Environ Sci Technol , IF:9.028 , 2023 Sep , V57 (37) : P13901-13911 doi: 10.1021/acs.est.3c03778
Polyethylene Degradation by a Rhodococcous Strain Isolated from Naturally Weathered Plastic Waste Enrichment.
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States.; Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States.; Marine College, Shandong University, Weihai 264105, China.; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States.; Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States.
Polyethylene (PE) is the most widely produced synthetic polymer and the most abundant plastic waste worldwide due to its recalcitrance to biodegradation and low recycle rate. Microbial degradation of PE has been reported, but the underlying mechanisms are poorly understood. Here, we isolated a Rhodococcus strain A34 from 609 day enriched cultures derived from naturally weathered plastic waste and identified the potential key PE degradation enzymes. After 30 days incubation with A34, 1% weight loss was achieved. Decreased PE molecular weight, appearance of C-O and C horizontal lineO on PE, palmitic acid in the culture supernatant, and pits on the PE surface were observed. Proteomics analysis identified multiple key PE oxidation and depolymerization enzymes including one multicopper oxidase, one lipase, six esterase, and a few lipid transporters. Network analysis of proteomics data demonstrated the close relationships between PE degradation and metabolisms of phenylacetate, amino acids, secondary metabolites, and tricarboxylic acid cycles. The metabolic roadmap generated here provides critical insights for optimization of plastic degradation condition and assembly of artificial microbial communities for efficient plastic degradation.
PMID: 37682848
Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Sci Total Environ , IF:7.963 , 2023 Sep , V905 : P167075 doi: 10.1016/j.scitotenv.2023.167075
Risk assessment framework for pine wilt disease: Estimating the introduction pathways and multispecies interactions among the pine wood nematode, its insect vectors, and hosts in China.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; The College of Forestry, Beijing Forestry University, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.; Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.; The College of Forestry, Beijing Forestry University, Beijing 100193, China. Electronic address: shi_juan@263.net.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: liuwanxue@caas.cn.
Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), a destructive, invasive forest pathogen, poses a serious threat to global pine forest ecosystems. The global invasion of PWN has been described based on three successive phases, introduction, establishment, and dispersal. Risk assessments of the three successive PWN invasion phases can assist in targeted management efforts. Here, we present a risk assessment framework to evaluate the introduction, establishment, and dispersal risks of PWD in China using network analysis, species distribution models, and niche concepts. We found that >88 % of PWN inspection records were from the United States, South Korea, Japan, Germany, and Mexico, and 94 % of interception records were primarily from the Jiangsu, Shanghai, Shandong, Tianjin, and Zhejiang ports. Based on the nearly current climate, the areas of PWN overlap with its host Pinus species were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions. Areas of PWN overlap with its insect vector Monochamus alternatus were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions, and those of PWN overlap with the insect vector Monochamus saltuarius were primarily distributed in eastern and northeastern China. The niche between PWN and the insect vector M. alternatus was the most similar (0.68), followed by that between PWN and the insect vector M. saltuarius (0.47). Climate change will increase the suitable probabilities of PWN and its two insect vectors occurring at high latitudes, further increasing their threat to hosts in northeastern China. This risk assessment framework for PWD could be influential in preventing the entry of the PWN and mitigating their establishment and dispersal risks in China. Our study provides substantial clues for developing a framework to improve the risk assessment and surveillance of biological invasions worldwide.
PMID: 37714356
Sci Total Environ , IF:7.963 , 2023 Nov , V900 : P165800 doi: 10.1016/j.scitotenv.2023.165800
Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields.
Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland. Electronic address: Mikhail.sofiev@fmi.fi.; Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center, Munich, Germany.; Federal Office of Meteorology and Climatology MeteoSwiss, Chemin de l'Aerologie 1, 1530 Payerne, Switzerland.; Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland.; Faculty of Geography and Earth Sciences, University of Latvia, Rainis bvld 19, Riga LV-1586, Latvia.; University of Worcester, UK.; Institute of Allergology, Charite - Universitatsmedizin Berlin, Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.; Department of Biology and Environmental Sciences, University of Gothenburg, Box 461, S-405 30 Gothenburg, Sweden.; Deutscher Wetterdienst, Berlin, Germany.; National Laboratory of Health, Environment and Food, Slovenia.; School of Chemical Sciences, Dublin City University, Ireland.; Department of Botany, Ecology and Plant Physiology, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Rabanales Campus, Celestino Mutis Building, E-14071 Cordoba, Spain; Andalusian Inter-University Institute for Earth System IISTA, University of Cordoba, Spain.; Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Pole of the Faculty of Sciences, University of Porto, Portugal.; German Pollen Information Service Foundation (PID), Berlin, Germany.
