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In the medical research domain, limited data and high annotation costs have made efficient classification under few-shot conditions a popular research area. This paper proposes a meta-learning framework, termed MedOptNet, for few-shot medical image classification. The framework enables the use of various high-performance convex optimization models as classifiers, such as multi-class kernel support vector machines, ridge regression, and other models. End-to-end training is then implemented using dual problems and differentiation in the paper. Additionally, various regularization techniques are employed to enhance the model's generalization capabilities. Experiments on the BreakHis, ISIC2018, and Pap smear medical few-shot datasets demonstrate that the MedOptNet framework outperforms benchmark models. Moreover, the model training time is also compared to prove its effectiveness in the paper, and an ablation study is conducted to validate the effectiveness of each module.

Introduction: Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang., Methods: Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed., Results: In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria , with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia . pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils., Discussion: These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wang, Yang, Nan, Guo, Tan, Shao and Tian.)

Introduction: Cabozantinib is one of the preferred treatment options in the latest metastatic renal cell carcinoma (mRCC) guidelines. Cabozantinib is also associated with high drug expenses irrespective of the used dose, because a flat-prizing model has been implemented. In addition, concomitant intake with a high-fat meal increases its bioavailability on average by 57%. Combined with the long terminal half-life of cabozantinib (99 h), this creates possibilities to extend the dosing interval to reduce drug expenses whilst maintaining equivalent exposure., Objectives: The primary objective was to evaluate the population pharmacokinetic (POPPK) model of cabozantinib developed for its registration using real-world patients' therapeutic drug monitoring (TDM) data. The secondary objective was to design, simulate, and evaluate alternative dose regimens with the aim to reduce drug expenses whilst maintaining comparable exposure., Methods: Retrospective TDM data from mRCC patients treated with cabozantinib were obtained. The data were evaluated using the published Food and Drug Administration (FDA) cabozantinib POPPK model, a two-compartment disposition model with a dual (fast and slow) lagged first-order absorption process derived from FDA registration documents, as a basis. Subsequently, simulations of alternative drug expenses saving regimens were evaluated., Results: Twenty-seven mRCC patients with 75 pharmacokinetic observations were included. Patients were treated for a median of 75 days with a median dose of 40 mg. Model evaluation results showed that the cabozantinib TDM concentrations were adequately predicted by the published FDA cabozantinib POPPK model, except for a slightly higher clearance (CL) of 3.11 L/h compared to the reported value (2.23 L/h). The simulation study indicated that an alternative dose regimen that consists of taking 60 mg of cabozantinib for 2 days and then skipping 1 day results in comparable average exposure when compared with a 40 mg daily dose, both without food interaction, while saving 33.3% of the total drug expenses per month. The food effect of a high-fat meal was also taken into account when simulating other alternative dose regimens; 40 mg every 72 h combined with a high-fat meal resulted in comparable exposure when compared with a 20 mg daily dose fasted, while saving 66.7% in drug expenses., Conclusions: In this study, the optimized cabozantinib POPPK model resulted in adequate prediction of real-world cabozantinib pharmacokinetic data. Alternative dosing regimens with and without using known food interactions were proposed that resulted in potential strategies to significantly reduce cabozantinib drug expenses., (© 2024. The Author(s).)

Introduction: Soil salinization poses a significant environmental challenge affecting plant growth and agricultural sustainability. This study explores the potential of salt-tolerant endophytes to mitigate the adverse effects of soil salinization, emphasizing their impact on the development and resistance of Arachis hypogaea L. (peanuts)., Methods: The diversity of culturable plant endophytic bacteria associated with Miscanthus lutarioriparius was investigated. The study focused on the effects of Bacillus tequilensis , Staphylococcus epidermidis , and Bacillus siamensis on the development and germination of A. hypogaea seeds in pots subjected to high NaCl concentrations (200 mM L -1 )., Results: Under elevated NaCl concentrations, the inoculation of endophytes significantly ( p < 0.05) enhanced seedling germination and increased the activities of enzymes such as Superoxide dismutase, catalase, and polyphenol oxidase, while reducing malondialdehyde and peroxidase levels. Additionally, endophyte inoculation resulted in increased root surface area, plant height, biomass contents, and leaf surface area of peanuts under NaCl stress. Transcriptome data revealed an augmented defense and resistance response induced by the applied endophyte ( B. tequilensis , S. epidermidis , and B. siamensis ) strain, including upregulation of abiotic stress related mechanisms such as fat metabolism, hormones, and glycosyl inositol phosphorylceramide (Na + receptor). Na + receptor under salt stress gate Ca 2+ influx channels in plants. Notably, the synthesis of secondary metabolites, especially genes related to terpene and phenylpropanoid pathways, was highly regulated., Conclusion: The inoculated endophytes played a possible role in enhancing salt tolerance in peanuts. Future investigations should explore protein-protein interactions between plants and endophytes to unravel the mechanisms underlying endophyte-mediated salt resistance in plants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liang, Tan, Chen, Guo, Afzal, Wang, Tan and Peng.)

