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A Gram-stain-negative, non-spore-forming, flagellated, motile, aerobic, rod-shaped bacteria strain, designated YY2XT, was isolated from chromium-contaminated soil. Phylogenetic analysis based on 16S rRNA gene, recA gene, and whole genome indicated that the strain represented a new member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. The phylogenetic trees based on 16 s rRNA gene, revealed that Falsochrobactrum ovis DSM26720T (96.7%), Ochrobactrum gallinifaecis DSM15295T (96.2%), and Pseudochrobactrum asaccharolyticum DSM25619T (96.2%) are the most closely related phylogenetic neighbors of strain YY2XT. The draft genome of YY2XT was approximately 4,650,646 bp in size with a G + C content of 53.0 mol%. Average nucleotide identity and digital DNA–DNA hybridization values among strain YY2XT and the selected Brucellaceae species were 71.4–83.1% and 13.5–42.7%, which are below the recommended cut-off values for species delineation. Growth of strain YY2XT occurred within pH 5–10 (optimum, pH 7–8), 4 ℃–42 °C (optimum, 30 °C), and NaCl concentrations of 0.0–6.0% (optimum, 1.0%). Major quinone system was ubiquinone 10, the major fatty acids were C16:0, C18:1ω7c, and C16:1ω7c and the major polyamines were spermidine and putrescine. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, and four undefined lipids. On the basis of the phenotypic, genotypic and chemotaxonomic traits, strain YY2XT was considered to represent a novel species of the genus Ochrobactrum, for which the name Ochrobactrum chromiisoli sp. nov. is proposed. The type strain is YY2XT (= CCTCC AB 2023035T = JCM 36000T). [ABSTRACT FROM AUTHOR]

A Gram-positive, aerobic, rod-shaped non-motile, non-sporulating bacterium, designated CSA2T, was isolated from chromium-containing soils collected from a chemical plant. The 16S rRNA gene sequence of strain CSA2T showed the highest homology with Leucobacter chromiireducens subsp. solipictus (97.85%), Leucobacter chromiireducens subsp. chromiireducens (97.85%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and the amino acid identity (AAI) values among strains CSA2T and the selected Leucobacter species were 20.6–23.4% (dDDH), 72.67–78.03% (ANI) and 66.39–76.16% (AAI), falling below the recommended thresholds for species delimitation. The principal fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected were MK-10 and MK-11. The cell-wall amino acids included 2,4-diaminobutyric acid, threonine, glutamic acid, alanine and glycine. Based on molecular feature, phenotypic and chemotaxonomic, strain CSA2T was considered to be a novel species of the genus Leucobacter., and the name Leucobacter edaphi sp. nov. is proposed. The type strain is CSA2T (= JCM 34360T = CGMCC 1.18747T). [ABSTRACT FROM AUTHOR]

MAP65 is a microtubule-binding protein family in plants and plays crucial roles in regulating cell growth and development, intercellular communication, and plant responses to various environmental stresses. However, MAP65s in Cucurbitaceae are still less understood. In this study, a total of 40 MAP65s were identified from six Cucurbitaceae species (Cucumis sativus L., Citrullus lanatus, Cucumis melo L., Cucurbita moschata, Lagenaria siceraria, and Benincasa hispida) and classified into five groups by phylogenetic analysis according to gene structures and conserved domains. A conserved domain (MAP65_ASE1) was found in all MAP65 proteins. In cucumber, we isolated six CsaMAP65s with different expression patterns in tissues including root, stem, leaf, female flower, male flower, and fruit. Subcellular localizations of CsaMAP65s verified that all CsaMAP65s were localized in microtubule and microfilament. Analyses of the promoter regions of CsaMAP65s have screened different cis-acting regulatory elements involved in growth and development and responses to hormone and stresses. In addition, CsaMAP65-5 in leaves was significantly upregulated by salt stress, and this promotion effect was higher in cucumber cultivars with salt tolerant than that without salt tolerant. CsaMAP65-1 in leaves was significantly upregulated by cold stress, and this promotion was higher in cold-tolerant cultivar than intolerant cultivar. With the genome-wide characterization and phylogenetic analysis of Cucurbitaceae MAP65s, and the expression profile of CsaMAP65s in cucumber, this study laid a foundation for further study on MAP65 functions in developmental processes and responses to abiotic stress in Cucurbitaceae species. [ABSTRACT FROM AUTHOR]

