Trends Plant Sci , IF:18.313 , 2022 Oct doi: 10.1016/j.tplants.2022.08.016
PANOMICS at the interface of root-soil microbiome and BNI.
Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.; Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: palak.chaturvedi@univie.ac.at.; Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan.; Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. Electronic address: wolfram.weckwerth@univie.ac.at.
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
PMID: 36229336
Trends Microbiol , IF:17.079 , 2022 Oct , V30 (10) : P922-924 doi: 10.1016/j.tim.2022.06.006
Synthetic plant microbiota challenges in nonmodel species.
Department of Biology, University of Florence, Florence, Italy.; Department of Biology, University of Florence, Florence, Italy. Electronic address: alessio.mengoni@unifi.it.
Plant-associated microbiota are becoming central in the development of ways to improve plant productivity and health. However, most research has focussed mainly on a few model plant species. It is essential to translate discoveries to the many nonmodel crops, allowing the design and application of effective synthetic microbiota.
PMID: 35843854
Biotechnol Adv , IF:14.227 , 2022 Oct , V59 : P107969 doi: 10.1016/j.biotechadv.2022.107969
Current status, and the developments of hosts and expression systems for the production of recombinant human cytokines.
Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.; Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India. Electronic address: veeranki@iitg.ac.in.
Cytokines consist of peptides, proteins and glycoproteins, which are biological signaling molecules, and boost cell-cell communication in immune reactions to stimulate cellular movements in the place of trauma, inflammation and infection. Recombinant cytokines are designed in such a way that they have generalized immunostimulation action or stimulate specific immune cells when the body encounters immunosuppressive signals from exogenous pathogens or other tumor microenvironments. Recombinant cytokines have improved the treatment processes for numerous diseases. They are also beneficial against novel toxicities that arise due to pharmacologic immunostimulators that lead to an imbalance in the regulation of cytokine. So, the production and use of recombinant human cytokines as therapeutic proteins are significant for medical treatment purposes. For the improved production of recombinant human cytokines, the development of host cells such as bacteria, yeast, fungi, insect, mammal and transgenic plants, and the specific expression systems for individual hosts is necessary. The recent advancements in the field of genetic engineering are beneficial for easy and efficient genetic manipulations for hosts as well as expression cassettes. The use of metabolic engineering and systems biology approaches have tremendous applications in recombinant protein production by generating mathematical models, and analyzing complex biological networks and metabolic pathways via simulations to understand the interconnections between metabolites and genetic behaviors. Further, the bioprocess developments and the optimization of cell culture conditions would enhance recombinant cytokines productivity on large scales.
PMID: 35525478
Mol Plant , IF:13.164 , 2022 Oct doi: 10.1016/j.molp.2022.10.016
MINI-EX: Integrative inference of single-cell gene regulatory networks in plants.
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium. Electronic address: klaas.vandepoele@psb.vib-ugent.be.
Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factor (TF) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell-types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell-types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell-types controlling a biological process of interest. We demonstrate MINI-EX's stability towards input data sets with low number of cells and its robustness towards missing data, and we show it infers state-of-the-art networks with a better performance compared to related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, Arabidopsis leaf development, and governing ear development in maize, enhancing our understanding of cell-type specific regulation and unraveling the role of different regulators controlling the development of specific cell-types in plants.
PMID: 36307979
New Phytol , IF:10.151 , 2022 Oct doi: 10.1111/nph.18564
Defining the scope for altering rice leaf anatomy to improve photosynthesis: A modelling approach.
Center of Excellence for Molecular Plant Science, Institute of Plant Physiology and Ecology, CAS, Shanghai, China, 200032.; Plants, Photosynthesis and Soil, Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.; Division of Agriculture and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.; Pacific Northwest National Laboratory, Richland, WA, 99354, USA.; Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia 43400, Serdang, Malaysia.
Leaf structure plays an important role in photosynthesis. However, the causal relationship and the quantitative importance of any single structural parameter to the overall photosynthetic performance of a leaf remains open to debate. In this paper we report on a mechanistic model, eLeaf, which successfully captures rice leaf photosynthetic performance under varying environmental conditions of light and CO2 . We developed a 3D reaction-diffusion model for leaf photosynthesis parameterized using a range of imaging data and biochemical measurements from plants grown under ambient and elevated CO2 , then interrogated the model to quantify the importance of these elements. The model successfully captured leaf-level photosynthetic performance in rice. Photosynthetic metabolism underpinned the majority of the increased carbon assimilation rate observed under elevated CO2 levels, with a range of structural elements making positive and negative contributions. Mesophyll porosity could be varied without any major outcome on photosynthetic performance, providing theoretical underpinning for experimental data. eLeaf allows quantitative analysis of the influence of morphological and biochemical properties on leaf photosynthesis. The analysis highlights a degree of leaf structural plasticity with respect to photosynthesis of significance in the context of attempts to improve crop photosynthesis.
PMID: 36271620
New Phytol , IF:10.151 , 2022 Oct doi: 10.1111/nph.18567
AabHLH113 integrates JA and ABA signalling to positively regulate artemisinin biosynthesis in Artemisia annua.
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & Southwest University, School of Life Sciences, Southwest University, Chongqing, 400715, China.; Chongqing Academy of Science and Technology, Chongqing, 401123, China.; College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China.; College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China.
Artemisinin, a sesquiterpene lactone isolated from Artemisia annua L., is in huge market demand due to its efficient anti-malarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via kinds of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA- induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed Artemisia annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that the AabZIP1 and AabHLH112, which respectively participate in ABA and JA signalling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelation role to integrate ABA- and JA-mediated regulating artemisinin biosynthesis.
PMID: 36271612
Plant Biotechnol J , IF:9.803 , 2022 Oct doi: 10.1111/pbi.13944
Multi-stress resilience in plants recovering from submergence.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.; Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition, and accelerated senescence. Plant responses to waterlogging and partial or complete submergence, have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and re-oxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals, and provide new perspectives for future studies.
PMID: 36217562
Elife , IF:8.14 , 2022 Sep , V11 doi: 10.7554/eLife.77058
A unified view of low complexity regions (LCRs) across species.
Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
PMID: 36098382
Elife , IF:8.14 , 2022 Sep , V11 doi: 10.7554/eLife.73031
Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root.
Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.; BioQuant, Heidelberg University, Heidelberg, Germany.; Center for Molecular Biology of Plants, University of Tubingen, Tubingen, Germany.; Department of Ecological and biological Science, Tuscia University, Viterbo, Italy.; Tasmanian Institute for Agriculture, University of Tasmania, Hobart, Australia.; International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China.