We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constraints for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data.
PMID: 37595925
Sci Total Environ , IF:7.963 , 2023 Nov , V897 : P165441 doi: 10.1016/j.scitotenv.2023.165441
Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers.
The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.; The National Key Laboratory of Water Disaster Prevention, Dayu College, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China. Electronic address: envly@hhu.edu.cn.
In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.
PMID: 37437635
Sci Total Environ , IF:7.963 , 2023 Oct , V896 : P165249 doi: 10.1016/j.scitotenv.2023.165249
Response of heavy-metal and antibiotic resistance genes and their related microbe in rice paddy irrigated with treated municipal wastewaters.
China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China. Electronic address: qyan2005@hotmail.com.
Paddy irrigation with secondary effluents from municipal wastewater treatment plants (MWTPs) is a well-established practice to alleviate water scarcity. However, the reuse might lead to more complicated contamination caused by interactions between residual antibiotics in effluents and heavy metals in paddy soil. To date, no information is available for the potential effects of dual stress of heavy metals and antibiotics on heavy-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Here, this study investigated the response of heavy metal and antibiotic resistance genes, and related microorganisms to the dual threat of antibiotics and heavy metals under the long-term MWTP effluent irrigation for rice paddy using metagenome. The results showed that there was not a negative effect on rice consumption if MWTP effluent was used to irrigate rice for a long time. The concentration of antibiotics could reshape the ARGs and MRG profiles in rice paddy soil. The findings revealed the co-occurrence of ARGs and MRGs in rice paddy soils, thus highlighting the need for simultaneous elimination of antibiotics and heavy metals to effectively reduce ARGs and MRGs. Acn and sul1 genes encoding Iron and sulfonamides resistance mechanisms are the most abundant MRG and ARG, respectively. Network analysis revealed the possibility that IntI1 plays a role in the co-transmission of MRG and ARG to host microbes, and that Proteobacteria are the most dominant hosts for MRG, ARG, and integrons. The presence of antibiotics in irrigated MWTP effluents has been found to stimulate the proliferation of heavy metal and antibiotic resistances by altering soil microbial communities. This study will enhance our comprehension of the co-selection between ARGs and MRGs, as well as reveal the concealed environmental impacts of combined pollution. The obtained results have important implications for food safety and human health in rice.
PMID: 37406708
Sci Total Environ , IF:7.963 , 2023 Oct , V895 : P165099 doi: 10.1016/j.scitotenv.2023.165099
Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry.
Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: liucongqiang@tju.edu.cn.; School of Environment Studies, China University of Geosciences, Wuhan 430074, China.; LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: fupingqing@tju.edu.cn.
Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.
PMID: 37379928
Sci Total Environ , IF:7.963 , 2023 Sep , V892 : P164506 doi: 10.1016/j.scitotenv.2023.164506
Diversity of fungal microbiome obtained from plant rhizoplanes.
Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA.; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA.; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.; Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA. Electronic address: dfrigirodrigues@uh.edu.
Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.
PMID: 37295515
Waste Manag , IF:7.145 , 2023 Sep , V172 : P33-42 doi: 10.1016/j.wasman.2023.09.003
Waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis promote tomato seedlings growth by benefiting properties, enzyme activities and rhizosphere bacterial community in coastal saline soil of Yellow River Delta, China.
College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China.; Citrus Research Institute, Southwest University, Chongqing 400712, China.; Weihai Academy of Agricultural Sciences, Weihai 264200, China.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: houxin.sdau@163.com.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: yanglong1020@163.com.
