16S DNA Sequencing Research Articles

The Diversity of Vibrios Associated with Vibriosis in Pacific White Shrimp (Litopenaeus vannamei) from Extensive Shrimp Pond in Kendal District, Indonesia

Vibriosis out breaks frequently occur in extensive shrimps farming. The study were commenced to find out the clinical signs of white shrimp that was infected by the Vibrio and to identify the bacterial associated with vibriosis in the pacific white shrimp, Litopenaeus vannamei. Bacterial isolates were gained from hepatopancreas and telson of moribund shrimps that were collected from extensive shrimp ponds of Kendal District, Indonesia and cultured on Thiosulfate Citrate Bile Salts Sucrose Agar (TCBSA). Isolates were clustered and identified using repetitive sequence-based polymerase chain reaction (rep-PCR). Three representative isolates (SJV 03, SJV 05 and SJV 19) were amplified with PCR using primers for 16S rRNA, and sequence for further identification. The clinical signs of shrimps affected by vibrio were pale hepatopancreas, weak of telson, dark and reddish coloration of smouth, patches of red colour in part of the body on the carapace, periopods, pleuopods, and telson. A total of 19 isolates were obtained and belong to three groups of genus Vibrios. Result of the 16S DNA sequence analysis, the vibrio found in this study related to vibriosis in white shrimps from extensive shrimp ponds of Kendal were closely related to Vibrio harveyi (SJV 03); V. parahaemolyticus (SJV 05) and V. alginolyticus (SJV 19).

Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding.

The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study, we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterize arthropod 16S and COI DNA sequences within bat faecal pellets collected across 16 Southern European localities, to first characterize the bat species' dietary niche, second measure the incidence of agricultural pests across their ranges and third assess whether geographical dietary variation responds to climatic, landscape diversity, agriculture type and vegetation productivity factors. We detected 12 arthropod orders, among which lepidopterans were predominant. We identified >200 species, 44 of which are known to cause agricultural damage. Pest species were detected at all but one sampling site and in 94% of the analysed samples. Furthermore, the dietary diversity of M. schreibersii exhibited a negative linear relation with the area of intensive agricultural fields, thus suggesting crops restrict the dietary niche of bats to prey taxa associated with agricultural production within their foraging range. Overall, our results imply that M. schreibersii might be a valuable asset for biological pest suppression in a variety of agricultural productions and highlight the dynamic interplay between wildlife and agricultural systems.

Protein profiling of Acanthamoeba species using MALDI-TOF MS for specific identification of Acanthamoeba genotype.

Acanthamoeba spp. are ubiquitous in the environment and have the potential to cause severe infections. The different genotypes of Acanthamoeba have been shown to influence the severity of the disease and response to therapy. Characterizing Acanthamoeba spp. upto genotype can aid in infection control practices. Twenty-five Acanthamoeba isolates, characterized by 18S rDNA sequencing, were subjected to MALDI-TOF MS analysis by creating a database for the individual genotypes. The differentiating features of the various spectra were observed; the coded samples were then tested against the created database. The results of identification were compared with sequencing. Five different genotypes were obtained-T3, T4, T5, T10, and T11. Spectral analysis revealed genus-specific and genotype-specific peaks. The peak patterns for individual genotype were discrete and reproducible. Clinical isolates produced different peaks from the environmental isolate of the same genotype. A concordance of 92% was obtained with MALDI-TOF MS in comparison with 18sDNA sequencing. MALDI-TOF MS, once optimized, has the potential to reliably identify the genotype of Acanthamoeba spp. and to differentiate clinical isolate from mere contaminant.