Brassinosteroids (BR) are key hormonal regulators of plant development. However, whereas the individual components of BR perception and signaling are well characterized experimentally, the question of how they can act and whether they are sufficient to carry out the critical function of cellular elongation remains open. Here, we combined computational modeling with quantitative cell physiology to understand the dynamics of the plasma membrane (PM)-localized BR response pathway during the initiation of cellular responses in the epidermis of the Arabidopsis root tip that are be linked to cell elongation. The model, consisting of ordinary differential equations, comprises the BR-induced hyperpolarization of the PM, the acidification of the apoplast and subsequent cell wall swelling. We demonstrate that the competence of the root epidermal cells for the BR response predominantly depends on the amount and activity of H(+)-ATPases in the PM. The model further predicts that an influx of cations is required to compensate for the shift of positive charges caused by the apoplastic acidification. A potassium channel was subsequently identified and experimentally characterized, fulfilling this function. Thus, we established the landscape of components and parameters for physiological processes potentially linked to cell elongation, a central process in plant development.
PMID: 36069528
Environ Pollut , IF:8.071 , 2022 Dec , V314 : P120344 doi: 10.1016/j.envpol.2022.120344
Effects of manure fertilization on human pathogens in endosphere of three vegetable plants.
Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. Electronic address: ygzhu@rcees.ac.cn.
Pathogens can colonize plant endosphere and, be transferred into human beings through the food chain. However, our understanding of the influences of agricultural activities, such as fertilization, on endophytic microbial communities and human pathogens is still limited. Here, we conducted a microcosm experiment using the combination of 16 S rRNA gene amplicon sequencing and high-throughput qPCR array to reveal the effects of manure fertilization on microbiomes of soils and plants and how such impact is translated into endophytic pathogens. Our results showed that manure fertilization significantly altered soil microbiomes, whereas with less influence on endophytic microbial communities. Soil is a vital source of both bacterial communities and human pathogens for the plant endosphere. The abundance of pathogens was increased both in soils and endosphere under manure fertilization. These findings provide an integrated understanding of the impact of manure fertilization on endophytic pathogens.
PMID: 36206891
Sci Total Environ , IF:7.963 , 2022 Sep , V838 (Pt 3) : P156426 doi: 10.1016/j.scitotenv.2022.156426
The combined effect of an integrated reclaimed water system on the reduction of antibiotic resistome.
Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China.; Beijing BHZQ Environmental Engineering Technology Co., LTD, Beijing 100176, China.; Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China. Electronic address: chen.haiyang@bnu.edu.cn.
The reuse of urban reclaimed water is conducive to alleviate the current serious shortage of water resources. However, antibiotic resistance genes (ARGs) in reclaimed water have received widespread attention due to their potential risks to public health. Deciphering the fate of ARGs in reclaimed water benefits the development of effective strategies to control resistome risk and guarantees the safety of water supply of reclaimed systems. In this study, the characteristics of ARGs in an integrated reclaimed water system (sewage treatment plant-constructed wetland, STP-CW) in Beijing (China) have been identified using metagenomic assembly-based analysis, as well as the combined effect of the STP-CW system on the reduction of antibiotic resistome. Results showed a total of 29 ARG types and 813 subtypes were found in the reclaimed water system. As expected, the STP-CW system improved the removal of ARGs, and about 58% of ARG subtypes were removed from the effluent of the integrated STP-CW system, which exceeded 43% for the STP system and 37% for the CW system. Although the STP-CW system had a great removal on ARGs, abundant and diverse ARGs were still found in the downstream river. Importantly, network analysis revealed the co-occurrence of ARGs, mobile genetic elements and virulence factors in the downstream water, implying potential resistome dissemination risk in the environment. Source identification with SourceTracker showed the STP-effluent was the largest contributor of ARGs in the downstream river, with a contribution of 45%. Overall, the integrated STP-CW system presented a combined effect on the reduction of antibiotic resistome, however, the resistome dissemination risk was still non-negligible in the downstream reclaimed water. This study provides a comprehensive analysis on the fate of ARGs in the STP-CW-river system, which would benefit the development of effective strategies to control resistome risk for the reuse of reclaimed water.
PMID: 35660592
Food Chem , IF:7.514 , 2022 Oct , V404 (Pt A) : P134545 doi: 10.1016/j.foodchem.2022.134545
Controlled mechanical stimuli reveal novel associations between basil metabolism and sensory quality.
School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden.; School of Hospitality, Culinary Arts and Meal Science, Sweden. Electronic address: anders.herdenstam@oru.se.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden; Department of Radiation Sciences, Radiation Physics, Umea University, 901 87 Umea, Sweden.; School of Science and Technology, Centre for Applied Autonomous Sensor Systems, Orebro University, 701 82 Orebro, Sweden.; School of Science and Technology, Man-Technology-Environment Research Centre, Orebro University, 701 82 Orebro, Sweden. Electronic address: victor.castro-alves@oru.se.
There is an increasing interest in the use of automation in plant production settings. Here, we employed a robotic platform to induce controlled mechanical stimuli (CMS) aiming to improve basil quality. Semi-targeted UHPLC-qToF-MS analysis of organic acids, amino acids, phenolic acids, and phenylpropanoids revealed changes in basil secondary metabolism under CMS, which appear to be associated with changes in taste, as revealed by different means of sensory evaluation (overall liking, check-all-that-apply, and just-about-right analysis). Further network analysis combining metabolomics and sensory data revealed novel links between plant metabolism and sensory quality. Amino acids and organic acids including maleic acid were negatively associated with basil quality, while increased levels of secondary metabolites, particularly linalool glucoside, were associated with improved basil taste. In summary, by combining metabolomics and sensory analysis we reveal the potential of automated CMS on crop production, while also providing new associations between plant metabolism and sensory quality.
PMID: 36252376
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6307-6333 doi: 10.1093/jxb/erac300
Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Rua do Matao, Sao Paulo, Brazil.; VIB Center for Plant Systems Biology, Ghent, Belgium.; VIB Metabolomics Core, Ghent, Belgium.; Joint BioEnergy Institute, Emeryville, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, Sao Paulo, Brazil.
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
PMID: 35788296
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6089-6102 doi: 10.1093/jxb/erac270
Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals.
National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China.; Sanya Institute of China Agricultural University, Sanya, Hainan, China.
Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.
PMID: 35724645
J Environ Manage , IF:6.789 , 2022 Oct , V319 : P115694 doi: 10.1016/j.jenvman.2022.115694
Optimization of vegetable waste composting and the exploration of microbial mechanisms related to fungal communities during composting.
Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. Electronic address: wangweiping119@126.com.
The application of additives to regulate the microbial functional composition during composting has attracted much research attention. However, little is known about the succession and role of the fungal community in the laboratory-scale composting of vegetable waste supplemented with pig manure and microbial agents. The purpose of this study was to identify effective additives for improving vegetable waste composting performance and product quality, and to analyze the microbial community succession during composting. The results showed that the combined addition of pig manure and microbial agents (T2 treatment) accelerated the pile temperature increase, enhanced total organic carbon degradation (23.36%), and promoted the maturation of the compost. Furthermore, the T2 treatment increased the activities of most enzymes, reshaped the microbial community, and reduced the relative abundance of potential animal (1.60%) and plant (0.095%) pathogens. The relative abundance of Firmicutes (71.23%) increased with the combined addition of pig manure and microbial agents in the thermophilic stage. In the middle and late stages, Saccharomonospora, Aspergillus, and Thermomyces, which were related to C/N and total phosphorus, were enriched in the T2 treatment. Network analysis demonstrated that the complexity and stability of the fungal network were more evidently increased in the T2 treatment, and Saccharomonospora, Aspergillus, and Microascus were identified as keystone taxa. The keystone taxa associated with extracellular enzymes contributed significantly to compost maturation. These results provide a reference for the application of additives to improve compost safety in pilot-scale composting.
PMID: 35841778
Cells , IF:6.6 , 2022 Oct , V11 (20) doi: 10.3390/cells11203250
Melatonin and Indole-3-Acetic Acid Synergistically Regulate Plant Growth and Stress Resistance.
Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, College of Pharmacy, BaoTou Medical College, Baotou 014040, China.; University Engineering Research Center of Chinese (Mongolia) Ecological Planting Medicinal Materials (Nurture) in Inner Mongolia Autonomous Region, College of agronomy, Inner Mongolia Minzu University, Tongliao 028000, China.; School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.; College of Pharmacy, Inner Mongolia Medical University, Hohhot 010110, China.; Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot 010020, China.; Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China.
Plant growth and development exhibit plasticity, and plants can adapt to environmental changes and stress. Various phytohormones interact synergistically or antagonistically to regulate these responses. Melatonin and indole-3-acetic acid (IAA) are widespread across plant kingdom. Melatonin, an important member of the neuroendocrine immune regulatory network, can confer autoimmunity and protect against viral invasion. Melatonin functions as a plant growth regulator and biostimulant, with an important role in enhancing plant stress tolerance. IAA has a highly complex stress response mechanism, which participates in a series of stress induced physiological changes. This article reviews studies on the signaling pathways of melatonin and IAA, focusing on specific regulatory mechanisms. We discuss how these hormones coordinate plant growth and development and stress responses. Furthermore, the interactions between melatonin and IAA and their upstream and downstream transcriptional regulation are discussed from the perspective of modulating plant development and stress adaptation. The reviewed studies suggest that, at low concentrations, melatonin promotes IAA synthesis, whereas at high levels it reduces IAA levels. Similarly to IAA, melatonin promotes plant growth and development. IAA suppresses the melatonin induced inhibition of germination. IAA signaling plays an important role in plant growth and development, whereas melatonin signaling plays an important role in stress responses.
PMID: 36291118
Environ Res , IF:6.498 , 2022 Dec , V215 (Pt 1) : P114238 doi: 10.1016/j.envres.2022.114238
The emerging potential of natural and synthetic algae-based microbiomes for heavy metal removal and recovery from wastewaters.
Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India.; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 34113, Daejeon, Republic of Korea.; Sustainable Resources Laboratory, Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod, Kerala, 671 316, India; Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, Republic of Korea. Electronic address: rishi@cukerala.ac.in.
Heavy Metal (HM) bioremoval by microbes is a successful, environment-friendly technique, particularly at low concentrations of HMs. Studies using algae, bacteria, and fungi reveal promising capabilities in isolation and when used in consortia. Yet, few reviews have emphasized individual and collective HM removal rates and the associated mechanisms in natural or synthetic microbiomes. Besides discussing the limitations of conventional and synthetic biology approaches, this review underscores the utility of indigenous microbial taxon, i.e., algae, fungi, and bacteria, in HM removal with adsorption capacities and their synergistic role in microbiome-led studies. The detoxification mechanisms studied for certain HMs indicate distinctive removal pathways in each taxon which points to an enhanced effect when used as a microbiome. The role and higher efficacies of the designer microbiomes with complementing and mutualistic taxa are also considered, followed by recovery options for a circular bioeconomy. The citation network analysis further validates the multi-metal removal ability of microbiomes and the restricted capabilities of the individual counterparts. In precis, the study reemphasizes increased metal removal efficiencies of inter-taxon microbiomes and the mechanisms for synergistic and improved removal, eventually drawing attention to the benefits of ecological engineering approaches compared to other alternatives.
PMID: 36108721
Plant J , IF:6.417 , 2022 Oct , V112 (1) : P68-83 doi: 10.1111/tpj.15928
A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid.
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2 s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.
PMID: 35912411
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810596
Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha.
Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.
PMID: 36142547
Front Plant Sci , IF:5.753 , 2022 , V13 : P1019709 doi: 10.3389/fpls.2022.1019709
An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean.
Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.; Department of Resource and Environment, Faculty of Science at Sriracha, Kasetsart University, Sriracha, Thailand.; Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.
PMID: 36247545
Front Plant Sci , IF:5.753 , 2022 , V13 : P976449 doi: 10.3389/fpls.2022.976449
Integrated metabolomic and transcriptomic analyses reveal molecular response of anthocyanins biosynthesis in perilla to light intensity.
Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
The perilla anthocyanins have important medicinal and ornamental value, and their contents are significantly affected by light intensity. In view of their molecular mechanisms were not well understood, we integrated the metabolomic and transcriptomic analyses of the light-sensitive perilla variety under different light intensity. The perilla leave color were obviously affected under different treatments. Totally 140 flavonoid metabolites and 2461 genes showed steady change, among which 60 flavonoid metabolites were increased accumulation and 983 genes were upregulated expression under elevated light intensity treatment. Light treatment prominently affected the expression of genes involved in the main anthocyanin metabolites accumulation in perilla leaves. Using WGCNA analysis, we identified 4 key genes in anthocyanin biosynthesis pathway (CHI, DFR, and ANS) and 147 transcription factors (MYB, bHLH, bZIP, ERF, and NAC) involved in malonylshisonin biosynthesis. Among them, 6 MYBs and 4 bZIPs were predicted to play important roles in light regulation of malonylshisonin biosynthesis based on phylogenetic construction, correlation analysis, cis-acting element identification and qPCR verification. The identified key genes and regulatory factors will help us to understand the potential mechanism of photo-regulated anthocyanin accumulation in perilla.
