<Emphasis Type="Italic">Talaromyces heiheensis</Emphasis> and <Emphasis Type="Italic">T. mangshanicus</Emphasis>, two new species from China

Two new species, Talaromyces heiheensis from rotten wood and T. mangshanicus isolated from soil, are illustrated and described as new to science in sections Trachyspermi and Talaromyces. The phylogenetic positions of the two new species inferred from the internal transcribed spacer, beta-tubulin, calmodulin and RNA polymerase II second largest subunit regions were carried out. Talaromyces heiheensis is phylogenetically closely related to T. albobiverticillius, T. rubrifaciens, T. solicola and T. erythromellis, and characterised by slow growth on Czapek yeast autolysate agar at 25 °C, orange conidia en masse on malt extract agar at 25 °C, biverticillate and terverticillate conidiophores, acerose phialides and subglobose to ellipsoidal, smooth-walled conidia. Talaromyces mangshanicus is related to T. kendrickii, T. qii and T. thailandensis, and characterised by slow-growing colonies with absent or sparse sporulation on CYA agar at 25 °C, conidia en masse greyish purple, purplish red soluble pigment on yeast extract agar (YES) at 25 °C, biverticillate conidiophores, ampulliform phialides and subglobose to ellipsoidal conidia with echinulate walls. They are distinguished from the known species in culture characteristics on four standard media, microscopic features and sequence data.     

Bacterial metabolites from intra- and inter-species influencing thermotolerance: the case of <Emphasis Type="Italic">Bacillus cereus</Emphasis> and <Emphasis Type="Italic">Geobacillus stearothermophilus</Emphasis>

Bacterial metabolites with communicative functions could provide protection against stress conditions to members of the same species. Yet, information remains limited about protection provided by metabolites in Bacillus cereus and inter-species. This study investigated the effect of extracellular compounds derived from heat shocked (HS) and non-HS cultures of B. cereus and Geobacillus stearothermophilus on the thermotolerance of non-HS vegetative and sporulating B. cereus. Cultures of B. cereus and G. stearothermophilus were subjected to HS (42 or 65 °C respectively for 30 min) or non-HS treatments. Cells and supernatants were separated, mixed in a combined array, and then exposed to 50 °C for 60 min and viable cells determined. For spores, D values (85 and 95 °C) were evaluated after 120 h. In most cases, supernatants from HS B. cereus cultures added to non-HS B. cereus cells caused their thermotolerance to increase (D ₅₀ 12.2–51.9) when compared to supernatants from non-HS cultures (D ₅₀ 7.4–21.7). While the addition of supernatants from HS and non-HS G. stearothermophilus cultures caused the thermotolerance of non-HS cells from B. cereus to decrease initially (D ₅₀ 3.7–7.1), a subsequent increase was detected in most cases (D ₅₀ 18–97.7). In most cases, supernatants from sporulating G. stearothermophilus added to sporulating cells of B. cereus caused the thermotolerance of B. cereus 4810 spores to decline, whereas that of B. cereus 14579 increased. This study clearly shows that metabolites in supernatants from either the same or different species (such as G. stearothermophilus) influence the thermotolerance of B. cereus.     

Physiological and Morphological Characteristics of Acidophilic Bacteria <Emphasis Type="Italic">Leptospirillum ferriphilum</Emphasis> and <Emphasis Type="Italic">Acidithiobacillus thiooxidans</Emphasis>, Members of a Chemolithotrophic Microbial Consortium