This study investigated the effects of waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis HCH2-3 on the tomato seedlings growth in coastal saline soils and chemical properties, enzyme activities, microbial communities of rhizosphere soil. Microcosmic experiment showed that the seaweed compost and rhizosphere bacteria (SC + HCH2-3) significantly alleviated the negative effects of salinity on the growth of tomato seedlings. SC + HCH2-3 amendment significantly increased the plant height and root fresh biomass of tomato seedling by 105.59% and 55.60% in the coastal saline soils, respectively. The soil properties and enzyme activities were also dramatically increased, indicating that the nutrient status of coastal saline soil was improved by SC + HCH2-3 amendment. In addition, Proteobacteria, Actinobacteriota and Firmicutes were the dominant phyla in the rhizosphere soil after adding seaweed compost and rhizosphere bacteria P. koreensis HCH2-3. The relative abundances of Massilia, Azospira, Pseudomonas and Bacillus increased in treatment SC + HCH2-3. Especially, the beneficial bacteria genera, such as Pseudomonas, Bacillus and Azospira, were significantly correlated with the increases of contents of total nitrogen, nitrate nitrogen and ammonium nitrogen in tomato rhizosphere soil samples. Consequently, adding waste seaweed compost and rhizosphere bacteria P. koreensis HCH2-3 into coastal saline soil was suggested as an effective method to relieve salt stress of tomato plants.
PMID: 37708810
Genes Dis , IF:7.103 , 2023 Sep , V10 (5) : P2049-2063 doi: 10.1016/j.gendis.2022.09.009
The transcriptional regulators of virulence for Pseudomonas aeruginosa: Therapeutic opportunity and preventive potential of its clinical infections.
College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.; Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, Guangdong 510006, China.; Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong 518057, China.
In Pseudomonas aeruginosa (P. aeruginosa), transcription factors (TFs) are important mediators in the genetic regulation of adaptability and pathogenicity to respond to multiple environmental stresses and host defences. The P. aeruginosa genome harbours 371 putative TFs; of these, about 70 have been shown to regulate virulence-associated phenotypes by binding to the promoters of their target genes. Over the past three decades, several techniques have been applied to identify TF binding sites on the P. aeruginosa genome, and an atlas of TF binding patterns has been mapped. The virulence-associated regulons of TFs show complex crosstalk in P. aeruginosa's regulatory network. In this review, we summarise the recent literature on TF regulatory networks involved in the quorum-sensing system, biofilm formation, pyocyanin synthesis, motility, the type III secretion system, the type VI secretion system, and oxidative stress responses. We discuss future perspectives that could provide insights and targets for preventing clinical infections caused by P. aeruginosa based on the global regulatory network of transcriptional regulators.
PMID: 37492705
J Exp Bot , IF:6.992 , 2023 Sep doi: 10.1093/jxb/erad348
Barley shows reduced Fusarium Head Blight under drought and modular expression of differential expressed genes under combined stress.
Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany.; Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany.; LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising-Weihenstephan, Germany.; Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3/I, 85354 Freising-Weihenstephan, Germany.; Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Strasse 34, 85354 Freising-Weihenstephan, Germany.; Institute of Phytopathology, Christian Albrecht University of Kiel, Hermann-Rodewald-Strasse 9, 24118 Kiel, Germany.
Plants often face simultaneous abiotic and biotic stress conditions. However, physiological and transcriptional responses of plants under combined stress situations still need to be understood. Spring barley is susceptible to Fusarium Head Blight (FHB), which is strongly affected by weather conditions. We therefore studied the potential influence of drought on FHB severity and responses in three differently susceptible spring barley varieties. We found strongly reduced FHB severity in susceptible varieties under drought. The number of differentially expressed genes (DEGs) and strength of transcriptomic regulation reflected the concentration of physiological stress markers such as abscisic acid or fungal DNA contents. Infection-related gene expression is associated with susceptibility rather than resistance. Weighted gene correlation network analysis uncovered 18 modules of co-expressed genes, which reflect the pathogen or drought response in the used varieties. A generally infection-related module contained co-expressed genes for defence, programmed cell death and mycotoxin-detoxification indicating that diverse genotypes use a similar defence strategy towards FHB, albeit with different success. Further, DEGs showed co-expression in drought or genotype-associated modules correlating with measured phytohormones or the osmolyte proline. The combination of drought stress with infection led to the highest numbers of DEGs and provoked a modular composition of single stress responses rather than a specific transcriptional readout.
PMID: 37668551
Int J Biol Macromol , IF:6.953 , 2023 Sep , V253 (Pt 1) : P126558 doi: 10.1016/j.ijbiomac.2023.126558
Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress.