One of the most concerning global environmental issues is the pollution of agricultural soils by heavy metals (HMs), especially cadmium, which not only affects human health through Cd-containing foods but also impacts the quality of rice. The soil's nitrification and denitrification processes, coupled with the release of volatile organic compounds by plants, raise substantial concerns. In this review, we summarize the recent literature related to the deleterious effects of Cd on both soil processes related to the N cycle and rice quality, particularly aroma, in different water management practices. Under both continuous flooding (CF) and alternate wetting and drying (AWD) conditions, cadmium has been observed to reduce both the nitrification and denitrification processes. The adverse effects are more pronounced in alternate wetting and drying (AWD) as compared to continuous flooding (CF). Similarly, the alteration in rice aroma is more significant in AWD than in CF. The precise modulation of volatile organic compounds (VOCs) by Cd remains unclear based on the available literature. Nevertheless, HM accumulation is higher in AWD conditions compared to CF, leading to a detrimental impact on volatile organic compounds (VOCs). The literature concludes that AWD practices should be avoided in Cd-contaminated fields to decrease accumulation and maintain the quality of the rice. In the future, rhizospheric engineering and plant biotechnology can be used to decrease the transport of HMs from the soil to the plant's edible parts.

Aims: Cetirizine is frequently administered at an increased dosage in clinical practice and recommended by several guidelines. Nonetheless, the pharmacokinetic (PK) profile and real-world safety data remain insufficient in the Chinese pediatric population. The objective of the current study is to develop a population pharmacokinetic (PPK) model for cetirizine in Chinese pediatric patients and to investigate the rationale behind its off-label usage. Methods: A prospective cohort study was conducted, enrolling children who had been diagnosed with allergic diseases and prescribed cetirizine. The outcomes were safety and pharmacokinetic (PK) parameters. Cetirizine concentrations were measured using a pre-established analytical method. Subsequently, a PK model was developed, followed by model evaluation and simulation. The developed PK model was employed to investigate the drug exposure differences across various age groups and to simulate scenarios of potential overdose. Results: Sixty-three children were enrolled, and 24 of them received a cetirizine dose exceeding the recommended dosage. A PPK model, based on published literature, served as the basis of our analysis, with adjustment made to estimate certain parameters. The final model evaluation and validation indicated accurate predictive performance and robust parameter estimation. Simulations conducted for the label-dose among age 1-12 indicated median maximum concentration at steady state (C max,ss ) of 7 year old children could be the highest. The model was also used to predict the off-label dose scenarios and overdose patient to support the clinical decision. There were no adverse drug reactions in either group. Conclusion: This study provides evidence-based and model-based exploration for optimizing cetirizine usage in Chinese pediatric patients. The cetirizine PPK model showed accurate predictive performance and could be utilized to simulate individual patient exposure in real-world clinical scenarios., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liu, Tan, Yang, Yu, Yao, Zhou, Liu and Zhou.)

Summary: Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA-seq datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 175 samples, 663 857 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, scCancer2 integrated a module to process the spatial transcriptomic data and analyze the spatial features of TME., Availability and Implementation: The package and user documentation are available at http://lifeome.net/software/sccancer2/ and https://doi.org/10.5281/zenodo.10477296., (© The Author(s) 2024. Published by Oxford University Press.)

Memristors, known for their adjustable and non-volatile resistance, offer a promising avenue for emulating synapses. However, achieving pulse frequency-dependent synaptic plasticity in memristors or memristive systems necessitates further exploration. In this study, we present a novel approach to modulate the conductance of a memristor in a capacitor-memristor circuit by finely tuning the frequency of input pulses. Our experimental results demonstrate that these phenomena align with the long-term depression (LTD) and long-term potentiation (LTP) observed in synapses, which are induced by the frequency of action potentials. Additionally, we successfully implement a Hebbian-like learning mechanism in a simple circuit that connects a pair of memristors to a capacitor, resulting in observed associative memory formation and forgetting processes. Our findings highlight the potential of capacitor-memristor circuits in faithfully replicating the frequency-dependent behavior of synapses, thereby offering a valuable contribution to the development of brain-inspired neural networks.

In this paper, we propose a pre-configured error pattern ordered statistics decoding (PEPOSD) algorithm and discuss its application to short cyclic redundancy check (CRC)-polar codes. Unlike the traditional OSD that changes the most reliable independent symbols, we regard the decoding process as testing the error patterns, like guessing random additive noise decoding (GRAND). Also, the pre-configurator referred from ordered reliability bits (ORB) GRAND can better control the range and testing order of EPs. An offline-online structure can accelerate the decoding process. Additionally, we also introduce two orders to optimize the search order for testing EPs. Compared with CRC-aided OSD and list decoding, PEPOSD can achieve a better trade-off between accuracy and complexity.

Introduction: Endophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia 'Hongsen' is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China's 'southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia 'Hongsen,' microbiome in detail by high-throughput sequencing and culture dependant., Methods: This study examined microbial species and functional diversity in Robinia pseudoacacia 'Hongsen' using culture-dependent (isolation) and culture-independent techniques., Results: A total of 210 isolates were isolated from R. pseudoacacia 'Hongsen.' These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia 'Hongsen'. ' Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia 'Hongsen' of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia 'Hongsen' plant., Discussion: It was predicted that R. pseudoacacia 'Hongsen' plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Huang, Chen, Ma, Mo, He, Liang, Peng and Tan.)

Mn-modified CeO 2 nanomaterials have attracted extensive attention as efficient and promising catalysts for soot combustion due to their low cost and high catalytic activity. However, a detailed mechanism of how Mn promotes soot oxidation over CeO 2 is still not clearly elucidated, which is crucial to further optimize the catalyst for achieving its practical applications. We here report a Mn-doped CeO 2 catalyst with tunable surface Mn chemical valence states to study the Mn-promoting mechanism for improving CeO 2 catalyst activity in soot oxidation. Experimental results show that Mn-doped CeO 2 nanorods with surface Mn chemical valence states being optimized (Mn 0.19 Ce 0.81 O 2 ) can lower the eliminating temperature of soot to 410 °C ( T 90 ) when in a loose contact and exhibit a strong resistance towards water molecules. The catalytic performances of Mn 0.19 Ce 0.81 O 2 nanorods are comparable with those of other reported oxide catalysts both in the mimetic realistic and ideal reaction environments. Detailed characterization and theoretical calculation results demonstrate that balanced multiple Mn valences can dramatically enhance the catalysts' redox properties and their ability to activate O 2 molecules, as well as improve the dynamic contact efficiency during the oxidation, which synergistically result in superior catalytic performances. This work might provide insight for the future design and preparation of catalysts to efficiently eliminate soot particles.