A thermoacidophilic consortium of chemolithotrophic microorganisms oxidizing the concentrate of high-pyrrhotite pyrite?arsenopyrite ore at 38–40°C was isolated. The most active members of the consortium were identified as Leptospirillum ferriphilum, Acidithiobacillus thiooxidans, Ferroplasma acidiphilum, and Sulfobacillus thermotolerans. Leptospirillum and Thiobacillus species were the most numerous members of the consortium and had the highest activity of ferrous iron and sulfur oxidation, respectively. The optimal temperature values for the growth of both isolates were within 35–38°C. The optimal ranges of initial pH were 1.0–1.2 and 1.75–1.85 for leptospirilla and 1.7–3.3 for thiobacilli with the pH optimum of 1.9. Significant polymorphism and specific cyclic growth with formation of vibrios, spirilla, rods with different end shape, spiral filaments, numerous “pseudococci,” and densely packed spiral filaments surrounded by a sheath were revealed for the Leptospirillum isolate. Two latter morphoforms of L. ferriphilum were not previously described. Differences in ability of the morphoforms to oxidize Fe²⁺ were revealed. For the first time, the possibility of growth in the presence of organic substances was demonstrated for A. thiooxidans. The rates of growth and substrate oxidation, cell size, and the maximal cell yield decreased insignificantly in comparison with the lithoautotrophic strain.     

Properties of Probiotics <Emphasis Type="Italic">Kocuria</Emphasis> SM1 and <Emphasis Type="Italic">Rhodococcus</Emphasis> SM2 Isolated from Fish Guts

This study characterized probiotics Kocuria SM1 and Rhodococcus SM2, which were recovered from the intestinal microbiota of rainbow trout (Oncorhynchus mykiss, Walbaum). The cultures were Gram-positive, non-motile, catalase-positive and oxidase-negative cocci or rods. Cell multiplication of SM1 and SM2 was observed at 4–37 °C (45 °C for SM1), in 0–20% (w/v) NaCl and at pH 2–11. The viability was not affected when exposed to pepsin at pH 2.0 and 3.0, and pancreatin at pH 8.0. Neither isolates were chrome azurol S-positive for siderophore production. Of the 19 common enzymes analysed using the API-ZYM system, only 8 were evident in the culture of SM1 compared to 11 enzymes for SM2. The secondary metabolites of both probiotics were inhibitory to Acinetobacter baumannii, Vibrio anguillarum and V. ordalii; SM2 inhibited Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. SM2 was resistant to penicillin and sulphatriad, out of six antimicrobial agents; SM1 was resistant to sulphatriad. These results suggest that Kocuria SM1 and Rhodococcus SM2 are able to grow over a wide range of temperature, salinity and pH, including in conditions that mimic the gastrointestinal environment of fish and produce extracellular enzymes that may have a role in the host digestive processes. Importantly, Rhodococcus SM2 displays a high degree of bacteriocinogenic potential against multi-drug-resistant human pathogens that have never been documented among the gut microbiota of fish.     

<Emphasis Type="Italic">Candida krusei</Emphasis> and <Emphasis Type="Italic">Candida glabrata</Emphasis> reduce the filamentation of <Emphasis Type="Italic">Candida albicans</Emphasis> by downregulating expression of <Emphasis Type="Italic">HWP1</Emphasis> gene

Pathogenicity of Candida albicans is associated with its capacity switch from yeast-like to hyphal growth. The hyphal form is capable to penetrate the epithelial surfaces and to damage the host tissues. Therefore, many investigations have focused on mechanisms that control the morphological transitions of C. albicans. Recently, certain studies have showed that non-albicans Candida species can reduce the capacity of C. albicans to form biofilms and to develop candidiasis in animal models. Then, the objective of this study was to evaluate the effects of Candida krusei and Candida glabrata on the morphogenesis of C. albicans. Firstly, the capacity of reference and clinical strains of C. albicans in forming hyphae was tested in vitro. After that, the expression of HWP1 (hyphal wall protein 1) gene was determined by quantitative real-time PCR (polymerase chain reaction) assay. For both reference and clinical strains, a significant inhibition of the hyphae formation was observed when C. albicans was incubated in the presence of C. krusei or C. glabrata compared to the control group composed only by C. albicans. In addition, the culture mixed of C. albicans-C. krusei or C. albicans-C. glabrata reduced significantly the expression of HWP1 gene of C. albicans in relation to single cultures of this specie. In both filamentation and gene expression assays, C. krusei showed the higher inhibitory activity on the morphogenesis of C. albicans compared to C. glabrata. C. krusei and C. glabrata are capable to reduce the filamentation of C. albicans and consequently decrease the expression of the HWP1 gene.     