Genetic structure and demographic history of the endemic Mediterranean scallop Pecten jacobaeus inferred from mitochondrial 16s DNA sequence analysis

espanolCon vistas a implementar un plan de gestion para las especies cuyas poblaciones estan menguando, es fundamental comprender la estructura genetica de dichas poblaciones. En el caso de Pecten jacobaeus, los estudios geneticos previos se han limitado a analizar poblaciones situadas en el Mediterraneo occidental (Espana) y en el mar Adriatico (Italia). Para comprobar la presencia de discontinuidades filogeograficas entre las dos cuencas del Mediterraneo, hemos estudiado la variabilidad del gen mitocondrial del ARNr 16S en dos poblaciones de la cuenca oriental (Tunez y Grecia) y la hemos analizado junto con la de las mencionadas anteriormente. Las dos poblaciones estudiadas recientemente compartieron los haplotipos mas frecuentes con las otras y no se encontraron indicios de que exista una discontinuidad filogeografica. Se observo un grado menor de variabilidad genetica en relacion con el Mediterraneo occidental en las poblaciones del Adriatico y el Egeo, pero no en Tunez. Las diferencias significativas observadas cuando se agruparon los datos sobre las frecuencias haplotipicas indicaron la existencia de una cierta diferenciacion genetica entre las poblaciones de Chioggia (Italia) y Vouliagmeni (Grecia) y las de las otras poblaciones. EnglishUnderstanding the genetic population structure of species going through population decline is primordial in implementing a management plan. In the case of Pecten jacobaeus, previous genetic studies have been limited to populations in the western Mediterranean (Spain) and the Adriatic Sea (Italy). To check the presence of phylogeographic breaks between the two Mediterranean basins, we scored the variability of the mitochondrial 16S rRNA gene in two populations from the eastern basin (Tunisia and Greece) and pooled them with those cited above. The two newly analyzed populations shared the most frequent haplotypes with the other populations and showed no evidence of phylogeographic breaks. We found lower levels of genetic variability in the Adriatic and the Aegean populations, but not in Tunisia, with respect to the Western Mediterranean. Significant differences in pooled haplotype frequencies indicated some genetic differentiation between the pooled Chioggia and Vouliagmeni populations and the other pooled populations.

IAA-producing Klebsiella variicola AY13 reprograms soybean growth during flooding stress

Soybean is known to be intolerant of waterlogged conditions. Flooding stress usually affects the crop via poor and retorted root development. The current study aimed to isolate indole acetic acid (IAA)-producing bacteria with potential to induce adventitious root growth and counteract flooding stress. The isolate AY-13 was identified as Klebsiella variicola using 16S DNA sequencing and phylogenetic analysis. A pure culture of AY-13 Klebsiella variicola was subjected to chromatography and mass spectrometry selected-ion monitoring (GC-MS/SIM) for IAA quantification. The results revealed the presence of (84.27±3.55 μg/mL) IAA in the AY-13 culture. The strain AY-13 was able to induce adventitious root initiation. Therefore, soybean seedlings were inoculated with AY-13 to examine its potential for promoting growth and reprograming after flooding stress. AY-13 application not only mitigated the flooding stress, but also significantly improved the plants’ growth, enhanced chlorophyll contents, and improved the quantum efficiency of chlorophyll fluorescence during and after flooding stress. Our findings were that AY-13 possesses great potential for mitigating flooding stress and improving soybean plant growth.

English

Several Bacillus strains were isolated from “Ouled Yelass” hot spring soil, located in Setif city (Eastern Algeria). Three isolates of them coded (4RH), (14 RH), and (Set-oxy), were screened for their ability to inhibit the growth of some phytopathogenic fungi, such as Fusarium oxysporium, Botrytis cinerea, Aspergillus niger, Cladosporium cucumerinium and Alternaria alternata. The molecular identification of the strain (4RH) based on the 16S-DNA and gyrase-A genes sequences analysis, showed that it is closely related (99.9%) to the Bacillus amyloliquefaciens species. This bacterium was characterized by a high sporulation yield reaching 22±0.86 × 108 spores/ml and had important inhibition rates up to 80 and 70%, against F. oxysporium and B. cinerea, respectively. The bacterium (4RH) was able to produce cell wall degrading enzymes of cellulase and protease, in contrast to chitinase activity which was negative. Furthermore, it produced the three lipopeptides families, which are, iturins A (C14; C15), fengycin A (C14, C15, C16, C17, and C18), and surfactin (C12, C13, C14, C15, C16). Interestingly, LC-MS profiles of 80% acetonitrile fengycin extract of the (4RH) strain, showed the presence of some new molecular ions (MH+) with masses different, but near to conventional fengycin variants, which correspond to new variants described for the first time in this work. The isolate (4RH) produced 5 µg/ml of the phytohormone (IAA), on TGE medium and sidérophores with more than 10 mm of yellow-orange zones, on CAS medium. To conclude, B. amyloliquefaciens (4RH) strain possessed interesting biocontrol and biofertilization characteristics, in vitro, in addition to its high sporulation yield, which make it a potential agent for future biopesticide that could be efficient in the integrate pest management and organic agricultural production systems.   Key words: Bacillus, biocontrol, biofertilization, plant protection, hot spring, lipopeptides.

