Molecular identification of temperate Cricetidae and Muridae rodent species using fecal samples collected in a natural habitat

Molecular species identification from biological material collected at field sites has become an established ecological tool. However, extracting and amplifying DNA from degraded field samples, such as prey remains and feces that have been exposed to the elements, remains a challenge and costly. We collected 115 fecal samples of unknown small mammals, resembling fecal droppings of voles and mice (i.e., Cricetidae and Muridae), from a salt marsh in The Netherlands. We modified a previously published protocol into a relatively low-cost method with a PCR success of 95%. We demonstrate that species identification is possible for both Cricetidae and Muridae species using fecal samples of unknown age deposited in the field. For 90 samples, sequences of the variable control region in the mitochondrial genome were obtained and compared to published DNA sequences of small mammals occurring in north European salt marshes. A single sample, probably environmentally contaminated, appeared as Sus scrofa (n?=?1). We positively identified house mouse Mus musculus, being the positive control (n?=?1), and common vole Microtus arvalis (n?=?88). In 81 sequences of 251 nt without ambiguous bases, ten haplotypes were present. These haplotypes, representing the central lineage of the western subspecies M. arvalis arvalis, were separated by 20 mutations from published control region haplotypes of the western European lineages sampled in France. Unlike earlier studies of cytochrome b variation in coastal European populations, we did not find indications of recent purging of genetic variation in our study area.     

Description of a new species of <Emphasis Type="Italic">Ixodes</Emphasis> Latreille, 1795 (Acari: Ixodidae) and redescription of <Emphasis Type="Italic">I. priscicollaris</Emphasis> Schulze, 1932, parasites of New Guinea rodents (Rodentia: Muridae)

Ixodes goliath n. sp. (Acari: Ixodidae), is described based on females collected from the eastern hyomys, Hyomys goliath (Milne-Edwards) (Rodentia: Muridae) from Papua New Guinea. Females of I. goliath n. sp. are similar to those of I. priscicollaris Schulze, 1932 but can be distinguished by the overall size, porose areas sculpture and shape of palpal segment I ventrally. For comparative purposes, the female of I. priscicollaris is redescribed. Studied females of I. priscicollaris were found on murid rodents and Phascogale sp. (Dasyuromorphia: Dasyuridae) from Indonesia (Papua Province) and Papua New Guinea.     

Diapausing egg banks,lake size,and genetic diversity in the rotifer <Emphasis Type="Italic">Brachionus plicatilis</Emphasis> Müller (Rotifera,Monogononta)

The fish from the family Anostomidae represent one of the most important groups of freshwater ichthyofauna from South America, with species of high economical value. The migratory characteristic of some species, through the several Amazonian environments, takes them into waters with different physico-chemical characteristics. Cytogenetic studies on the Anostomidae demonstrate that these fishes have a conserved diploid number and karyotype macrostructure. So, to verify if this conservation occurs also in the genomic level, the current study aimed at a chromosomal comparative physical mapping, using 45S and 5S rDNA, of seven species of anostomids: Leporinus fasciatus, L. agassizi, L. friderici, L. trifasciatus, Rhytiodus macrolepis, Laemolyta taeniata, and Schizodon fasciatus, collected in different Amazonian environments. The results obtained corroborate the conservation of the karyotype macrostructure. However, significant differences were found in the distribution of heterochromatin and on the pair bearing the nucleolus organizer region. The staining of 45S and 5S rDNA by FISH highlighted, for four of the seven species, more than one chromosome pair bearing the site 45S. The 5S rDNA, although present in only one chromosome pair, varied in its chromosome and karyotype position. Thus, although the Anostomidae family has a conserved chromosomic macrostructure the use of molecular techniques revealed the presence of chromosomic translocation during the evolution of these fishes.     

New species of the bristletail families Ateluridae and Lepismatidae (Zygentoma) from Abkhazia and Adygea

Four new species of the bristletail families Ateluridae (Atelura abkhazica sp. n. and Nipponatelurina caucasica sp. n.) and Lepismatidae (Lepisma xylophila sp. n. and L. adygei sp. n.) are described. Atelura abkhazica sp. n. differs from the other species of the genus Atelura in a smaller size, smaller number of ovipositor divisions, in the presence of apical sensory cones on the male parameres, which are absent in the other species of the genus, and in a fewer number of lateral pegs on urotergite X. The genus Nipponatelurina comprises two species (N. kurosai Mendes et Machida, 1994 and N. caucasica sp. n.). The distinguishing features of N. caucasica sp. n. include a significant number of short minute thin cilia on the head capsule, a longer ultimate segment of the maxillary palp, and a fewer number of setae at the posterior margin of urosternites IV–VII. Lepisma xylophila sp. n. differs from L. saccharinum and L. chlorosoma in the distribution of epidermic pigment and in the urotergites chaetom. Lepisma adygei sp. n. is most closely related to the synanthropic species L. saccharinum, but differs in the size of the body, color of scales on the upper surface of the body, and in the structure of the labial palps, urotergite X, ovipositor, and parameres.     