Purification and antibacterial mechanism of fish-borne bacteriocin and its application in shrimp (<Emphasis Type="Italic">Penaeus vannamei</Emphasis>) for inhibiting <Emphasis Type="Italic">Vibrio parahaemolyticus</Emphasis>

Vibrio parahaemolyticus: is recognized as the main cause of gastroenteritis associated with consumption of seafood. Bacteriocin-producing Lactobacillus plantarum FGC-12 isolated from golden carp intestine had strong antibacterial activity toward V. parahaemolyticus. The fish-borne bacteriocin was purified by a three-step procedure consisting of ethyl acetate extraction, gel filtration chromatography and high performance liquid chromatography. Its molecular weight was estimated at 4.1 kDa using SDS-PAGE. The fish-borne bacteriocin reached the maximum production at stationary phase after 20 h. It was heat-stable (30 min at 121?°C) and remained active at pH range from 3.0 to 5.5, but was sensitive to nutrasin, papain and pepsin. Its minimum inhibitory concentration for V. parahaemolyticus was 6.0 mg/ml. Scanning electron microscopy analysis showed that the fish-borne bacteriocin disrupted cell wall of V. parahaemolyticus. The antibacterial mechanism of the fish-borne bacteriocin against V. parahaemolyticus might be described as action on membrane integrity in terms of the leakage of electrolytes, the losses of Na⁺K⁺-ATPase, AKP and proteins. The addition of the fish-borne bacteriocin to shrimps leaded V. parahaemolyticus to reduce 1.3 log units at 4?°C storage for 6 day. Moreover, a marked decline in total volatile base nitrogen and total viable counts was observed in bacteriocin treated samples than the control. It is clear that this fish-borne bacteriocin has promising potential as biopreservation for the control of V. parahaemolyticus in aquatic products.     

<Emphasis Type="Italic">Pedobacter panacis</Emphasis> sp. nov., isolated from <Emphasis Type="Italic">Panax ginseng</Emphasis> soil

A novel strain, DCY108^T was isolated from soil of a Panax ginseng field, Yeoncheon province (38°04′N 126°57′E), Republic of Korea. Strain DCY108^T is Gram-negative, non-motile, non-flagellate, rod-shaped, and aerobic. The bacterium grows optimally at 25–30 °C, pH 6.5–7.0 and 1 % NaCl. Phylogenetically, strain DCY108^T is closely related to Pedobacter jejuensis JCM 18824^T, Pedobacter aquatilis JCM 13454^T, Pedobacter kyungheensis LMG 26577^T and the type strain of the genus Pedobacter heparinus DSM 2366^T. The DNA–DNA relatedness values between strain DCY108^T and its close phylogenetic neighbors were below 30.0 %. The DNA G+C content of strain DCY108^T was determined to be 45.1 mol%. The predominant quinone was menaquinone 7 (MK-7). The major polar lipids were identified as phosphatidylethanolamine and three unidentified aminolipids AL1, AL13 and AL17. Iso-C_15:00, iso-C_17:03OH and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) were identified as the major fatty acids present in strain DCY108^T. The results of physiological and biochemical tests allowed strain DCY108^T to be differentiated phenotypically from other recognized species belonging to the genus Pedobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Pedobacter panacis sp. nov is proposed with the type strain designated as DCY108^T (=CCTCCAB 2015196^T = KCTC 42748^T).     