PMID: 36212297
Front Plant Sci , IF:5.753 , 2022 , V13 : P985088 doi: 10.3389/fpls.2022.985088
Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat.
Key Laboratory of High-Quality Crops Cultivation and Safety Control of Yunnan Province, Honghe University, Honghe, China.; Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, China.; College of Life Science, Guizhou Normal University, Guiyang, China.; Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region of Ministry of Education, Guizhou University, Guiyang, China.
Drought stress is one of the major abiotic stress factors that affect plant growth and crop productivity. Tartary buckwheat is a nutritionally balanced and flavonoid-rich pseudocereal crop and also has strong adaptability to different adverse environments including drought. However, little is known about its drought tolerance mechanism. In this study, we performed comparative physiological and transcriptomic analyses of two contrasting drought-resistant Tartary buckwheat genotypes under nature drought treatment in the reproductive stage. Under drought stress, the drought-tolerant genotype XZSN had significantly higher contents of relative water, proline, and soluble sugar, as well as lower relative electrolyte leakage in the leaves than the drought-susceptible LK3. A total of 5,058 (2,165 upregulated and 2,893 downregulated) and 5,182 (2,358 upregulated and 2,824 downregulated) potential drought-responsive genes were identified in XZSN and LK3 by transcriptome sequencing analysis, respectively. Among the potential drought-responsive genes of XZSN, 1,206 and 1,274 genes were identified to be potential positive and negative contributors for XZSN having higher drought resistance ability than LK3. Furthermore, 851 out of 1,206 positive drought-resistant genes were further identified to be the core drought-resistant genes of XZSN based on WGCNA analysis, and most of them were induced earlier and quicker by drought stress than those in LK3. Functional annotation of the 851 core drought-resistant genes found that a large number of stress-responsive genes were involved in TFs, abscisic acid (ABA) biosynthesis, signal transduction and response, non-ABA signal molecule biosynthesis, water holding, oxygen species scavenging, osmotic adjustment, cell damage prevention, and so on. Transcriptional regulatory network analyses identified the potential regulators of these drought-resistant functional genes and found that the HD-ZIP and MYB TFs might be the key downstream TFs of drought resistance in Tartary buckwheat. Taken together, these results indicated that the XZSN genotype was more drought-tolerant than the LK3 genotype as evidenced by triggering the rapid and dramatic transcriptional reprogramming of drought-resistant genes to reduce water loss, prevent cell damage, and so on. This research expands our current understanding of the drought tolerance mechanisms of Tartary buckwheat and provides important information for its further drought resistance research and variety breeding.
PMID: 36262653
Front Plant Sci , IF:5.753 , 2022 , V13 : P1001357 doi: 10.3389/fpls.2022.1001357
Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress.
Research Institute of Oil Tea Camellia, Hunan Academy of Forestry, Changsha, China.; National Engineering Research Center for Oil Tea Camellia, Changsha, China.
Camellia oleifera Abel. (C. oleifera) is an edible oil tree species that provide an important guarantee for targeted poverty alleviation strategy in China. Severe difficulties in irrigation leading to drought stress have become a major obstacle to the development of the C. oleifera planting industry. Breeding of drought-tolerant cultivars is the main idea for solving the problem of water shortage stress in C. oleifera cultivation. The photosynthetic physiology traits of C. oleifera cultivars 'Xianglin No.1' and 'Hengdong No.2' were affected by drought stress to different degrees, which demonstrated that the two cultivars suffered different degrees of damage. In the present study, we applied mRNA-seq and miRNA-seq to analyze the difference in molecular responses between drought stress and control, drought-tolerant and -sensitive cultivars, at mRNA and miRNA levels. The differentially expressed genes (DEGs) involved in photosynthesis-related, porphyrin, and chlorophyll metabolism, circadian rhythm system, and plant hormone signal transduction pathways were identified that might be candidates for drought stress tolerance genes. Subsequently, the miRNA-mRNA regulatory networks connected the differentially expressed miRNAs (DEMs) to their predicted target genes were established. miR398 and miR408-3p in C. oleifera showed that associated with the response to drought stress by negatively regulating genes encoding Downy Mildew Resistance 6 (DMR6) and Enhanced Disease Resistance 2 (EDR2), respectively, which might further improve drought tolerance via crosstalk between different stress-responsive pathways. The quantitation results of miRNA and mRNA were validated by quantitative real-time PCR (qRT-PCR). In summary, the integrated mRNA-seq and miRNA-seq analysis deepen our understanding of the regulatory network response to drought stress and variety-specific responses improving drought tolerance in C. oleifera.
PMID: 36247533
Front Plant Sci , IF:5.753 , 2022 , V13 : P952698 doi: 10.3389/fpls.2022.952698
An integrated metabolome and transcriptome approach reveals the fruit flavor and regulatory network during jujube fruit development.
Beijing Academy of Agriculture and Forestry Sciences, Institute of Forestry and Pomology, Beijing, China.; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.; Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China.
The fruit flavor is a key economic value attribute of jujube. Here we compared metabolomes and transcriptomes of "Mazao" (ST) and "Ping'anhuluzao" (HK) with unique flavors during fruit development. We identified 437 differential metabolites, mainly sugars, acids, and lipids. Fructose, glucose, mannose and citric acid, and malic acid are the determinants of sugar and acid taste of jujube fruit. Based on the transcriptome, 16,245 differentially expressed genes (DEGs) were identified, which were involved in "glucosyltransferase activity," "lipid binding," and "anion transmembrane transporter activity" processes. Both transcriptome and metabolome showed that developmental stages 2 and 3 were important transition periods for jujube maturation. Based on WGCNA and gene-metabolite correlation analysis, modules, and transcription factors (ZjHAP3, ZjTCP14, and ZjMYB78) highly related to sugar and acid were identified. Our results provide new insights into the mechanism of sugar and acid accumulation in jujube fruit and provide clues for the development of jujube with a unique flavor.
PMID: 36212371
Front Plant Sci , IF:5.753 , 2022 , V13 : P1008829 doi: 10.3389/fpls.2022.1008829
Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.; School of Forestry, Northeast Forestry University, Harbin, China.; State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China.; College of Life Sciences, Northeast Forestry University, Harbin, China.
Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.