Vermicompost and biochar have been widely used to improve soil conditions. However, little information is available regarding the efficiency and effectiveness of in situ vermicomposting with biochar (IVB) in monoculture soils. In this study, we estimated the effects of IVB on soil physiochemical and microbial properties, crop yields, and fruit quality under the tomato monoculture system. The soil treatments considered were (i) untreated monoculture soil (MS, control), (ii) MS plus 1.5 t/ha biochar applied to soil surface (MS+1.5BCS), (iii) MS plus 3 t/ha biochar applied to soil surface (MS+3BCS), (iv) MS mixed with 1.5 t/ha biochar (MS+1.5BCM), (v) MS mixed with 3 t/ha biochar (MS+3BCM), (vi) in situ vermicomposting (VC), (vii) VC plus 1.5 t/ha biochar applied to VC surface (VC+1.5BCS), (viii) VC plus 3 t/ha biochar applied to VC surface (VC+3BCS), (ix) VC mixed with 1.5 t/ha biochar (VC+1.5BCM), and (x) VC mixed with 3 t/ha biochar (VC+3BCM). In general, soil pH varied from 7.68 to 7.96 under VC-related treatments. The microbial diversity was much higher in bacterial communities (OTU: 2284-3194, Shannon index: 8.81-9.91) than in fungal communities (OTU: 392-782, Shannon index: 4.63-5.71) in VC-related treatments. Specifically, Proteobacteria was the dominant bacterial phylum, followed by Bacteroidota, Chloroflexi, Patescibacteria, Acidobacteriota, Firmicutes, and Myxococcota. It is worth noting that IVB-related treatments could increase the relative abundance of Acidobacteria and reduced the relative abundance of Bacteroidetes. In addition, the VC+1.5BCM treatment exhibited the greatest yield (9377.6 kg/667m2) and simultaneously showed higher fruit quality (vitamin C, 28.94 mg/100g; soluble sugar, 20.15%) as compared to other treatments. Our results suggested that in situ vermicomposting with biochar can improve soil properties and enhance both crop yields and fruit quality under the tomato monoculture system. [ABSTRACT FROM AUTHOR]

Exopolysaccharides (EPSs) are naturally occurring high-molecular-weight carbohydrates that have been widely studied for their biological activities, including antioxidant, immunomodulatory, anticancer and gut microbiota regulation activities. Polysaccharides are abundant in nature and can be derived from animals, plants, algae, and microorganisms, but among polysaccharides with potential uses, EPSs from microorganisms have the advantages of a short production cycle, high yield, and independence of production from season and climate and thus have broad prospects. While the safety of the producing microorganism can represent a problem in application of microbial EPSs, lactic acid bacteria (LAB) have been used by humans for thousands of years, and they and their products are generally recognized as safe. This makes LAB excellent sources for exopolysaccharides. EPS-producing LAB are readily found in nature. Through screening of strains, optimization of culture conditions, and improvement of the growth medium, the yield of EPSs from LAB can be increased and the scope of application broadened. This review summarizes EPSs from LAB in terms of structure, function and applications, as well as yield optimization, and introduces recent research on the biological activities and practical applications of LAB EPSs, aiming to provide references for researchers in related areas. [ABSTRACT FROM AUTHOR]

Key message: A mutation of CsARC6 not only causes white fruit color in cucumber, but also affects plant growth and fruit quality. Fruit color of cucumber is a very important agronomic trait, but most of the genes affecting cucumber white fruit color are still unknow, and no further studies were reported on the effect of cucumber fruit quality caused by white fruit color genes. Here, we obtained a white fruit mutant em41 in cucumber by EMS mutagenesis. The mutant gene was mapped to a 548 kb region of chromosome 2. Through mutation site analysis, it was found to be a null allele of CsARC6 (CsaV3_2G029290). The Csarc6 mutant has a typical phenotype of arc6 mutant that mesophyll cells contained only one or two giant chloroplasts. ARC6 protein was not detected in em41, and the level of FtsZ1 and FtsZ2 was also reduced. In addition, FtsZ2 could not form FtsZ ring-like structures in em41. Although these are typical arc6 mutant phenotypes, some special phenotypes occur in Csarc6 mutant, such as dwarfness with shortened internodes, enlarged fruit epidermal cells, decreased carotenoid contents, smaller fruits, and increased fruit nutrient contents. This study discovered a new gene, CsARC6, which not only controls the white fruit color, but also affects plant growth and fruit quality in cucumber. [ABSTRACT FROM AUTHOR]