<Emphasis Type="Italic">t</Emphasis>-Specific <Emphasis Type="Italic">D17Leh66</Emphasis> DNA Elements in the Family Muridae

Blot-hybridization analysis with the use of the t-specific probe D17Leh66 has been used to study DNA of various representatives of family Muridae. Hamsters from genus Phodopus have no homologs of this probe, whereas African rats from genus Lophuromys have some homologous elements. This indicates that sequence D17Leh66 is ancient and was probably present in the common ancestor of family Muridae.     

Bacterial diversity of the outflows of a Polichnitos (Lesvos,Greece) hot spring,laboratory studies of a <Emphasis Type="Italic">Cyanobacterium</Emphasis> sp. strain and potential medical applications

The bacterial diversity of the outflows of Polichnitos (Lesvos, Greece) hot spring has been investigated. Cyanobacteria showing high sequence homologies with Phormidium sp. and Cyanobacterium aponinum were found. Members of the Alphaproteobacteria closely related to Rhodobium sp. Albidovulum sp., Rhodobacter sp., Microvigra sp., Nitratireductor sp. and Phaeobacter sp. Gammaproteobacteria, Betaproteobacteria and Firmicutes were represented by members of Idiomarina sp., Marinobacter sp., Shinella sp., Bacillus sp. and Clostridium sp. with sequence homologies ranging from 92% to 100%. Members of the Bacteroidetes and Planctomycetes were represented by sequences of novel phylogenetic linkages exhibiting 87–90% sequence homology with type strains. When the hot spring consortium was cultivated in bioreactor repeated batch culture under photo-autotrophic growth conditions at temperature < 30 °C, Cyanobacterium sp. dominated over Phormidium sp. Cyanobacterium sp. seems to have biotechnological potential since its extracellular broth exhibited a strong insecticidal activity against larvae of Aedes aegypti (a vector of important human diseases) and significant anti-cancer activity against the PC3 human prostate cancer cell line, while its toxicity against human endothelial cells was relatively low.     

Occurrence of two types of larvae of the Asian seaperch (<Emphasis Type="Italic">Lateolabrax</Emphasis>) in the estuaries of northern Vietnam

Lateolabrax sp. larvae were collected in the Tien Yen and Kalong estuaries of northern Vietnam, the southernmost locality for this genus distribution. Vietnamese Lateolabrax sp. larvae could be distinguished from those of L. japonicus by pigmentation patterns. Their morphological, meristic and pigmentation characters were closer to those of Chinese Lateolabrax than L. japonicus, so Vietnamese Lateolabrax is likely situated as a population of the Chinese one. Morphometric and pigmentation characters of larvae from the two estuaries differed, suggesting that Lateolabrax of northern Vietnam are diversified and consist of at least two different breeding stocks.     

Descriptions of eight new species of <Emphasis Type="Italic">Ligophorus</Emphasis> Euzet &; Suriano, 1977 (Monogenea: Ancyrocephalidae) from Red Sea mullets

Eight new species of Ligophorus Euzet &; Suriano, 1977 (Monogenea: Ancyrocephalidae) are described from two species of mullets from the Red Sea. Ligophorus bykhowskyi n. sp. and L. zhangi n. sp. from Crenimugil crenilabris (Forsskål) differ from other species of the genus in the structure of the male copulatory organ, which has a simple accessory piece and a wide copulatory tube that arises from a large, single-chambered, expanded base. Ligophorus simpliciformis n. sp., L. bipartitus n. sp., L. campanulatus n. sp., L. mamaevi n. sp., L. lebedevi n. sp. and L. surianoae n. sp. from Liza carinata (Valenciennes) are differentiated on the basis of the morphometrics of the hard parts of the haptor and male copulatory organ. The eight species represent the first records of species directly attributed to Ligophorus from the Red Sea. Measurements of the haptoral hard-parts and the male copulatory organ of the new species are analysed with the aid of Principal Component Analysis. Three morphological types of male copulatory organ, five types of anchor, and two types of ventral and three types of dorsal bars were distinguished among these species. L. bykhowskyi and L. zhangi from C. crenilabris have the same type of male copulatory organ and anchors. Those species from Liza carinata have only one common morphological character, a thick copulatory tube, but have two types of accessory piece, four types of anchors and three types of bars. All species of Ligophorus found on mullets in the Red Sea have an accessory piece without a distal bifurcation and thus differ from most species of this genus from other regions of the world’s oceans.     

