16S rDNA Sequence Analysis Research Articles

Characteristics of a novel thermophilic heterotrophic bacterium, Anoxybacillus contaminans HA, for nitrification-aerobic denitrification.

A strain bacterium that is thermophilic, heterotrophic nitrifying, and aerobic denitrifying was isolated and identified as Anoxybacillus contaminans HA for the first time. The identification was based on morphological and physiological characterizations, together with phylogenetic analysis of 16S rDNA sequence. The strain possessed excellent tolerance to high temperatures, with 55°C as its optimum and 60°C as viable. Moreover, NH4 (+)-N and NO3 (-)-N could be efficiently removed under thermophilic and solely aerobic conditions, with little intermediate accumulation. Average removal efficiencies of NH4 (+)-N and NO3 (-)-N at 55°C reached 71.0 and 74.7%, respectively, with removal rates of 5.83 and 32.08mgl(-1)h(-1), respectively. Single-factor experiments suggested that the optimal conditions for both heterotrophic nitrification and aerobic denitrification were glucose as carbon source, NH4 (+)-N range of 50-200mgl(-1), and wide NO3 (-)-N range of 200-1000mgl(-1). These results indicated that strain HA had heterotrophic nitrification and aerobic denitrification abilities, as well as the notable ability to remove ammonium under thermophilic condition. Thus, this strain has potential application in waste-gas treatment.

Dollfustrema durum n. sp. and Heterobucephalopsis perardua n. sp. (Digenea: Bucephalidae) from the giant moray eel, Gymnothorax javanicus (Bleeker) (Anguilliformes: Muraenidae), and proposal of the Heterobucephalopsinae n. subfam

Two new species of bucephalid trematode (Platyhelminthes: Digenea) are described from the giant moray eel, Gymnothorax javanicus (Anguilliformes: Muraenidae), from off Lizard Island, Australia. We used a combined morphological and molecular-based approach targeting the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) and the D1–D3 region of the large subunit (28S) of rDNA to circumscribe the species. Dollfustrema durum n. sp. is distinguished from seven congeners in having 5–6 rows of enlarged body spines circling the anterior portion of the rhynchus. From the remaining 10 species, D. durum n. sp. differs in body length, and in having a caecum that terminates posteriorly to the confluent arc formed by the vitelline follicles, gonads predominantly anterior to the pharynx, testes in tandem, an anterior testis positioned posteriorly to the vitelline follicles, and the pre-vitelline field 23–40% of the body length. Heterobucephalopsis perardua n. sp. differs from Heterobucephalopsis gymnothoracis, the type- and only other reported species, in being two to three times smaller. Heterobucephalopsis, currently considered a genus inquirendum, is confirmed as valid and is rediagnosed. Bayesian inference analysis of 28S rDNA sequences representing 28 species from nine genera and four subfamilies of bucephalid, indicates that i) subfamily classifications previously based on morphological characters are broadly robust, ii) the sequence representing H. perardua n. sp. is resolved as distinct, and basal, to sequences representing the Bucephalinae, the Prosorhynchinae, the Paurorhynchinae, and the Dolichoenterinae, iii) the Dolichoenterinae and the Prosorhynchinae are monophyletic sister clades, basal to the Bucephalinae and the Paurorhynchinae, iv) sequences representing Grammatorcynicola, Prosorhynchus, and Dollfustrema are also monophyletic, v) the Bucephalinae is paraphyletic relative to the Paurorhynchinae, and vi) the bucephaline genera Prosorhynchoides, Rhipidocotyle, and Bucephalus are each polyphyletic. The morphological and molecular differences observed among the four previously recognised subfamilies in this study lead us to propose Heterobucephalopsinae n. subfam. to accommodate the genus Heterobucephalopsis.