Sequence analysis of <Emphasis Type="Italic">KmXYL1</Emphasis> genes and verification of thermotolerant enzymatic activities of xylose reductase from four <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis> strains

Kluyveromyces marxianus has the capability of producing xylitol from xylose because of the endogenous xylose reductase (KmXYL1) gene. In this study, we cloned KmXYL1 genes and compared amino acid sequences of xylose reductase (XR) from four K. marxianus strains (KCTC 7001, KCTC 7155, KCTC 17212, and KCTC 17555). Four K. marxianus strains showed high homologies (99%) of amino acid sequences with those from other reported K. marxianus strains and around 60% homologies with that from Scheffersomyces stipitis. For XR enzymatic activities, four K. marxianus strains exhibited thermostable XR activities up to 45°C and K. marxianus KCTC 7001 showed the highest XR activity. When reaction temperatures were increased from 30 to 45°C, NADH-dependent XR activity from K. marxianus KCTC 7001 was highly increased (46%). When xylitol fermentations were performed at 30 or 45°C, four K. marxianus strains showed very poor xylitol production capabilities regardless fermentation temperatures. Xylitol productions from four K. marxianus strains might be limited because of low xylose uptake rate or cell growth although they have high thermostable XR activities.     

Expression and characterization of glutamate decarboxylase from <Emphasis Type="Italic">Lactobacillus brevis</Emphasis> HYE1 isolated from <Emphasis Type="Italic">kimchi</Emphasis>

A putative gene (gadlbhye1) encoding glutamate decarboxylase (GAD) was cloned from Lactobacillus brevis HYE1 isolated from kimchi, a traditional Korean fermented vegetable. The amino acid sequences of GADLbHYE1 showed 48% homology with the GadA family and 99% identity with the GadB family from L. brevis. The cloned GADLbHYE1 was functionally expressed in Escherichia coli using inducible expression vectors. The expressed recombinant GADLbHYE1 was successfully purified by Ni–NTA affinity chromatography, and had a molecular mass of 54 kDa with optimal hydrolysis activity at 55 °C and pH 4.0. Its thermal stability was determined to be higher than that of other GADs from L. brevis, based on its melting temperature (75.18 °C). Kinetic parameters including K_m and V_max values for GADLbHYE1 were 4.99 mmol/L and 0.224 mmol/L/min, respectively. In addition, the production of gamma-aminobutyric acid in E. coli BL21 harboring gadlbhye1/pET28a was increased by adding pyridoxine as a cheaper coenzyme.     

<Emphasis Type="Italic">Rhizobium</Emphasis> strains in the biological control of the phytopathogenic fungi <Emphasis Type="Italic">Sclerotium</Emphasis> (<Emphasis Type="Italic">Athelia</Emphasis>) <Emphasis Type="Italic">rolfsii</Emphasis> on the common bean

Aims

To identify Rhizobium strains’ ability to biocontrol Sclerotium rolfsii, a fungus that causes serious damage to the common bean and other important crops, 78 previously isolated rhizobia from common bean were assessed.

Methods

Dual cultures, volatiles, indole-acetic acid (IAA), siderophore production and 16S rRNA sequencing were employed to select strains for pot and field experiments.

Results

Thirty-three antagonistic strains were detected in dual cultures, 16 of which were able to inhibit ≥84% fungus mycelial growth. Antagonistic strains produced up to 36.5 μg mL^?1 of IAA, and a direct correlation was verified between IAA production and mycelium inhibition. SEMIA 460 inhibited 45% of mycelial growth through volatile compounds. 16S rRNA sequences confirmed strains as Rhizobium species. In pot condition, common bean plants grown on S. rolfsii-infested soil and inoculated with SEMIA 4032, 4077, 4088, 4080, 4085, or 439 presented less or no disease symptoms. The most efficient strains under field conditions, SEMIA 439 and 4088, decreased disease incidence by 18.3 and 14.5% of the S. rolfsii-infested control.