Studying factors involved in biogenesis of <Emphasis Type="Italic">Lysobacter</Emphasis> sp. XL1 outer membrane vesicles

The Gram-negative bacterium Lysobacter sp. XL1 produces outer membrane vesicles that are heterogeneous in size, density, and protein composition. One of the subpopulations is secretory vesicles for lytic protease L5 of Lysobacter sp. XL1 (Kudryakova et al. (2015) FEMS Microbiol. Lett., 362, fnv137). Protein L5 was assumed to influence biogenesis of these secretory vesicles that contain it. Using a Pseudomonas fluorescens Q2-87/B expression system, it was shown that the recombinant L5 protein may act as a factor of vesicle biogenesis. This points to a possible involvement of L5 protein in Lysobacter sp. XL1 vesicle biogenesis. Furthermore, it was established that the main phospholipid of Lysobacter sp. XL1 vesicles is cardiolipin, and vesicles are formed predominantly of outer membrane regions enriched with this phospholipid. This indicates that cardiolipin participates in biogenesis of all vesicle subpopulations in Lysobacter sp. XL1.     

Two species of <Emphasis Type="Italic">Neometadena</Emphasis> Hafeezullah &amp; Siddiqi, 1970 (Digenea: Cryptogonimidae) from Moreton Bay,Australia, including the description of <Emphasis Type="Italic">Neometadena paucispina</Emphasis> n. sp. from Australian Lutjanidae

A survey of the trematode fauna of lutjanid fishes off the east coast of Queensland (QLD), Australia revealed the presence of two species of Neometadena Hafeezullah & Siddiqi, 1970 (Digenea: Cryptogonimidae). Neometadena paucispina n. sp. is described from the intestine and pyloric caeca of Lutjanus fulviflamma (Forsskål) and L. russellii (Bleeker) from Moreton Bay, in southeast QLD. Specimens of the type- and only other species, N. ovata (Yamaguti, 1952) Miller & Cribb, 2008, were recovered from L. carponotatus (Richardson), L. fulviflamma, L. fulvus (Forster), L. russellii, and L. vitta (Quoy & Gaimard) off Lizard Island, on the northern Great Barrier Reef (GBR). Neometadena paucispina is distinguished from N. ovata in having fewer oral spines (55–65 vs 67–80). Alignment of novel molecular data for these two taxa revealed that they differ consistently by 13 nucleotides (1.5%) over the partial large subunit (LSU), 34 nucleotides (6.6%) over the internal transcribed spacer 1 (ITS1), 0 nucleotides over the 5.8S, and 21 nucleotides (7.3%) over the ITS2 rDNA regions. Despite relatively large samples of L. carponotatus, L. fulviflamma and L. russellii from three distinct locations along the east coast of QLD (i.e. Moreton Bay in the south, Heron Island in central QLD and Lizard Island in northern QLD), these two species have been found at only one site each with neither species at Heron Island. These distributions are discussed in the context of the wide distribution of other cryptogonomid species in the same hosts elsewhere in the Indo-West Pacific.     

New and little known species of the dance-fly subgenus <Emphasis Type="Italic">Xanthempis</Emphasis> Bezzi,genus <Emphasis Type="Italic">Empis</Emphasis> L. (Diptera,Empididae), from the Caucasus

Five new species of the subgenus Xanthempis Bezzi are described from the Caucasus: Empis (Xanthempis) annae sp. n. (Russia: Krasnodar Territory), E. (X.) grichanovi sp. n. (Russia: Krasnodar Territory; Georgia), E. (X.) pseudoconcolor sp. n. (Russia: Krasnodar and Stavropol territories; Georgia: Abkhazia), E. (X.) teberdaensis sp. n. (Russia: Karachay-Cherkessia), and E. (X.) zamotajlovi sp. n. (Russia: Krasnodar Territory and Adygea). The females of E. (X.) alanica Shamshev and E. (X.) kovalevi Shamshev are described for the first time. New data on the distribution of some previously described species are reported. The geographical distribution of Xanthempis is discussed. A key to Xanthempis species from the Caucasus is compiled.     