Streptomyces somaliensis mediated green synthesis of silver nanoparticles

Objective(s): The development of reliable and ecofriendly process for the synthesis of nano-metals is an important aspect in the field of nanotechnology. Nano-metals are a special group of materials with broad area of applications. Materials and Methods: In this study, extracellular synthesis of silver nanoparticles (SNPs) performed by use of the gram positive soil Streptomycetes. Streptomycetes isolated from rice fields of Guilan Province, Iran (5 isolates). Initial characterization of SNPs was performed by visual change color. To determine the bacterium taxonomical identity, its colonies characterized morphologically by use of scanning electron microscope. The PCR molecular analysis of active isolate represented its identity partially. In this regard, 16S rDNA of isolate G was amplified using universal bacterial primers FD1 and RP2. The PCR products were purified and sequenced. Sequence analysis of 16S rDNA was then conducted using NCBI GenBank database using BLAST. Also SNPs were characterized by, transmission electron microscopy (TEM) and X-ray diffraction spectroscopy (XRD). Results: From all 5 collected Streptomyces somaliensis isolates, isolate G showed highest extracellular synthesis of SNPs via in vitro. SNPs were formed immediately by the addition of (AgNO3) solution (1 mM). UV-visible spectrophotometry for measuring surface plasmon resonance showed a single absorption peak at 450 nm, which confirmed the presence of SNPs. TEM revealed the extracellular formation of spherical silver nanoparticles in the size range of 5-35 nm. Conclusions: The biological approach for the synthesis of metal nanoparticles offers an environmentally benign alternative to the traditional chemical and physical synthesis methods. So, a simple, environmentally friendly and cost-effective method has been developed to synthesize AgNPs using Streptomycetes.

First report of Tragopogon dubius witches' broom disease associated with a subgroup 16SrI‐B phytoplasma in Iran

Tragopogon dubius (yellow salsify, Asteraceae) is a perennial herb in Iran. In a survey conducted for phytoplasma diseases in 2014, T. dubius witches' broom disease was observed in vineyards and green areas of Bajgah and Zarghan localities (Fars province, Iran). The characteristic symptoms of T. dubius witches' broom were flower virescence and phyllody, crown proliferation and witches' broom (Fig. 1). Since the symptoms were suggestive of phytoplasma infection, plants were assayed for presence of phytoplasma by PCR amplification. Total DNA was extracted from 0.3 g of midrib tissue of four witches' broom affected and two symptomless T. dubius plants (two plants per location), using the procedure of Zhang et al. (6). Total DNA samples were tested by both direct and nested PCR assays using phytoplasma universal 16S rDNA primer pairs P1/P7 (Deng & Hiruki, 1; Schneider et al., 4) and R16F2n/R16R2 (Gundersen & Lee, 2) that amplify fragments of 1800 bp and 1250 bp, respectively. Expected fragments were amplified following direct and nested PCR from all symptom-bearing but not from symptomless plants. P1/P7-primed PCR products amplified from four witches' broom-affected T. dubius plants were separately cloned and sequenced. The full-length 16S rDNA sequences displayed 100% sequence identity with each other. A consensus sequence corresponding to the Bajgah T. dubius witches' broom was deposited in GenBank (Accession No. KR262955). A Blast search showed that this sequence had 100% identity with Oenothera phytoplasma (‘Candidatus Phytoplasma asteris‘) (M30790), representative of subgroup 16SrI-B. Virtual RFLP analysis using iPhyClassifier online tool (http://www.ba.ars.usda.gov/data/mppl/iphyclassifier), carried out with 17 restriction enzymes, indicated the presence of a 16SrI-B phytoplasma in witches' broom-affected T. dubius plants (Fig. 2). Phylogenetic analysis of full length 16S rDNA sequences using MEGA version 5 (Tamura et al., 5) grouped T. dubius witches' broom phytoplasma with onion yellows phytoplasma (GenBank Accession No. D12569), a member of 16SrI-B subgroup (Fig. 3). To our knowledge this is the first report of natural occurrence and partial molecular characterisation of a phytoplasma associated with T. dubius witches' broom disease. A 16SrI-B subgroup phytoplasma has previously been reported as causal agent of rapeseed phyllody disease in Zarghan (Salehi et al., 3). The significance of diseased T. dubius as natural reservoir of rapeseed phyllody phytoplasma remains to be determined. Aster yellows phytoplasmas were reported in grapevine in several countries. However, possible transmission of T. dubius witches' broom phytoplasma to grapevine is yet to be tested.

