Reexamination of the Species Assignment of Diacavolinia Pteropods Using DNA Barcoding

Thecosome pteropods (Mollusca, Gastropoda) are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals) and one from the Eastern tropical North Pacific (15 individuals). Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the “DNA barcoding” region of the cytochrome c oxidase subunit I (COI). Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of <3% (K2P distance) whereas the Pacific and Atlantic samples were more distant (∼19%). Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (∼24%). These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to environmental variability; furthermore, the apparent variation of the pteropods shell may have implications for our understanding of the species’ sensitivity to ocean acidification.     

Mesophotic communities of the insular shelf at Tutuila, American Samoa

An investigation into the insular shelf and submerged banks surrounding Tutuila, American Samoa, was conducted using a towed camera system. Surveys confirmed the presence of zooxanthellate scleractinian coral communities at mesophotic depths (30–110 m). Quantification of video data, separated into 10-m-depth intervals, yielded a vertical, landward-to-seaward and horizontal distribution of benthic assemblages. Hard substrata composed a majority of bottom cover in shallow water, whereas unconsolidated sediments dominated the deep insular shelf and outer reef slopes. Scleractinian coral cover was highest atop mid-shelf patch reefs and on the submerged bank tops in depths of 30–50 m. Macroalgal cover was highest near shore and on reef slopes approaching the bank tops at 50–60 m. Percent cover of scleractinian coral colony morphology revealed a number of trends. Encrusting corals belonging to the genus Montipora were most abundant at shallow depths with cover gradually decreasing as depth increased. Massive corals, such as Porites spp., displayed a similar trend. Percent cover values of plate-like corals formed a normal distribution, with the highest cover observed in the 60–70 m depth range. Shallow plate-like corals belonged mostly to the genus Acropora and appeared to be significantly prevalent on the northeastern and eastern banks. Deeper plate-like corals on the reef slopes were dominated by Leptoseris, Pachyseris, or Montipora genera. Branching coral cover was high in the 80–110 m depth range. Columnar and free-living corals were also occasionally observed from 40–70 m.     

Diet of five species of the family Myctophidae caught off the Mariana Islands

Myctophids are important components of marine food webs, but little is known about the diets of many species in large stretches of the ocean. To fill this knowledge gap, Myctophum lychnobium, Symbolophorus evermanni, Centrobranchus andreae, Myctophum aurolaternatum, and Myctophum nitidulum were collected off the previously unsampled Mariana Islands in 2007. Myctophum lychnobium predominately consumed pelagic molluscs (28 % by number), amphipods (26 %), and copepods (24 %). Symbolophorus evermanni consumed copepods (53 %) and larval fishes (22 %). Centrobranchus andreae consumed molluscs (90 %). Little dietary overlap occurred among these fishes, and the reliance on molluscs was unusual compared to results from previous studies.     

Scleractinia (Cnidaria: Anthozoa) from INDEMARES 2010–2012 expeditions to the Avilés Canyon System (Bay of Biscay,Spain, northeast Atlantic)

Twenty-eight species of scleractinian corals were collected between 55 and 2,291 m depth during INDEMARES 2010–2012 expeditions to the Avilés Canyon System and the near continental shelf (Bay of Biscay). Most interesting species are described and all depicted. All species were already known from the northeast Atlantic, although some are seldom reported. Deltocyathus eccentricus and Flabellum chunii are northernmost records in the eastern Atlantic, and species first collected from the Bay of Biscay. From a literature review and new records given herein, 31 species of Scleractinia are known from the Avilés Canyon System. Live specimens of six species were recorded outside their previously known bathymetric ranges in the Bay of Biscay and nearby areas, either at shallower depths (Caryophyllia sarsiae, Monomyces pygmaea, Stephanocyathus nobilis), or deeper depths (C. atlantica, C. sarsiae, Enallopsammia rostrata, Solenosmilia variabilis). Desmophyllum cristagalli has the widest bathymetric range (551–2,291 m), and Lophelia pertusa is the most widely distributed species (24 stations). Tabulating the number of live species occurring in each 100-m depth interval of the canyon system, highest species richness occurs in the 700–800-, 800–900-, and 1,400–1,500-m depth intervals (11 species). The habitat-forming species L. pertusa and Madrepora oculata were abundant in some stations building well-developed coral banks. Live colonies of the big-sized species S. variabilis and E. rostrata co-occurred at the deepest station sampled that yielded scleractinia (2,291 m).     