Genetic structuring in the Pyramid Elimia, Elimia potosiensis (Gastropoda, Pleuroceridae), with implications for pleurocerid conservation

The Interior Highlands, in southern North America, possesses a distinct fauna with numerous endemic species. Many freshwater taxa from this area exhibit genetic structuring consistent with biogeography, but this notion has not been explored in freshwater snails. Using mitochondrial 16S DNA sequences and ISSRs, we aimed to examine genetic structuring in the Pyramid Elimia, Elimia potosiensis, at various geographic scales. On a broad scale, maximum likelihood and network analyses of 16S data revealed a high diversity of mitotypes lacking biogeographic patterns across the range of E. potosiensis. On smaller geographic scales, ISSRs revealed significant population structure, even over the distance of a few hundred meters. Unlike other freshwater mollusks like mussels, E. potosiensis showed no evolutionary patterns relating to biogeography. The species does show population-level genetic structure, which may have implications in conservation efforts.

Cryptic diversity and speciation in endemic Cytherissa (Ostracoda, Crustacea) from Lake Baikal

Lake Baikal (Siberia) is the most ancient and deepest of all ancient lakes on Earth. It holds a (mostly endemic) diversity of thousands of animal species, including a speciose radiation of ostracods of the genus Cytherissa. Applying molecular tools to this crustacean group reveals that several morphological species are actually species clusters. Based on combined 16S and 28S DNA sequence data from thirteen classic Cytherissa species and one subspecies sensu Mazepova (1990), we recognize 26 different genetic Cytherissa species, 18 with morphological variation and eight truly cryptic species. These results suggest that the actual specific diversity of Cytherissa in Lake Baikal might easily be double of what is presently known. Baikalian endemic species most likely live in the cradle in which they originated and this opens perspectives to infer modes of speciation. Our current distribution data of Cytherissa species provide first indications for both geographic (lakes basins and shores) and ecological (sediment type, water depth) separation. Our present data thus provide the first steps towards future, rigorous testing of focussed hypotheses on the causality of speciation through either allopatric isolation or parapatric ecological clines.

Characterization Physiology and Molecular Bacteria Symbiont- Entomopathogenic Nematodes based of Gene Sequences Encoding the 16S rRNA District of Bromo Probolinggo


 
 
 This study aims to identify entomopathogenic nematodes symbiotic bacteria phenotypically and based on the gene encoding 16S rRNA sequences. Bacterial symbionts of entomopathogenic nematodes, obtained from isolates from the area Wonokerto (WN01) and isolates Sukapura (SP01), Bromo, Probolinggo, two symbiont bacteria was found in entomopathogenic nematodes Steinernema sp. The method used in this study are: the isolation of entomopathogenic nematodes Steinernema sp. and bacterial symbionts conventionally for the identification of phenotypically, after the characterization of bacterial isolates, the isolation of genomic DNA, 16S rRNA PCR, DNA purification and DNA sequence analysis. The results based on phenotypic characterization showed that isolates WN01 and SP01, yellowish white, gram positive, negative bioluminenscene, catalase positive, can not hydrolyze urea, and also can not produce H2S. The results of the gene encoding 16S rRNA sequence can be deduced WN01 isolates have in common with the bacteria Bacillus strain toyonensis BCT 7112, while the SP01 isolates have in common with the bacteria Bacillus strain cereus ATCC 14 579.
 