Wet-salted skin, as a special artificial high-salt environment, is rich in protein, fat, collagen and other nutrient substrates, and is a rich resource of halotolerant and halophilic microorganisms. However, knowledge gaps regarding the microbial community structure and inter taxa associations of wet-salted skin are large. In this study, the spatiotemporal dynamics and community structure of microorganisms present on wet-salted goatskins were investigated using 16S rRNA gene amplicon sequencing and culturable technique. Alpha diversity analysis based on Sobs, Chao, Ace and Shannon indices revealed that microbial diversity on the wet-salted goatskins exhibited a trend of 'down → up → down → flat' with time. During preservation, genera belonging to the bacteria domain such as Acinetobacter, Weissella and Streptococcus were slowly dying out, whereas those belonging to halophilic archaea such as Natrialba and Haloterrigena were gradually flourishing. Moreover, to resist high-salt stress, microorganisms on the wet-salted goatskin gradually migrated from the outside to the inside, eventually leading to the microbial diversity inside the skin being the same as or even higher than that on the skin surface. Venn diagram analysis revealed that the strains of some genera, including Psychrobacter, Salimicrobium, Salinicola, Ornithinibacillus, Halomonas, Bacillus and Chromohalobacter, were distributed throughout the interior and exterior of the wet-salted goatskin and existed during various periods. Accordingly, 45 protease-producing halophilic or halotolerant microorganisms were isolated and screened from the wet-salted goatskin using the gradient dilution plate method. Importantly, 16S rRNA genes of some bacteria exhibited less than 99.5% similarity to valid published species, indicating that they likely are novel species and have a good potential for application. [ABSTRACT FROM AUTHOR]

In the current work, a novel thermophilic serine protease gene (P3862) from Ornithinibacillus caprae L9T was functionally expressed in Bacillus subtilis SCK6. The monomeric enzyme of about 29 kDa was purified to homogeneity with 43.91% of recovery and 2.81-folds of purification. Characterization of the purified protease revealed the optimum activity at pH 7 and 65 °C. The protease exhibited excellent activity and stability in the presence of Na+, Mg2+, Ca2+, ethanediol, n-hexane, Tween-20, Tween-80 and Triton X-100. P3862 displayed favorable caseinolytic activity, moderate keratinolytic activity but no collagenolytic activity. Besides, the homology model of P3862 possessed a globular configuration and characteristic of α/β hydrolase fold, and displayed stable interactions with casein, glycoprotein and keratin rather than collagen. Moreover, the crude enzyme could completely dehair goatskin within 6 h, resulting in decrease in BOD5, COD and TSS loads by 72.86, 74.07, and 73.79%, respectively, as compared with Na2S treatment. Biocatalytic applications revealed that it could effectively remove egg-stains from fabrics at 37 °C for 30 min with low supplementation (300 U/mL), and was able to degrade the feathers of duck and chicken. Overall, these outstanding properties make P3862 valuable in the development of environmentally friendly biotechnologies. [ABSTRACT FROM AUTHOR]

Deep Neural Network (DNN) models are widely used for image classification. While they offer high performance in terms of accuracy, researchers are concerned about if these models inappropriately make inferences using features irrelevant to the target object in a given image. To address this concern, we propose a metamorphic testing approach that assesses if a given inference is made based on irrelevant features. Specifically, we propose two metamorphic relations (MRs) to detect such unreliable inferences. These relations expect (a) the classification results with different labels or the same labels but less certainty from models after corrupting the relevant features of images, and (b) the classification results with the same labels after corrupting irrelevant features. The inferences that violate the metamorphic relations are regarded as unreliable inferences. Our evaluation demonstrated that our approach can effectively identify unreliable inferences for single-label classification models with an average precision of 64.1% and 96.4% for the two MRs, respectively. As for multi-label classification models, the corresponding precision for MR-1 and MR-2 is 78.2% and 86.5%, respectively. Further, we conducted an empirical study to understand the problem of unreliable inferences in practice. Specifically, we applied our approach to 18 pre-trained single-label image classification models and 3 multi-label classification models, and then examined their inferences on the ImageNet and COCO datasets. We found that unreliable inferences are pervasive. Specifically, for each model, more than thousands of correct classifications are actually made using irrelevant features. Next, we investigated the effect of such pervasive unreliable inferences, and found that they can cause significant degradation of a model's overall accuracy. After including these unreliable inferences from the test set, the model's accuracy can be significantly changed. Therefore, we recommend that developers should pay more attention to these unreliable inferences during the model evaluations. We also explored the correlation between model accuracy and the size of unreliable inferences. We found the inferences of the input with smaller objects are easier to be unreliable. Lastly, we found that the current model training methodologies can guide the models to learn object-relevant features to certain extent, but may not necessarily prevent the model from making unreliable inferences. We encourage the community to propose more effective training methodologies to address this issue. [ABSTRACT FROM AUTHOR]