Relationships of osmerid fishes (Osmeridae) of Russia: divergence of nucleotide sequences of mitochondrial and nuclear genes

Relationships of seven species of smelts (family Osmeridae) inhabiting Russian waters were analyzed on the basis of nucleotide sequence divergence of cytb, COI and intron 1 of rpS7 genes. Nuclear sequence divergence between the species within of the genera Osmerus, Mallotus and Hypomesus was 1.6–2.6, 2.9 and 6.6–11.8 %, respectively, and mitochondrial sequence divergence was 8.9–9.7, 3.9 and 15.1–18.3 %, respectively. The mtDNA divergence was 20.4 % between the genera Hypomesus and Mallotus, 18.47 % between Hypomesus and Osmerus, and 17.62 % between Mallotus and Osmerus. Nuclear DNA divergence was 11.58, 11.19, and 11.37 %, respectively. MP, ML and Bayesian analyses coupled with inclusion in analyses of GenBank-derived sequences of osmerid species that do not inhabit this region suggest that the lineage of the genus Mallotus was the first to separate from the common hypothetic ancestor of the smelts and is sister to the Osmerus–Hypomesus clade. The position of Hypomesus olidus is not resolved and points to the need for further research.     

Effects of temperature and rainfall variation on population structure and sexual dimorphism across the geographical range of a dioecious species

The effects of climate (precipitation and temperature) on sexual dimorphism and population structure were analysed along a broad-scale environmental gradient covering the distributional range of the endemic dioecious species Corema album, along the west coast of the Iberian Peninsula. We aimed to assess distribution constraints and sex-related differences in demography and size associated with higher reproductive investment in females. Nine populations were chosen from across the geographic range of C. album and ten 10 × 10 m plots were established (10 m apart) along a 200-m transect. All male, female and non-reproductive shrubs were quantified within each plot and plant size, photosynthetic layer, height, sex ratio, population density and structure, and spatial segregation of sexes, under environmental conditions ranging from temperate to Mediterranean climate, were recorded and analysed. Increased aridity was related to lower population density and less structured populations, indicating an effect of higher temperature and lower precipitation on regeneration. Sexual dimorphism was influenced by climate, with size differences between sexes varying with aridity. However, demographic differences between sexes reflected in sex ratio deviations or the occurrence of spatial segregation were unrelated to any climatic variable, suggesting the existence of compensatory mechanisms that may counterbalance the higher reproductive effort of female plants. The results show the vulnerability of this endemic species to the increase in aridity expected in the southernmost limit of the biogeographical area due to global climate change, and demonstrate the importance of broad scale studies in the assessment of sexual dimorphism.     

Responses of small vertebrates to linear clearings in a South Australian woodland

This work assesses whether the width and “permanence” of linear clearings affects the distribution and movement patterns of small, terrestrial vertebrates in a native South Australian woodland. We examined the influence of narrow (1.5 and 4.2 m), non-permanent seismic exploration tracks; and wide (6–7 and 12–15 m), permanent fire tracks. There were 1,007 captures of 14 species (four amphibians, six reptiles, four mammals) from 18,000 trap days/nights across 15 sites. Total species richness was highest adjacent to 6–7 m wide permanent tracks (8.3) and lowest in areas without clearings (5.3). There was heterogeneity of captures between track types (p < 0.008), species (p < 0.001), and species by track type (p < 0.001). Antechinus flavipes was most abundant adjacent to both types of permanent tracks, probably as a result of increased habitat complexity at these sites. Twenty-four percent of movements by recaptured A. flavipes involved track crossings. Animals crossed all track types; nevertheless, individuals were more likely to be recaptured on the same side of a track. Individuals were less likely to cross permanent tracks (p = 0.025 for 6–7 m and p = 0.008 for 12 to 15-m-wide tracks), with females being particularly inhibited. Although 11 % of 56 recaptured Rattus spp. had crossed a track, no individuals crossed the 12 to 15-m permanent tracks. In the habitat type studied here, narrow seismic lines may have a slightly positive effect on some ground-dwelling vertebrates, and do not appear to substantially inhibit movement. However, there is a need to carefully manage permanent tracks, which could isolate faunal populations.     

