in particular, to the species of the African continent. Despite the current absence of evidence for the existence of planktonic species, several conditions are suggested that could lead to intrusion of the planktonic habitat, e.g. turbulent shallow waters, high food densities and preadaptations such as swimming ability and negative geotaxis. A new and more practical ecological classification of the inland free-living nematodes is proposed to avoid further incoherency in this regard. All the free-living inland aquatic species described in Africa are presented here in a checklist, including notes on their ecology and distribution. Many of the cosmopolitan species, included in the checklist, are now increasingly being recognized as conglomerates of species, each species of which occupies a restricted area. Finally the distribution of free-living inland aquatic species in Africa is discussed and some preliminary notes are presented.     

The Distribution of Isopoda in the Delaware Bay Region

The distributions of 24 marine and estuarine isopods have been reviewed. Lironeca ovalis, Aegathoa medialis, Olencira praegustator, and Probopyrus pandalicola were the only parasitic species found. Of the 20 free-living isopods, Asellus communis and Chiridotea almyra were the only fresh to brackish water species, and Chiridotea arenicola, C. stenops, Cirolana impressa, C. polita and Edotea montosa were the true marine species. The salinity range of Cyathura burbancki was extended and the range of Chiridotea stenops was extended northward while the ranges of Chiridotea nigrescens and C. arenicola were extended southward. The contribution of isopod distributions to the concept of a shallow water Transatlantic zoogeographic province is discussed.     

Free-living nematodes of the Tra Ly River in the Red River mouth,Vietnam

In samples of the Tra Ly River in the Red River mouth (Northern Vietnam), 46 species of free-living nematodes have been found, five of which are new to science. The species dominant in abundance were Ptycholaimellus adocius Dashchenko et Belogurov, 1984; Dichrocuadora affinis Gagarin et Nguyen Vu Thanh, 2011; and Tripyloides minor sp.n. The species composition of nematodes is listed and the new species Tripyloides minor sp. n. is described and illustrated. The nematode described and illustrated by Riemann (1970) from watercourses of Colombia as Tripyloides amazonicus (Gerlach, 1957) is recognized as a valid species (Tripyloides riemanni nom.n).     

Strongyloides spearei n. sp. (Nematoda: Strongyloididae) from the common wombatVombatus ursinus (Marsupialia: Vombatidae)

Strongyloides spearei n. sp. is described from the small intestine of the common wombatVombatus ursinus from Healesville, Victoria. The new species is distinguished from all known congeners by: the triangular shape of the stoma and the length of the parasitic female; the blunt spicules in the free-living male; and the presence of eggs in the faeces of the host.S. spearei andS. thylacis Mackerras, 1959 form a separate group withinStrongyloides based on both species infecting marsupials, having directly recurrent ovaries in the parasitic female and having blunt spicules in the free-living male. The histological localisation ofS. spearei is predominantly within the crypts of the small intestine.     

First record of a free-living dalyellioid turbellarian from the pacific:Balgetia pacifica nov. spec.

Balgetia pacifica nov. spec. from coarse sand beaches along the west coast of San Juan Island (Washington) is described and its taxonomy discussed. The species is characterized by its large bursal apparatus with a strengthened copulatory bursa.B. pacifica is the first free-living species of the Turbellaria Dalyellioida recorded from the Pacific Ocean.     

Newcastle disease virus and Chlamydia psittaci in free-living raptors from eastern Germany

Organ samples from free-living raptors from the federal states of Berlin and Brandenburg in eastern Germany were tested for Newcastle disease virus (NDV; n = 331) and Chlamydia psittaci (n = 39) by polymerase chain reaction (PCR). In 18 individuals NDV nucleic acids were detected. These samples originated from barn owls (Tyto alba; n = 15, 28%), tawny owl (Strix aluco; n = 1, 5%), common buzzard (Buteo buteo, n = 1, 1%), and European kestrel (Falco tinnunculus; n = 1, 4%). In 29 (74%) of 39 samples C. psittaci was detected. Chlamydia psittaci is common in free-living birds of prey in the investigated area.     

NEMATOLOGY IN RETROSPECT AND PROSPECT

The first small nematodes to be described, free-living in the seventeenth century and plant-parasitic in the eighteenth, are identifiable only from their peculiar habitats; taxonomy came relatively late in nematology because adequate optical equipment was a prerequisite. In the study of the free-living and the plant-parasitic species, the development of two readily-presented aspects of taxonomy, figure drawing and mensuration (each showing oscillation between paucity and excess of detail), is traced in the work of five founders, all of whom were living in 1904: Bastian, Bütschli, de Man, Cobb and Goodey. Possible future developments in the identification of species and strains, the investigation of host-parasite relationships, and the training of nematologists are briefly discussed.     

A new genus and two new species of marine free-living nematodes from the coastal waters of Southern Vietnam

A new genus and two new species of free-living marine nematodes from sediments in the coastal zone of the South China Sea (Vietnam) are described. Cyartonemoides gen. n. morphologically resembles Cyartonema Cobb, 1920, but differs from it in having a well-developed cephalic capsule. Cyartonemoides foetidus gen. n., sp. n. is the type and the only species of the genus. Campylaimus abnormis sp. n. differs from all species of the genus Campylaimus Cobb, 1920 by the shape of the amphidial fovea and shorter lateral fields.     

Formicitylenchus oregonensis n. g., n. sp. (Allantonematidae: Nematoda), the first tylenchid parasite of ants,with a review of nematodes described from ants

The first tylenchid parasite of ants, Formicitylenchus oregonensis n. g., n. sp., is described from a queen carpenter ant Camponotus vicinus Mayr in Western Oregon, USA. The new genus is characterised by the excretory pore anterior to the nerve-ring and rounded tails in the free-living adults, a stylet bearing basal thickenings in the free-living female, a smaller stylet lacking basal thickenings in the male and a short, crenulate leptoderan bursa. The mature parasitic female is light yellow and ovoviviparous. F. oregonensis n. sp. is closely related to members of Metaparasitylenchus Wachek, 1955, with species parasitising beetles living under bark or in rotten wood, a habitat similar to that of carpenter ants. However, males of Metaparasitylenchus are characterised by a fairly long tail with a broad peloderan bursa. It is suggested that this case of tylenchid parasitism in ants is an example of environmental host selection. A review of the described nematode parasites of ants is presented.