As a common heavy metal, chromium and its compounds are widely used in industrial applications, e.g., leather tanning, electroplating, and in stainless steel, paints and fertilizers. Due to the strong toxicity of Cr(VI), chromium is regarded as a major source of pollution with a serious impact on the environment and biological systems. The disposal of Cr(VI) by biological treatment methods is more favorable than traditional treatment methods because the biological processes are environmentally friendly and cost-efficient. This review describes how bacteria tolerate and reduce Cr(VI) and the effects of some physical and chemical factors on the reduction of Cr(IV). The practical applications for Cr(VI) reduction of bacterial cells are also included in this review. [ABSTRACT FROM AUTHOR]

Planococcus halotolerans, recently described as a novel species with SCU63T as the type strain, is capable of thriving in up to 15% NaCl and temperatures as low as 0 °C. To better understand its adaptation strategies at the genomic level, strain SCU63T was subjected to whole-genome sequencing and data mining. The high-quality assembly yielded 17 scaffolds with a genome size of 3,622,698 bp. Its genome harbors 3683 protein-coding sequences and 127 RNA genes, as well as three biosynthetic gene clusters and 25 genomic islands. The phylogenomic tree provided compelling insights into the evolutionary relationships of Planococcus. Comparative genomic analysis revealed key similarities and differences in the functional gene categories among Planococcus species. Strain SCU63T was shown to have diverse stress response systems for high salt and cold habitats. Further comparison with three related species showed the presence of numerous unique gene clusters in the SCU63T genome. The strain might serve as a good model for using extremozymes in various biotechnological processes. [ABSTRACT FROM AUTHOR]

A novel Gram-stain-negative, moderately halotolerant, rod-shaped bacterium, designated strain L3T, was isolated from a wetsalted hide in Chengdu, China. The organism grew optimally at 30 °C, at pH 8 and with 5–10% (w/v) NaCl. The major cellular fatty acids were C16:0, C16:1ω7c, C18:1ω7c and C19:0 cyclo ω8c; the predominant respiratory quinone was Q-9; the phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and three unidentified phospholipids. Phylogenetic trees based on the 16S rRNA, gyrB and rpoD genes' sequences, obtained using three different algorithms, clearly revealed the isolate belonged to the genus Salinicola, and was found to be closely related to Salinicola acroporae JCM 30412T, Salinicola socius CGMCC 1.12383T and Salinicola lusitanus CR50T. The draft genome was approximately 4.5 Mb in size with 4486 predicted coding sequences, and the G+C content was 62.6 mol%. The maximum values of ANI and dDDH between strain L3T and the three above-mentioned type species were 89.2% and 63.8%, respectively. Differential phenotypic properties, together with the genome analysis, support the view that strain L3T represents a novel species, Salinicola corii sp. nov., with the type strain L3T (=CGMCC 1.17272T=KCTC 72572T). [ABSTRACT FROM AUTHOR]