PMID: 36147236
Ambio , IF:5.129 , 2022 Oct , V51 (10) : P2137-2154 doi: 10.1007/s13280-022-01733-z
Trees as brokers in social networks: Cascades of rights and benefits from a Cultural Keystone Species.
Jalan CIFOR Situ Gede, Bogor Barat, Bogor, 16115, Indonesia. h.djoudi@cgiar.org.; Jalan CIFOR Situ Gede, Bogor Barat, Bogor, 16115, Indonesia.; Cirad, UPR Forets et Societes, Univ Montpellier, TA C105-D, 34398, Montpellier Cedex5, France.; Center for International Forestry Research (CIFOR), 06 BP 9478, Ouagadougou, Burkina Faso.; Fenner School of Environment and Society, Australian National University, Bldg, 141, Linnaeus Way, Canberra, ACT, 2601, Australia.; The Alliance of Bioversity International and International Center for Tropical Agriculture, Via di San Domenico, 1, 00153, Rome, Italy.; CSIRO Land and Water, Ngunnawal Country GPO, Box 1700, Canberra, ACT, 2601, Australia.
Indigenous trees play key roles in West African landscapes, such as the nere tree (Parkia biglobosa (Jacq.) R.Br. ex G.Don). We applied social-ecological network analysis to understand the social-ecological interactions around nere. We documented the benefits nere provides and the multiple social interactions it creates amongst a large range of actors. The flows of rights over the trees and benefits from them formed two hierarchical networks, or cascades, with different actors at the top. The two forms of power revealed by the two cascades of rights and benefits suggest possible powers and counter-powers across gender, ethnicity, and age. We documented how the tree catalyses social interactions across diverse groups to sustain vital social connections, and co-constitute places, culture, and relationships. We argue that a paradigm shift is urgently needed to leverage the remarkable untapped potential of indigenous trees and Cultural Keystone Species in current global restoration and climate change agendas.
PMID: 35737271
Metabolites , IF:4.932 , 2022 Sep , V12 (9) doi: 10.3390/metabo12090871
Regulation Mechanism of Plant Pigments Biosynthesis: Anthocyanins, Carotenoids, and Betalains.
Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China.; College of Tropical Crops, Hainan University, Haikou 570228, China.
Anthocyanins, carotenoids, and betalains are known as the three major pigments in the plant kingdom. Anthocyanins are flavonoids derived from the phenylpropanoid pathway. They undergo acylation and glycosylation in the cytoplasm to produce anthocyanin derivatives and deposits in the cytoplasm. Anthocyanin biosynthesis is regulated by the MBW (comprised by R2R3-MYB, basic helix-loop-helix (bHLH) and WD40) complex. Carotenoids are fat-soluble terpenoids whose synthetic genes also are regulated by the MBW complex. As precursors for the synthesis of hormones and nutrients, carotenoids are not only synthesized in plants, but also synthesized in some fungi and bacteria, and play an important role in photosynthesis. Betalains are special water-soluble pigments that exist only in Caryophyllaceae plants. Compared to anthocyanins and carotenoids, the synthesis and regulation mechanism of betalains is simpler, starting from tyrosine, and is only regulated by MYB (myeloblastosis). Recently, a considerable amount of novel information has been gathered on the regulation of plant pigment biosynthesis, specifically with respect to aspects. In this review, we summarize the knowledge and current gaps in our understanding with a view of highlighting opportunities for the development of pigment-rich plants.
PMID: 36144275
Plant Cell Physiol , IF:4.927 , 2022 Sep doi: 10.1093/pcp/pcac133
The Alteration Of Tomato CHLOROPLAST VESICULATION Positively Affects Whole-Plant Source-Sink Relations And Fruit Metabolism Under Stress Conditions.
School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978 Israel.; Equal contribution.; Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.; Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.; Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.; Department of Plant Sciences, University of California, Davis, CA 95616, USA.
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato CHLOROPLAST VESICULATION (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit-development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. CRISPR/CAS9 knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the L-glutamine and L-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress, and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
PMID: 36161338
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111459 doi: 10.1016/j.plantsci.2022.111459
ZmDWF1 regulates leaf angle in maize.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China; Henan Academy of Agricultural Science, Zhengzhou, Henan 450002, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China. Electronic address: kulixia0371@163.com.
Leaf angle (LA) is a critical agronomic trait enhancing grain yield under high-density planting in maize. A number of researches have been conducted in recent years to investigate the quantitative trait loci/genes responsible for LA variation, while only a few genes were identified through map-based cloning. Here we cloned the ZmDWF1 gene, which was previously reported to encode Delta24-sterol reductase in the brassinosteroids (BRs) biosynthesis pathway. Overexpression of ZmDWF1 resulted in enlarged LA, indicating that ZmDWF1 is a positive regulator of LA in maize. To reveal the regulatory framework of ZmDWF1, we conducted RNA-Sequencing and yeast-two hybrid (Y2H) screening analysis. RNA-Sequencing analyzing results indicate ZmDWF1 mainly affected expression level of genes involved in cell wall associated metabolism and hormone metabolism including BR, gibberellin, and auxin. Y2H screening with Bi-FC assay confirmed three proteins (ZmPP2C-1, ZmROF1, and ZmTWD1) interacting with ZmDWF1. We revealed a new regulatory network of ZmDWF1 gene in controlling plant architecture in maize.
PMID: 36113675
Mol Plant Microbe Interact , IF:4.171 , 2022 Oct : PMPMI07220148A doi: 10.1094/MPMI-07-22-0148-A
Complete Genome Sequence Resource of Bacillus cereus Gsicc 30237, Isolated from Cabbage Planting Soil.
Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, China.; State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430000, China.; College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China.
PMID: 36306438
Genes (Basel) , IF:4.096 , 2022 Oct , V13 (10) doi: 10.3390/genes13101851
Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine.
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
Grapevine (Vitisvinifera L.) fruit ripening is a complex biological process involving a phase transition from immature to mature. Understanding the molecular mechanism of fruit ripening is critical for grapevine fruit storage and quality improvement. However, the regulatory mechanism for the critical phase transition of fruit ripening from immature to mature in grapevine remains poorly understood. In this work, to identify the key molecular events controlling the critical phase transition of grapevine fruit ripening, we performed an integrated dynamic network analysis on time-series transcriptomic data of grapevine berry development and ripening. As a result, we identified the third time point as a critical transition point in grapevine fruit ripening, which is consistent with the onset of veraison reported in previous studies. In addition, we detected 68 genes as being key regulators involved in controlling fruit ripening. The GO (Gene Ontology) analysis showed that some of these genes participate in fruit development and seed development. This study provided dynamic network biomarkers for marking the initial transcriptional events that characterizes the transition process of fruit ripening, as well as new insights into fruit development and ripening.