The Internet of Things (IoT) is a paradigm that connects a range of physical smart devices to provide ubiquitous services to individuals and automate their daily tasks. IoT devices collect data from the surrounding environment and communicate with other devices using different communication protocols such as CoAP, MQTT, DDS, etc. Study shows that these protocols are vulnerable to attack and prove a significant threat to IoT telemetry data. Within a network, IoT devices are interdependent, and the behaviour of one device depends on the data coming from another device. An intruder exploits vulnerabilities of a device's interdependent feature and can alter the telemetry data to indirectly control the behaviour of other dependent devices in a network. Therefore, securing IoT devices have become a significant concern in IoT networks. The research community often proposes intrusion Detection Systems (IDS) using different techniques. One of the most adopted techniques is machine learning (ML) based intrusion detection. This study suggests a stacking-based ensemble model makes IoT devices more intelligent for detecting unusual behaviour in IoT networks. The TON-IoT (2020) dataset is used to assess the effectiveness of the proposed model. The proposed model achieves significant improvements in accuracy and other evaluation measures in binary and multi-class classification scenarios for most of the sensors compared to traditional ML algorithms and other ensemble techniques.

The increased use of social media among digitally anonymous users, sharing their thoughts and opinions, can facilitate participation and collaboration. However, this anonymity feature which gives users freedom of speech and allows them to conduct activities without being judged by others can also encourage cyberbullying and hate speech. Predators can hide their identity and reach a wide range of audience anytime and anywhere. According to the detrimental effect of cyberbullying, there is a growing need for cyberbullying detection approaches. In this survey paper, a comparative analysis of the automated cyberbullying techniques from different perspectives is discussed including data annotation, data preprocessing, and feature engineering. In addition, the importance of emojis in expressing emotions as well as their influence on sentiment classification and text comprehension leads us to discuss the role of incorporating emojis in the process of cyberbullying detection and their influence on the detection performance. Furthermore, the different domains for using self-supervised learning (SSL) as an annotation technique for cyberbullying detection are explored., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2022 Lulwah M. Al-Harigy et al.)

Aims: A lot of medication risks related to high-dose methotrexate (HDMTX) therapy still remain to be identified and standardized. This study aims to establish an evidence-based practice guideline for individualized medication of HDMTX., Methods: The practice guideline was launched by the Division of Therapeutic Drug Monitoring, Chinese Pharmacological Society. The guideline was developed following the WHO handbook for guideline development and the methodology of evidence-based medicine (EBM). The guideline was initially registered in the International Practice Guidelines Registry Platform (IPGRP-2017CN021). Systematic reviews were conducted to synthesize available evidence. A multicentre cross-sectional study was conducted using questionnaires to evaluate patients' perception and willingness concerning individualized medication of HDMTX. The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach was used to rate the quality of evidence and to grade the strength of recommendations., Results: Multidisciplinary working groups were included in this guideline, including clinicians, pharmacists, methodologists, pharmacologists and pharmacoeconomic specialists. A total of 124 patients were involved to integrate patient values and preferences. Finally, the guideline presents 28 recommendations, regarding evaluation prior to administration (renal function, liver function, pleural effusion, comedications, genetic testing), pre-treatment and routine dosing regimen, therapeutic drug monitoring (necessity, method, timing, target concentration), leucovorin rescue (initial timing, dosage regimen and optimization), and management of toxicities. Of these, 12 are strong recommendations., Conclusions: We developed an evidence-based practice guideline with respect to HDMTX medication using a rigorous and multidisciplinary approach. This guideline provides comprehensive and practical recommendations involving the whole process of HDMTX administration to health care providers., (© 2021 British Pharmacological Society.)

A novel phage vB&#95;VpP&#95;DE17, which infects Vibrio parahaemolyticus, was isolated from the sewer of the Huangsha aquatic market in Guangzhou. Transmission electron microscopy indicated that DE17 had an icosahedral head (47 ± 2 nm diameter) and a short, non-contractile tail (17 ± 2 nm). The genome of DE17 was a double-stranded linear DNA with a length of 43,397 bp and GC content of 49.23%. In total, 49 putative open reading frames (ORFs) were predicted and could be divided into six modules: DNA metabolism, lysis, packaging, structure, additional function, and hypothetical proteins. Taxonomic analysis revealed that the phage belonging to the genus of Maculvirus, Autographivirinae subfamily, Podoviridae family. DE17 had a short latent period of 5 min with burst size of 80 pfu/cell. Its optimum temperature and pH ranges were 4 °C-50 °C and 5-10, respectively; it was completely inactivated after 20 min of ultraviolet irradiation. No transfer RNA (tRNA), virulence associated, or antibiotic resistance genes were identified. Bacterial challenge test revealed that DE17 had a certain inhibitory effect on V. parahaemolyticus within 6 h. Characterization, genomic analysis and in vitro antibacterial assays of DE17 will further enhance our understanding of phage biology and diversity., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

A reliable, rapid, and effective bioanalytical method is essential for the determination of the pharmacokinetic, pharmacodynamic, and toxicokinetic parameters that inform the safety and efficacy profile of investigational drugs. The overall goal of bioanalytical method development is to elucidate the procedure and operating conditions under which a method can sufficiently extract, qualify, and/or quantify the analyte(s) of interest and/or their metabolites for the intended purpose. Given the difference in the physicochemical properties of small and large molecule drugs, different strategies need to be adopted for the development of an effective and efficient bioanalytical method. Herein, we provide an overview of different sample preparation strategies, analytical platforms, as well as procedures for achieving high throughput for bioanalysis of small and large molecule drugs.