A novel Gram-stain-positive, motile, moderate halophile, strain L9T, was isolated from hides of white goat in China. The isolate grew optimally at 30 °C, at pH 7 and with 5–10% (w/v) NaCl. The predominant menaquinone was MK-7, and the major cellular fatty acids were identified as iso-C15:0 and anteiso-C15:0. The peptidoglycan amino acid type was determined to be A4β, containing l-ornithine and d-aspartic as diagnostic amino acids. The phospholipids were dominated by diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid and two unidentified phospholipids. Genome sequencing resulted in a genome size of 4.0 Mbp and a DNA G + C content of 35.9 mol%. Phylogenetic trees based on the 16S rRNA gene sequences showed the isolate to be closely related to Oceanobacillus limi H9BT (98.2% similarity) and Ornithinibacillus halophilus G8BT (97.5% similarity). The ANI and dDDH values between strain L9T and the closely related species were 69.8–76.1% and 13.0–20.5%, respectively. On the basis of the data presented, strain L9T represents a novel species of the genus Ornithinibacillus, for which the name Ornithinibacillus caprae sp. nov. is proposed. The type strain is L9T (= KCTC 43176T = CGMCC 1.17659T). [ABSTRACT FROM AUTHOR]

In this work, we present the draft genome sequence of Actinocorallia populi A251T consisting of 8,253,402 bp with a G + C content of 71.5 mol%. The genome sequence includes 3 5S rRNA genes, 54 tRNA genes, 28 snRNA genes and 19 CRISPRs in 26 contigs. Using the Rapid Annotation using Subsystem Technology, a total of 7766 coding DNA sequences, which were assigned to 436 subsystems, were found in the genome. And 6743 protein-coding sequences with designated functions were assigned to 19 categories in the Cluster of Orthologous Groups database. The genome contains 20 gene clusters responsible for the synthesis of secondary metabolites, including two type I polyketide synthase (PKS) gene clusters, two type III PKS gene clusters, three nonribosomal peptide synthetase (NRPS) gene clusters and two hybrid PKS/NRPS gene clusters. These results indicate that strain A251 has the ability to produce several nonribosomal polypeptides and diverse polyketides, which was verified by liquid chromatography-mass spectrometry analysis of the extraction from fermentation broth. In addition, lactones, indole and many unknown natural products are present in the metabolites. Bioactivity testing revealed anticancer and antidiabetic activities of the crude extract towards the cancer cell line HepG2. In summary, the genomic sequences and bioactive fermentation products demonstrate the potential of strain A251 in biotechnology. [ABSTRACT FROM AUTHOR]

A novel endophytic actinobacterium strain, A217T, was isolated from the bulbil of Dioscorea bulbifera L. Its taxonomic position was characterized using a polyphasic study. Morphological and chemotaxonomic characteristics of strain A217T were consistent with those of members of the genus Streptomyces: long straight to flexuous spore chain; cellular components contained LL-diaminopimelic acid, ribose, and small traces of glucose in whole-cell hydrolysates; MK-9(H6) and MK-9(H8) as predominant menaquinones. The patterns of major fatty acids are C16:0, anteiso-C15:0, C15:0, iso-C14:0, C16:1ω7c, anteiso-C17:0, and iso-C17:1ω5c. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannoside, and glycolipid, as well as two unidentified phospholipids, one unidentified aminolipid, and one unidentified aminophospholipid. The DNA G + C content of draft genome is 70.7 mol%. Analysis of the 16S rRNA gene sequence and phylogenetic trees revealed that the isolate was most closely related to S. aurantiacus JCM 4453T (99.0%), S. glomeroaurantiacus JCM 4677T (99.0%), and S. tauricus JCM 4837T (98.8%). The DNA-DNA hybridization values between the strain A217T and three reference strains ranged from 34.6% to 51.7%. On the basis of phenotypic and genotypic differentiation from all tested strains, isolate A217T is proposed to represent a novel species of the genus Streptomyces, named Streptomyces dioscori sp. nov. The type strain is A217T (= CGMCC 4.7415T = JCM 32173T). [ABSTRACT FROM AUTHOR]

All locust epiphytic bacteria were screened and a total of 62 epiphytic bacteria were obtained from samples of Acrida cinerea. Via phylogenetic analysis, the 62 epiphytic bacteria were allocated to 27 genera, 18 families, 13 orders, six classes, and four phylums. Then, cyhalothrin degradation experiments were conducted, and the 10 strains that degraded more than 30% cyhalothrin and Paracoccus acridae SCU-M53 showed the highest cyhalothrin degradation rate of 70.5%. Furthermore, Paracoccus acridae SCU-M53 was selected for optimal cyhalothrin biodegradation conditions via the response surface method (Design-Expert). Under the optimum conditions (28 °C, 75 mg/L, and 180 rpm), the cyhalothrin degradation rate reached 79.84% after 2 days. This suggests the possibility that isolating biodegradation cyhalothrin strains from Acrida cinerea is feasible. [ABSTRACT FROM AUTHOR]

Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant ( P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities. [ABSTRACT FROM AUTHOR]

Solar greenhouse is a common facility type used for horticultural crop production in China. However, most solar greenhouse fields have been degraded due to continuous cropping and excessive fertilizer use. Therefore, we investigated solar greenhouse soils covering a wide range of cultivation years and environmental conditions in Round-Bohai Bay-Region to test the effects of cultivation year and biogeography on nutrients, heavy metals, and phthalate acid esters (PAEs). In general, soil pH decreased while soil electrical conductivity (EC), organic matter (OM), total nitrogen (TN), NO-N, NH-N, mineral nitrogen (MN), Olsen-P, and NHOAc-K contents increased as time of cultivation increased. However, this trend was influenced by sampling sites. Among sampling sites, Jiangsu showed a relatively low soil pH and high Olsen-P content, while Hebei showed a relatively high soil EC value, NO-N, NH-N, MN, and NHOAc-K contents. Liaoning was characterized by relatively high soil OM and TN contents. The nutrient level indexes in evaluation of soil quality on Olsen-P and NHOAc-K exceeded the standard seriously. The maximum values of the heavy metals Cd, Cu, and Zn were 4.87, 2.78, and 1.15 times higher than the threshold values, respectively. There was a rising trend on the heavy metal contents with the increasing cultivation years, and this trend was significantly influenced by sampling sites. Both Cu and Zn had relative high heavy metal indexes in evaluation of soil pollution. The PAEs were not detected in almost all sampling soils. Overall, the excessive fertilizer application was an important cause of nutrient accumulation and heavy metal pollution, resulting in soil degradation in solar greenhouses. [ABSTRACT FROM AUTHOR]

Two moderately halophilic strains, PT-11 and PT-20, were isolated from saline alkali soil samples collected in Shache County, Xinjiang Province, China. Both strains are aerobic, Gram-positive, motile rods. Strain PT-11 grows at 15-40 °C and at pH 6.5-10.0, while PT-20 grows at 15-40 °C and at pH 6.5-11.0. The major cellular fatty acids in both strains include anteiso-C, anteiso-C and iso-C. For both strains, the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and several unidentified lipids. In addition, strain PT-20 also contains phosphatidylcholine. The major isoprenoid quinone for both strains is MK-7. The genomic G+C content is 36.7 % for PT-11 and 39.2 % for PT-20. Phylogenetic analyses of 16S rRNA gene sequences indicated that these two isolates are members of the genus Oceanobacillus. DNA-DNA hybridization indicated that strains PT-11 and PT-20 should be considered two distinct species. On the basis of both phylogenetic and chemotaxonomic data analyses, therefore, we conclude that PT-11 and PT-20 represent two novel species within the genus Oceanobacillus, for which we propose the names Oceanobacillus rekensis sp. nov. and Oceanobacillus damuensis sp. nov., respectively. The type strains are PT-11 (=KCTC 33144 = DSM 26900) and PT-20 (=KCTC 33146 = DSM 26901). [ABSTRACT FROM AUTHOR]

Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber. [ABSTRACT FROM AUTHOR]

