Proc Natl Acad Sci U S A , IF:9.412 , 2020 May , V117 (19) : P10234-10245 doi: 10.1073/pnas.1917471117
Global control of bacterial nitrogen and carbon metabolism by a PTS(Ntr)-regulated switch.
Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom.; Soil Ecology, Rheinisch-Westfalische Technische Hochschule (RWTH) Aachen, D-52056 Aachen, Germany.; Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom.; Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom; philip.poole@plants.ox.ac.uk.
The nitrogen-related phosphotransferase system (PTS(Ntr)) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTS(Ntr) constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTS(Ntr) is widely conserved in proteobacteria, highlighting its global importance.
PMID: 32341157
J Hazard Mater , IF:9.038 , 2020 May , V389 : P122082 doi: 10.1016/j.jhazmat.2020.122082
Changes in microbial community structure during pig manure composting and its relationship to the fate of antibiotics and antibiotic resistance genes.
Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand.; Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China.; College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; Scion, Private Bag 29237, Christchurch, New Zealand.; Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand.; Scion, Private Bag 29237, Christchurch, New Zealand.; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. Electronic address: lizhaojun@caas.cn.
Animal manure containing veterinary antibiotics is a significant source of microbial antibiotic resistance genes (ARGs). Composting of animal manure with wheat straw and sawdust was explored as a means to reduce ARGs load in the final material. The effects of ciprofloxacin, oxytetracycline, sulfamerazine on the bacterial community composition, and how this then affected the removal of seven tetracycline resistance genes (TARGs), four sulfonamide resistance genes (SARGs), and two fluoroquinolone resistance genes (QARGs) were investigated. Treatments receiving either ciprofloxacin or the three mixed antibiotics had reduced bacterial alpha-diversity and displayed shifts in the abundance of Proteobacteria and Firmicutes. This demonstrated that different antibiotics played an important role in bacterial community composition. Furthermore, variation in the physicochemical properties of compost, particularly pH and temperature, was also strongly linked to shifts in bacterial composition over time. Based on network analysis, the reduction of TARGs were associated with loss of Pseudomonas, Pseudoxanthomonas, Pusillimonas, Aquamicrobium, Ureibacillus, Lysinibacillus, Bacillus and Brachybacterium during the thermophilic stage. However, QARGs and SARGs were more strongly affected by the presence of multiple antibiotics. Our results have important implications for reducing the spread of certain ARGs by controlling the composting temperature, pH or the antibiotics species used in husbandry.
PMID: 32004835
Addiction , IF:6.343 , 2020 May , V115 (5) : P944-945 doi: 10.1111/add.14949
Commentary on Pacek et al. (2019): Cannabis and major depression-a network theory proposal.
Department of Psychological Medicine, University of Otago, Christchurch, New Zealand.
PMID: 31981263
J Exp Bot , IF:5.908 , 2020 May , V71 (10) : P2943-2955 doi: 10.1093/jxb/eraa052
ZmIBH1-1 regulates plant architecture in maize.
College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China.
Leaf angle (LA) is a critical agronomic trait in maize, with more upright leaves allowing higher planting density, leading to more efficient light capture and higher yields. A few genes responsible for variation in LA have been identified by map-based cloning. In this study, we cloned maize ZmIBH1-1, which encodes a bHLH transcription factor with both a basic binding region and a helix-loop-helix domain, and the results of qRT-PCR showed that it is a negative regulator of LA. Histological analysis indicated that changes in LA were mainly caused by differential cell wall lignification and cell elongation in the ligular region. To determine the regulatory framework of ZmIBH1-1, we conducted RNA-seq and DNA affinity purification (DAP)-seq analyses. The combined results revealed 59 ZmIBH1-1-modulated target genes with annotations, and they were mainly related to the cell wall, cell development, and hormones. Based on the data, we propose a regulatory model for the control of plant architecture by ZmIBH1-1 in maize.
PMID: 31990030
Pest Manag Sci , IF:3.75 , 2020 May , V76 (5) : P1881-1892 doi: 10.1002/ps.5719
Relevance of the ecological traits of parasitoid wasps and nectariferous plants for conservation biological control: a hybrid meta-analysis.
Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agriculture Sciences, Hangzhou, China.; School of Agricultural and Wine Sciences, Charles Sturt University, Orange, NSW, Australia.; Jinhua Plant Protection Station, Jinhua, China.; Research Office, Charles Sturt University, Wagga Wagga, NSW, Australia.
BACKGROUND: Ecosystem services are key to human survival. In agriculture, they offer potential to intensify production while reducing reliance on hazardous inputs, including pesticides. Nectar plants can nourish natural enemies of pests and thereby promote the ecosystem service of biological control. To date, however, the selection of optimal plants has been reliant on laborious testing of multiple candidate species for use in each new agroecosystem. We report a hybrid meta-analysis of published literature, employing Bayesian network analysis. RESULTS: The hybrid meta-analysis identified the particular plant and parasitoid traits that were most predictive of promoted or suppressed parasitoid longevity. Integrating trait effects identified a combination of plant-parasitoid traits that had the highest impact on parasitoid longevity: compound umbel or raceme inflorescence form and shallow corolla, together with high potential fecundity of the parasitoid. CONCLUSION: Unlike earlier analyses focusing on taxonomic categories, we analyzed effect sizes in relation to the ecological traits of parasitoids and plants. This generated the first generalizable guidelines for selecting nectar plants as well as appropriate parasitoid targets for the enhancement of biological control. Within the guidelines, optimal outcomes resulted when plants with compound umbel or raceme inflorescences and shallow corollas were combined with fecund parasitoids. More widely, this type of ecological trait-based meta-analysis opens a new avenue for optimizing the delivery of other types of ecosystem services. (c) 2019 Society of Chemical Industry.