Effects of water flow on growth and energetics of the scleractinian coral<Emphasis Type="Italic"> Agaricia tenuifolia</Emphasis> in Belize

The branching scleractinian coral Agaricia tenuifolia is abundant on reefs in Belize, over an exceptionally broad range of depth, flow regime, and irradiance. Photosynthesis and respiration of coral branches were measured over a range of irradiance and unidirectional flow speeds (1–10 cm s^–1) using a small-volume respirometry chamber designed for flat coral branches. Respiration rate increased significantly with flow speed; however, there was no significant effect of flow on either α or P_max, indicating that this coral could thus carry out maximum photosynthesis even at very low flow. This result contrasts with published results for other coral species that experience a significant increase in net photosynthesis with flow speed. Growth rates of A. tenuifolia were measured using branch fragments in a variety of reef habitats, over a range of water flow speeds. Growth rates were comparable over most habitat types, across a depth range of 1–15 m. Compared to 1 m, flow and irradiance at 15 m decreased to less than 20% and less than 50%, respectively. Reduced growth was observed only at 24-m depth, and in low-flow microhabitats (concavities) at 15 m. Transplants to 1 m, in the surf zone, also had reduced growth and were the only group to suffer significant colony mortality. At 8- and 15-m depth, growth rate of flat coral branches was not affected by orientation (parallel or perpendicular to flow) or shading. Compared with studies of other species, A. tenuifolia displays an ability to utilize a greater range of habitats and flow speeds, suggesting that it may have specific adaptations that allow it to tolerate very low flow conditions.     

Responses of native plant populations on an unprotected beach to disturbance by storm-induced overwash events

Extreme climatic events disturb plant communities, altering species composition, and abundance. For herbaceous populations on coastal beaches, responses to disturbance are often spatially heterogeneous and depend on species’ life history. This study documents the effects of two overwash events, caused by Hurricane Irene in August 2011 and Superstorm Sandy in October 2012, on the abundance of native species on a low-lying, unprotected beach on Staten Island, New York, USA. Temporary plots (33 cm diameter) spaced at 3-m intervals along 30-m transects perpendicular to shoreline, were used in September 2007, 2011, 2012, and 2013 to survey lower (0–9 m), middle (12–21 m), and upper (24–30 m) regions of the same beach. The same procedure was used to quantify seedling recruitment in spring (May) after each overwash. Complex changes in density the year after each overwash were specific for distinct beach regions and depended on species’ life history. Rhizomatous perennial grasses (Ammophila breviligulata and Panicum amarum) maintained or increased ramet populations, possibly stimulated by sand deposition on the middle and upper beach. The first overwash was early enough in the growing season to permit subsequent seed production during autumn, and seedling recruitment occurred for three native annuals (Cenchrus tribuloides, Heterotheca subaxillaris, and Triplasis purpurea), and the tall perennial Solidago sempervirens the next spring. The second overwash was later in autumn and probably removed seeds from the site and/or deeply buried the seeds of two annuals (Cenchrus and Heterotheca) which did not recruit seedlings the next spring. Triplasis seedlings were abundant in a blowout on the lower beach. Given more frequent storms and sea-level rise in the future, it becomes imperative to maintain an assemblage of native plant species with diverse life histories when restoring coastal beaches.     

