Detection of Laribacter hongkongensis using species-specific duplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (ISR)

Aims: For the rapid detection of Laribacter hongkongensis, which is associated with human community‐acquired gastroenteritis and traveller’s diarrhoea, we developed a duplex species‐specific PCR assay. Methods and Results: Full‐length of the 16S–23S rRNA intergenic spacer region (ISR) sequences of 52 L. hongkongensis isolates were obtained by PCR‐based sequencing. Two species‐specific primer pairs targeting 16S rRNA gene and ISR were designed for duplex PCR detection of L. hongkongensis. The L. hongkongensis species‐specific duplex PCR assay showed 100% specificity, and the minimum detectable level was 2·1 × 10^?2 ng μl^?1 genomic DNA which corresponds to 5000 CFU ml^?1. Conclusions: The high specificity and sensitivity of the assay make it suitable for rapid detection of L. hongkongensis. Significance and Impact of the Study: This species‐specific duplex PCR method provides a rapid, simple, and reliable alternative to conventional methods to identify L. hongkongensis and may have applications in both clinical and environmental microbiology.     

Co-occurrence and commensal feeding between Little Egrets Egretta garzetta and Eurasian Spoonbills Platalea leucorodia

Capsule: The spatial distribution and feeding efficiency of Little Egrets Egretta garzetta wintering in the gulf of Gabès, Tunisia, are affected by a commensal association with the Eurasian Spoonbills Platalea leucorodia.

Aims: To investigate the role of the interspecific interaction between Little Egrets and Eurasian Spoonbills in shaping the spatial distribution and feeding efficiency of Little Egrets.

Methods: Using count and behavioural data, we examined the co-occurrence of these species in flocks, and compared the foraging efficiency of Little Egrets feeding with Eurasian Spoonbills with that of solitary Little Egrets.

Results: We found that the presence of Eurasian Spoonbills doubled the chance of Little Egrets being present. Within mixed flocks, the number of Little Egrets increased with the number of Spoonbills. Moreover, Little Egrets foraging in association with Eurasian Spoonbills took fewer steps, had higher pecking rates and higher prey intake rates than solitary Little Egrets.

Conclusion: Little Egrets appear to obtain foraging efficiency benefits by following Eurasian Spoonbills. This interaction seems to play a role in determining the spatial distribution of Little Egrets.     

Unravelling Diaporthe species associated with Camellia

The genus Diaporthe (syn. Phomopsis) comprises important pathogens, endophytes or saprobes with diverse host associations and worldwide distribution. Phomopsis theae is the first and hitherto the only recorded Diaporthe species on Camellia in China. The aim of this study was to investigate the Diaporthe species associated with symptomatic and asymptomatic tissues of Camellia spp. from several provinces in China. Eighty-three strains were isolated in the present study. Based on the multi-locus (ITS, HIS, TEF1, TUB) phylogenetic analyses and phenotypic characters, four novel species (D. apiculata Y.H. Gao & L. Cai, D. compacta Y.H. Gao & L. Cai, D. oraccinii Y.H. Gao & L. Cai, D. penetriteum Y.H. Gao & L. Cai), and three known species (D. discoidispora, D. hongkongensis, D. ueckerae) were identified. Five strains were assigned to D. amygdali species complex and 17 strains to D. eres species complex respectively, but they could not be further identified to species level using current multi-locus phylogenetic analysis and morphological characters. Of the identified species, D. compacta and D. discoidispora are only known as endophytes. Diaporthe hongkongensis is the dominant species on Camellia, accounting for 53.3% of the frequency of occurrence. Diaporthe lithocarpus is synonymized with D. hongkongensis; D. miriciae is synonymized with D. ueckerae. Our study revealed a high diversity of undescribed Diaporthe species on Camellia.     

The Complete Genome and Proteome of Laribacter hongkongensis Reveal Potential Mechanisms for Adaptations to Different Temperatures and Habitats

Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish–borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors—such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases—are present. Proteomes of L. hongkongensis HLHK9 cultured at 37°C (human body temperature) and 20°C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)—NAGK-20 and NAGK-37—in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20°C, whereas NAGK-37 showed higher expression at 37°C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other bacteria. Genome and proteome analysis of L. hongkongensis revealed novel mechanisms for adaptations to survival at different temperatures and habitats.     

