New Phytol , IF:10.151 , 2024 Feb , V241 (3) : P1193-1209 doi: 10.1111/nph.19420
A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1.
Bioscience, Wageningen Plant Research, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Laboratory of Molecular Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autonoma de Madrid, 28049, Madrid, Spain.; Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Cientificas, Ave. Americo Vespucio 49, 41092, Seville, Spain.; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Ave. Reina Mercedes s/n, 41012, Seville, Spain.; Bioinformatics, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Department of Systems Biology, Centro Nacional de Biotecnologia/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autonoma de Madrid, 28049, Madrid, Spain.
The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::beta-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.
PMID: 38009929
New Phytol , IF:10.151 , 2024 Feb , V241 (4) : P1421-1434 doi: 10.1111/nph.19527
Receptor-like kinases and their signaling cascades for plant male fertility: loyal messengers.
Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China.; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China.; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China.
Receptor-like kinases (RLKs) are evolved for plant cell-cell communications. The typical RLK protein contains an extracellular and hypervariable N-terminus to perceive various signals, a transmembrane domain to anchor into plasma membrane, and a cytoplasmic, highly conserved kinase domain to phosphorylate target proteins. To date, RLKs have manifested their significance in a myriad of biological processes during plant reproductive growth, especially in male fertility. This review first summarizes a recent update on RLKs and their interacting protein partners controlling anther and pollen development, pollen release from dehisced anther, and pollen function during pollination and fertilization. Then, regulatory networks of RLK signaling pathways are proposed. In addition, we predict RLKs in maize and rice genome, obtain homologs of well-studied RLKs from phylogeny of three subfamilies and then analyze their expression patterns in developing anthers of maize and rice to excavate potential RLKs regulating male fertility in crops. Finally, current challenges and future prospects regarding RLKs are discussed. This review will contribute to a better understanding of plant male fertility control by RLKs, creating potential male sterile lines, and inspiring innovative crop breeding methods.
PMID: 38174365
Sci Total Environ , IF:7.963 , 2024 Mar , V914 : P169824 doi: 10.1016/j.scitotenv.2023.169824
The impact of various forms of silver nanoparticles on the rhizosphere of wheat (Triticum aestivum L.) - Shifts in microbiome structure and predicted microbial metabolic functions.
Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, 10-720 Olsztyn, Poland. Electronic address: sebastian.przemieniecki@uwm.edu.pl.; Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland. Electronic address: karolina.ruraz@ujk.edu.pl.; Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawochenskiego 17, 10-720 Olsztyn, Poland. Electronic address: olga.kosewska@uwm.edu.pl.; Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland. Electronic address: magdalena.ocwieja@ikifp.edu.pl.; Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, 31-120 Krakow, Poland. Electronic address: anna.gorczyca@urk.edu.pl.
The study investigated the effects of different silver nanoparticles (AgNPs) on the soil microbiome and wheat growth. For comparison purposes, a commercial fungicide and silver nitrate (AgNO(3)) were used. The results revealed three distinct groups of nanoparticles based on their impacts. Small-size AgNPs (10 nm) with a negative charge, as well as fungicide had limited effects on the microbiome, similar to the no-treatment control. Bigger in size (30-60 nm) and a negative charge AgNPs showed the most beneficial effects on soil microbiota shifts. These AgNPs increased the abundance of bacteria with beneficial traits such as nitrogen-fixing, urease, protease, and lignin degradation bacteria. The third type of AgNPs had a positive charge of nanostructure and influenced specific microbial populations, increasing the abundance of anaerobic and autotrophic groups of microorganisms, which could be assessed as a harmful shift for plants growth promotions and was similar to the AgNO(3) treatment. Overall, the study emphasized the potential of AgNPs in agriculture not only as biocidal. The conducted study proved that AgNPs with bigger size/negative charge, used in low concentration can have a surprisingly stimulating effect on the positive characteristics of the rhizosphere microbiome. Moreover, the surface charge of AgNPs is a significant factor affecting microbial activity of wheat rhizosphere soil, which in this treatment is significantly similar to the AgNO(3) treatment.