Earthworm Communities in the Bamboo Plantations of West Tripura (India)

Present study revealed the presence of 16 earthworm species belonging to 11 genera and four families viz. Megascolecidae (Amynthus alexandri, Metaphire houlleti, Lampito mauritii, Kanchuria sp1, Perionyx excavatus), Octochaetidae (Eutyphoeus gigas, Eutyphoeus comillahnus, Eutyphoeus orientalis, Octochaetona beatrix, Dichogaster bolaui, Lennogaster chittagongensis, Lennogaster yeicus), Moniligastridae (Drawida papillifer papillifer, Drawida assamensis, Drawida nepalensis) and Glossoscolecidae (Pontoscolex corethrurus) in the soils of five bamboo species [Bambusa balcooa (Sil Barak), Melocanna baccifera (Muli), Bambusa polumorpha (Bari), Bambus cacharensis (Bom) and Bambus bambus (Katabarak)] of West-Tripura. While four earthworm species viz. Metaphire houlleti, Drawida assamensis, Drawida papillifer papillifer and Pontoscolex corethrurus were common to all species of bamboo plantations, the rest showed restricted distribution. Among the earthworm species 4 were exotic (Amynthus alexandri, Metaphire houlleti, Dichogaster bolaui and Pontoscolex corethrurus) and the others were native to the Indian sub-continent. In general, earthworms under the bamboo plantations occurred within temperature range of 21.6 °C–28.0 °C, pH 4.0–7.0, organic matter 0.56–5.99 %, moisture 9.6–31.7 %, water holding capacity 14.6–43.9 % and bulk density 0.7–1.8 g cm^?3. The average density and biomass of the earthworms in the studied places were 108 ind m^?2 and 44 g m^?2 respectively. Earthworm diversity, dominance and evenness indices showed the values 1.00, 0.47 and 0.70 respectively. Earthworm density and biomass showed a negative correlation with temperature whereas those had a strong positive correlation with pH, moisture and organic matter of the soils.     

The comparative pollen morphology of genera Matricaria L. and Tripleurospemum Sch. Bip. (Asteraceae) in Turkey

Pollen morphology of four Matricaria species and 28 Tripleurospermum species was investigated with light microscopies (LM) and scanning electron microscopies (SEM). Pollen slides were prepared using Wodehouse technique. Measurements were based on 20 or more pollen grains per specimen. For SEM studies, dried pollen grains were transferred on aluminum stubs and coated with gold for 4 min in a sputter-coater. The pollen grains of Matricaria and Tripleurospermum are radially symmetric and isopolar. The pollen grains of the Matricaria are oblate-spheroidal with the polar axes 16.6–31.2 μm and the equatorial axes 18.7–23.9 μm. Tripleurospermum is oblate-spheroidal, suboblate and prolate-spheroidal with the polar axes 15.6–32.2 μm and the equatorial axes 17.7-38.5 μm. The pollen grains of Tripleurospermum are operculate and tricolporate. Matricaria is operculate and usually tricolporate or rarely syncolporate, tricolpate and tetracolporate. The pollen grain of both taxa shows echinate ornamentation. The spines are commonly conical with a broadened base and a tapered apical portion. The spine length varies between 1.8–4 μm in Tripleurospermum and 2.3–3.3 μm in Matricaria. The width of spines varies between 2.8–4.6 μm in Tripleurospermum and 2.4–3.6 μm in Matricaria. Inter-spinal area shows granulate–perforate, reticulate–perforate, rugulate–perforate ornamentations and the tectum surrounding the spine base is micro perforate. Overall exine thickness ranges from 2.8 to 4.8 μm in Tripleurospermum, 3.6 to 5.2 μm in Matricaria. Intine is thicker under pores in Tripleurospermum (0.3–0.62 μm) than in Matricaria (0.6–0.8 μm). Inter-spinal ornamentations, pollen shape and the numbers of perforations at the spin base have been observed as important morphological characters.     