PMID: 31840379
FEMS Microbiol Ecol , IF:3.675 , 2020 May , V96 (5) doi: 10.1093/femsec/fiaa060
Aggregate size-dependence of bacterial community separation in a full-scale membrane bioreactor plant.
School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China.; Division of Energy and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China.
The size of bacterial aggregates can determine both nutrient removal and sludge/water separation in activated sludge processes. In this study, the bacterial community structures and network associations of different sized aggregates obtained from a full-scale membrane bioreactor plant over a one-year period were investigated. Our results showed that biodiversity of larger sized aggregates was significantly higher than that of smaller ones and that the bacterial compositions of different sized aggregates differed significantly from each other. Bacteria related to nutrient removal (e.g. denitrification, hydrolysis and fermentation) were found to be significantly more abundant in larger aggregates than smaller ones. Network analysis revealed significant difference in species-species interactions, topological roles of individual OTU and keystone populations among different sized aggregates. Moreover, the occurrence of keystone OTUs affiliated with denitrifiers (Thermomonas) in networks of large and medium aggregates may suggest that denitrification influences bacterial interactions in large and medium aggregates. Overall, our results indicate the aggregates size-dependence of bacterial community separation in activated sludge. The current findings not only can provide guidance for process design and operation optimization, but also highlight the necessity for paying more attentions to the aggregate-based community, metabolic function and gene expression of activated sludge in future studies.
PMID: 32275301
BMC Plant Biol , IF:3.497 , 2020 May , V20 (1) : P193 doi: 10.1186/s12870-020-02419-y
Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency.
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China. yangxinghai514@163.com.; Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.; Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.; Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.; Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.; Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China. ricegl@163.com.; Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China. dengguofu@gxaas.net.
BACKGROUND: Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS: We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. CONCLUSIONS: In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.
PMID: 32375632
Epilepsy Behav , IF:2.508 , 2020 May , V106 : P107013 doi: 10.1016/j.yebeh.2020.107013
Interictal structural and functional connectivity in idiopathic generalized epilepsy: A systematic review of graph theoretical studies.
Department of Neurology, Manchester Centre for Clinical Neurosciences, United Kingdom; Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom. Electronic address: Emily-pegg@doctors.org.uk.; Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom; Manchester Academic Health Sciences Centre, United Kingdom.; Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, United Kingdom; The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom.; Department of Neurology, Manchester Centre for Clinical Neurosciences, United Kingdom; Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom.
The evaluation of the role of anomalous neuronal networks in epilepsy using a graph theoretical approach is of growing research interest. There is currently no consensus on optimal methods for performing network analysis, and it is possible that variations in study methodology account for diverging findings. This review focuses on global functional and structural interictal network characteristics in people with idiopathic generalized epilepsy (IGE) with the aim of appraising the methodological approaches used and assessing for meaningful consensus. Thirteen studies were included in the review. Data were heterogenous and not suitable for meta-analysis. Overall, there is a suggestion that the cerebral neuronal networks of people with IGE have different global structural and functional characteristics to people without epilepsy. However, the nature of the aberrations is inconsistent with some studies demonstrating a more regular network configuration in IGE, and some, a more random topology. There is greater consistency when different data modalities and connectivity subtypes are compared separately, with a tendency towards increased small-worldness of networks in functional electroencephalography/magnetoencephalography (EEG/MEG) studies and decreased small-worldness of networks in structural studies. Prominent variation in study design at all stages is likely to have contributed to differences in study outcomes. Despite increasing literature surrounding neuronal network analysis, systematic methodological studies are lacking. Absence of consensus in this area significantly limits comparison of results from different studies, and the ability to draw firm conclusions about network characteristics in IGE.
PMID: 32193094
Yi Chuan , IF:2.412 , 2020 May , V42 (5) : P506-518 doi: 10.16288/j.yczz.20-070
Analysis of rice root bacterial microbiota of Nipponbare and IR24.
School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
The root-associated bacterial microbiota is closely related to life activities of land plants, and its composition is affected by geographic locations and plant genotypes. However, the influence of plant genotypes on root microbiota in rice grown in northern China remains to be explained. In this study, we performed 16S rRNA gene amplicon sequencing to generate bacterial community profiles of two representative rice cultivars, Nipponbare and IR24. They are planted in Changping and Shangzhuang farms in Beijing and have reached the reproductive stage. We compared their root microbiota in details by Random Forest machine learning algorithm and network analysis. We found that the diversity of rice root microbiota was significantly affected by geographic locations and rice genotypes. Nipponbare and IR24 showed distinct taxonomic composition of the root microbiota and the interactions between different bacteria. Moreover, the root bacteria could be used as biomarkers to distinguish Nipponbare from IR24 across regions. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota in Northern China and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.
PMID: 32431301