Background: Pharmacist-led clinical pathways/order sets (PLCOs) were first applied for designated diseases and surgical operations, such as cancer. They were not used in pharmacotherapy until recently. After screening a large number of publications, we found that PLCOs were rarely accessible. Objective: To evaluate the effects and the changes of relevant medical outcomes of PLCOs. Methods: Articles from PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure, Wanfang database, and China Biology Medicine disc (CBM) were systematically retrieved. Clinical research comparing cancer patients' clinical effects with or without clinical pathway/order sets was performed. Two reviewers performed quality assessment, and the data were abstracted independently. A narrative synthesis of the extracted data was performed due to heterogeneity. Results: Nine studies were identified, including six uncontrolled before-after studies and three case-series studies. The scopes of PLCOs of included research can be divided into two types, one focusing on chemotherapy agents and the other on the managements of chemotherapy-induced complications. The PLCOs shortened hospital length of stay, decreased initial antibiotic time intervals in patients with febrile neutropenia, reduced medication error incidence, and increased physicians' adherence rate to clinical pathway/order sets. Moreover, three articles included economic effects showing positive savings on medication costs through PLCOs. Conclusion: PLCOs can have beneficial effects on medication effectiveness, safety, and economic outcomes. Nevertheless, clinical pathway/order sets need to be further optimized and expanded to other clinical areas., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. All authors stated that they had no potential conflicts., (Copyright © 2021 Tan, Yu, Chen, Liu and Zhao.)

Accumulating evidence has indicated that the multiple drug resistant Vibrio parahaemolyticus may pose a serious threat to public health and economic concerns for humans globally. Here, two lytic bacteriophages, namely vB&#95;VpS&#95;BA3 and vB&#95;VpS&#95;CA8, were isolated from sewage collected in Guangzhou, China. Electron microscopy studies revealed both virions taxonomically belonged to the Siphoviridae family with icosahedral head and a long non-contractile tail. The double-stranded DNA genome of phage BA3 was composed of 58648 bp with a GC content of 46.30% while phage CA8 was 58480 bp with an average GC content of 46.42%. In total, 85 putative open reading frames (ORFs) were predicted in the phage BA3 genome while 84 were predicted in that of CA8. The ORFs were associated with phage structure, packing, host lysis, DNA metabolism, and additional functions. Furthermore, average nucleotide identity analysis, comparative genomic features and phylogenetic analysis revealed that BA3 and CA8 represented different isolates but novel members of the family, Siphoviridae . Regarding the host range of the 61 V. parahaemolyticus isolates, BA3 and CA8 had an infectivity of 8.2 and 36.1%, respectively. Furthermore, ∼100 plaque-forming units (pfu)/cell for phage BA3 and ∼180 pfu/cell for phage CA8 were determined to be the viral load under laboratory growth conditions. Accordingly, the phage-killing assay in vitro revealed that phage CA8 achieved approximately 3.65 log unit reductions. The present results indicate that CA8 is potentially applicable for biological control of multidrug resistant V. parahaemolyticus ., (Copyright © 2020 Yang, Liang, Huang, Zhang, Wang, Chen, Ye, Gao, Wu and Tan.)

The hotspot issue in wireless sensor networks, with nodes nearest the sink node losing energy fastest and degrading network lifetime, is a well-referenced problem. Mobile sink nodes have been proposed as a solution to this. They do not completely remove the hotspot problem though, with nodes the sink passes most closely still expending more energy than others. This study proposes a lightweight algorithm, located in the media access control (MAC) layer of static nodes and utilising knowledge of predictable sink node mobility. This is in order to create a dynamic communication threshold between static nodes and the sink, within which static nodes awaken, lessening competition for sink communication between nodes. In utilising predictable mobility and factors already known to the static node, such as location and interference range, there is no need for energy-consuming messaging. Analysis and simulation results, tested on a lightweight implementation of a carrier-sense multiple-access-based MAC protocol, show a significant improvement in energy consumption in both controlled and random environments, with frame delivery improved to the point where sink speed is negated. This is when compared to the existing duty cycling approach.

The Internet of Things (IoT) is an emerging technology that aims to enable the interconnection of a large number of smart devices and heterogeneous networks. Ad hoc networks play an important role in the designing of IoT-enabled platforms due to their efficient, flexible, low-cost and dynamic infrastructures. These networks utilize the available resources efficiently to maintain the Quality of Service (QoS) in a multi-hop communication. However, in a multi-hop communication, the relay nodes can be malicious, thus requiring a secured and reliable data transmission. In this paper, we propose a QoS-aware secured communication scheme for IoT-based networks (QoS-IoT). In QoS-IoT, a Sybil attack detection mechanism is used for the identification of Sybil nodes and their forged identities in multi-hop communication. After Sybil nodes detection, an optimal contention window (CW) is selected for QoS provisioning, that is, to achieve per-flow fairness and efficient utilization of the available bandwidth. In a multi-hop communication, the medium access control (MAC) layer protocols do not perform well in terms of fairness and throughput, especially when the nodes generate a large amount of data. It is because the MAC layer has no capability of providing QoS to prioritized or forwarding flows. We evaluate the performance of QoS-IoT in terms of Sybil attack detection, fairness, throughput and buffer utilization. The simulation results show that the proposed scheme outperforms the existing schemes and significantly enhances the performance of the network with a large volume of data. Moreover, the proposed scheme is resilient against Sybil attack.