PMID: 36292736
Genes (Basel) , IF:4.096 , 2022 Sep , V13 (10) doi: 10.3390/genes13101767
Mining Candidate Genes Related to Heavy Metals in Mature Melon (Cucumis melo L.) Peel and Pulp Using WGCNA.
Xinjiang Key Laboratory of Agricultural Product Quality and Safety/Agricultural Product Quality and Safety Risk Assessment Laboratory of the Ministry of Rural Agriculture/Institute of Agricultural Quality Standards and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.; School of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830091, China.; New Plant Variety Testing (Urumqi) Branch Center of the Ministry of Agriculture and Rural Affairs, Crop Variety Resources Institute, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.; Xinjiang Key Laboratory of Agricultural Product Quality and Safety/Agricultural Product Quality and Safety Risk Assessment Laboratory of the Ministry of Rural Agriculture, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China.
The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H(+)-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT-PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.
PMID: 36292652
Genes (Basel) , IF:4.096 , 2022 Sep , V13 (10) doi: 10.3390/genes13101713
Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis.
National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.; The Shennong Laboratory, Zhengzhou 450002, China.
The developmental phase changes of maize are closely associated with the life span, environmental adaption, plant height, and disease resistance of the plant and eventually determines the grain yield and quality of maize. A natural mutant, Early Phase Change 1 (ZmEPC1), was selected from the inbred line KN5585. Compared with the wild type plant, the ZmEPC1 mutant exhibits deceased plant stature, accelerated developmental stages, and decreased leaf size. Through the transcriptome sequencing analysis of leaf samples at flowering stage, a total of 4583 differentially expressed genes (DEGs) were screened between the mutant and wild type, including 2914 down-regulated genes and 1669 up-regulated genes. The GO enrichment and KEGG enrichment analysis revealed that the DEGs were mainly involved in hormone response, hormone signal transduction, autophagy, JA response and signal response, photosynthesis, biotic/abiotic stress, and circadian rhythms. The RT-qPCR results revealed that the most tested DEGs display consistent expression alterations between V5 and FT stages. However, several genes showed opposite expression alterations. Strikingly, most of the JA biosynthesis and signaling pathway-related genes displayed diametrically expression alterations between V5 and FT stages. miR156, a key regulator of plant phase transition, exhibited significant down-regulated expression at V5 and FT stages. The expression of two miR156 target genes were both significantly different between mutants and wild type. In conclusion, ZmEPC1 was identified to be mainly involved in the regulation of JA-mediated signaling pathways and hormone response and signaling, which is possible to confer developmental phase change through miR156-SPLs pathway.
PMID: 36292598
Plants (Basel) , IF:3.935 , 2022 Oct , V11 (19) doi: 10.3390/plants11192614
Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.
UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia.; Institute of System Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia.; Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Malaysia.
In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
PMID: 36235479
J Plant Physiol , IF:3.549 , 2022 Nov , V278 : P153827 doi: 10.1016/j.jplph.2022.153827
MicroRNA miR1118 contributes to wheat (Triticum aestivum L.) salinity tolerance by regulating the Plasma Membrane Intrinsic Proteins1;5 (PIP1;5) gene.
Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran. Electronic address: shamloor@gmail.com.; Department of Plant Production and Genetics, College of Agricultural Engineering, Isfahan University of Technology, Isfahan, Iran.; Institute of Biotechnology, Shiraz University, Shiraz, Iran.
microRNAs (miRNAs) are important regulators of various adaptive stress responses in crops; however, many details about associations among miRNAs, their target genes and physiochemical responses of crops under salinity stress remain poorly understood. We designed this study in a systems biology context and used a collection of computational, experimental and statistical procedures to uncover some regulatory functions of miRNAs in the response of the important crop, wheat, to salinity stress. Accordingly, under salinity conditions, wheat roots' Expressed Sequence Tag (EST) libraries were computationally mined to identify the most reliable differentially expressed miRNA and its related target gene(s). Then, molecular and physiochemical evaluations were carried out in a separate salinity experiment using two contrasting wheat genotypes. Finally, the association between changes in measured characteristics and wheat salinity tolerance was determined. From the results, miR1118 was assigned as a reliable salinity-responsive miRNA in wheat roots. The expression profiles of miR1118 and its predicted target gene, Plasma Membrane Intrinsic Proteins1,5 (PIP1;5), significantly differed between wheat genotypes. Moreover, results revealed that expression profiles of miR1118 and PIP1;5 significantly correlate to Relative Water Content (RWC), root hydraulic conductance (Lp), photosynthetic activities, plasma membrane damages, osmolyte accumulation and ion homeostasis of wheat. Our results suggest a plausible regulatory node through miR1118 adjusting the wheat water status, maintaining ion homeostasis and mitigating membrane damages, mainly through the PIP1;5 gene, under salinity conditions. To our knowledge, this is the first report on the role of miR1118 and PIP1;5 in wheat salinity response.
PMID: 36206620
Funct Integr Genomics , IF:3.41 , 2022 Sep doi: 10.1007/s10142-022-00899-9
"KRiShI": a manually curated knowledgebase on rice sheath blight disease.
Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.; Department of Plant Pathology, Assam Agricultural University, Assam, 785013, India.; University of Horticultural Sciences, Karnataka, 587315, India.; Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India. barah@tezu.ernet.in.
Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface. KRiShI collects and integrates widely scattered and unstructured information from various scientific literatures, stores it under a single window, and makes it available to the community in a user-friendly manner. From basic information, best management practices, host resistance, differentially expressed genes, proteins, metabolites, resistance genes, pathways, and OMICS scale experiments, KRiShI presents these in the form of easy and comprehensive tables, diagrams, and pictures. The "Search" tab allows users to verify if their input rice gene id(s) are Rhizoctonia solani (R. solani) responsive and/or resistant. KRiShI will serve as a valuable resource for easy and quick access to data and information related to rice SB disease for both the researchers and the farmers. To encourage community curation a submission facility is made available. KRiShI can be found at http://www.tezu.ernet.in/krishi .
PMID: 36109405
OMICS , IF:3.374 , 2022 Sep doi: 10.1089/omi.2022.0107
Systems Biology of COVID-19 and Human Diseases: Beyond a Bird's Eye View, and Toward One Health.
Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad, India.