Phytoplankton blooms occurring in the Jiangdong Reservoir of Jiulong River, Fujian Province, South China, are a potential source of contamination of the drinking water of Xiamen (Amoy) City. To understand the main factors governing phytoplankton composition and succession, we sampled phytoplankton and measured environmental parameters in the reservoir, weekly or biweekly from Jan. 2010 to Feb. 2012. We identified 123 species of phytoplankton from 7 phyla and 74 genera. The major phyla were Chlorophyta, Bacillariophyta, Cryptophyta, Cyanophyta, and Dinophyta. The main trend in the succession of phytoplankton was from prevalence of Cryptophyta-Bacillariophyta communities to those of Chlorophyta-Cyanophyta. High cell concentrations of Cryptophyta, predominantly Komma caudate, Cryptomonas marssonii, and Cryptomonas erosa, were present in winter, associated with low river discharge and cold water. Bacillariophyta, primarily Cyclotella meneghiniana, Aulacoseira granulata, and Aulacoseira granulata var. angustissima, dominated in early spring, coinciding with high turbulence and low irradiance. During early summer and autumn, Chlorophyta, comprising Scenedesmus quadricauda, Dictyosphaerium ehrenbergianum, and Pandorina sp. were prevalent during conditions of warmer water temperatures and low turbulence. Cyanophyta, with dominance of Pseudanabaena mucicola, Merismopedia tenuissima and Raphidiopsis sp. increased throughout the summer, coinciding with higher water temperatures and lower nutrient concentrations. Dinophyta content was occasionally high during winter and summer. Peridiniopsis penardii (Dinophyta) bloomed during winter 2009, with a persistently high biomass recorded into early spring. Canonical correspondence analysis indicated that phytoplankton communities were influenced by river discharge, irradiance, water temperature, and nutrient concentrations. [ABSTRACT FROM AUTHOR]

Trueperella pyogenes (formerly Arcanobacterium) is commonly isolated from domesticated or wild ruminants as an opportunistic pathogen. To investigate the role of virulence determinants (VDs) and biofilm production in T. pyogenes isolates, a total of 36 T. pyogenes were collected from abscesses of forest musk deer in Miyaluo Farm (Sichuan Province, China). The prevalence of VDs and associations with clonal types, antibiotic resistance and biofilm production were analyzed by PCR and bioassay. Finally, T. pyogenes isolates were separated into three clonal types based on the DNA fingerprinting of BOX-PCR. Isolates with less VDs obtained from sick forest musk deer were mainly belonged to Type 1, and the isolates with robust VD repertoire obtained from dead forest musk deer were included in Type 3. Accordingly, resistant isolates exhibited significant lower virulence than susceptible ones. Majority of T. pyogenes isolates of this study were capable of producing a biofilm. However, no VDs presence and antibiotic resistance were statistically associated with biofilm production. In conclusion, the current study demonstrated that T. pyogenes was probably the primary pathogen of abscesses in the forest musk deer. Moreover, as an animal origin pathogen, the increasing resistance of T. pyogenes isolates could also associate with a decreased virulence. [ABSTRACT FROM AUTHOR]

Nitrogen nutrient management is crucially important in shallow-rooted vegetable production systems characterized by high input and high environmental risk. To investigate the effects of summer catch crop (sweet corn, common bean, garland chrysanthemum and edible amaranth), residue management, and soil temperature and water on the succeeding cucumber rhizosphere nitrogen mineralization in intensive production systems, we determined the rates of net nitrogen mineralization and nitrification in a 4-year field experiment on greenhouse cucumber double-cropping systems. Summer catch crop and its residue significantly increased the succeeding cucumber rhizosphere mineral nitrogen contents, when compared to conventional practices. In general, summer catch crop and its residue significantly increased the rates of both net nitrogen mineralization and net nitrogen nitrification at 4 or 40°C, and increased the rates of net nitrogen immobilization (negative mineralization) and net nitrogen nitrification at 15 or 28°C, in succeeding cucumber rhizosphere after four-year treatment. Soil temperature and water had more influence than catch crops and residue management on N mineralization. The effect of carbon on nitrogen mineralization was more pronounced than that of nitrogen, and the effect of microbial carbon on the different forms of inorganic N was more pronounced than that of organic carbon. When the effects of soil temperature and water content were eliminated, cumulative net nitrogen mineralization and nitrification in catch crop and residue management plots were 296-784 and 57-84% higher, respectively, than conventional practices plots. Catch crops and residue management influenced change of ammonium-N more significantly than that of nitrate-N. Additionally, there were complex relationships between fruit yield and soil N mineralization in catch crop- and residue management-induced systems. [ABSTRACT FROM AUTHOR]

Investigates the expression of a fundamental molecule of integrin-dependent signal transduction pathways, focal adhesion kinase, in mouse blastocysts and its influence on mouse blastocyst adhesion. Use of in vitro blastocyst culture and indirect immunocytochemistry, matrix metalloproteinases zymography and antisense oligodeoxynucleotide.