A Gram-stain-negative, aerobic, nitrogen-fixing bacterium, designated strain L461 T , was isolated from leaves of Bryophyllum pinnatum growing at the South China Agricultural University. Phylogenetic analysis of the 16S rRNA gene sequence indicated it as a member of the genus Azotobacter closely related to Azotobacter beijerinckii JCM 20725 T (97.82 % similarity) and Azotobacter chroococcum ATCC 9043 T (97.34 %). Its major fatty acid components were C16 : 1 ω9c and C16 : 0. Its predominant isoprenoid quinone was Q-9. Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, phospholipid and one unknown lipid. Its DNA G+C content was 64.9 mol% (Tm). DNA-DNA relatedness values between strain L461 T and the reference strains of A. beijerinckii and A. chroococcum were 46.43 and 28.23 %, respectively. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, and comparison of cellular fatty acids distinguished strain L461 T from the closely related Azotobacter species. Based on these data, the novel species Azotobacter bryophylli sp. nov. is proposed, with the type strain L461 T (=KCTC 62195 T =GDMCC 1.1250 T ).

A novel strain, designated K23C18032701 T , was isolated from a sample of forest soil collected from Dinghushan Biosphere Reserve, Guangdong Province, PR China. The strain was Gram-stain-negative, aerobic, motile and showed a shape change from a filamentous cell to coccobacilli. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain belongs to the family Chitinophagaceae, and showed the highest similarities to Arvibacter flaviflagrans JCM 31293 T (95.0 %) and Filimonas aurantiibacter LMG 29039 T (94.4 %). The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The predominant polar lipid was phosphatidylethanolamine (PE). The predominant respiratory quinone was menaquinone-7. The major polyamine was sym-homospermidine. The draft genome size of strain K23C18032701 T was 5.84 Mb with a DNA G+C content of 47.2 mol%. Based on phenotypic, genotypic and phylogenetic analysis, strain K23C18032701 T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Deminuibacter soli is proposed. The type strain is K23C18032701 T (=GDMCC 1.1403 T =KCTC 62913 T ). We also propose the reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. (type strain 1458 T =NRRL B-65305 T =LMG 29039 T ).

A Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901 T , was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10' 24'' N; 112° 32' 10'' E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901 T belongs to the genus Chitinophaga, and showed the highest similarities to Chitinophaga sancti NBRC 15057 T (98.6 %) and Chitinophaga oryziterrae JCM 16595 T (96.9 %). The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901 T was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain K20C18050901 T and C. sancti NBRC 15057 T were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901 T represents a novel species of the genus Chitinophaga, for which the name Chitinophagasilvisoli sp. nov. is proposed. The type strain is K20C18050901 T (=GDMCC 1.1411 T =KCTC 62860 T ).

A nitrogen-fixing, endospore-forming bacterium, designated strain L201 T was isolated from the leaves of Bryophyllum pinnatum growing in South China Agricultural University. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L201 T is affiliated with the genus Paenibacillus, and closely related to Paenibacillus albidus Q4-3 T (97.4%), Paenibacillus odorifer DSM 15391 T (97.3%) and Paenibacillus borealis DSM 13188 T (97.2%). The main fatty acids components was anteiso-C 15:0 (48.1%). The predominant isoprenoid quinone was MK-7. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of strain L201 T was 43.9%. DNA-DNA relatedness between L201 T and the reference strain was 29.8%. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting and comparison of cellular fatty acids distinguished strain L201 T from the closely related Paenibacillus species. Based on these data, the novel species Paenibacillus bryophyllum sp. nov. is proposed, with the type strain L201 T (= KCTC 33951 T  = GDMCC 1.1251 T ).

Three bacterial isolates, designated W44 T , W15 and W11, were isolated from the root of Oryza officinalis grown in Wuzhou, China. These isolates were Gram-negative, aerobic, motile and rod-shaped; demonstrated cellulase and urea activities; and formed cream-coloured colonies. The 16S rRNA gene sequence analysis indicated that the similarities between strain W44 T and strains W15 and W11 were 100 %; all of them belonged to the genus Rhizobium and had the highest sequence similarity to Rhizobium rosettiformans W3 T (98.7 %), followed by Rhizobium ipomoeae shin9-1 T (98.2 %). Sequencing of housekeeping genes (recA, atpD, rpoB and glnA) of the novel isolates revealed similarities to members of established Rhizobium species to be less than 94.3 %. The values of DNA-DNA hybridization between strain W44 T and the reference strains (R. rosettiformans W3 T and R. ipomoeae shin9-1 T ) were 41.3 and 29.2 %, respectively. The major cellular fatty acid of strain W44 T was summed feature 8 (C18 : 1ω9t and/or C18 : 1ω9c and/or C18 : 1ω7c). The polar lipid profile of strain W44 T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified lipids and two unidentified aminophospholipids. The G+C content of strain W44 T was 62.4 mol%. In nodulation tests, none of the three strains could induce nodule formation in Glycine max, Phaseolus vulgaris or Medicago sativa. The nodulation gene (nodA), nitrogenase reductase gene (nifH) and virulence gene (virC) were not detected by PCR in these strains. Based on the above results and phenotypic features, a novel species, Rhizobium wuzhouense sp. nov., is proposed, with strain W44 T (=CCTCC AB 2017179 T =GDMCC 1.1257 T =KCTC 62194 T ) as the type strain.