Taxonomy and phylogeny of Pyramimonas vacuolata sp. nov. (Pyramimonadales, Chlorophyta)

:Pyramimonas vacuolata Suda, Horiguchi & Sym sp. nov. is described from Okinawa-jima Island, Japan. The species has been characterized using light and electron microscopy and its phylogenetic position inferred based on 18S rDNA and rbcL gene sequences relative to other species. Strains of P. vacuolata were isolated from coastal sand samples collected from two localities in Okinawa-jima. The cells are quadriflagellate but remarkably large for the genus, and the posterior half of the cell is vacuolated. The single parietal chloroplast is olive-green and contains two conspicuous pyrenoids lying on the same transverse plane, slightly anterior to the equatorial region of the cell. The pyrenoids are surrounded by numerous starch grains, and thylakoids randomly traverse the pyrenoid matrix. Two monolayered eyespots are present, situated on the same transverse plane as the pyrenoids. The alga possesses three types of body scales and four types of flagellar scales, inclusive of two types of hair scales. This species is readily distinguished from known species of Pyramimonas by its large cell size, the conspicuous posterior vacuole and the presence of two pyrenoids. The most obvious character of this species is its large posterior vacuole, and this prompted the adoption of the specific epithet ‘vacuolata’. Analysis of 18S rDNA and rbcL gene sequences of P. vacuolata relative to those of other species of Pyramimonas shows that it falls, with strong support, in a monophyletic clade representing the subgenus Pyramimonas.

A diverse group of halophilic bacteria exist in Lunsu, a natural salt water body of Himachal Pradesh, India.

Five halophilic bacterial isolates namely SS1, SS2, SS3, SS5 and SS8 were isolated from soil sediments of Lunsu, a salty water body. All the bacterial isolates showed growth in LB medium containing up to 8.7% NaCl, pH 7–8 and at temperature range of 30–37°C. The bacterial isolates SS1 and SS3 require at least 3.8% NaCl for their growth, indicating their strict halophilic nature. Interestingly, bacterial isolates SS2, SS5 and SS8 but not SS1 and SS3 exhibited growth in medium supplemented with KCl. Accordingly, Na+ and K+ ions were detected at 1.39 and 0.0035%, respectively in Lunsu water. All the bacterial isolates were analyzed by random amplification of polymorphic DNA (RAPD) using four different random primers and produced PCR fragments ranging from 0.1 to 5 kb in size. Phylogenetic tree based on RAPD finger prints showed that SS1 and SS3 formed one group, while SS2 and SS5 formed the second group, whereas SS8 was out group. Sequence analysis of 16S rDNA identified SS1 and SS3 as Halobacillus trueperi, SS2 as Shewanella algae, SS5 as Halomonas venusta, and SS8 as Marinomonas sp. were deposited in GenBank with accession numbers of KM260166, KF751761, KF751760, KF751762 and KF751763, respectively. This is the first report on the presence of diverse halophilic bacteria in the foot hills of Himalayas.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1028-1) contains supplementary material, which is available to authorized users.

Enhanced production of prodigiosin by Serratia marcescens MO-1 using ram horn peptone.