Monitoring of the bacterial and fungal biodiversity and dynamics during Massa Medicata Fermentata fermentation

The microbial community dynamics play an important role during Massa Medicata Fermentata (MMF) fermentation. In this study, bacterial and fungal communities were investigated based on the culture-dependent method and polymerase chain reaction-denaturing gradient gel electrophoresis analysis. Meanwhile the dynamic changes of digestive enzyme activities were also examined. Plating results showed that MMF fermentation comprised two stages: pre-fermentation stage (0–4 days) was dominated by bacterial community and post-fermentation stage (5–9 days) was dominated by fungal community. The amount of bacteria reached the highest copy number 1.2?×?10¹⁰ CFU/g at day 2, but the fungi counts reached 6.3?×?10⁵ CFU/g at day 9. A total of 170 isolates were closely related to genera Enterobacter, Klebsiella, Acinetobacter, Pseudomonas, Mucor, Saccharomyces, Rhodotorula, and Amylomyces. DGGE analysis showed a clear reduction of bacterial and fungal diversity during fermentation, and the dominant microbes belonged to genera Enterobacter, Pediococcus, Pseudomonas, Mucor, and Saccharomyces. Digestive enzyme assay showed filter paper activity; the activities of amylase, carboxymethyl cellulase, and lipase reached a peak at day 4; and the protease activity constantly increased until the end of the fermentation. In this study, we carried out a detailed and comprehensive analysis of microbial communities as well as four digestive enzymes' activities during MMF fermentation process. The monitoring of bacterial and fungal biodiversity and dynamics during MMF fermentation has significant potential for controlling the fermentation process.     

Morphology of pollen and orbicules in the tribe Spiraeeae (Rosaceae) and its systematic implications

This study provides pollen data for 38 representative taxa belonging to all nine genera in the current classification of the tribe Spiraeeae (Rosaceae) including the monotypic Korean endemic genus Pentactina, and considers the distribution of orbicules for the first time. Pollen morphology and wall stratification were investigated using light, scanning electron and transmission electron microscopy. Spiraeeae pollen grains are small to medium in size (P = 6.9–34.0 μm, E = 7.1–28.0 μm), oblate to prolate in shape (P/E = 0.66–1.48) and tri-colporate. Spiraeeae pollen is generally characterised by striate sexine ornamentation, but four ornamentation types are recognised based on the length and direction of the ridge patterns. The observed variation in sexine ornamentation is particularly valuable at the generic level. The exine stratification of the representative Spiraeeae studied is similar and characterised by unbranched columellae and a continuous endexine. Orbicules are present in three genera of the tribe (Luetkea, Sibiraea and Xerospiraea). Orbicule distribution patterns indicate that the absence of orbicules is a synapomorphic condition of the more derived clade, comprising Pentactina + Petrophytum + Kelseya + Spiraea.     

Distribution of Chironomidae in a Semiarid Intermittent River of Brazil

The effects of the intermittency of water flow on habitat structure and substrate composition have been reported to create a patch dynamics for the aquatic fauna, mostly for that associated with the substrate. This study aims to describe the spatial distribution of Chironomidae in an intermittent river of semiarid Brazil and to associate assemblage composition with environmental variables. Benthic invertebrates were sampled during the wet and dry seasons using a D-shaped net (40?cm wide and 250???m mesh), and the Chironomidae were identified to genus level. The most abundant genera were Tanytarsus, Polypedilum, and Saetheria with important contributions of the genera Procladius, Aedokritus, and Dicrotendipes. Richness and density were not significantly different between the study sites, and multiple regression showed that the variation in richness and density explained by the environmental variables was significant only for substrate composition. The composition of genera showed significant spatial segregation across the study sites. Canonical Correspondence Analysis showed significant correspondence between Chironomidae composition and the environmental variables, with submerged vegetation, elevation, and leaf litter being important predictors of the Chironomidae fauna. This study showed that Chironomidae presented important spatial variation along the river and that this variation was substantially explained by environmental variables associated with the habitat structure and river hierarchy. We suggest that the observed spatial segregation in the fauna results in the high diversity of this group of organisms in intermittent streams.     