The Dirichlet multinomial mixtures mode was used to analyse illumina sequencing data to reveal both temporal and spatial variations of the fungi community present in the aerobic composting. Results showed that 670 operational taxonomic units (OTUs) were detected, and the dominant phylum was Ascomycota. There were four types of samples fungi communities during the composting process. Samples from the early composting stage were mainly grouped into type I and Saccharomycetales sp. was dominant. Fungi community in the medium composting stage were fallen into type II and III, Sordariales sp. and Acremonium alcalophilum, Saccharomycetales sp. and Scedosporium minutisporum were the dominant OTUs respectively. Samples from the late composting stage were mainly grouped into type IV and Scedosporium minutisporum was the dominant OTU; Scedosporium minutisporum was significantly affected by depth (P<0.05). Results indicate that time and depth both are factors that influence fungi distribution and variation in c waste during static aerobic composting., (Copyright © 2017. Published by Elsevier Ltd.)

Background: One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits., Results: A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits., Conclusions: With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.

Key Message: Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao. Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F 2 individuals and 196 F 7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F 2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.

To achieve tumor-specific delivery of doxorubicin, TiO 2 @Fe 3 O 4 /PEI/delivery of doxorubicin conjugates were designed and synthesized. Fe 3 O 4 could act as magnetically responsive carriers and enhance the visible light photodynamic activities of TiO 2 Delivery of doxorubicin was conjugated via coordination bond. The drug release rate at pH 5.2 was much faster than that at pH 7.4, due to pH-sensitive coordination bond. Besides, TiO 2 @Fe 3 O 4 /PEI/delivery of doxorubicin showed high antitumor efficacy combining with phototherapy, good bio-safety, higher cellular uptake with an external magnetic field, and less toxicity in vitro and in vivo. These results suggested that TiO 2 @Fe 3 O 4 /PEI/delivery of doxorubicin may be promising for high tumor treatment efficacy with minimal side effects in future., (© The Author(s) 2016.)

Nodulation is an essential process for biological nitrogen (N2) fixation in legumes, but its regulation remains poorly understood. Here, a β-expansin gene, GmEXPB2, was found to be critical for soybean (Glycine max) nodulation. GmEXPB2 was preferentially expressed at the early stage of nodule development. β-Glucuronidase staining further showed that GmEXPB2 was mainly localized to the nodule vascular trace and nodule vascular bundles, as well as nodule cortical and parenchyma cells, suggesting that GmEXPB2 might be involved in cell wall modification and extension during nodule formation and development. Overexpression of GmEXPB2 dramatically modified soybean root architecture, increasing the size and number of cortical cells in the root meristematic and elongation zones and expanding root hair density and size of the root hair zone. Confocal microscopy with green fluorescent protein-labeled rhizobium USDA110 cells showed that the infection events were significantly enhanced in the GmEXPB2-overexpressing lines. Moreover, nodule primordium development was earlier in overexpressing lines compared with wild-type plants. Thereby, overexpression of GmEXPB2 in either transgenic soybean hairy roots or whole plants resulted in increased nodule number, nodule mass, and nitrogenase activity and thus elevated plant N and phosphorus content as well as biomass. In contrast, suppression of GmEXPB2 in soybean transgenic composite plants led to smaller infected cells and thus reduced number of big nodules, nodule mass, and nitrogenase activity, thereby inhibiting soybean growth. Taken together, we conclude that GmEXPB2 critically affects soybean nodulation through modifying root architecture and promoting nodule formation and development and subsequently impacts biological N2 fixation and growth of soybean., (© 2015 American Society of Plant Biologists. All Rights Reserved.)

Uniform dispersion of Au-Ag alloy nanoparticles underneath the surface of a Si wafer is realized via Au film pre-deposition and Ag ion implantation. The Au-Ag nanoparticles are used as catalysts in metal assisted chemical etching for fabricating Si nanowire arrays with average diameters of less than 10 nm. We find that the alloy catalysts introduced by ion implantation are the key to obtaining thin nanowire arrays and we also demonstrate that SiNWAs with various diameters could be simply produced by changing the thickness of the pre-deposited Au layer. Compared with the traditional process, ion beam assisted chemical etching is proven to be a convenient and efficient approach to fabricate ultra-thin SiNWAs on a large scale.

Objective: The longer the Pericarpium Citri Reticulatae is preserved, the better medicinal values will be. The present work aims to isolate beneficial microbes isolated from the 7-year orange peel that might be used to produce high quality Pericarpium Citri Reticulatae., Methods: The microbes isolated from the 7-year orange peel using 4 mediums were grouped by SDS-PAGE patterns of the whole-cell protein electrophoresis and IS-PCR DNA fingerprinting. The representative strains were further studied by physiological and biochemical tests, and phylogeny analysis., Results: Total 23 bacteria were obtained from the 7-year orange peel. These strains were classified into 4 groups: the strains of group I belonged to Bacillus; the strains of group II, group III and group IV were closed to Paenibacillus., Conclusion: Among the representative strains of group I, II, III and IV, only the representative strain cp20 of group II has the ability of strong utilizing citrate obviously. The strain cp20 of group II were further applied to making Pericarpium Citri Reticulatae.