Conclusions

Rhizobium strains could be strong antagonists towards S. rolfsii growth. SEMIA 4032, 4077, 4088, 4080, 4085, and 439 are effective in the biological control of the collar rot of the common bean.

     

<Emphasis Type="Italic">Hoeflea prorocentri</Emphasis> sp. nov., isolated from a culture of the marine dinoflagellate <Emphasis Type="Italic">Prorocentrum mexicanum</Emphasis> PM01

A Gram-stain negative, aerobic, rod-shaped, non-motile, yellow-pigmented and non-spore-forming bacterial strain, designated PM5-8^T, was isolated from a culture of a marine toxigenic dinoflagellate Prorocentrum mexicanum PM01. Strain PM5-8^T grew at 15–35 °C (optimum, 25–30 °C) and pH 6–11 (optimum, 7.5–8). Cells required at least 1.5% (w/v) NaCl for growth, and can tolerate up to 7.0% with the optimum of 4%. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the strain PM5-8^T is closely related to members of the genus Hoeflea, with high sequence similarities with Hoeflea halophila JG120-1^T (97.06%) and Hoeflea alexandrii AM1V30^T (97.01%). DNA–DNA hybridization values between the isolate and other type strains of recognized species of the genus Hoeflea were between 11.8 and 25.2%, which is far below the value of 70% threshold for species delineation. The DNA G?+?C content was 50.3 mol%. The predominant cellular fatty acids of the strain were identified as summed feature 8 (C_16:1 ω7c and/or C_16:1 ω6c; 51.5%), C_18:1 ω7c 11-methyl (20.7%), C_16:0 (17.2%) and C_18:0 (5.7%). The major respiratory quinone was Q-10. Polar lipids profiles contained phosphatidylcholine, phosphatidylglycerol, sulfoquinovosyl diacylglycerol, phosphatidylmono- methylethanolamine, phosphatidylethanolamine and four unidentified lipids. On the basis of the polyphasic taxonomic data presented, strain PM5-8^T (=?CCTCC AB 2016294^T?=?KCTC 62490^T) represents a novel species of the genus Hoeflea, for which the name Hoeflea prorocentri sp. nov. is proposed.     

Regional chronologies of <Emphasis Type="Italic">Cedrela</Emphasis><Emphasis Type="Italic">fissilis</Emphasis> and <Emphasis Type="Italic">Cedrela angustifolia</Emphasis> in three forest types and their relation to climate

Key message

Although tree-ring chronologies of Cedrela fissilis and Cedrela angustifolia showed a common climatic signal, local conditions influence growth, suggesting that forest guidelines should be appropriate to the species and context.

Abstract

Cedrela species are highly valued because of the quality of their timber. Understanding the behaviour of each different Cedrela species and their ecology is of importance to ensuring that forest harvesting and management do not endanger the survival of natural populations. These species grow in a wide range of environmental gradients and different types of forests in Bolivia. This study used dendrochronological methods to analyse growth–precipitation relationships of two Cedrela species coming from three locations with different environmental conditions: dry Chiquitano (Concepción), Chiquitano transitional Amazonian (Guarayos), and Bolivian-Tucuman montane forests (Postrervalle). The rainy season in all locations runs from October to April and the dry season runs from May to September. Twelve Cedrela fissilis specimens were sampled from dry Chiquitano, 11 Cedrela fissilis specimens from Chiquitano transitional Amazonian, and 30 Cedrela angustifolia specimens from Bolivian-Tucuman montane forests. The samples were crossdated and exhibited a common signal between trees from three sites, despite tree rings from the Chiquitano transitional Amazonian forest being narrower and displaying blurred bands of parenchyma in the boundaries. Significant inter-series correlation was found for the C. fissilis species series from dry Chiquitano with r = 0.261 (p < 0.01) and Chiquitano transitional Amazonian forests with r = 0.284 (p < 0.01), and for Cedrela angustifolia from Bolivian-Tucuman montane forests with r = 0.374 (p < 0.01). Mean annual growth was 2.07, 1.92, and 2.82 mm year^?1 at the three sites, respectively. Cedrela species from dry Chiquitano and Bolivian-Tucuman montane forests were sensitive to precipitation from October to April of the current growth year (wettest season) and to low temperatures from May to July of the current growth year (driest season). Samples from Chiquitano transitional Amazonian were more sensitive to precipitation during late rainy season (March, April, and May of the current growth year) and high temperatures during the rainy months (November–December). Growth differences between sites and species in response to climate variations and local conditions should be taken into account and handled with different forest management guidelines.