Predation on crown-of-thorns starfish larvae by damselfishes

Examining the functional response of predators can provide insight into the role of predation in structuring prey populations and ecological communities. This study explored feeding behaviour and functional responses of planktivorous damselfishes when offered captive reared larvae of crown-of-thorns starfish, Acanthaster sp., with the aim of determining whether these predators could ever play a role in moderating outbreaks of Acanthaster sp. We examined predatory behaviour of 11 species of planktivorous damselfish, testing: (1) the relationship between predator size and predation rate, both within and among fish species; (2) consumption rates on larvae of Acanthaster sp. versus larvae of a common, co-occurring coral reef asteroid Linckia laevigata; (3) maximal feeding rates upon both Acanthaster sp. and L. laevigata; and (4) functional responses of planktivorous fishes to increasing densities of Acanthaster sp. Consumption rates of crown-of-thorns larvae by damselfishes were independent of predator size; however, there was a significant negative relationship between predator size and consumption rate of L. laevigata, when pooling across all predatory species. Some damselfishes, including Acanthochromis polyacanthus and Amblyglyphidodon curacao, consumed larval Acanthaster sp. at a greater rate than for L. laevigata. Most predatory species (all except A. curacao and Pomacentrus amboinensis) exhibited a Type II functional response whereby the increasing feeding rate decelerated with increasing prey density. In addition to revealing that a wide range of planktivorous fishes can prey upon larvae of Acanthaster sp., these data suggest that planktivorous damselfishes may have the capacity to buffer against population fluctuations of Acanthaster sp. Importantly, predators with Type II functional responses often contribute to stability of prey populations, though planktivorous fishes may be swamped by an abnormally high influx of larvae, potentially contributing to the characteristic population fluctuations of Acanthaster sp.     

Genome sequences and comparative genomics of two <Emphasis Type="Italic">Lactobacillus ruminis</Emphasis> strains from the bovine and human intestinal tracts

Background

The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade.

Results

The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group.

Conclusions

The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli.

     

Identification of the di-<Emphasis Type="Italic">n</Emphasis>-butyl phthalate-biodegrading strains and the biodegradation pathway in strain LMB-1

DNA isolated from a greenhouse soil (Nanjing, Jiangsu Province, China) was suitable for PCR amplification of gene segment coding for the 16S rRNA. Diverse PCR products were characterized by cloning and sequencing, and analysis of bacterial colonies showed the presence over 26 phyla. The most bacteria belonged to Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetes. Furthermore, after the enrichment procedure of DBP-degrading microorganisms, 4 strains were isolated from the soil sample with di-n-butyl phthalate (DBP) biodegradability, and they were identified to be Rhizobium sp., Streptomyces sp., Pseudomonas sp. and Acinetobacter sp. Analysis of the degradation products by LC-MS led to identification of metabolites of DBP in strain LMB-1 (identified as Rhizobium sp.) which suggests that DBP was degraded through β-oxidation, demethylation, de-esterification and cleavage of aromatic ring.     

Nitrogen fixing bacterial diversity in a tropical estuarine sediments

Microorganisms play a significant role in biogeochemical cycles, especially in the benthic and pelagic ecosystems. Role of environmental parameters in regulating the diversity, distribution and physiology of these microorganisms in tropical marine environment is not well understood. In this study, we have identified dinitrogen (N₂) fixing bacterial communities in the sediments by constructing clone libraries of nitrogenase (nifH) gene from four different stations in the Cochin estuary, along the southeastern Arabian Sea. N₂ fixing bacterial clones revealed that over 20 putative diazotrophs belong to alpha-, beta-, gamma-, delta- and epsilon- proteobacteria and firmicutes. Predominant genera among these were Bradyrhizobium sp. (α-proteobacteria), Dechloromonas sp. (β-proteobacteria); Azotobactor sp., Teredinibacter sp., Methylobacter sp., Rheinheimera sp. and Marinobacterium sp. (γ-proteobacteria); Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio sp. (δ -proteobacteria); Arcobacter sp. and Sulfurospirillum sp. (ε-proteobacteria). Nostoc sp. was solely identified among the cyanobacterial phylotype. Nitrogen fixing Sulfate reducing bacteria (SRBs) such as Desulfobulbus sp., Desulfovibrio sp., Desulfuromonas sp., Desulfosporosinus sp., Desulfobacter sp., were also observed in the study. Most of the bacterial nifH sequences revealed that the identities of N₂ fixing bacteria were less than 95% similar to that available in the GenBank database, which suggested that the sequences were of novel N₂ fixing microorganisms. Shannon-Weiner diversity index of nifH gene ranged from 2.95 to 3.61, indicating an inflated diversity of N₂ fixing bacteria. Canonical correspondence analysis (CCA) implied positive correlation among nifH diversity, N₂ fixation rate and other environmental variables.     

A review of sciarids of the genus <Emphasis Type="Italic">Leptosciarella</Emphasis> Tuomikoski 1960 (Diptera,Sciaridae) in the Altai fauna,with description of three new species

The taxonomy of the genus Leptosciarella Tuomikoski, 1960 in the Altai Area within Altai Territory and the Altai Republic was studied. Eleven species were recognized, including three new species which are described and illustrated here: Leptosciarella (L.) ulagana Komarova sp. n., L. (L.) angustistylus Komarova sp. n., L. (L.) senex Komarova sp. n. Additionally, L. (L.) fuscipalpa (Mohrig et Mamaev 1979) and L. (L.) truncata (Tuomikoski 1960) are recorded from Altai for the first time. A key to the Altai species is provided.