Comparative morphology of leaf epidermis in the genus Lithocarpus and its implication in leaf epidermal feature evolution in Fagaceae

Leaf epidermal features are considered to be taxonomically important in Fagaceae. In this study, we examined and compared leaf epidermal features of 112 specimens, representing 105 species and one variety of Lithocarpus from China and adjacent areas and Notholithocarpus densiflorus. As a result of the different interpretations of terms in previous studies, trichome terminology in Lithocarpus and its relatives was re-assessed aiming to reveal the trichome evolutionary patterns in Fagaceae. Twelve types of trichomes and five types of trichome bases were detected in Lithocarpus, among which the broad-based trichome (BBT) is newly reported. Stomata in Lithocarpus are restricted to the cyclocytic type and their size range is 28.6 ± 8.2 μm × 26.5 ± 9.3 μm. The distribution of epidermal features in Lithocarpus revealed three distinct morphological groups: glabrous, BBT, and appressed parallel tufts (APT). The importance of epidermal features across Fagaceae for taxon delimitation is evaluated. Species of Lithocarpus can be accurately identified by the presence of APT or flat epidermal cells combined with non-dark stained subsidiary cells and non-cutinized trichome bases only, or in addition, fasciculate trichome bases. The phylogenetic distribution of epidermal features and their evolutionary trends in Fagaceae is also discussed.     

Genome size in Dipsacaceae and Morina longifolia (Morinaceae)

Dipsacaceae and Morinaceae have for a long time been regarded as separate but related families, whereas according to APG III they are included within the larger family Caprifoliaceae. Although genome size studies seldom provide conclusive characters for higher level systematics, they can yield useful information at a lower taxonomy level. In this study, we used DNA flow cytometry (supplemented by Feulgen densitometry) for measurement of genome size variation in the Dipsacaceae genera Cephalaria, Dipsacus, Knautia, Lomelosia, Pterocephalus, Scabiosa, Sixalix, Succisa, and Succisella, and Morina of the Morinaceae. At the monoploid level the Dipsacaceae genera (x = 7–10) vary 5.94-fold between 0.902 and 5.362 pg DNA (1Cx-value), whereas Morina longifolia (x = 17) has only 0.670 pg DNA. At the holoploid level 11.58-fold variation occurs between 0.902 and 10.446 pg DNA (1C-value). In Knautia sect. Trichera ploidy levels 2x, 4x, 6x are accompanied by corresponding increments of C-values, but genome downsizing is observed. In Knautia sect. Tricheroides the only investigated species K. integrifolia (2n = 20) has only 0.60-fold the mean genome size of sect. Trichera. Scabiosa canescens (2n = 2x = 16) has approximately double the C-value of all other Austrian Scabiosa species at the diploid level (pseudopolyploidy). These values raise concern against DNA-ploidy estimations at the interspecific level when chromosome numbers are unknown. The species sorted into two major clades of an existing phylogenetic tree of Dipsacaceae differ characteristically in their range of Cx-values. The Knautia–Cephalaria–Dipsacus–Succisella clade has the great majority of its Cx-values larger than those of the Scabiosa–Pterocephalus–Lomelosia clade.     

Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis

An investigation of bacterial diversity in compost was performed using molecular chronometer in order to reveal its phylogeny. Thirty-three bacterial isolates isolated from compost were analyzed by 16S rRNA gene sequencing which revealed phylogenetic lineage of class Bacilli, γ, β-Proteobacteria, and Actinobacteria. Among these lineages, isolates belonging to class Bacilli consisted of species from genera Staphylococcus, Bacillus, Terribacillus, and Lysinibacillus. From phylum Actinobacteria: Microbacterium barkeri and Kocuria sp. were identified. Other bacterial groups had phylogenetic linkage with genera Comamonas and Acidovorax (class β-Proteobacteria); Serratia, Klebsiella, and Enterobacter (class γ-Proteobacteria). Similar isolates were analyzed through ARDRA. Amplified product of 16S rRNA gene from each isolates was subjected to cleavage by enzymes HpaII, HinfI, and MspI in separate reaction tubes. HpaII generated 2–6 bands ranging from 90–688 bp, HinfI generated 2–5 bands of 71–1,038 bp, and MspI 2–7 bands of 69–793 bp. The restriction patterns from HpaII, HinfI, and MspI were normalized separately and combined by means of pattern recognition software “Diversity Database.” HpaII had highest discrimination index (0.72) than HinfI (0.68) and MspI (0.65), and the combination of all three showed discrimination index (0.69). Numerical analysis of ARDRA patterns demonstrated sufficient phylogenetic information for characterizing bacterial diversity. Phylogenetic relationship obtained among isolates through ARDRA was compared with 16S rRNA gene sequence and ARDRA results showed sufficiently similar 16S rRNA gene sequence analysis, but not an overlapping. It has been observed that ARDRA technique facilitates the identification of bacteria in less than 36 h as compared to traditional 16S rRNA gene sequencing.     