     

<Emphasis Type="Italic">Vibrio injenensis</Emphasis> sp. nov., isolated from human clinical specimens

Vibrio species are well known as motile, mostly oxidase-positive, facultative anaerobic Gram-negative bacteria. They are abundant in aquatic environments and are a common cause of human infections including diarrhea, soft tissue diseases, and bacteremia. Here, two Gram-negative bacteria, designated M12-1144^T and M12-1181, were isolated from human clinical specimens and identified using a polyphasic taxonomic approach. Phylogenetic study based on 16S rRNA gene sequence analysis revealed that the isolates belong to the genus Vibrio, and are closely related to Vibrio metschnikovii KCTC 32284^T (98.3%) and Vibrio cincinnatiensis KCTC 2733^T (97.8%). The major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c, 38.0%), C_16:0 (23.0%), and summed feature 8 (C_18:1 ω7c or C_18:1 ω6c, 19.3%) and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The G + C content of the genomic DNA was determined to be 44.1 mol%. DNA–DNA relatedness between the two newly isolated strains and V. metschnikovii KCTC 32284^T and V. cincinnatiensis KCTC 2733^T was between 42.6 to 47.5%. The similarities of genome-to-genome distance between M12-1144^T and related species ranged from 18.4-54.8%. Based on these results, a new species of the genus Vibrio, Vibrio injenensis is proposed. The type strain is M12-1144 ^T(=KCTC 32233^T =JCM 30011^T).     

Low temperature and <Emphasis Type="Italic">Daphnia</Emphasis>-associated infochemicals promote colony formation of <Emphasis Type="Italic">Scenedesmus obliquus</Emphasis> and its harvesting

Objective

To explore the combined effects of temperature and Daphnia-associated infochemicals on colony formation of Scenedesmus obliquus to faciliate harvesting the algal biomass.

Results

A three-parameter modified Gaussian model fitted the changes of the number of cells per particle in S. obliquus induced by Daphnia culture filtrate well under any temperature. Decreases in temperature enhanced the induced–colony formation of Scenedesmus. The maximum colony size at 15–25 °C was significantly larger than those at 30–35 °C. An additional 1 or 2 days at low temperature was needed to reach the maximum colony size, which indicates the best harvest time for algal biomass.

Conclusion

Induced-colony formation of Scenedesmus by Daphnia culture filtrate at 15–25 °C is recommended to settle algal cells. This condition facilitates harvesting the biomass.

     

Multilocus phylogeny of <Emphasis Type="Italic">Clonostachys</Emphasis> subgenus <Emphasis Type="Italic">Bionectria</Emphasis> from Brazil and description of <Emphasis Type="Italic">Clonostachys chloroleuca</Emphasis> sp. nov.

Phylogenetic analyses based on protein-encoding gene exons and introns of ATP citrate lyase (ACL1), beta tubulin (TUB), the largest subunit of RNA polymerase II (RPB1), and translation elongation factor 1-α (TEF1) are used for inferring the existence of a new Clonostachys species from the Cerrado biome in Brazil, described here as C. chloroleuca. The species produces dimorphic, primary, and secondary conidiophores that form consistently greenish conidial masses on artificial media. It resembles therefore C. rosea f. catenulata although it differs from this species by less adpressed branches in the secondary conidiophores. The new species is also phylogenetically related to C. byssicola and C. rhizophaga. Our inventory suggests that C. byssicola, C. chloroleuca, C. pseudochroleuca, C. rhizophaga, C. rogersoniana, and C. rosea commonly occur in native and agriculturally used soils of the Cerrado and Amazon Forest. Using sequences available from two genome-sequenced strains employed as biological control agents, we confirm the identity of the European strain IK726 as C. rosea and identify strain 67-1 from China as C. chloroleuca.     