This work addresses the production of prodigiosin from ram horn peptone (RHP) using MO-1, a local isolate in submerged culture. First, a novel gram-negative and rod-shaped bacterial strain, MO-1, was isolated from the body of the grasshopper (Poecilemon tauricola Ramme 1951), which was collected from pesticide-contaminated fields. Sequence analysis of 16S rDNA classified the microbe as Serratia marcescens. The substrate utilization potential (BIOLOG) and fatty acid methyl ester profile (FAME) of S. marcescens were also determined. The effect of RHP on the production of prodigiosin by S. marcescens MO-1 was investigated, and the results showed that RHP supplementation promoted the growth of MO-1 and increased the production of prodigiosin. A concentration of 0.4% (w/v) RHP resulted in the greatest yield of prodigiosin (277.74 mg/L) after 48 h when mannitol was used as the sole source of carbon. The pigment yield was also influenced by the types of carbon sources and peptones. As a result, RHP was demonstrated to be a suitable substrate for prodigiosin production. These results revealed that prodigiosin could be produced efficiently by S. marcescens using RHP.

A new bacterial disease observed onQuercus myrsinifolia

This is the first report of a new bacterial disease occurring on Quercus myrsinifolia in the nurseries of the Kyushu district in Japan. The main symptoms are shoot and twig blight, which begins with black necrotic lesions. In addition, unclear blackish discolorations, bacterial ooze and water-soaked lesions were observed as early symptoms, and spindle-shaped cankers and stem cankers with irregular surface were observed as secondary symptoms. The blight symptoms observed on the current-year shoots were first observed during the rainy season and continued until autumn (June–October). In summer, the symptoms were pronounced. A yellowish bacterium was consistently isolated from the affected shoots of Q. myrsinifolia, and on inoculation into healthy trees, it caused the same symptoms, which were more severe after wound inoculation than after non-wound inoculation. Wound inoculation also caused the disease symptoms on Quercus spp., Fagus crenata and Lithocarpus glaber, but not on several other species of Fagaceae. The causal bacterium was identified as Xanthomonas arboricola based on its morphological, cultural and biochemical characteristics and genetic sequence analysis of 16S rDNA, 16S-23S spacer regions and gyrB. To our knowledge, there are no previous records of xanthomonads causing shoot blight on fagaceous plants like Q. myrsinifolia. Therefore, we postulate that the shoot blight of Q. myrsinifolia is a new bacterial disease. We propose the name of the disease to be ‘bacterial shoot blight’ based on its main symptoms.

Redox-specialized bacterioplankton metacommunity in a temperate estuary.

This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilities to utilize different electron receptors and donors (including trace metal and single carbon compounds). On the other hand, temporal shifts in the bacterioplankton community composition at the surface layer were mainly connected to the seasonal succession of phytoplankton and the inflow of freshwater species. We also conclude that many relatively abundant populations are indigenous and well-established in the area.

Monophyletic group of unclassified γ-Proteobacteria dominates in mixed culture biofilm of high-performing oxygen reducing biocathode

Several mixed microbial communities have been reported to show robust bioelectrocatalysis of oxygen reduction over time at applicable operation conditions. However, clarification of electron transfer mechanism(s) and identification of essential micro-organisms have not been realised. Therefore, the objective of this study was to shape oxygen reducing biocathodes with different microbial communities by means of surface modification using the electrochemical reduction of two different diazonium salts in order to discuss the relation of microbial composition and performance. The resulting oxygen reducing mixed culture biocathodes had complex bacterial biofilms variable in size and shape as observed by confocal and electron microscopy. Sequence analysis of ribosomal 16S rDNA revealed a putative correlation between the abundance of certain microbiota and biocathode performance. The best performing biocathode developed on the unmodified graphite electrode and reached a high current density for oxygen reducing biocathodes at neutral pH (0.9A/m2). This correlated with the highest domination (60.7%) of a monophyletic group of unclassified γ-Proteobacteria. These results corroborate earlier reports by other groups, however, higher current densities and higher presence of these unclassified bacteria were observed in this work. Therefore, members of this group are likely key-players for highly performing oxygen reducing biocathodes.