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China. Electronic address: bqli@mail.hzau.edu.cn.; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China. Electronic address: yxy@mail.hzau.edu.cn.
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
PMID: 37659489
Environ Res , IF:6.498 , 2023 Oct , V234 : P116499 doi: 10.1016/j.envres.2023.116499
Community recovery of benthic macroinvertebrates in a stream influenced by mining activity: Importance of microhabitat monitoring.
Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: mjbae@nnibr.re.kr.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: ejkim@nnibr.re.kr.
The decrease in freshwater biodiversity owing to anthropogenic disturbances such as mining activity is a global challenge; hence, there is an urgent need for systematic approaches to continuously monitor such disturbances and/or the recovery of biodiversity in freshwater habitats. The Hwangjicheon Stream is the source of South Korea's longest river and has been subjected to runoff from coal mining. We investigated changes in the diversity of the benthic macroinvertebrate community in various microhabitats, including riffle, run, and pool, to monitor the recovery of biodiversity in the stream following the improvement of a mining water treatment plant in 2019. The dataset comprised 111 samples obtained from four types of microhabitats (riffle, run, pool, and riparian) over a four-year period from 2018 to 2021. The mining-affected sites had lower macroinvertebrate community complexities according to a network analysis, and grouped into the same cluster based on self-organizing map (SOM) analysis. Moreover, 51 taxa selected as indicator species represented each cluster obtained through the SOM analysis. Among them, only Limnodrilus gotoi and Radix auricularia were included as indicator species at the mining-affected sites. However, after 2020, the benthic macroinvertebrate community complexity increased, and some of the microhabitats at the mining-affected sites were included in the same cluster as the reference sites in the SOM analysis, indicating that the recovery of benthic macroinvertebrate communities had initiated in certain microhabitats (e.g., riparian). Further analysis confirmed that the macroinvertebrate community clearly differed according to the survey year, even in different microhabitats at the same sites. This suggests that more acute microhabitat monitoring may be necessary to quickly confirm biodiversity restoration when assessing the degree of the recovery in river biodiversity from anthropogenic disturbances.
PMID: 37429394
mSystems , IF:6.496 , 2023 Aug , V8 (4) : Pe0044023 doi: 10.1128/msystems.00440-23
Paired associated SARS-CoV-2 spike variable positions: a network analysis approach to emerging variants.
Department of Microbiology, Medical School, National and Kapodistrian University of Athens , Athens, Greece.; ELGO-Demeter, Plant Protection Division of Patras, Laboratory of Virology , Patras, Greece.; Department of Medicine, Stanford University , Stanford, California, USA.; Departments of Epidemiology and Population Health, Stanford University , Stanford, California, USA.; Department of Biomedical Data Science, Stanford University , Stanford, California, USA.; Department of Statistics, Stanford University , Stanford, California, USA.
Amino acids in variable positions of proteins may be correlated, with potential structural and functional implications. Here, we apply exact tests of independence in R x C contingency tables to examine noise-free associations between variable positions of the SARS-CoV-2 spike protein, using as a paradigm sequences from Greece deposited in GISAID (N = 6,683/1,078 full length) for the period 29 February 2020 to 26 April 2021 that essentially covers the first three pandemic waves. We examine the fate and complexity of these associations by network analysis, using associated positions (exact P /= 2) as links and the corresponding positions as nodes. We found a temporal linear increase of positional differences and a gradual expansion of the number of position associations over time, represented by a temporally evolving intricate web, resulting in a non-random complex network of 69 nodes and 252 links. Overconnected nodes corresponded to the most adapted variant positions in the population, suggesting a direct relation between network degree and position functional importance. Modular analysis revealed 25 k-cliques comprising 3 to 11 nodes. At different k-clique resolutions, one to four communities were formed, capturing epistatic associations of circulating variants (Alpha, Beta, B.1.1.318), but also Delta, which dominated the evolutionary landscape later in the pandemic. Cliques of aminoacidic positional associations tended to occur in single sequences, enabling the recognition of epistatic positions in real-world virus populations. Our findings provide a novel way of understanding epistatic relationships in viral proteins with potential applications in the design of virus control procedures. IMPORTANCE Paired positional associations of adapted amino acids in virus proteins may provide new insights for understanding virus evolution and variant formation. We investigated potential intramolecular relationships between variable SARS-CoV-2 spike positions by exact tests of independence in R x C contingency tables, having applied Average Product Correction (APC) to eliminate background noise. Associated positions (exact P /= 2) formed a non-random, epistatic network of 25 cliques and 1-4 communities at different clique resolutions, revealing evolutionary ties between variable positions of circulating variants and a predictive potential of previously unknown network positions. Cliques of different sizes represented theoretical combinations of changing residues in sequence space, allowing the identification of significant aminoacidic combinations in single sequences of real-world populations. Our analytic approach that links network structural aspects to mutational aminoacidic combinations in the spike sequence population offers a novel way to understand virus epidemiology and evolution.