A review of the history of research and control of <Emphasis Type="Italic">Rhipicephalus</Emphasis> (<Emphasis Type="Italic">Boophilus</Emphasis>) <Emphasis Type="Italic">microplus</Emphasis>, babesiosis and anaplasmosis in Uruguay

The effect of five constant temperatures (16, 20, 24, 28 and 32 °C) on the development, survival and reproduction of Tetranychus cinnabarinus (Boisduval) [=?Tetranychus urticae Koch (red form)] fed on cassava leaves was examined in the laboratory at 85% relative humidity. Development time of various immature stages decreased with increasing temperature, with total egg-to-adult development time varying from 27.7 to 6.7 days. The lower thermal threshold for development was 10.8 °C and the thermal constant from egg to adult was 142.4 degree-days. Pre- and post-oviposition period and female longevity all decreased as temperature increased. The longest oviposition period was observed at 20 °C with 20.4 days. Under different temperatures, mated females laid, on average, 1.0, 2.9, 4.7, 4.7 and 4.9 eggs per day, respectively. The maximum fecundity (81.5 eggs per female) was at 28 °C and the intrinsic rate of increase (r _m ) was highest (0.25) at 32 °C. The results of this study indicate that T. cinnabarinus population could increase rapidly when cassava leaves serve as a food source. At the appropriate temperature T. cinnabarinus could seriously threaten growth of cassava.     

Revision of the genus <Emphasis Type="Italic">Melamphaes</Emphasis> (Melamphaidae): 7. oligo-raker species: <Emphasis Type="Italic">M. danae</Emphasis> and <Emphasis Type="Italic">M. pumilis</Emphasis>

Two species, M. danae Ebeling and M. pumilis Ebeling, belonging to the species group “M. simus” are described in the final part of the revision of oligo-raker species of the genus Melamphaes (Melamphaidae) (≤19 gill rakers on the first gill arch). The species M. danae is distributed in the Indian and Pacific oceans between 30° N and 30° S. In the Pacific Ocean, it is known up to 112° W. The species M. pumilis is distributed in the North Atlantic between 17° and 45° N, and the main catches have been conducted in the western part of the ocean. In the eastern part of the ocean, the catches are registered up to 28° W. A key for the identification of 21 oligo-raker species of the genus Melamphaes is presented.     

Association between <Emphasis Type="Italic">cagA</Emphasis>, <Emphasis Type="Italic">vacAi</Emphasis>, and <Emphasis Type="Italic">dupA</Emphasis> genes of <Emphasis Type="Italic">Helicobacter pylori</Emphasis> and gastroduodenal pathologies in Chilean patients