Evidence for the hybrid origin of Lathyrus plitmannii (Leguminosae)

ABSTRACT

The hypothesis that Lathyrus plitmannii may be of hybrid origin was tested on a morphological data set, derived from measurements of 50 herbarium specimens, by employing the computer program HYWIN. Results showed that all the specimens of L. plitmannii were putative hybrids and that the highest ranked pair of specimens that best matches the morphologies of its parents was L. gorgonei and L. pseudocicera. Examination of the distribution patterns of the three species shows that L. plitmannii is confined to regions common to both putative parents and that hybrids could be formed, assuming that genetic barriers were overcome. Additional supporting evidence includes overlaps in the edaphic requirements and the habitats of the three species. Lathyrus plitmannii is recognised as a distinct species that should be regarded as derivative of hybridisation between L. gorgonei and L. pseudocicera.     

Breeding biology of the Little Egret Egretta garzetta on the southern coast of the Bay of Biscay

ABSTRACT

Capsule: Annual reproductive parameters of Little Egrets Egretta garzetta in an Atlantic coastal colony showed strong variation in a 20-year study, mainly due to extreme events.

Aims: To describe the breeding biology of Little Egrets in the Bay of Biscay and compare it with that of the Mediterranean basin. Also, to explore relationships between breeding parameters and colony size with some climatic indicators.

Methods: Phenology, number of nests, clutch size, number of hatchlings, brood size, and hatching and breeding success were recorded over 20 years.

Results: Median laying date of 214 nests was 1 May (range: 1 April–25 June) and 54% of the clutches were laid in the second half of April and the first half of May. Over the 20-year study period mean clutch size of 270 nests was 4.0, mean number of hatchlings was 3.1, and mean brood size was 2.3. Hatching success ranged from 46.1% to 100% and breeding success from zero to 100%. Number of nests was negatively associated with clutch and brood size. The highest clutch size and lowest brood size were recorded at the beginning of the season. Significant relationships were found between the number of hatchlings and the rainfall during the pre-breeding season, and between brood size and the summer rainfall.

Conclusions: Reproductive parameters showed significant variation over the study period, which highlights the importance of using long-term data sets. Breeding occurred one month later than in natural colonies of the Mediterranean basin. Negative relationships between the number of nests and clutch and brood size suggest some degree of density-dependent effects. Ranges of clutch size, number of hatchlings, and brood size were within those reported in Mediterranean populations. The effect of rainfall on reproductive parameters was weak. Extreme weather and predation events caused low rates of hatching and breeding success that affected the growth of the colony.     

Investigation of the immunomodulatory effects of Lactobacillus casei and Bifidobacterium lactis on Helicobacter pylori infection

Background: Lactobacillus and Bifidobacterium species have shown beneficial effects in the treatment of Helicobacter pylori infection; however, the mechanisms behind such effects are not fully understood. In this study, we have investigated the immunomodulatory effects of probiotics in a mouse model of H. pylori infection. Materials and methods: H. pylori‐infected C57BL/6 mice were treated with L. casei L26, B. lactis B94, or no probiotics for 5 weeks, respectively. Mice not infected with H. pylori were included as normal controls. Gastric histology, protein levels of interleukin (IL)‐1β, IL‐10, IL‐12/23p40, and H. pylori colonization density in the gastric tissues, as well as H. pylori‐specific antibodies were examined. Results: In mice receiving L. casei L26 and B. lactis B94, gastric neutrophil infiltration and IL‐1β were significantly decreased and IL‐10 was significantly increased as compared with mice receiving no probiotics. In mice receiving B. lactis B94, IL‐12/23p40 was significantly increased and H. pylori IgG was significantly reduced as compared with mice receiving no probiotics. No significant difference of H. pylori colonization was observed among the three groups of mice. Conclusion: The reduced level of IL‐1β and neutrophil infiltration observed in mice infected with H. pylori following treatment with L. casei L26 and B. lactis B94 resulted from a modulation of immune response rather than a decrease of H. pylori colonization. Furthermore, B. lactis B94 has the intrinsic ability to promote a Th1 immune response through an increase in IL‐12/IL‐23.     

Reintroduction of rare arable plants by seed transfer. What are the optimal sowing rates?

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Two new species of genus Chablisea Gauld et Dubois, 2006 (Hymenoptera: Ichneumonidae: Pimplinae) from China

Chablisea concave sp. n. and C. Varicolor sp. n. from China are described and illustrated. A key to the world species of the genus is provided. Type specimens are deposited in the Parasitic Hymenoptera Collection of Zhejiang University, Hangzhou, China (ZJUH).     