As we gaze into the future beyond the current coronavirus disease 2019 (COVID-19) pandemic, there is a need to rethink our priorities in planetary health, research funding, and, importantly, the concepts and unchecked assumptions by which we attempt to understand health and prevent illness. Next-generation quantitative omics technologies promise a more profound and panoptic understanding of the dynamic pathophysiological processes and their aberrations in diverse diseased conditions. Systems biology research is highly relevant for COVID-19, a systemic disease affecting multiple organs and biological pathways. In addition, expanding the concept of health beyond humans so as to capture the importance of ecosystem health and recognizing the interdependence of human, animal, and plant health are enormously relevant and timely in the current historical moment of the pandemic. Notably, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, can affect our body clock, and the circadian aspects of this viral infection and host immunity need to be considered for its effective clinical management. Finally, we need to rethink and expand beyond the false binaries such as humans versus nature, and deploy multiomics systems biology research if we intend to design effective, innovative, and socioecological planetary health interventions to prevent future pandemics and ecological crises. We argue here that juxtaposing ecology and human health sciences scholarship is one of the key emerging tenets of 21st-century integrative biology.
PMID: 36095163
J Appl Genet , IF:3.24 , 2022 Sep doi: 10.1007/s13353-022-00722-y
Genome-wide post-transcriptional regulation of bovine mammary gland response to Streptococcus uberis.
Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran.; Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran. ss.sharifi2015@gmail.com.; Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran. pakdel@iut.ac.ir.; Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, 3391653755, Iran.; Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, 84156-83111, Iran.; Institute of Biotechnology, Shiraz University, Shiraz, 71946-84334, Iran.; Novocraft Technologies Sdn Bhd, Petaling Jaya, Malaysia.
MicroRNAs (miRNAs) as post-transcriptionally regulators of gene expression have been shown to be critical regulators to fine-tuning immune responses, besides their criteria for being an ideal biomarker. The regulatory role of miRNAs in responses to most mastitis-causing pathogens is not well understood. Gram-positive Streptococcus uberis (Str. uberis), the leading pathogen in dairy herds, cause both clinical and subclinical infections. In this study, a system biology approach was used to better understand the main post-transcriptional regulatory functions and elements of bovine mammary gland response to Str. uberis infection. Publicly available miRNA-Seq data containing 50 milk samples of the ten dairy cows (five controls and five infected) were retrieved for this current research. Functional enrichment analysis of predicted targets revealed that highly confident responsive miRNAs (4 up- and 19 downregulated) mainly regulate genes involved in the regulation of transcription, apoptotic process, regulation of cell adhesion, and pro-inflammatory signaling pathways. Time series analysis showed that six gene clusters significantly differed in comparisons between Str. uberis-induced samples with controls. Additionally, other bioinformatic analysis, including upstream network analysis, showed essential genes, including TP53 and TGFB1 and some small molecules, including glucose, curcumin, and LPS, commonly regulate most of the downregulated miRNAs. Upregulated miRNAs are commonly controlled by the most important genes, including IL1B, NEAT1, DICER1 enzyme and small molecules including estradiol, tamoxifen, estrogen, LPS, and epigallocatechin. Our study used results of next-generation sequencing to reveal key miRNAs as the main regulator of gene expression responses to a Gram-positive bacterial infection. Furthermore, by gene regulatory network (GRN) analysis, we can introduce the common upregulator transcription factor of these miRNAs. Such milk-based miRNA signature(s) would facilitate risk stratification for large-scale prevention programs and provide an opportunity for early diagnosis and therapeutic intervention.
PMID: 36066834
JMIR Form Res , 2022 Oct , V6 (10) : Pe39582 doi: 10.2196/39582
Social Media Mining of Long-COVID Self-Medication Reported by Reddit Users: Feasibility Study to Support Drug Repurposing.
Department of Management and Entrepreneurship, Faculty of Management, Economics and Society, Witten/Herdecke University, Witten, Germany.
BACKGROUND: Since the beginning of the COVID-19 pandemic, over 480 million people have been infected and more than 6 million people have died from COVID-19 worldwide. In some patients with acute COVID-19, symptoms manifest over a longer period, which is also called "long-COVID." Unmet medical needs related to long-COVID are high, since there are no treatments approved. Patients experiment with various medications and supplements hoping to alleviate their suffering. They often share their experiences on social media. OBJECTIVE: The aim of this study was to explore the feasibility of social media mining methods to extract important compounds from the perspective of patients. The goal is to provide an overview of different medication strategies and important agents mentioned in Reddit users' self-reports to support hypothesis generation for drug repurposing, by incorporating patients' experiences. METHODS: We used named-entity recognition to extract substances representing medications or supplements used to treat long-COVID from almost 70,000 posts on the "/r/covidlonghaulers" subreddit. We analyzed substances by frequency, co-occurrences, and network analysis to identify important substances and substance clusters. RESULTS: The named-entity recognition algorithm achieved an F1 score of 0.67. A total of 28,447 substance entities and 5789 word co-occurrence pairs were extracted. "Histamine antagonists," "famotidine," "magnesium," "vitamins," and "steroids" were the most frequently mentioned substances. Network analysis revealed three clusters of substances, indicating certain medication patterns. CONCLUSIONS: This feasibility study indicates that network analysis can be used to characterize the medication strategies discussed in social media. Comparison with existing literature shows that this approach identifies substances that are promising candidates for drug repurposing, such as antihistamines, steroids, or antidepressants. In the context of a pandemic, the proposed method could be used to support drug repurposing hypothesis development by prioritizing substances that are important to users.
PMID: 36007131
Biomed Pharmacother , 2022 Nov , V155 : P113798 doi: 10.1016/j.biopha.2022.113798
Therapeutic efficacy of Scutellaria baicalensis Georgi against psoriasis-like lesions via regulating the responses of keratinocyte and macrophage.
Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.; Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.; Pharmaceutics Laboratory, Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan.; National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan.; School of Traditional Chinese Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan. Electronic address: pan@mail.cgu.edu.tw.