Soil and water quality is greatly affected by environmental pollution due to the increasing trend of urbanization and industrialization. In many developing countries, including Pakistan, the situation is more alarming as no preventive measures are still taken to tackle the problem. Although in developed countries, many techniques are used to remediate the environment including phytoremediation. It is the most eco-friendly technique in which plants are used to remove pollutants from the environment. Pakistan has also a great diversity of plants which could be used for the remediation of environmental pollutants. To our knowledge, few studies from Pakistan were reported about the use of flora for phytoremediation. According to recent literature, 50 plant species from Pakistan are studied for remediation purposes. In this review, the potential of different plant species for phytoremediation from Pakistan has been discussed along with their comparison to other countries to relate future perspectives.

Objective: We isolated myxobacteria and explored their diversity from the rhizosphere soils of some medicinal plants., Methods: We used the helper bacteria baiting technique to isolate myxobacteria from the rhizosphere soils collected in South China Botanical Garden and Nanling National Forest Park. The myxobacteria were identified by morphological characteristics and 16S rDNA gene sequences analysis., Results: A total of 50 strains were isolated from 22 soil samples, which were identified into 7 genera, Myxococcus (18), Corallococcus (11), Cystobacter (7), Archangium (8), Stigmatella (1), Chondromyces (4) and Pyxidicoccus (1). The dominant genera were Myxococcus and Corallococcus., Conclusion: Environmental factors were associated with the diversity of myxobactria. Myxobacteria better adapt in high organic matter content and neutral pH environments. The strains of Myxococcus and Corallococcus had a good adaptability for different pH. Meanwhile, the dependence of the strains of Myxococcus and Cystobacter on organic carbon content was not too obvious, and they can also be found in the poor soils. Our findings provided an important scientific base for the development and utilization of myxobacteria resources.

Thirty-three endophytic diazotrophs were isolated from surface-sterilized leaves, stem, and roots of wild rice Oryza alta. The SDS-PAGE profile of total protein and insertion sequence-based polymerase chain reaction (IS-PCR) fingerprinting grouped the isolates into four clusters (I-IV). The 16S rRNA gene sequence homology of the representative strains B21, B31, B1, and B23 of clusters I, II, III, and IV were assigned to Pseudomonas oleovorans (99.2% similarity), Burkholderia fungorum (99.4% similarity), Enterobacter cloacae (98.9% similarity), and Acinetobacter johnsonii (98.4% similarity), respectively. The results showed wide genetic diversity of the putative diazotrophic strains of the wild rice, O. alta, and the strains of cluster IV are the first report of nitrogen-fixing Acinetobacter species. The cell size, phenotypic characters, total protein profile, genomic DNA fingerprinting, DNA-DNA hybridization, and antibiotic resistance differentiated strain B23(T) from its closest relatives A. johnsonii LMG999(T) and Acinetobacter haemolyticus LMG996(T). The DNA-DNA hybridization also distinguished the strain B23(T) from the closely related Acinetobacter species. Based on these data, a novel species, Acinetobacter oryzae sp. nov., and strain B23(T) (=LMG25575(T) = CGMCC1.10689(T)) as the type strain were proposed.

Objective: To isolate myxobacteria and investigate their diversity in saline-alkaline soils from Akesu in Xinjiang., Methods: Conventional culture-dependent methods, e. g. baiting technique, water agar, soil extract agar and mineral agar, were used to isolate myxobacteria from 25 soil samples collected from Akesu areas of Xinjiang. Combining with physicochemical properties (acidity/alkalinity, salt concentration, vegetation and geographical locations) of the soil samples, myxobacterial diversity was studied., Results: In total 58 strains were isolated, and identified as belonging to 6 different genera, i.e. Myxococcus, Cystobacter, Corallococcus, Sorangium, Nannocystis and Polyangium of Myxococcales. The most frequent genus isolated was Myxococcus which may better adapt in harsh environments. Different myxobacterial diversity was detected in different habitat., Conclusion: Myxobacteria diversity was low in saline-alkaline soils of Akesu in Xinjiang.

Objective: Vetiver zizanioides is a perennial grass of the Poaceae family, known of its silage, soil and water conservation role. The aim of the study was to collect and identify the resources of the nitrogen-fixing bacteria associated with Vetiver zizanioides., Methods: Associated nitrogen-fixing bacteria isolated from Vetiver zizanioides were studied by SDS-PAGE whole-cell protein patterns, insert sequence (IS)-PCR finger printing, utilization of sole carbon sources and 16S rRNA gene sequence analysis., Results: Based on the results of finger printing analysis, protein patterns and biological test, isolates were grouped into 6 clusters, except 4 single strains. Phylogenetic analysis of 16S rDNA sequences indicated that isolates belonged to Herbaspirillum frisingense, Enterobacter ludwigii, Pseudacidovorax intermedius, Mitsuaria chitosanitabida, Pseudomonas putida, Pseudomonas fluorescens, Burkholderia vietnamiensis and Enterobacter cloacae., Conclusion: The nitrogen fixers associated with Vetiver zizanioides showed great diversity and may have a potential application for the grass forage and agriculture.