Foraging behavior and energetics of Great Egrets and Snowy Egrets at interior rivers and weirs

ABSTRACT.   Wading birds may use different foraging methods and prey capture techniques in particular habitats or under specific conditions. We measured foraging behavior and its energetic costs for Great Egrets ( Ardea alba ) and Snowy Egrets ( Egretta thula ) at two weirs (small overflow dams that raise water levels in a stream or river) and in two naturally flowing rivers in Kansas in May and June 2000 and 2005. We observed 99 randomly selected birds (38 Great Egrets and 61 Snowy Egrets) for 1513 min, and noted strike rate, prey capture rate, capture efficiency, prey size, and social interactions. In addition, 30 of these birds were observed for 504 min to estimate ambulation velocities and foraging energetics. Both species had higher strike rates and prey capture rates in rivers, but caught larger fish at weirs. Capture efficiency was higher for Snowy Egrets at weirs, but did not differ between microhabitats for Great Egrets. Snowy Egrets had higher rates of conspecific aggression at weirs than in rivers, but little aggression was documented for Great Egrets. Established algorithms suggest that, while foraging in rivers, Snowy Egrets had similar costs for changes in velocity. Changes in ambulation velocity for Great Egrets were greater at weirs than rivers. For both species, the percentage of time spent standing was twice as high at weirs as in rivers. Both species also used low-cost foraging strategies at weirs that yielded larger fish, so net energetic gains at weirs were higher than in rivers. Weirs appear to be more important to Snowy Egrets than to Great Egrets. Estimates of energy gains and expenses provide valuable predictive power for understanding egret behavior.     

Life cycle of Spongilla lacustris (Porifera,Spongillidae): a cue for environment-dependent phenotype

We studied the life cycle and growth of Spongilla lacustris in a stream with three distinct habitats. Sponge populations in the habitats exhibited different adaptive strategies. Growth forms of S. lacustris ranged from encrusting to digitate and branched. Environmental factors controlled the appearance of each growth form. In the most hospitable habitat, a variety of colonization strategies and different growth forms were present. In the less hospitable habitat growth was restricted to small and encrusting specimens. In the optimal habitat, the largest and most luxuriant specimens developed. Gemmulation and hatching were dephased among specimens in the three habitats; hence gemmules were present for long periods of time. S. lacustris was found capable of displaying two life strategies: r in the short run, K in the long run.     

The allopolyploid origin of Spiranthes hongkongensis (Orchidaceae)

Morphological and ecological similarities between Spiranthes hongkongensis Hu et Barretto and S. sinensis (Pers.) Ames suggest a close evolutionary relationship. The hypothesis that S. hongkongensis evolved through natural hybridization between S. sinensis and S. spiralis was tested using isozyme electrophoresis. A total of 28 isozyme loci were interpreted in the diploid species S. sinensis and S. spiralis, and “fixed heterozygosity” owing to gene duplication was observed at ten of these loci in S. hongkongensis. Isozyme phenotypes provided strong evidence for an allotetraploid origin of S. hongkongensis, with S. sinensis and most likely S. spiralis as its diploid progenitors. Chromosomal counts of S. hongkongensis gave a tetraploid number of ≈60. The allotetraploid species is self-fertile, and completely isolated by sterility barriers from S. sinensis. Premating isolation also exists between S. hongkongensis and S. sinensis due to earlier flowering and autogamy in S. hongkongensis, which may account for the rarity of natural hybrids in the sites of sympatry. The role of the autogamous breeding system in the establishment and spread of S. hongkongensis is discussed.     

Genetic structure of cherry fruit fly (Rhagoletis cingulata) populations across managed,unmanaged, and natural habitats

The cherry fruit fly (CFF), Rhagoletis cingulata Loew (Diptera: Tephritidae: Trypetini), is endemic to eastern North America and Mexico, where its primary native host is black cherry [Prunus serotina Ehrh. (Rosaceae)]. Cherry fruit fly is also a major economic pest of the fruit of cultivated sweet (Prunus avium L.) and tart (Prunus cerasus L.) cherries. Adult CFF that attack wild black cherry and introduced, domesticated cherries in commercial and abandoned orchards are active at different times of the summer, potentially generating allochronic isolation that could genetically differentiate native from sweet and tart CFF populations. Here, we test for host‐related genetic differences among CFF populations in Michigan attacking cherries in managed, unmanaged, and native habitats by scoring flies for 10 microsatellite loci. Little evidence for genetic differentiation was found across the three habitats or between the northern and southern Michigan CFF populations surveyed in the study. Local gene flow between native black cherry, commercial, and abandoned orchards may therefore be sufficient to overcome seasonal differences in adult CFF activity and prevent differentiation for microsatellites not directly associated with (tightly linked to) genes affecting eclosion time. The results do not support the existence of host‐associated races in CFF and imply that flies attacking native, managed, and unmanaged cherries should be considered to represent a single population for pest management purposes.     