 

The prevalence of Anaplasma platys and a potential novel Anaplasma species exceed that of Ehrlichia canis in asymptomatic dogs and Rhipicephalus sanguineus in Taiwan.

Canine anaplasmosis is regarded as an infection by Anaplasma platys rather than zoonotic Anaplasma phagocytophilum in subtropical areas based on the assumption that the common dog tick species is Rhipicephalus sanguineus, which transmits E. canis and presumably A. platys. We investigated asymptomatic dogs and dog ticks from 16 communities in Nantou County, Taiwan to identify common dog tick species and to determine the prevalence of Anaplasma and Ehrlichia spp. Of total 175 canine blood samples and 315 ticks, including 306 R. sanguineus and 9 Haemaphysalis hystricis, 15 dogs and 3 R. sanguineus ticks were positive for E. canis, while 47 dogs and 71 R. sanguineus ticks were positive for A. platys, via nested PCR for 16S rDNA and DNA sequencing of selected positive amplicons. However, among the dogs and ticks that were positive to A. platys 16S rDNA, only 20 dogs and 11 ticks were positive to nested PCR for A. platys groEL gene. These results revealed the importance of searching for novel Anaplasma spp. closely related to A. platys in dogs and ticks. Seropositivity to a commercial immunochromatographic test SNAP 4Dx Anaplasma sp. was not significantly associated with PCR positivity for A. platys but with infestation by ticks carrying A. platys (P<0.05). Accordingly, R. sanguineus may be involved in transmission of A. platys but may not act as a reservoir of E. canis and PCR results for 16S rDNA could be a problematic diagnostic index for A. platys infection.

Molecular identification of Sarcocystis species in imported frozen beef in Egypt

In the present study, we set out to implement and compare the different detection methods that include the peptide digestion, histopathological examination and PCR, to identify Sarcocystis species that can be found in the imported frozen beef. Comparing results from the three identification methods, along with their compatibility and accuracy in diagnosing Sarcocystis spp. are also presented. Finally, a special focus is given to the use of PCR followed by sequencing and the bioinformatics analysis in detecting and comparing Sarcocystis found in the imported frozen beef. A total number of 384 samples of imported frozen beef (280 Indian buffalo and 104 Brazilian cattle meat) were collected from different retail meat shops in Alexandria province, Egypt. Visual meat inspection revealed a low prevalence of macroscopic Sarcocystis spp. in buffalo beef (3.9%) and no macrocysts were detected in cattle beef. Fifty samples were taken from buffalo beef and subjected to peptic digestion, histopathology and PCR resulting in 24%, 38% and 34% positive samples respectively. While the same number of samples were taken from cattle beef resulting in lower infection rates (6%, 2% and 2% respectively). There were no significance difference found between the infection rate according to diagnostic method or type of meat cut. For molecular characterization newly designed primer sets were used to specifically amplify the 18S DNA sequences of the four Sarcocystis spp. in both buffalo and cattle (S.fusiformis, S.buffalonis, S.hirsuta and S.hominis) using the primer BLAST tool on the NCBI of the Genbank. Aligning the 18S rDNA sequences of three positive PCR products revealed high identity percents with three Sarcocystis spp.; S. fusiformis, S. buffalonis and S. hominis. (85%, 92% and 100% respectively).

Extracellular Components in Culture Media of Mycobacterium Avium Subspecies and Staphylococci with Implications for Clinical Microbiology and Blood Culture