First Hemolivia from southern Africa: reassigning chelonian Haemogregarina parvula Dias, 1953 (Adeleorina: Haemogregarinidae) to Hemolivia (Adeleorina: Karyolysidae)

To date, only a single species of Hemolivia, Hemolivia mauritanica (Sergent & Sergent, 1904), has been described from African terrestrial tortoises. Although various haemogregarines have been described from southern African terrapins and tortoises, including species from the genus Haemogregarina and one from the genus Hepatozoon, no species of Hemolivia have been identified previously from southern Africa. Since its morphological redescription, the taxonomic placement of one of these species, Haemogregarina parvula Dias, 1953, was in doubt. Hence, research was undertaken to resolve the true taxonomic position of this haemogregarine. Blood smears from nine wild tortoises of two species, Stigmochelys pardalis and Kinixys zombensis, from South Africa were screened, with the focus on H. parvula. Parasite DNA was extracted from ethanol-preserved blood samples, and fragments of the 18S rDNA gene were amplified by PCR using the primer sets HepF300/HepR900 and 4558/2733. Maximum likelihood and maximum parsimony analyses of 18S rDNA sequences showed that Haemogregarina parvula formed a monophyletic clade with species of Hemolivia within the Hepatozoon clade, not with species of Haemogregarina. It is thus recommended that this haemogregarine be reassigned to the genus Hemolivia, rendering Hemolivia parvula (Dias, 1953) the first species of the genus recorded from southern African tortoises.

Biosynthesis of gold nanoparticles using streptomyces fulvissimus isolate

Objective(s): In recent years, the biosynthesis of gold nanoparticles has been the focus of interest because of their emerging application in a number of areas such as biomedicine. In the present study we report the extracellular biosynthesis of gold nanoparticles (AuNPs) by using a positive bacterium named Streptomyces fulvissimus isolate U from rice fields of Guilan Province, Iran. Materials and Methods: From over 20 Streptomyces isolates collected, isolate U showed high AuNPs biosynthesis activity. To determine its taxonomical identity, its morphology was characterized by scanning electron microscope and partial molecular analysis performed by PCR. In this regard, 16S rDNA of isolate U was amplified using universal bacterial primers FD1 and RP2. The PCR products were purified and sequenced. Sequence analysis of 16S rDNA was then conducted using NCBI BLAST method. In biosynthesis of AuNPs by this bacterium, the biomass of bacterium exposed to the HAuCl4 solution. Results: The nanoparticles obtained were characterized by UV-Visible spectroscopy, transmission electron microscopy (TEM) and Energy dispersive X-ray (EDX) spectroscopy and X-ray diffraction spectroscopy (XRD) analyses. Our results indicated that Streptomyces fulvissimus isolate U bio-synthesizes extracellular AuNPs in the range of 20-50 nm. Conclusions: This technique of green synthesis of AuNPs by a microbial source may become a promising method because of its environmental safety. Its optimization may make it a potential procedure for industrial production of gold nanoparticles.

Ecology and genetic variation of Amblyomma tonelliae in Argentina.

The ecology of Amblyomma tonelliae (Ixodida: Ixodidae), including its seasonal distribution and the development periods of each stage, was investigated during a study carried out over two consecutive years in northwestern Argentina. In addition, the genetic variation of this tick was studied through analyses of 16S rDNA sequences. Amblyomma tonelliae has a 1-year lifecycle characterized by a long pre-moult period in larvae with no development of morphogenetic diapause. Larvae peak in abundance during late autumn and early winter; nymphs peak in abundance in spring, and adults do so from late spring to early summer. Amblyomma tonelliae shows a marked ecological preference for the driest areas of the Chaco ecoregion. In analyses of 16S rDNA sequences in genes from different populations of A. tonelliae, values for nucleotide diversity and the average number of nucleotide differences showed genetic diversity within this species to be low. No significant differences were found in comparisons among populations.

Isolation and Identification of a Heterotrophic Nitrifying Bacteria and Study on Removal of Nitrite Nitrogen

A bacteria strain for efficiently removing nitrite nitrogen was isolated and purified from sediment in shrimp pond, and the morphology of bacteria was observed using scanning electron microscopy, and the homology analysisof 16SrDNA sequence of the strain was conducted. The results showed that the strain was identified as Acinetobacter baumanii according to the morphological characteristics, physiological and biochemical characteristics and 16SrDNA sequence analysis. The isolated strain had a high heterotrophic nitrification function, the removal rate of nitrite nitrogen reached 97.17% after 12 h.