PMID: 38185142
Sci Total Environ , IF:7.963 , 2024 Jan , V906 : P167544 doi: 10.1016/j.scitotenv.2023.167544
Deterioration of sludge characteristics and promotion of antibiotic resistance genes spread with the co-existing of polyvinylchloride microplastics and tetracycline in the sequencing batch reactor.
School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.; School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.. Electronic address: shishengnan013@163.com.; School of Life Sciences, Liaoning Normal University; Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.. Electronic address: 103596@lnnu.edu.cn.
With the continuous increase in microplastics (MPs) and tetracycline (TC) entering wastewater treatment plants (WWTPs) along with sewage, the co-existence of MPs and TC in the biological treatment of wastewater has attracted extensive attention. This study investigated the effect of 1 mg/L polyvinyl chloride (PVC) MPs and 100 ng/L TC co-existing on sequencing batch reactors (SBRs) (S2) treating phenol wastewater in contrast to the control with TC alone (S1). The phenol removal efficiency was significantly inhibited by the co-existence of PVC MPs and TC. Sludge characteristics were also distinctively influenced. The decreased zone sludge velocity (ZSV) and increased sludge volume index (SVI) indicated that the combined effect of PVC MPs and TC deteriorated sludge settleability, which had positive and negative linear correlations with extracellular polymeric substances (EPS) content and the protein (PN)/polysaccharide (PS) ratio, respectively. Moreover, the decreased and increased relative abundances of potential phenol-degraders and antibiotic resistance gene (ARG) carriers may elucidate the inhibition of phenol removal and promotion of ARGs propagation with the co-occurrence of PVC MPs and TC. In addition, the enhanced potential ARGs hosts, loss of the EPS protective effect, and increased membrane permeability induced by reactive oxygen species (ROS) jointly promoted ARGs dissemination in the co-existence of PVC MPs and TC. Notably, the co-occurrence of ARGs and mobile genetic element (MGEs) indicated that the co-existence of PVC MPs and TC promoted the spread of some transposase-associated ARGs mediated by horizontal gene transfer (HGT).
PMID: 37797771
Microbiol Spectr , IF:7.171 , 2024 Jan , V12 (1) : Pe0337423 doi: 10.1128/spectrum.03374-23
Saccharomyces cerevisiae biofactory to produce naringenin using a systems biology approach and a bicistronic vector expression strategy in flavonoid production.
School of Engineering and Science, Tecnologico de Monterrey , Monterrey, Nuevo Leon, Mexico.; Department of Chemical and Food Engineering, Grupo de Diseno de Productos y Procesos (GDPP), Universidad de los Andes , Bogota, Colombia.; Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry , Halle, Germany.
Flavonoids are a group of compounds generally produced by plants with proven biological activity, which have recently beeen recommended for the treatment and prevention of diseases and ailments with diverse causes. In this study, naringenin was produced in adequate amounts in yeast after in silico design. The four genes of the involved enzymes from several organisms (bacteria and plants) were multi-expressed in two vectors carrying each two genes linked by a short viral peptide sequence. The batch kinetic behavior of the product, substrate, and biomass was described at lab scale. The engineered strain might be used in a more affordable and viable bioprocess for industrial naringenin procurement.
PMID: 38088543
Int J Biol Macromol , IF:6.953 , 2023 Dec , 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
Front Plant Sci , IF:5.753 , 2023 , V14 : P1249122 doi: 10.3389/fpls.2023.1249122
Transcriptomic landscape of staminate catkins development during overwintering process in Betula platyphylla.
Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.
Betula platyphylla, belonging to the cold-specialized lineage Betulaceae, exhibits a unique reproductive strategy where staminate catkins emerge in the first summer and undergo an overwintering process, culminating in flowering in the following year. However, the underlying regulatory mechanism remains unclear. In this study, we investigated the male germline development of B. platyphylla in four distinct stages: microsporocytes in Oct. (S1), uninuclear microspores from Dec. (S2) to Mar. of the following year (S3), and bicellular microspores in Apr. (S4). We performed RNA sequencing on mature pollen and the four stages of staminate catkins. Using weighted gene co-expression network analysis (WGCNA), we identified five highly correlated gene modules with distinct expression profiles. These modules exhibited strong correlations with sugar metabolism, cell cycle, flowering, and cell wall dynamics, highlighting their dynamic roles during male germline developmental stages. During the overwintering process, we observed that the expression of transcription factors such as BpDUO1 and BpAMS at the appropriate developmental stages, suggests their significant roles in male germline development. The expression patterns of BpFLC and BpFT suggest their potential involvement in temperature perception during male reproductive development. These findings offer valuable insights into the reproductive success of plants adapting to cold environments.