Rapid culture of Mycobacterium avium subspecies paratuberculosis (MAP) from patients remain a challenge. During the process of developing a rapid culture method for MAP, we found extracellular bacterial DNA, RNA and proteins for MAP, MAH (Mycobacterium avium subspecies hominissuis) and other bacteria such as Staphylococcus aureus, and Staphylococcus pseudintermedius in the supernatants of our liquid culture media. When cultured on the solid media plate, there are a limited number of colonies developed for MAP and MAH disproportionate to the expected numbers of mycobacterial growth. The presence of extracellular components within the liquid culture media raises the possibility of an unknown biological process or a cell death process during the culture that has not been previously described. Based on the presence of extracellular bacterial DNA, RNA and proteins in the liquid media of various bacterial/mycobacterial cultures, and the fact that automated clinical blood culture system consistently gives rise to a low yield, we tested 62 blood culture specimens that have been reported negative by a routine automated blood culture method after 5 days of incubation. We used high sucrose culture media and molecular diagnostic techniques to test these negative culture bottles, and we found a large percentage of bacterial growth by high sucrose culture media (32%) and by molecular PCR amplification using 16S rDNA primers and DNA sequencing (69%). The bacteria identified by PCR/sequencing methods from these culture-negative bottles are diverse and may play roles in pathogenesis of these clinically ill patients. The sensitivity of detection by an alternative culture media and the molecular PCR/sequencing method are significantly higher than by routine automated blood culture. We suspect the low yield of automated blood culture in hospital setting may result from cell death of bacteria under the culture conditions. Our study demonstrates a potential alternative bacterial growth/death pattern in liquid media and provides an area of needs for more sensitive and faster diagnostic tools to guide clinical practice and improve the outcome of sepsis management.

Ultrastructural and biomolecular detection of Rickettsiales-like organisms in tissues of rainbow trout with Red Mark Syndrome.

Red mark syndrome (RMS) and US strawberry disease (US SD) are skin disorders affecting rainbow trout farmed in Europe and USA. The disease etiology has not yet been established. In spite of specific investigations, identifying Rickettsia-like organism (RLO)- and Midichloria-like organism (MLO)-related DNA in affected individuals, these pathogens have never been observed. We performed histological, ultrastructural and biomolecular analysis on skin and spleen samples of trout with RMS. Examination by TEM revealed the presence of intracytoplasmic microorganisms resembling Rickettsiales within macrophages, fibroblasts and erythrocytes. The microorganisms were oval or short rod shaped (400-800nm in length and 100-200nm in width) and often showed a cell wall similar to Gram-negative bacteria. PCR analysis for Rickettsiales supported these findings: 53% of affected trout were positive by both PCR and TEM The primers RiFCfw-RiFCrev were used to anneal both the RLO 16S DNA sequence and the MLO 16S DNA sequence. For this reason, and in agreement with previous studies confirming the presence of Rickettsiales-related DNA in trout with RMS, we assume that TEM detected microorganisms morphologically consistent with bacteria belonging to Rickettsiales order and couldbe considered as possible causative agents of RMS.

Pigments from UV-resistant Antarctic bacteria as photosensitizers in Dye Sensitized Solar Cells

Here we report the use of pigments produced by UV-resistant Antarctic bacteria as photosensitizers in Dye Sensitized Solar Cells (DSSCs). Pigments were obtained from red and yellow colored psychrotolerant bacteria isolated from soils of King George Island, Antarctica. Based on metabolic characteristics and 16s DNA sequence, pigmented bacteria were identified as Hymenobacter sp. (red) and Chryseobacterium sp. (yellow). Pigments produced by these microorganisms were extracted and classified as carotenoids based on their spectroscopic and structural characteristics, determined by UV–Vis spectrophotometry and infrared spectroscopy (FTIR), respectively.With the purpose of develop green solar cells based on bacterial pigments, the photostability and capacity of these molecules as light harvesters in DSSCs were determined. Absorbance decay assays determined that bacterial carotenoids present high photostability. In addition, solar cells based on these photosensitizers exhibit an open circuit voltage (VOC) of 435.0 [mV] and a short circuit current density (ISC) of 0.2 [mA·cm−2] for the red pigment, and a VOC of 548.8 [mV] and a ISC of 0.13 [mA·cm−2] for the yellow pigment.This work constitutes the first approximation of the use of pigments produced by non-photosynthetic bacteria as photosensitizers in DSSCs. Determined photochemical characteristics of bacterial pigments, summed to their easy obtention and low costs, validates its application as photosensitizers in next-generation biological solar cells.

Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe

AbstractWide‐scale application of biochar to soil has been suggested as a mechanism to offset increases inCO2emissions through the long‐term sequestration of a carbon rich and inert substance to the soil, but the implications of this for soil diversity and function remain to be determined. Biochar is capable of inducing changes in soil bacterial communities, but the exact impacts of its application are poorly understood. Using three European sites [UK SRC, short rotation coppice, French grassland (FR) and ItalianSRF, short rotation forestry (IT)] treated with identical biochar applications, we undertook 16S andITSampliconDNAsequencing. In addition, we carried out assessments of community change over time and N and P mobilization in theUK. Significant changes in bacterial and community structure occurred due to treatment, although the nature of the changes varied by site.STAMPdifferential abundance analysis showed enrichment ofGemmatimonadeteandAcidobacteriainUKbiochar plots 1 year after application, whilst control plots exhibited enrichedGemmataceae, IsosphaeraceaeandKoribacteraceae. Increased mobility of ammonium and phosphates was also detected after 1 year, coupled with a shift from acid to alkaline phosphomonoesterase activity, which may suggest an ecological and functional shift towards a more copiotrophic ecology. Italy also exhibited enrichments, in both theProteobacteria(driven by an increase in the orderRhizobiales) and theGemmatimonadetes. No significant change in the abundance of individual taxa was noted inFR, although a small significant change in unweightedUNIFRACoccurred, indicating variation in the identities of taxa present due to treatment. Fungalβdiversity was affected by treatment inITandFR, but was unaffected inUKsamples. The effects of time and site were greater than that of biochar application inUKsamples. Overall, this report gives a tantalizing view of the soil microbiome at several sites across Europe and suggests that although application of biochar has significant effects on microbial communities, these may be small compared with the highly variable soil microbiome that is found in different soils and changes with time.

EFFICACY OF THREE OF THE MOST EFFECTIVE FACULTATIVE OLIGOTROPHIC PUTATIVEN2-FIXING BACTERIAL STRAINS IN CONTROLLING DAMPING-OFF DISEASE OF TWO CAUSABLE PATHOGENIC FUNGI IN TOMATO.

Complete identification was made for three strains of the facultativeputative N2-fixing bacteria using the 16s DNA sequencing studies andby detailed conventional API kit and other possible geneticdetermination. The efficacy of Bacillus subtilis subsp. spizizenii strainNRRL B-23049T (S4), Naxobacter varians strain CCUG 35299 (S5)and Bacillus megatherium strain IAM 13418. (S6), their potency againsttwo pathogenic fungi causing damping-off and their effect on N-contentof tomato plant. Inoculated tomato plants with any of the three bacterialstrains, each alone or together, in presence of 1/3 N-recommended dose,significantly increased N- content and yield production. The fungiinfested plants (Py. altimum and R. solani) showed pronounceddecreases in yield and N-content. Incorporation of the three putative N2-fixers antagonizer strains partially alleviated the adverse effect of any ofthe infested fungi. The presence of the three antagonizer strains togetherincreased the defense mechanism principles of plants like PO, PPO andphenol content. In case of the presence of the three antagonizers and 1/3N-dose, survived plants reached 100% while other treatments showedfluctuated estimates between 20 and 96.7% due to the treatment and theplant used.

Larval Morphology and Biology of the New Zealand-Chilean GeneraCylomissusBroun andAnticuraSpangler (Coleoptera: Hydrophilidae: Rygmodinae)

Abstract Larval morphology of the monotypic rygmodine genera Anticura Spangler, 1979 from Chile and Cylomissus Broun, 1903 from New Zealand is described, based on field-collected larvae associated with adults and authenticated by CO1 and 18S DNA sequences. General morphology and chaetotaxy of the head capsule is described and illustrated for all three instars of Anticura flinti Spangler, 1979 and the first and third instar of Cylomissus glabratus Broun, 1903. Both genera are similar in larval morphology, sharing several unique larval characters (e.g., bidentate nasale in the first instar, presence of numerous additional setae on parietale in the first instar), which support their close phylogenetic relationship and provides morphological support for the transfer of Anticura to the Rygmodinae. The presence of numerous additional setae on the parietale of all instars and characteristic chaetotaxy of the maxillary stipes are hypothesized as potential larval synapomorphies of the subfamily Rygmodinae. Field o...