Twelve facultatively anaerobic, endophytic diazotrophs were isolated from surface-sterilized roots of the wild rice species Oryza latifolia and characterized by phenotypic and molecular methods. Six isolates were grouped together as group A by phenotypic characters, and this grouping was confirmed by SDS-PAGE whole-cell protein patterns and insertion sequence-based PCR (IS-PCR) methods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that group A, represented by strain Ola 51(T), is closely related to Enterobacter radicincitans D5/23(T) (98.9 % similarity, except that E. radicincitans D5/23(T) has a 70 bp insertion) and Enterobacter cloacae (98.0 % similarity to the type strain). rpoB gene sequence analysis also showed strain Ola 51(T) has the highest sequence similarity to E. radicincitans DSM 16656(T) (98.3 %), but supported the distinct position. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, antibiotic resistance and comparison of cellular fatty acids showed differences among group A, E. radicincitans DSM 16656(T) and E. cloacae ATCC 13047(T). DNA-DNA hybridization distinguished strain Ola 51(T) from closely phylogenetically related Enterobacter species. Based on these data, the novel species Enterobacter oryzae sp. nov. is proposed, with strain Ola 51(T) (=LMG 24251(T) =CGMCC 1.7012(T)) as the type strain.

Objective: Bermuda grass white leaf is an important disease on Bermuda grass all over the world. The aim of this research is to identify the pathogen which leads to Bermuda grass white leaf occurring on the Chinese mainland., Methods: PCR amplification technique, sequence analysis and Southern hybridization were used., Results: A 1.3 kb fragment was amplified by PCR phytoplasma universal primers and total DNA sample extracted from ill Bermuda grass as the amplified template. Sequence analysis of the amplified fragment indicated it clustered into Candidatus Phytoplasm Cynodontis. Southern hybridization analysis showed differential cingulums., Conclusion: The pathogen of Bermuda grass white leaf on the Chinese mainland contains phytoplasma, which provides a scientific basis for further identification, prevention and control of the disease.

During a study of endophytic nitrogen-fixing bacteria present in the wild rice species Oryza alta, eight novel isolates were obtained from surface-sterilized roots and classified in the genus Rhizobium on the basis of almost-complete 16S rRNA gene sequence analysis. These strains can nodulate Phaseolus vulgaris and Glycine max. The highly similar protein patterns, DNA fingerprint patterns of insertion sequence-based PCR (IS-PCR) and DNA-DNA hybridizations showed that these novel isolates were members of the same species. The closest phylogenetic relatives of the representative strain Alt 505(T) of the novel group were Rhizobium etli CFN 42(T) and Rhizobium indigoferae CCBAU 71714(T), with 96.2 and 96.0% 16S rRNA gene sequence similarity, respectively. Low DNA-DNA relatedness with the type strains of R. etli, R. indigoferae, Rhizobium hainanense, Rhizobium mongolense and Rhizobium galegae and differences in IS-PCR fingerprinting patterns, SDS-PAGE of proteins, antibiotic resistance, phenotypic tests and comparison of cellular fatty acids with Rhizobium species indicated that the novel group of isolates were distinct from previously described species. Based on these results, we propose to place them in a novel species, as Rhizobium oryzae sp. nov. The type strain is Alt 505(T) (=LMG 24253(T) =CGMCC 1.7048(T)).

Fifteen bacterial strains isolated from molasses grass (Melinis minutiflora Beauv.) were identified as nitrogen-fixers by using the acetylene-reduction assay and PCR amplification of nifH gene fragments. These strains were classified as a unique group by insertion sequence-PCR fingerprinting, SDS-PAGE protein patterns, DNA-DNA hybridization, 16S rRNA gene sequencing and morphological characterization. Phylogenetic analysis of the 16S rRNA gene indicated that these diazotrophic strains belonged to the genus Azospirillum and were closely related to Azospirillum lipoferum (with 97.5 % similarity). In all the analyses, including in addition phenotypic characterization using Biolog MicroPlates and comparison of cellular fatty acids, this novel group was found to be different from the most closely related species, Azospirillum lipoferum. Based on these data, a novel species, Azospirillum melinis sp. nov., is proposed for these endophytic diazotrophs of M. minutiflora, with TMCY 0552(T) (=CCBAU 5106001(T) = LMG 23364(T) = CGMCC 1.5340(T)) as the type strain.

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified nitrogenase gene (nifH) fragments is a rapid technique for profiling of diazotrophic microbial communities without the necessity of cultures for study. Here, we examined the impact of N-fertilization, plant genotype and environmental conditions on diazotrophic microbial populations in association with roots of rice (Oryza species) by T-RFLP community profiling and found marked effects on the composition of the microbial community. We found a rapid change of the diazotrophic population structure within 15 days after application of nitrogen fertilizer and a strong effect of environmental conditions and plant genotype. Control experiments revealed that phylogenetically distantly related nifH genes were proportionately amplified, and that signal strength reflected the relative abundance of nifH genes in the sample within a 10-fold range of template concentrations. These results clearly demonstrated that our T-RFLP method was suitable to reflect compositional differences in the diazotrophic community in a semiquantitative manner and that the diazotrophic rhizosphere communities of rice are not static but presumably rather highly dynamic.

In order to clarify the taxonomic position of Dechlorosoma suillum, which shares 99.9% 16S rDNA sequence identity (1433 of 1435 bp) with Azospira oryzae, we compared the two species in a polyphasic taxonomic approach. Results of 122 physiological and biochemical tests for D. suillum DSM 13638T and Azospira oryzae 6a3T were identical, except for the lack of growth of Azospira oryzae 6a3T with perchlorate as the terminal electron acceptor. Presence of a nifH gene and nitrogenase activity, a key feature of Azospira, were also detected in D. suillum by Southern hybridization and by the acetylene reduction assay, respectively. Whole-cell SDS-PAGE profiles of SDS-soluble proteins of strains DSM 13638T and 6a3T were almost identical. DNA-DNA hybridization studies showed more than 90% binding between D. suillum and two strains of Azospira oryzae. These data provide evidence that the two bacteria belong to the same species and that D. suillum is a later subjective synonym of Azospira oryzae.