Determines the effects of vascular endothelial growth factor (VEGF) on matrix metalloprotenaises during embryo implantation in mice. Describes VEGF as a specific mitogen of endothelial cells; Importance of VEGF in vasculogenesis and angiogenesis; Regulation of the anility for metastasis, invasion of blastocysts, and the receptiveness of the uterus through VEGF.

Studies the effect of matrix metallo-proteinase-26 (MMP-26) during embryo implantation in the mouse. Use of uterine horn injection, immunohistochemistry and in situ hybridization; Strong expression of MMP-26 mRNA and protein in the mouse embryo; Inhibition of mouse embryo implantation by the MMP-26 antibody.

Presents a study on the importance of insulin-like growth factor (IGF)-II and IGF binding protein (IGFBP)-1, members of IGF family in the cyclic development of endometrium and the blastocyst implantation. Specific expression of IGF-II and IGFBP-1 at the maternal-fetal interface; Results of zymography, which showed that IGF-II enhanced the activities of MMP-2 and MMP-9, while IGFBP-1 did not affect the activities of MMP-2 and MMP-9; Conclusion that the equilibrium between the invasion of trophoblast and the inhibition of deciduas may be regulated by the interaction between the IGF-II-expressing invading cytotrophoblast and maternal deciduas-derived IGFBP-1.

Chromium is widely used in industry, and improper disposal of wastewater and industrial residues containing excessive chromium can contaminate water and soil, endangering both environmental and human health. Natural biopolymers and their derivatives have been investigated for removal of chromium (Cr) from wastewater. Cellulose, lignin, tannin, chitin, chitosan, and polypeptides are abundant in nature, and have high potential as adsorbents due to their easy access, low cost, and the recyclability of the captured heavy metals. In order to improve their mechanical strength, recyclability, specific surface area, binding site number, and adsorption rate as adsorbents, native materials have also been modified. This review discusses the source of chromium contamination and the main species of interest, as well as their toxicity. The structures of the aforementioned biopolymers were analyzed, and the adsorption mechanism of chromium and the main influencing factors on this process are discussed. The modification methods of various adsorbents and their adsorption effects on chromium are also detailed, and the developmental direction of research on the use of biopolymer adsorption remediation to control chromium contamination is discussed. [ABSTRACT FROM AUTHOR]

Human oral streptococci, particularly the mitis group, often dwell in the upper respiratory tracts, oral mucosa, and tooth surfaces of healthy individuals. In this work, an α-hemolytic strain, designated LQJ-218, was isolated from the human oral cavity and evaluated for its ability to produce exopolysaccharides. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain is a potentially novel species belonging to the mitis group streptococci. Whole-genome sequence-based analysis indicated that the genome sequence of Streptococcus sp. LQJ-218 was 1,935,194 bp in length, with a mol% G + C content of 40.0, and contained 1897 coding DNA sequences and 91 RNA genes. Furthermore, four biosynthetic gene clusters relevant to exopolysaccharide production were identified in the genome. Both digital DNA-DNA hybridization (yielding a value of 56.60% between strain LQJ-218 and its nearest relative S. mitis) and average nucleotide identity analysis (revealing 91.29% identity of LQJ-218 with its nearest relative S. mitis) suggested that strain LQJ-218 should be classified as a novel Streptococcus species. This potentially novel strain may possess great potential for contributing to the development of new exopolysaccharides. The present study provides valuable genetic information that may be useful in comparative genomics and biotechnological applications. [ABSTRACT FROM AUTHOR]

Planococcus halotolerans, recently described as a novel species with SCU63T as the type strain, is capable of thriving in up to 15% NaCl and temperatures as low as 0 °C. To better understand its adaptation strategies at the genomic level, strain SCU63T was subjected to whole-genome sequencing and data mining. The high-quality assembly yielded 17 scaffolds with a genome size of 3,622,698 bp. Its genome harbors 3683 protein-coding sequences and 127 RNA genes, as well as three biosynthetic gene clusters and 25 genomic islands. The phylogenomic tree provided compelling insights into the evolutionary relationships of Planococcus. Comparative genomic analysis revealed key similarities and differences in the functional gene categories among Planococcus species. Strain SCU63T was shown to have diverse stress response systems for high salt and cold habitats. Further comparison with three related species showed the presence of numerous unique gene clusters in the SCU63T genome. The strain might serve as a good model for using extremozymes in various biotechnological processes. [ABSTRACT FROM AUTHOR]