PMID: 38259941
Front Plant Sci , IF:5.753 , 2023 , V14 : P1252885 doi: 10.3389/fpls.2023.1252885
Identification of candidate regulators of the response to early heat stress in climate-adapted wheat landraces via transcriptomic and co-expression network analyses.
Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, United Kingdom.
INTRODUCTION: Climate change is likely to lead to not only increased global temperatures but also a more variable climate where unseasonal periods of heat stress are more prevalent. This has been evidenced by the observation of spring-time temperatures approaching 40 degrees C in some of the main spring-wheat producing countries, such as the USA, in recent years. With an optimum growth temperature of around 20 degrees C, wheat is particularly prone to damage by heat stress. A warming climate with increasingly common fluctuations in temperature therefore threatens wheat crops and subsequently the lives and livelihoods of billions of people who depend on the crop for food. To futureproof wheat against a variable climate, a better understanding of the response to early heat stress is required. METHODS: Here, we utilised DESeq2 to identify 7,827 genes which were differentially expressed in wheat landraces after early heat stress exposure. Candidate hub genes, which may regulate the transcriptional response to early heat stress, were identified via weighted gene co-expression network analysis (WGCNA), and validated by qRT-PCR. RESULTS: Two of the most promising candidate hub genes (TraesCS3B02G409300 and TraesCS1B02G384900) may downregulate the expression of genes involved in the drought, salinity, and cold responses-genes which are unlikely to be required under heat stress-as well as photosynthesis genes and stress hormone signalling repressors, respectively. We also suggest a role for a poorly characterised sHSP hub gene (TraesCS4D02G212300), as an activator of the heat stress response, potentially inducing the expression of a vast suite of heat shock proteins and transcription factors known to play key roles in the heat stress response. DISCUSSION: The present work represents an exploratory examination of the heat-induced transcriptional change in wheat landrace seedlings and identifies several candidate hub genes which may act as regulators of this response and, thus, may be targets for breeders in the production of thermotolerant wheat varieties.
PMID: 38235195
Plant Physiol Biochem , IF:4.27 , 2024 Jan , V207 : P108399 doi: 10.1016/j.plaphy.2024.108399
Non-coding RNAs and leaf senescence: Small molecules with important roles.
State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.; State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China. Electronic address: lizhonghai@bjfu.edu.cn.
Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.
PMID: 38277833
Tree Physiol , IF:4.196 , 2024 Jan doi: 10.1093/treephys/tpae011
Na2CO3-responsive mechanism insight from quantitative proteomics and SlRUB gene function in Salix linearistipularis seedlings.
Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China.; Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China.; College of Life Sciences and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China.
Mongolian willow (Salix linearistipularis) is a naturally occurring woody dioecious plant in the saline soils of northeastern China that has a high tolerance to alkaline salts. Although transcriptomics studies have identified a large number of salinity-responsive genes, the mechanism of salt tolerance in Mongolian willow is not clear. Here, we found that in response to Na2CO3 stress, Mongolian willow regulates osmotic homeostasis by accumulating proline and soluble sugars, and scavenges ROS by antioxidant enzymes and non-enzymatic antioxidants. Our quantitative proteomics study identified 154 salt-sensitive proteins mainly involved in maintaining the stability of the photosynthetic system and ROS homeostasis to cope with Na2CO3 stress. Among them, Na2CO3-induced rubredoxin (RUB) was predicted to be associated with 122 proteins for modulation of these processes. The chloroplast-localized SlRUB was highly expressed in leaves and significantly induced under Na2CO3 stress. Phenotypic analysis of overexpression, mutation, and complementation materials of RUB in Arabidopsis suggests that SlRUB is critical for the regulation of photosynthesis, ROS scavenging, and other metabolisms in the seedlings of Mongolian willow to cope with Na2CO3 stress. This provides more clues to better understand the alkali-responsive mechanism and RUB functions in the woody Mongolian willow.