Large-Scale Purification,Characterization, and Spore Outgrowth Inhibitory Effect of Thurincin H,a Bacteriocin Produced by Bacillus thuringiensis SF361

Large-scale purification of the highly hydrophobic bacteriocin thurincin H was accomplished via a novel and simple two-step method: ammonia sulfate precipitation and C18 solid-phase extraction. The inhibition spectrum and stability of thurincin H as well as its antagonistic activity against Bacillus cereus F4552 spores were further characterized. In the purification method, secreted proteins contained in the supernatant of a 40 h incubated culture of B. thuringiensis SF361 were precipitated by 68 % ammonia sulfate and purified by reverse-phase chromatography, with a yield of 18.53 mg/l of pure thurincin H. Silver-stained SDS–PAGE, high-performance liquid chromatography, and liquid chromatography–mass spectrometry confirmed the high purity of the prepared sample. Thurincin H exhibited a broad antimicrobial activity against 22 tested bacterial strains among six different genera including Bacillus, Carnobacterium, Geobacillus, Enterococcus, Listeria, and Staphylococcus. There was no detectable activity against any of the selected yeast or fungi. The bacteriocin activity was stable for 30 min at 50 °C and decreased to undetectable levels within 10 min at temperatures above 80 °C. Thurincin H is also stable from pH 2–7 for at least 24 h at room temperature. Thurincin H is germicidal against B. cereus spores in brain heart infusion broth, but not in Tris–NaCl buffer. The efficient purification method enables the large-scale production of pure thurincin H. The broad inhibitory spectrum of this bacteriocin may be of interest as a potential natural biopreservative in the food industry, particularly in post-processed and ready-to-eat food.     

Analysis of the Gut Microbiota by High-Throughput Sequencing of the V5–V6 Regions of the 16S rRNA Gene in Donkey

Considerable evidence suggests that the gut microbiota is complex in many mammals and gut bacteria communities are essential for maintaining gut homeostasis. To date the research on the gut microbiota of donkey is surprisingly scarce. Therefore, we performed high-throughput sequencing of the 16S rRNA genes V5–V6 hypervariable regions from gut fecal material to characterize the gut microbiota of healthy donkeys and compare the difference of gut microbiota between male and female donkeys. Sixty healthy donkeys (30 males and 30 females) were enrolled in the study, a total of 915,691 validated reads were obtained, and the bacteria found belonged to 21 phyla and 183 genera. At the phylum level, the bacterial community composition was similar for the male and female donkeys and predominated by Firmicutes (64 % males and 64 % females) and Bacteroidetes (23 % males and 21 % females), followed by Verrucomicrobia, Euryarchaeota, Spirochaetes, and Proteobacteria. At the genus level, Akkermansia was the most abundant genus (23 % males and 17 % females), followed by Sporobacter, Methanobrevibacter, and Treponema, detected in higher distribution proportion in males than in females. On the contrary, Acinetobacter and Lysinibacillus were lower in males than in females. In addition, six phyla and 15 genera were significantly different between the male and female donkeys for species abundance. These findings provide previously unknown information about the gut microbiota of donkeys and also provide a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in donkey and other animals.