Psoriasis is a chronic and recurrent skin problem that affects 3% of the global population. Nowadays, most medicines may not promise a complete cure for patients with psoriasis because of the development of pharmacoresistance and the side effects of drugs due to the microenvironment impact in the context of skin imbalance. Herein, we attempt to explore the pharmaceutical efficacy of Scutellaria baicalensis (S. baicalensis) in modulating the microenvironment created by macrophages and keratinocytes in psoriasis. The results indicated that treatment of S. baicalensis extract significantly reduced the thickness of epidermis and attenuated psoriatic lesions. Moreover, S. baicalensis extract obviously inhibited the activation and infiltration of macrophages by alleviating inflammatory factors such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappaB) and cyclooxygenase-2 (COX-2). The administration of S. baicalensis extract also remarkably abolished oxidative damage upon DNA and proteins, which attributed to the activation of nuclear factor erythroid 2-related factor-2 (Nrf2) and heme oxygenase-1 (HO-1). The network analysis of redox proteomics and cytokine profiles suggested that S. baicalensis administration regulated the specific pathways associated with oxidative stress, inflammation and cytokine signaling cascades to ameliorate the macrophage-targeted responses and subsequently arrest proliferation of keratinocytes. Collectively, our findings highlighted the importance of S. baicalensis application in reprogramming microenvironment to provide an alternative and complementary intervention for long-term psoriatic therapy.
PMID: 36271574
Huan Jing Ke Xue , 2022 Oct , V43 (10) : P4755-4764 doi: 10.13227/j.hjkx.202201210
[Effects of Long-term Straw Returning on Fungal Community, Enzyme Activity and Wheat Yield in Fluvo-aquic Soil].
Key Laboratory of Wastes Matrix Utilization, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Ji'nan 250100, China.; Dezhou Academy of Agricultural Sciences, Dezhou 253015, China.
To illustrate the effects of long-term straw returning on the fungal community, soil enzyme activity, and crop yield in a fluvo-aquic soil area typical of the Huang-Huai-Hai Plain, a 10-year field experiment (established in 2010) located in Dezhou City, Shandong province, was performed, including three fertilization regimes (NF, no fertilization control; NPK, fertilization with chemical N, P, and K fertilizers; NPKS, straw returning combined with chemical N, P, and K fertilizers). This study aimed to explore the regulation mechanisms of fungal communities on soil fertility, enzyme activities, and crop yield by employing co-occurrence network and structural equation model analyses. Our results showed that long-term straw returning significantly improved soil nutrients, enzyme activity, and wheat yield. Compared with the NPK and NF treatments, soil organic matter (SOM) increased by 9.20% and 34.75%, alkali-hydrolyzed nitrogen (AN) increased by 12.03% and 39.17%, dehydrogenase (DHA) increased by 37.21% and 50.91%, beta-glucosidase (beta-GC) increased by 17.29% and 73.48%, and wheat production increased by 16.22% and 125.53%, respectively. Different long-term fertilization regimes did not significantly change soil fungal alpha-diversity but resulted in significant differences in beta-diversity. Available phosphorus (AP), SOM, and AN were the main driving factors of fungal community differentiation based on redundancy analysis and hierarchical partitioning analysis. Different abundance analyses revealed significantly different fungal community compositions among fertilization regimes. The long-term NF treatment resulted in a significant enrichment of phosphate/potassium-solubilizing species (i.e., Mortierella, Aspergillus, Ceriporia, and Acremonium) and symbiotic species (i.e., Leohumicola and Hyalodendriella). The relative abundance of pathogenic fungi, namely Sarocladium, Fusarium, and Fusicolla, increased significantly in the NPK treatment. Long-term straw returning in the NPKS treatment significantly stimulated the growth of plant growth-promoting species (i.e., Pseudogymnoascus and Schizothecium) and straw-degrading species (i.e., Trichocladium and Lobulomyces). Co-occurrence network analysis showed that the fungal network was composed of four main modules; the cumulative relative abundance of module 2 was significantly increased under the NPKS treatment and showed a positive linear correlation with DHA and beta-GC. The structural equation model further indicated that the wheat yield was mainly regulated by SOM, whereas species of module 2 could indirectly affect SOM and wheat yield by positively regulating DHA and beta-GC. Taken together, long-term straw returning to the fluvo-aquic soil area of the Huang-Huai-Hai Plain could regulate fungal interspecific interactions, stimulate the growth of specific species groups, inhibit the activity of pathogens, increase the activity of soil enzymes, promote the accumulation of SOM, and achieve high crop yield.
PMID: 36224161
Huan Jing Ke Xue , 2022 Oct , V43 (10) : P4536-4544 doi: 10.13227/j.hjkx.202201136
[Historical Antibiotic Stress Changed the Effects of Sulfamethoxazole and Trimethoprim on Activated Sludge: ARGs and Potential Hosts].
Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing 100124, China.
The co-exposure of antibiotics has important effects on antibiotic resistance genes (ARGs) and microbial community aggregation in wastewater treatment plants (WWTPs). However, it is unclear whether differences in historical antibiotic exposure stress can determine responses of microbes and ARGs to combined antibiotics. By selecting a high concentration (30 mg.L(-1)) of sulfamethoxazole (SMX) and trimethoprim (TMP) as historical exposure stress conditions, the effects of SMX and TMP-combined pollution on ARGs, bacterial communities, and their interactions were explored in short-term experiments. Based on high-throughput quantitative PCR, a total of 13 ARGs were detected, and the absolute abundance was 2.21-5.42 copies.muL(-1) (logarithm, DNA, the same below). Among them, sul2, ermB, mefA, and tetM-01 were the main subtypes in the samples, and the absolute abundance was between 2.95 and 5.40 copies.muL(-1). The combined contamination of SMX and TMP could cause the enrichment of ARGs and mobile genetic elements (MGEs); however, their effects on each subtype were different, and the historical legacy effect of SMX was higher than that of TMP. Under the different exposure histories, the co-occurrence and co-exclusion patterns existed between ARGs. Moreover, MGEs (especially intI-1) were significantly correlated with sulfonamides (sul1 and sul2), tetracyclines[tet(32)], and macrolide-lincosamide-streptogramin (MLSB) resistance genes (ermB). Based on the full-scale classification of microorganisms, it was found that the microbial community structure of various groups responded differently to combined pollution, and the conditionally abundant taxa (CAT) were obviously enriched. Thauera, Pseudoxanthomonas, and Paracoccus were the dominant resistant bacterial genera. Furthermore, a total of 31 potential hosts of ARGs were identified with network analysis, which were dominated with conditionally rare taxa (CRT). Particularly, Candidatus_Alysiosphaera and Fusibacter were positively correlated with most of the ARGs, being the common protentional hosts. Importantly, some rare genera (RT, Variibacter, Aeromonas, Cloacibacterium, etc.) were potential hosts of transposon IS613, which played an important role in the proliferation and spread of ARGs. In conclusion, this study revealed the legacy effects of historical antibiotic stress on ARGs and their hosts, which could provide new ideas and theoretical basis for reducing ARGs pollution in WWTPs.
PMID: 36224139