PMID: 38263488
BMC Genomics , IF:3.969 , 2024 Jan , V25 (1) : P29 doi: 10.1186/s12864-023-09906-0
Intergrative metabolomic and transcriptomic analyses reveal the potential regulatory mechanism of unique dihydroxy fatty acid biosynthesis in the seeds of an industrial oilseed crop Orychophragmus violaceus.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. wangray1987@scu.edu.cn.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. wangjing2019@scu.edu.cn.
BACKGROUND: Orychophragmus violaceus is a potentially important industrial oilseed crop due to the two 24-carbon dihydroxy fatty acids (diOH-FA) that was newly identified from its seed oil via a 'discontinuous elongation' process. Although many research efforts have focused on the diOH-FA biosynthesis mechanism and identified the potential co-expressed diacylglycerol acyltranferase (DGAT) gene associated with triacylglycerol (TAG)-polyestolides biosynthesis, the dynamics of metabolic changes during seed development of O. violaceus as well as its associated regulatory network changes are poorly understood. RESULTS: In this study, by combining metabolome and transcriptome analysis, we identified that 1,003 metabolites and 22,479 genes were active across four stages of seed development, which were further divided into three main clusters based on the patterns of metabolite accumulation and/or gene expression. Among which, cluster2 was mostly related to diOH-FA biosynthesis pathway. We thus further constructed transcription factor (TF)-structural genes regulatory map for the genes associated with the flavonoids, fatty acids and diOH-FA biosynthesis pathway in this cluster. In particular, several TF families such as bHLH, B3, HD-ZIP, MYB were found to potentially regulate the metabolism associated with the diOH-FA pathway. Among which, multiple candidate TFs with promising potential for increasing the diOH-FA content were identified, and we further traced the evolutionary history of these key genes among species of Brassicaceae. CONCLUSION: Taken together, our study provides new insight into the gene resources and potential relevant regulatory mechanisms of diOH-FA biosynthesis uniquely in seeds of O. violaceus, which will help to promote the downstream breeding efforts of this potential oilseed crop and advance the bio-lubricant industry.
PMID: 38172664
Plant Commun , 2024 Jan , V5 (1) : P100645 doi: 10.1016/j.xplc.2023.100645
Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites that modulate defense against pathogens.
Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, C/Vall Moronta, Edifici CRAG, 08193 Bellaterra (Cerdanyola del Valles), Barcelona, Spain. Electronic address: antoni.garcia@cragenomica.es.; Department of Biology, Biochemistry, and Natural Sciences, School of Technology and Experimental Sciences, Universitat Jaume I, 12006 Castello de la Plana, Spain.
Understanding plant immune responses is complex because of the high interdependence among biological processes in homeostatic networks. Hence, the integration of environmental cues causes network rewiring that interferes with defense responses. Similarly, plants retain molecular signatures configured under abiotic stress periods to rapidly respond to recurrent stress, and these can alter immunity. Metabolome changes imposed by abiotic stressors are persistent, although their impact on defense remains to be clarified. In this study, we profiled metabolomes of Arabidopsis plants under several abiotic stress treatments applied individually or simultaneously to capture temporal trajectories in metabolite composition during adverse conditions and recovery. Further systemic analysis was performed to address the relevance of metabolome changes and extract central features to be tested in planta. Our results demonstrate irreversibility in major fractions of metabolome changes as a general pattern in response to abiotic stress periods. Functional analysis of metabolomes and co-abundance networks points to convergence in the reconfiguration of organic acid and secondary metabolite metabolism. Arabidopsis mutant lines for components related to these metabolic pathways showed altered defense capacities against different pathogens. Collectively, our data suggest that sustained metabolome changes configured in adverse environments can act as modulators of immune responses and provide evidence for a new layer of regulation in plant defense.
PMID: 37403356
Huan Jing Ke Xue , 2024 Jan , V45 (1) : P543-554 doi: 10.13227/j.hjkx.202303078
[Response Characteristics of Soil Fungal Community Structure to Long-term Continuous Cropping of Pepper].
Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren 554300, China.; College of Resources and Environment, Shanxi Agricultural University, Jinzhong 030801, China.; Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Agro-Environment and Safe-Product, Tianjin 300191, China.