Breeding populations of Little Ringed Plover Charadrius dubius and Ringed Plover Charadrius hiaticula in the United Kingdom in 2007

Capsule: The 2007 national survey of the UK breeding population of Little Ringed Plovers shows a further spread into Scotland and Wales since the previous survey in 1984. In contrast, there has been a significant decrease in the Ringed Plover breeding population.

Aims: To provide new breeding population estimates in the UK and Great Britain for Little Ringed Plover Charadrius dubius and Ringed Plover Charadrius hiaticula in 2007 and investigate changes in breeding distribution and habitat use since 1984.

Methods: Breeding population estimates were made by combining counts of pairs from ‘key sites’ (2?×?2?km tetrads known to be occupied in/since 1984) and estimates of the numbers of pairs away from these sites based on stratified sampling. Survey periods for Little Ringed Plover: 15 April to 15 July, three visits; Ringed Plover: 15 April to 30 June, two visits.

Results: Population estimates, for 2007, of 1239 (95% confidence intervals: 1175–1311) pairs of Little Ringed Plover and 5291 (5106–5478) pairs of Ringed Plovers were calculated for Great Britain, with 5438 (5257–5622) pairs of Ringed Plover estimated in the UK. Counts of Ringed Plover at inland and coastal sites, covered in both 1984 and 2007, decreased by 83% and 53%, respectively. The Little Ringed Plover population has expanded in range northward and westward since 1984. Main habitats used in 2007 by Little Ringed Plover were inland gravel and sand (25.9%) and river shingle (17.8%); and, for Ringed Plover, coastal shingle and sand (38.5% and 13.7%, respectively) and machair plus associated habitats (23.8%) in the Outer Hebrides.

Conclusions: Between 1984 and 2007, the Little Ringed Plover breeding population in the UK increased considerably, expanding northward and westward, with increased use of river shingle habitats. During the same period Ringed Plover breeding numbers in the UK declined considerably in both coast and inland habitats, likely to be due to human disturbance and habitat change, respectively.     

Laribacter hongkongensis: an emerging pathogen of infectious diarrhea

Laribacter hongkongensis is relatively a new name in the list of bacterial pathogens for gastroenteritis and travelers’ diarrhea. Addition of another name increases burden on the enteric infections as a whole. L. hongkongensis belongs to Neisseriaceae family of β subclass Proteobacteria. L. hongkongensis was initially isolated in Hong Kong from blood and empyema of an alcoholic cirrhotic patient in 2001, followed by reports from Korea and China, representing a total of 38 articles in PubMed until April 2013. As of now, there is no report from Indian subcontinent where infectious diarrhea is very much prevalent and a major burden. This review provides information about the microbiological characteristics, consideration of an emerging pathogen, relative pathogenicity, genome and proteome content, resistance toward multiple antibiotics, adaptability to different stress, and other features since its time of discovery. Investigation for this bacterium may avoid misidentification as other microbial flora. Further studies like the geographical distribution, type of infection, disease burden, pathogenicity, or genomic exploration of this bacterium will be useful in characterizing them properly. This bacterium may possibly be the emerging threat to public health.     

Spatial and temporal habitat partitioning by calliphorid blowflies

Calliphorid blowflies perform an essential ecosystem service in the consumption, recycling and dispersion of carrion nutrients and are considered amongst the most important functional groups in an ecosystem. Some species are of economic importance as facultative agents of livestock myiasis. The interspecific ecological differences that facilitate coexistence within the blowfly community are not fully understood. The aim of this work was to quantify differences in habitat use by calliphorid species. Thirty traps were distributed among three habitats at two sites in southwest England for collections made during March–August 2016. A total of 17 246 specimens were caught, of which 2427 were Lucilia sericata, 51 Lucilia richardsi, 6580 Lucilia caesar, 307 Lucilia ampullacea, 4881 Calliphora vicina and 2959 Calliphora vomitoria (all: Diptera: Calliphoridae). Lucilia sericata was the dominant species in open habitats, whereas L. caesar was the most abundant species in shaded habitats. Calliphora specimens were more abundant in the cooler months. These findings suggest that Calliphora and Lucilia species show strong temporal segregation mediated by temperature, and that species of the genus Lucilia show differences in the use of habitats that are likely to be driven by differences in humidity tolerance and light intensity. These factors in combination result in effective niche partitioning.     

Do Chinese cavefish show intraspecific variability in morphological traits?