In addition to the already known cagA gene, novel genetic markers have been associated with Helicobacter pylori (H. pylori) virulence: the dupA and vacAi genes. These genes might play an important role as specific markers to determine the clinical outcome of the disease, especially the vacAi gene, which has been expected to be a good marker of severe pathologies like gastric adenocarcinoma. In the present study, the association of cagA, dupA, and vacAi genes with gastroduodenal pathologies in Chilean patients was studied. One hundred and thirty-two patients positive for H. pylori were divided into two groups—non-severe and severe gastric pathologies—and investigated for the presence of cagA, dupA, and vacAi H. pylori virulence genes by PCR. The cagA gene was detected in 20/132 patients (15.2%), the vacAi1 gene was detected in 54/132 patients (40.9%), the vacAi2 gene was detected in 26/132 patients (19.7%), and the dupA gene was detected in 50/132 (37.9%) patients. Logistic regression model analysis showed that the vacAi1 isoform gene in the infected strains and the severity of the diseases outcome were highly associated, causing severe gastric damage that may lead to gastric cancer (p < 0.0001; OR = 8.75; 95% CI 3.54–21.64). Conversely, cagA (p = 0.3507; OR = 1.62; 95% CI 0.59–4.45) and vacAi2 (p = 0.0114; OR = 3.09; 95% CI 1.26–7.60) genes were not associated with damage, while the dupA gene was associated significantly with non-severe clinical outcome (p = 0.0032; OR = 0.25; 95% CI 0.09–0.65). In addition, dupA gene exerts protection against severe gastric pathologies induced by vacAi1 by delaying the outcome of the disease by approximately 20 years.     

<Emphasis Type="Italic">Sphingorhabdus buctiana</Emphasis> sp. nov., isolated from fresh water,and reclassification of <Emphasis Type="Italic">Sphingopyxis contaminans</Emphasis> as <Emphasis Type="Italic">Sphingorhabdus contaminans</Emphasis> comb. nov.

A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated T5^T, was isolated from the Chishui River in Maotai town, Guizhou Province, Southwest of China. Strain T5^T was found to grow optimally at pH 9.0 and 25 °C. The 16S rRNA gene sequence analysis indicated that strain T5^T belongs to the family Sphingomonadaceae within the phylum Proteobacteria; the strain T5^T clustered with the type strains of Sphingopyxis contaminans, Sphingorhabdus wooponensis and Sphingorhabdus rigui, with which it exhibits 16S rRNA gene sequence similarity values of 96.2–96.9%. The DNA G+C content was 58.5 mol%. The major respiratory quinone was Q-10 and the major polar lipid was phosphatidylethanolamine. The major polyamine was homospermidine and the major fatty acids were C_18:1 ω7c (37.5%) and C_16:1 ω7c (30.1%). On the basis of phylogenetic, phenotypic and genetic data, strain T5^T represents a novel species of the genus Sphingorhabdus, for which the name Sphingorhabdus buctiana sp. nov. is proposed. The type strain is T5^T (= CGMCC 1.12929^T = JCM 30114^T). It is also proposed that Sphingopyxis contaminans should be reclassified as a member of the genus Sphingorhabdus.     

Taxonomic composition of bacteria associated with cultivated mollusks <Emphasis Type="Italic">Crassostrea lugubris</Emphasis> and <Emphasis Type="Italic">Perna viridis</Emphasis> and with the water of the Gulf of Nha Trang lagoon,Vietnam

One hundred and four strains of heterotrophic bacteria have been isolated and characterized from two species of bivalve mollusks cultivated in the Gulf of Nha Trang (Vietnam) and from the water of a mariculture farm. The isolates have been identified on the basis of morphological, physiological, biochemical, and chemotaxonomic properties, as well as by the content of G+C bases in DNA. In the microflora of mollusks, Vibrio alginolyticus was predominant; the pathogenic species V. harveyi and V. splendidus were found as well. Staphylococci and bacilli occupied the second place in abundance after vibrios. In addition, coryneforms and enterobacteria, as well as Pseudomonas spp. and Pseudoalteromonas spp., were revealed. The composition of the water microflora was more diverse as compared with the microflora of mollusks. In the water, Bacillus spp., Vibrio spp., and Pseudomonas spp. were predominant. Brevibacterium spp. and other coryneform bacteria, as well as enterobacteria, occurred in significant amounts. In addition, Pseudoalteromonas spp., Marinococcus sp., Halobacillus sp., Shewanella sp., Sulfitobacter sp., and bacteria of the CFB cluster were noticed. The presence of pathogenic and conditionally pathogenic bacterial species in the water and mollusks is probably the reason for the high death rate of cultivated animals at the mariculture farm.