SEQUENCE ANALYSIS OF 18s DNA OF Melosira sp., Dunaliella sp., Isochrysis sp. AND Porphyridium sp.

&lt;p&gt;Phytoplankton has high level of biodiversity. In previous years phytoplankton was identified by their morphological characters. However, their morphology might change in different environments. These difficulties can be overcome by comparing their 18S rDNA sequences. This research is aimed to verify the identity of Melosira sp., Dunaliella sp., Isochrysis sp. and Porphyridium sp. Here, PCR method was used to amplify 18s DNA sequences. Three primer pairs were used, i.e. 18S-F and 18S-R; 501F and 1700R; 18S-2F and 18S-2R. PCR products were sequenced. MEGA5 was used to make phylogenetic tree. Genus verification for Isochrysis sp., Dunaliella sp. and Melosira sp. were conducted successfully using Blast and phylogenetic tree. 18s DNA sequence of Porphyridium sp. shows an interesting result and needs further verification.&lt;/p&gt;&lt;p&gt;&lt;br /&gt;&lt;strong&gt;Keywords&lt;/strong&gt;: Phytoplankton, Melosira sp., Dunaliella sp., Isochrysis sp., Porphyridium sp.&lt;/p&gt;

Bacterial endophytes of sweet potato tuberous roots affected by the plant genotype and growth stage

This study aimed to characterize the endophytic bacterial communities in the tuberous roots of three sweet potato genotypes, IPB-149, IPB-137 and IPB-052. The hypothesis is that plant genotype and growth stage influence bacterial composition. Using cultivation-independent (Polymerase chain reaction-denaturing gradient gel electrophoresis–PCR-DGGE–based on 16S rRNA gene fragments and DNA sequencing) and cultivation-dependent (bacterial isolation) methods it was shown that plant growth stage influenced the endophytic bacterial communities, and that plant genotypes also significantly influenced these communities, but only at the first sampling (three months after planting). A total of 93 strains were isolated from the roots of the different genotypes, and 59 groups were revealed by BOX-PCR. Bacteria from the Proteobacteria, Actinobacteria and Firmicutes phyla were found, and Bacillus strains predominated in the roots of IPB-052 and IPB-149 (72% and 79%, respectively). Almost half of the strains isolated from IPB-137 roots (47%) were Gammaproteobacteria. In addition, the isolates were tested for antimicrobial substance and indole acetic acid production, organic and inorganic phosphate solubilization, siderophore production and for the presence of nitrogenase gene. All isolates with antagonistic activity against the sweet potato-pathogenic fungus Plenodomus destruens belong to the genus Bacillus. Indole acetic acid production was predominantly found among the strains isolated from IPB-137; once again suggesting an influence of the sweet potato genotype on its endophytes.

Melioidosis in Hainan, China: a restrospective study

Melioidosis is a tropical disease caused by infection with Burkholderia pseudomallei. Here, we report an 11 year (2002-2013) retrospective study of melioidosis cases in China. A total of 170 culture-confirmed melioidosis cases were included in our analysis, with culture-positive confirmation, biochemical identification and 16S DNA sequencing. A retrospective study design was employed and a correlational analysis of potential risk factors for mortality was carried out with logistic regression. We observed a year-over-year increasing trend in the incidence of melioidosis in Hainan, particularly after 2007 (annual peak of 64 cases in 2012). Farmers and fishers were the main group susceptible to melioidosis (75/170; 44.1%). Forty-six (27.1%) of the cases were fatal. Pneumonia (58/170; 34.1%) and septicaemia (44/170; 25.9%) were common presentations. Meanwhile, pre-existing diabetes (74/170; 43.5%) and being employed in a job that involves outdoor labour (148/170; 87.1%) emerged as common factors among affected patients. We did not observe a significant effect of seasonal variation on melioidosis mortality, but the greatest number of cases did occur in the rainiest season. This was the first clinical retrospective study of melioidosis in Hainan, China. The present data will be a useful resource to melioidosis researchers worldwide.