This study aimed to clarify the effect of long-term continuous cropping of pepper on soil fungal community structure, reveal the mechanism of continuous cropping obstacles, and provide a theoretical basis for the ecological safety and sustainable development of pepper industry. We took the pepper continuous cropping soil in the vegetable greenhouse planting base of Tongren City as the research object. The diversity and community structure of fungi in farmland soil were analyzed using Illumina MiSeq high-throughput sequencing, the responses of soil physio-chemical properties and fungal community characteristics to long-term continuous pepper cropping were discussed, and the relationships between the characteristics of fungal community structure and environmental factors were determined using CCA and correlation network analysis. The results showed that with the extension of pepper continuous cropping years, the soil pH value and organic matter (OM) content decreased, total phosphorus (TP) and available phosphorus (AP) contents increased, hydrolyzed nitrogen (AN) and available potassium (AK) contents decreased first and then increased, and total nitrogen (TN) and total potassium (TK) contents did not change significantly. Long-term continuous cropping decreased the Chao1 index and observed species index and decreased the Shannon index and Simpson index. The change in continuous cropping years had a significant effect on the relative abundance of soil fungal dominant flora. At the phylum level, the relative abundance of Mortierellomycota decreased with the extension of pepper continuous cropping years, the relative abundance of Ascomycota increased first and then decreased, and the relative abundance of Basidiomycota decreased first and then increased. At the genus level, with the increasing of pepper continuous cropping years, the relative abundance of Fusarium increased, and the relative abundance of Mortierella and Penicillium decreased. In addition, long-term continuous cropping simplified the soil fungal symbiosis network. CCA analysis indicated that pH, OM, TN, AN, AP, and AK were the driving factors of soil fungal community structure, and correlation network analysis showed that pH, OM, TN, TP, TK, AN, AP, and AK were the driving factors of soil fungal community structure, including Fusarium, Lophotrichus, Penicillium, Mortierella, Botryotrichum, Staphylotrichum, Plectosphaerella, and Acremonium. In conclusion, continuous cropping changed the soil physical and chemical properties, affected the diversity and community structure of the soil fungal community, changed the interaction between microorganisms, and destroyed the microecological balance of the soil, which might explain obstacles associated with continuous cropped pepper.
PMID: 38216503
Biochem Biophys Rep , 2024 Mar , V37 : P101620 doi: 10.1016/j.bbrep.2023.101620
Trancriptome data mining in combination with co-expression network analysis identifies the functional modules and critical regulators in Hordeum vulgare L. in response to cold stress.
Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.; Faculty of Agriculture (Meshgin-Shahr Campus), University of Mohaghegh Ardabili, Ardabil, Iran.
Cold stress, as an abiotic stress, is one of the most limiting factors which pose a great threat to the plant's productivity. To understand the transcriptional regulation and connectivity pattern of genes involved in barley cold stress responses, co-expression network analysis was performed based on the global transcriptome profiling. The microarray datasets related to cold stress treatments were retrieved from the Gene Expression Omnibus (GEO) and Array express databases. Four microarray datasets related to cold stress-responsive transcriptome in barley were included in our study. Gene co-expression analysis was constructed using WGCNA method. Module-Trait Relationships (MTR) analysis and hub genes determination and validation were carried out. Finally, transcription factor and kinase regulatory networks were Inferred using machine learning algorithm. The co-expression modules were determined using beta index = 10. In total 13 co-expressed modules were identified with an average size of 153 genes. Functional enrichment based on gene ontology (GO) showed that each of the stress related significant modules were enriched in different biological processes. Annotation of significant modules identifies some TFs and Kinases such as ethylene-responsive transcription factor 1-like, transcription factor PCL1-like, transcription factor MYC2, WRKY, serine/threonine-protein kinase PBL7, and receptor-like protein kinase At2g42960 were contributed in barley cold stress response. Our analysis highlighted the functional importance of ABA signaling pathway, ROS signaling, defensive and protective proteins, degrading protein, Ca2(+) related signaling, ribosome-mediated translation and etc. in responding of barley to cold stress condition. The current findings add substantially to our understanding of the cold responsive underlying mechanism of barley which can serve in future studies and breeding programs.
PMID: 38155945