Cavefishes represent one of the most bizarre and intriguing life forms inhabiting groundwater environments. One‐third of the known cavefishes worldwide is endemic to China, and almost half of those belongs to a single genus, Sinocyclocheilus (Cypriniformes: Cyprinidae). Analyzing the morphometrics of three Sinocyclocheilus species, we aimed to assess whether variability among conspecific populations exists. We predict that populations inhabiting different subterranean habitats (shallow vs. deep) show divergences in specific morphological traits to better cope with the local ecological conditions. Our results showed that the populations showing bigger eyes and reduced humpback were those occurring close to the cave entrance (habitats with light and high food availability), while specimens with smaller eyes and increased humpback were collected from deeper groundwater areas (habitats laying in darkness with food scarcity). This explorative study paves the way for further researches aiming to collect novel data on Chinese cavefishes and highlights the usefulness of these species in evolutionary studies.     

Isolation and characterization of fourteen novel microsatellite loci in the Hong Kong oyster, Crassostrea hongkongensis

Fourteen polymorphic microsatellite markers were isolated from the Hong Kong oyster, Crassostrea hongkongensis, with a partial genomic library enriched for tandem repeat sequences of (CA)₁₂, (GA)₁₂, (ATG)₆ and (TAGA)₄. Polymorphism of these loci was assessed in a sample of 48 wild unrelated individuals. The average allelic number of these polymorphic loci was 6.36 per locus, with a range of 4–16. The observed and expected heterozygosity varied from 0.208 to 0.729 (averaging 0.502) and from 0.193 to 0.789 (averaging 0.615), respectively. After Bonferroni correction (P > 0.0036), 11 of the 14 loci accorded with Hardy–Weinberg equilibrium, and the rest three were detected significant departure from HWE. Additionally, two loci (Ch103 and Ch104) showed significant linkage disequilibrium (P < 0.01). This is the first set of microsatellite loci developed in this species and would be useful for studies of population genetics, stock management and other relevant research in C. hongkongensis.     

The diversity and paleoenvironmental significance of Calophyllum (Clusiaceae) from the Miocene of southeastern China

Abstract

Three species within the genus Calophyllum collected from middle Miocene Fotan Group sediments in Zhangpu County, Fujian, southeastern China are described in this paper. These fossils include Calophyllum zhangpuensis sp. nov., Calophyllum striatum, and Calophyllum suraikholaensis. The new fossil species C. zhangpuensis sp. nov. is oval, possesses entire leaves with closely spaced parallel secondary veins and has a round, or slightly retuse, apex. These specimens represent the first known fossil records of this relative wide leaf-type form of Calophyllum from China and have a length:width (L:W) ratio less than 3:1. In combination with the known modern geographic distribution and habitats of this wide leaf-type Calophyllum and other plants, data suggest that the middle Miocene Fotan flora is indicative of a warm climate. Thus, based on available fossil data, we speculate that this genus probably originated in India during the Paleocene before spreading from India to Bangladesh and into China, Sumatra, Malaysia, Indonesia, and Java during the Neogene, leading to its modern distribution. At least, the 3 fossil species in this region can explain floristic exchange between India, Fujian, and South China, which is consistent with previous studies; the occurrence of these 3 species indicates that Calophyllum began to diversity in China no later than the Miocene.     

Photoperiodic response of diapause induction in the pine caterpillar, Dendrolimus punctatus

The pine caterpillar, Dendrolimus punctatus (Walker) (Lepidoptera: Lasiocampidae), is a multivoltine pest of pine trees in China, overwintering as larvae. Winter diapause was induced by short day length. The critical night length was about 10 h 40 min at 25, 28, and 31 °C in the field, showing a temperature‐compensated diapause induction. Transfer experiments from a short night (L16:D8) to a long night (L12:D12) or vice versa at different times after hatching showed that sensitivity to day length was restricted to the first 14 days; the required day number for a 50% response at 25 °C was about 3.5 days for short nights but 7.5 days for long nights, indicating that short nights are photoperiodically more effective. When four successive short nights (L16:D8) were used to interrupt the long‐night regime (L12:D12) at different development stages and vice versa, the results showed that the highest sensitivity to photoperiod occurred on the 4th?8th day, corresponding to the second larval instar. Experiments of alternating short‐night (L16:D8) and long‐night (L12:D12) cycles during the larval period showed that the information of short nights as well as long nights could be accumulated. By rearing the larvae under conditions other than 24‐h light–dark cycles, we clearly showed that the dark period (scotophase) played a major role in the determination of diapause. The Nanda‐Hamner and Bünsow experiments failed to reveal rhythmic fluctuations with a period of about 24 h in the occurrence of diapause. Therefore, the photoperiodic clock in D. punctatus is an hourglass timer or a damped circadian oscillator.