Two new species of Ornithodoros (Ixodida; Argasidae) from the Southern Cone of South America.

Two new species of the genus Ornithodoros were described from larvae collected in Argentina and Chile. Ornithodoros xerophylus n. sp. was described from specimens collected on the small rodent Graomys centralis in Argentina. The diagnostic characters for this species are a combination of dorsal plate slightly oval with a length of approximately 250 µm, 16 pairs of dorsal setae, hypostome with apex rounded and dental formula 2/2 in most rows, 3/3 apically, and capsule of the Haller's organ oval in shape without reticulations. Larvae of Ornithodoros lahillei n. sp. were collected on the reptiles Philodryas chamissonis and Callopistes maculatus in Chile. The diagnostic characters for O. lahillei are a combination of dorsal plate subtriangular with margins corrugated and posterior margin convex, dorsal surface with 14 pairs of setae, absence of postcoxal setae, and hypostome with apex pointed and dental formula 3/3 in anterior third and 2/2 in the middle and basal portion. Phylogenetic analysis of 16S rDNA sequences and a Principal Component Analysis based on morphometric characters provided additional support to the description of O. lahillei and O. xerophylus as two independent lineages within the genus Ornithodoros.

Archaeal community structure in the tropical coastal waters of Peninsular Malaysia

In this study, we used a direct cloning method to explore the archaeal diversity at four locations along the Straits of Malacca. Four 16S rDNA clone libraries were constructed with archaeal specific primers (Arc21F and Arc958R) and, in total, 1,074 randomly selected clones were screened by PCR-restriction fragment length polymorphism analysis using three different restriction enzymes (RsaI, CfoI and DdeI). Good’s coverage suggested that >85 % of archaeal sequence types were obtained in our libraries. The majority of the sequences from Port Dickson and Sungai Muar were affiliated to Euryarchaeota, whereas Port Klang and Kuala Selangor clone libraries were dominated by Thaumarchaeota sequences. Phylogenetic analysis of 16S rDNA sequences showed high archaeal diversity, with a Shannon index ranging from 2.16 to 3.24. Using weighted, non-normalized principal coordinate analysis, the archaeal communities of the four sites were clearly separated from each other. We also showed via canonical correspondence analysis that the distribution of archaeal operational taxonomic units could be related to environmental variables (salinity and chlorophyll a).

In vitro screening of lactic acid bacteria for multi-strain probiotics

The aim of this research was to screen and evaluate some probiotic properties of lactic acid bacteria strains isolated from 150 animal fecal samples, such as cows, pigs, chickens, and ducks. To achieve an objective, 81 isolates were tested for antimicrobial activity, tolerance to bile salts and acid, potential adhesion to cell surface, and in vitro adhesion. The results of the antimicrobial activity against pathogenic bacteria showed that, out of 81 isolates, 61, 59, 43, 78, and 79 isolates had antimicrobial activity against Escherichia coli, Staphylococcus aureus, Salmonella sp., Shigella sp., and Kiebsiella sp., respectively. Most lactic acid bacteria (LAB) isolates were tolerant to 1.0% bile salts and were able to survive at pH 3.5 for 3h. Twelve isolates were then evaluated on their hydrophobic character. Five isolates with probiotic properties were subsequently selected. Sequence analysis of 16S rDNA demonstrated that 2 isolates belong to Lactobacillus reuteri (strains P8 and P30), 2 to Lactobacillus plantarum (strains P6 and P31), and another one to Lactobacillus paraplantarum (strain P25). To assess their viability in broiler chicken diets, 3 strains, L. plantarum (strain P6), L. paraplantarum (strain P25), and L. reuteri (strain P30), containing 108cfu/g were inoculated into a commercial chicken diet in the form of single strain and multi-strain preparations. We found that in all of the treatments, the numbers of viable cells of LAB (cfu/g of diet) were decreased below 107cfu/g after 3d of incubation. Therefore, based on our study, the single- and multi-strains may have a potential use as novel probiotics in broiler chicken diets.

Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet.

Biological processes in the supraglacial ecosystem, including cryoconite, contribute to nutrient cycling within the cryosphere and may affect surface melting, yet little is known of the diversity of the active microbes in these environments. We examined the bacterial abundance and community composition of cryoconite over a melt season at two contrasting sites at the margin and in the interior of the Greenland ice sheet, using sequence analysis and quantitative polymerase chain reaction of coextracted 16S rDNA and rRNA. Significant differences were found between bulk (rDNA) and potentially active (rRNA) communities, and between communities sampled from the two sites. Higher concentrations of rRNA than rDNA were detected at the interior site, whereas at the margin several orders of magnitude less rRNA was found compared with rDNA, which may be explained by a lower proportion of active bacteria at the margin site. The rRNA communities at both sites were dominated by a few taxa of Cyanobacteria and Alpha- and/or Betaproteobacteria. The bulk alpha diversity was higher in the margin site community, suggesting that local sources may be contributing towards the gene pool in addition to long distance transport.

First Report of Corn Whorl Rot Caused by Serratia marcescens in China

AbstractWhorl rot is a novel disease of corn found in the Huang‐Huai‐Hai Plain, China. Common symptoms of the disease in fields include yellowing and water‐soaked brown necrosis of young leaves in the whorl of corn plants, which often results in rot of the whorl. Bacterial streaming was always observed from diseased samples. Bacterial isolates were obtained from symptomatic tissue and further confirmed to be the casual agent of the disease using Koch's Postulates. Sequence analysis of 16S rDNA, housekeeping gene groES‐groEL and BIOLOG tests revealed that the isolate B3R3 belongs to the bacterium Serratia marcescens. None of the corn cultivars evaluated showed acceptable resistance to the disease. To our knowledge, this is the first report on corn whorl rot caused by Serratia marcescens.

Myroides odoratimimus, a biocontrol agent from the rhizosphere of tobacco with potential to control Alternaria alternata

Bacteria from the tobacco rhizosphere were isolated and evaluated for their potential of producing volatile compounds against tobacco brown spot pathogen Alternaria alternata. Among the 82 strains of bacteria isolated from tobacco rhizosphere, 22 produced volatiles against the fungal pathogen A. alternata and showed an inhibition rate of over 50 % on A. alternata. The inhibition rate of strain T45 was the most pronounced, reaching 78.89 %. Sequence analysis of 16S rDNA of T45 identified it as Myroides odoratimimus. Scanning electron microscopy revealed that the volatile compounds it produced strongly suppressed mycelial growth, conidial germination, and sporulation, leading to mycelial fragmentation, surface crumpling, and damage to hyphae morphology. A sealed plate experiment showed volatile compounds generated from M. odoratimimus T45 exhibited inhibitory effect on the growth of eight plant pathogenic fungi (10.52–88.20 %), the inhibition was most pronounced on Valsa mali while the least pronounced inhibitory effect was on Colletotrichum orbiculare. Headspace solid-phase microextraction gas chromatography mass spectrometry analysis revealed a total of 24 compounds in the volatiles produced by M. odoratimimus. The main components of volatiles primarily included alcohols, aldehydes, acids, ketones, esters, and hydrocarbons. At a concentration of 100 µl per dish, isoamyl alcohol, isobutyric acid and isovaleric acid were able to completely inhibit the mycelial growth of A. alternata. This is the first report on using volatiles produced by M. odoratimimus T45 as biocontrol agents against A. alternata. The studies indicated M. odoratimimus T45 and volatile compounds isoamyl alcohol, isobutyric acid and isovaleric acid it produced could be potential biocontrol agents suitable for use against A. alternata.