PMID: 37432011
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1408-1427 doi: 10.1111/tpj.16330
A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.
Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan.; Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
PMID: 37247130
Front Plant Sci , IF:5.753 , 2023 , V14 : P1222414 doi: 10.3389/fpls.2023.1222414
Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways.
Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, Hainan, China.; College of Ecology and Environment, Hainan University, Haikou, Hainan, China.; Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China.; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
Light serves not only as a signaling cue perceived by plant photoreceptors but also as an essential energy source captured by chloroplasts. However, excessive light can impose stress on plants. Fern gametophytes possess the unique ability to survive independently and play a critical role in the alternation of generations. Due to their predominantly shaded distribution under canopies, light availability becomes a limiting factor for gametophyte survival, making it imperative to investigate their response to light. Previous research on fern gametophytes' light response has been limited to the physiological level. In this study, we examined the light response of Adiantum flabellulatum gametophytes under different photosynthetic photon flux density (PPFD) levels and identified their high sensitivity to low light. We thereby determined optimal and stress-inducing light conditions. By employing transcriptome sequencing, weighted gene co-expression network analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified 10,995 differentially expressed genes (DEGs). Notably, 3 PHYBs and 5 Type 1 CRYs (CRY1s) were significantly down-regulated at low PPFD (0.1 mumol m(-2) s(-1)). Furthermore, we annotated 927 DEGs to pathways related to photosynthesis and 210 to the flavonoid biosynthesis pathway involved in photoprotection. Additionally, we predicted 34 transcription factor families and identified a close correlation between mTERFs and photosynthesis, as well as a strong co-expression relationship between MYBs and bHLHs and genes encoding flavonoid synthesis enzymes. This comprehensive analysis enhances our understanding of the light response of fern gametophytes and provides novel insights into the mechanisms governing their responses to light.
PMID: 37746005
Plant Sci , IF:4.729 , 2023 Sep , V336 : P111855 doi: 10.1016/j.plantsci.2023.111855
Involvement of plant signaling network and cell metabolic homeostasis in nitrogen deficiency-induced early leaf senescence.
Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China.; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, China. Electronic address: chengfm@zju.edu.cn.
Nitrogen (N) is a basic building block that plays an essential role in the maintenance of normal plant growth and its metabolic functions through complex regulatory networks. Such the N metabolic network comprises a series of transcription factors (TFs), with the coordinated actions of phytohormone and sugar signaling to sustain cell homeostasis. The fluctuating N concentration in plant tissues alters the sensitivity of several signaling pathways to stressful environments and regulates the senescent-associated changes in cellular structure and metabolic process. Here, we review recent advances in the interaction between N assimilation and carbon metabolism in response to N deficiency and its regulation to the nutrient remobilization from source to sink during leaf senescence. The regulatory networks of N and sugar signaling for N deficiency-induced leaf senescence is further discussed to explain the effects of N deficiency on chloroplast disassembly, reactive oxygen species (ROS) burst, asparagine metabolism, sugar transport, autophagy process, Ca(2+) signaling, circadian clock response, brassinazole-resistant 1 (BZRI), and other stress cell signaling. A comprehensive understanding for the metabolic mechanism and regulatory network underlying N deficiency-induced leaf senescence may provide a theoretical guide to optimize the source-sink relationship during grain filling for the achievement of high yield by a selection of crop cultivars with the properly prolonged lifespan of functional leaves and/or by appropriate agronomic managements.
PMID: 37678563
Photochem Photobiol Sci , IF:3.982 , 2023 Sep doi: 10.1007/s43630-023-00478-2
Metabolomic response to high light from pgrl1 and pgr5 mutants of Chlamydomonas reinhardtii.
Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.; The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 8499000, Beersheba, Israel.; National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.; Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India. srgsl@uohyd.ernet.in.
Chlamydomonas (C.) reinhardtii metabolomic changes in cyclic electron flow-dependent mutants are still unknown. Here, we used mass spectrometric analysis to monitor the changes in metabolite levels in wild-type, cyclic electron-deficient mutants pgrl1 and pgr5 grown under high-light stress. A total of 55 metabolites were detected using GC-MS analysis. High-light stress-induced selective anaplerotic amino acids in pgr5. In addition, pgr5 showed enhancement in carbohydrate, polyamine, and polyol metabolism by 2.5-fold under high light. In response to high light, pgr5 triggers an increase in several metabolites involved in regulating osmotic pressure. Among these metabolites are glycerol pathway compounds such as glycerol-3-phosphate and glyceryl-glycoside, which increase significantly by 1.55 and 3.07 times, respectively. In addition, pgr5 also enhanced proline and putrescine levels by 2.6- and 1.36-fold under high light. On the other hand, pgrl1-induced metabolites, such as alanine and serine, are crucial for photorespiration when subjected to high-light stress. We also observed a significant increase in levels of polyols and glycerol by 1.37- and 2.97-fold in pgrl1 under high-light stress. Both correlation network studies and KEGG pathway enrichment analysis revealed that metabolites related to several biological pathways, such as amino acid, carbohydrate, TCA cycle, and fatty acid metabolism, were positively correlated in pgrl1 and pgr5 under high-light stress conditions. The relative mRNA expression levels of genes related to the TCA cycle, including PDC3, ACH1, OGD2, OGD3, IDH3, and MDH4, were significantly upregulated in pgrl1 and pgr5 under HL. In pgr5, the MDH1 level was significantly increased, while ACS1, ACS3, IDH2, and IDH3 levels were reduced considerably in pgrl1 under high-light stress. The current study demonstrates both pgr5 and prgl1 showed a differential defense response to high-light stress at the primary metabolites and mRNA expression level, which can be added to the existing knowledge to explore molecular regulatory responses of prg5 and pgrl1 to high-light stress.
PMID: 37751074
In Silico Pharmacol , 2023 , V11 (1) : P25 doi: 10.1007/s40203-023-00163-3
In-vitro antibacterial, antioxidant and anti-inflammatory and In-silico ADMET, molecular docking study on Hardwickia binata phytocompunds with potential inhibitor of skin cancer protein.
Department of Botany, Periyar University, Salem, 636 011 Tamil Nadu India. ROR: https://ror.org/05crs8s98. GRID: grid.412490.a. ISNI: 0000 0004 0538 1156; Department of Biotechnology, Periyar University, Salem, 636 011 Tamil Nadu India. GRID: grid.412490.a. ISNI: 0000 0004 0538 1156; Sri Paramakalyani Centre for Excellence and Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi, 627 412 Tamil Nadu India. ROR: https://ror.org/02qgw5c67. GRID: grid.411780.b. ISNI: 0000 0001 0683 3327
The new sources of antimicrobial and antioxidant agents for methanol extracts of Hardwickia binata Roxb were evaluated systematically. The present investigation is antibacterial, antioxidant, ADMET and molecular docking studies. Our results show the good polyphenol content (total phenol, total flavonoid) and antioxidant capacity of methanol extracts. The free radical scavenging activities of the methanol extracts also were highest, with the antioxidant activity becoming significantly greater. Furthermore, in-vitro antibacterial experiments against phytopathogens, Enterococcus faecalis have a high zone of inhibition (14 +/- 0.54) compared with other pathogens. The functional groups of methanol extract were identified using FTIR. The active molecules from GCMS involved in ADMET and docking study for skin cancer proteins (1P7K and 5OTE) among the phytocompounds, Hexadecanoic acid, methyl ester (- 6.2; - 6.6 kcal/mol) and 5-Phenyl-2,4-pyrimidinediamine, 2TMS derivative (- 7.50; - 8.11 kcal/mol) is the best compound for the human skin cancer possessed higher binding energy. Our results indicate that the plants can provide sources of natural compounds used for moderate good anticancer drug.
PMID: 37750071