J Adv Res , IF:10.479 , 2023 Nov , V53 : P17-31 doi: 10.1016/j.jare.2022.12.003
Chilling-induced peach flavor loss is associated with expression and DNA methylation of functional genes.
Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.; Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China.; Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; Shandong (Linyi) Institute of Morden Agriculture, Zhejiang University, Linyin 276000, China. Electronic address: bozhang@zju.edu.cn.
INTRODUCTION: Flavor is a major contributor to consumer preference. Despite being effective at extending the fruit's commercial life, cold storage also results in a significant loss of flavor volatiles. To date, there has been few studies on the metabolic dynamics and the mechanism underlying the regulatory networks that modulate flavor loss during cold storage for fruit. METHODS: The volatile contents were detected by Gas Chromatography-Mass Spectrometer (GC-MS). Weighted gene co-expression network analysis (WGCNA) was used to identify structure genes and transcription factors (TFs). DNA methylation was analyzed by whole-genome methylation sequencing during cold storage. RESULTS: We generated a temporal map, over hourly to weekly timescales, for the effects of chilling on flavor volatiles by combining metabolome, transcriptome, and DNA methylome in peach fruit. Based on the big data analysis, we developed a regulatory network for volatile formation and found that a decrease in volatiles during cold storage was significantly correlated with a decrease in the expression of synthesis genes. Moreover, TFs associated with these structure genes were identified. Expression of genes involved in ethylene biosynthesis was reduced while cold tolerance pathway was activated in response to low temperature. Functions of those genes were confirmed through transgenic experiments and across peach cultivars, suggesting our dataset is a useful tool for elucidating regulatory factors that have not yet been clarified in relation to flavor and cold tolerance. Genome wide DNA methylation was induced by chilling and peaked at 7 d followed by a decline during 28 d cold storage. Reduction of gene expression was accompanied by major changes in the methylation status of their promoters, including PpACS1, PpAAT1, PpTPS3 and PpMADS2. CONCLUSION: Our study revealed the mechanism for chilling-induced flavor loss of peach fruit through time-course transcriptome and DNA methylome analysis.
PMID: 36496174
New Phytol , IF:10.151 , 2023 Nov 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
Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Elife , IF:8.14 , 2023 Nov , V12 doi: 10.7554/eLife.86576
100 years of anthropogenic impact causes changes in freshwater functional biodiversity.
Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, United Kingdom.; School of Geography, Earth & Environmental Sciences, University of Birmingham, Birmingham, United Kingdom.; Department Evolutionary Ecology & Environmental Toxicology, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany.; Lake Group, Department of Ecoscience, Aarhus University, Aarhus, Denmark.; School of Natural Sciences, Environment Centre Wales, Deiniol Road, Bangor University, Bangor, United Kingdom.; Department Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, United States.; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.; Department Media-related Toxicology, Institute for Molecular Biology and Applied Ecology (IME), Frankfurt, Germany.; The Alan Turing Institute, British Library, London, United Kingdom.
Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high-throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.
PMID: 37933221
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
Sci Total Environ , IF:7.963 , 2023 Dec , V905 : P167075 doi: 10.1016/j.scitotenv.2023.167075
Risk assessment framework for pine wilt disease: Estimating the introduction pathways and multispecies interactions among the pine wood nematode, its insect vectors, and hosts in China.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; The College of Forestry, Beijing Forestry University, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.; Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.; The College of Forestry, Beijing Forestry University, Beijing 100193, China. Electronic address: shi_juan@263.net.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China. Electronic address: liuwanxue@caas.cn.
Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), a destructive, invasive forest pathogen, poses a serious threat to global pine forest ecosystems. The global invasion of PWN has been described based on three successive phases, introduction, establishment, and dispersal. Risk assessments of the three successive PWN invasion phases can assist in targeted management efforts. Here, we present a risk assessment framework to evaluate the introduction, establishment, and dispersal risks of PWD in China using network analysis, species distribution models, and niche concepts. We found that >88 % of PWN inspection records were from the United States, South Korea, Japan, Germany, and Mexico, and 94 % of interception records were primarily from the Jiangsu, Shanghai, Shandong, Tianjin, and Zhejiang ports. Based on the nearly current climate, the areas of PWN overlap with its host Pinus species were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions. Areas of PWN overlap with its insect vector Monochamus alternatus were primarily distributed in southern, eastern, Yangtze River Basin, central, and northeastern China regions, and those of PWN overlap with the insect vector Monochamus saltuarius were primarily distributed in eastern and northeastern China. The niche between PWN and the insect vector M. alternatus was the most similar (0.68), followed by that between PWN and the insect vector M. saltuarius (0.47). Climate change will increase the suitable probabilities of PWN and its two insect vectors occurring at high latitudes, further increasing their threat to hosts in northeastern China. This risk assessment framework for PWD could be influential in preventing the entry of the PWN and mitigating their establishment and dispersal risks in China. Our study provides substantial clues for developing a framework to improve the risk assessment and surveillance of biological invasions worldwide.
PMID: 37714356
Sci Total Environ , IF:7.963 , 2023 Nov , V900 : P165800 doi: 10.1016/j.scitotenv.2023.165800
Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields.
Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland. Electronic address: Mikhail.sofiev@fmi.fi.; Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center, Munich, Germany.; Federal Office of Meteorology and Climatology MeteoSwiss, Chemin de l'Aerologie 1, 1530 Payerne, Switzerland.; Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland.; Faculty of Geography and Earth Sciences, University of Latvia, Rainis bvld 19, Riga LV-1586, Latvia.; University of Worcester, UK.; Institute of Allergology, Charite - Universitatsmedizin Berlin, Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.; Department of Biology and Environmental Sciences, University of Gothenburg, Box 461, S-405 30 Gothenburg, Sweden.; Deutscher Wetterdienst, Berlin, Germany.; National Laboratory of Health, Environment and Food, Slovenia.; School of Chemical Sciences, Dublin City University, Ireland.; Department of Botany, Ecology and Plant Physiology, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Rabanales Campus, Celestino Mutis Building, E-14071 Cordoba, Spain; Andalusian Inter-University Institute for Earth System IISTA, University of Cordoba, Spain.; Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Pole of the Faculty of Sciences, University of Porto, Portugal.; German Pollen Information Service Foundation (PID), Berlin, Germany.
We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constraints for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data.
PMID: 37595925
Sci Total Environ , IF:7.963 , 2023 Nov , V897 : P165441 doi: 10.1016/j.scitotenv.2023.165441
Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers.
The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.; The National Key Laboratory of Water Disaster Prevention, Dayu College, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China. Electronic address: envly@hhu.edu.cn.
In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.
PMID: 37437635
Plant Cell Environ , IF:7.228 , 2023 Nov , V46 (11) : P3628-3643 doi: 10.1111/pce.14672
Dynamic gene regulatory networks improving spike fertility through regulation of floret primordia fate in wheat.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.; College of Biological Sciences, China Agricultural University, Beijing, China.; Texas A&M AgriLife Research and Extension Center at Amarillo, Amarillo, Texas, USA.; Engineering Technology Research Center for Agriculture in Low Plain Areas, Hebei Province, China.
The developmental process of spike is critical for spike fertility through affecting floret primordia fate in wheat; however, the genetic regulation of this dynamic and complex developmental process remains unclear. Here, we conducted a high temporal-resolution analysis of spike transcriptomes and monitored the number and morphology of floret primordia within spike. The development of all floret primordia in a spike was clearly separated into three distinct phases: differentiation, pre-dimorphism and dimorphism. Notably, we identified that floret primordia with meiosis ability at the pre-dimorphism phase usually develop into fertile floret primordia in the next dimorphism phase. Compared to control, increasing plant space treatment achieved the maximum increasement range (i.e., 50%) in number of fertile florets by accelerating spike development. The process of spike fertility improvement was directed by a continuous and dynamic regulatory network involved in transcription factor and genes interaction. This was based on the coordination of genes related to heat shock protein and jasmonic acid biosynthesis during differentiation phase, and genes related to lignin, anthocyanin and chlorophyll biosynthesis during dimorphism phase. The multi-dimensional association with high temporal-resolution approach reported here allows rapid identification of genetic resource for future breeding studies to realise the maximum spike fertility potential in more cereal crops.
PMID: 37485926
Waste Manag , IF:7.145 , 2023 Dec , V172 : P33-42 doi: 10.1016/j.wasman.2023.09.003
Waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis promote tomato seedlings growth by benefiting properties, enzyme activities and rhizosphere bacterial community in coastal saline soil of Yellow River Delta, China.
College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China.; Citrus Research Institute, Southwest University, Chongqing 400712, China.; Weihai Academy of Agricultural Sciences, Weihai 264200, China.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: houxin.sdau@163.com.; College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Taian 271018, China. Electronic address: yanglong1020@163.com.
This study investigated the effects of waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis HCH2-3 on the tomato seedlings growth in coastal saline soils and chemical properties, enzyme activities, microbial communities of rhizosphere soil. Microcosmic experiment showed that the seaweed compost and rhizosphere bacteria (SC + HCH2-3) significantly alleviated the negative effects of salinity on the growth of tomato seedlings. SC + HCH2-3 amendment significantly increased the plant height and root fresh biomass of tomato seedling by 105.59% and 55.60% in the coastal saline soils, respectively. The soil properties and enzyme activities were also dramatically increased, indicating that the nutrient status of coastal saline soil was improved by SC + HCH2-3 amendment. In addition, Proteobacteria, Actinobacteriota and Firmicutes were the dominant phyla in the rhizosphere soil after adding seaweed compost and rhizosphere bacteria P. koreensis HCH2-3. The relative abundances of Massilia, Azospira, Pseudomonas and Bacillus increased in treatment SC + HCH2-3. Especially, the beneficial bacteria genera, such as Pseudomonas, Bacillus and Azospira, were significantly correlated with the increases of contents of total nitrogen, nitrate nitrogen and ammonium nitrogen in tomato rhizosphere soil samples. Consequently, adding waste seaweed compost and rhizosphere bacteria P. koreensis HCH2-3 into coastal saline soil was suggested as an effective method to relieve salt stress of tomato plants.
PMID: 37708810
J Exp Bot , IF:6.992 , 2023 Nov , V74 (21) : P6820-6835 doi: 10.1093/jxb/erad348
Barley shows reduced Fusarium head blight under drought and modular expression of differentially expressed genes under combined stress.
Chair of Phytopathology, TUM School of Life Sciences, HEF World Agricultural Systems Center, Technical University of Munich, Emil-Ramann Str. 2, 85354 Freising-Weihenstephan, Germany.; Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany.; LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising-Weihenstephan, Germany.; Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3/I, 85354 Freising-Weihenstephan, Germany.; Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Strasse 34, 85354 Freising-Weihenstephan, Germany.; Institute of Phytopathology, Christian Albrecht University of Kiel, Hermann-Rodewald-Strasse 9, 24118 Kiel, Germany.
Plants often face simultaneous abiotic and biotic stress conditions; however, physiological and transcriptional responses under such combined stress conditions are still not fully understood. Spring barley (Hordeum vulgare) is susceptible to Fusarium head blight (FHB), which is strongly affected by weather conditions. We therefore studied the potential influence of drought on FHB severity and plant responses in three varieties of different susceptibility. We found strongly reduced FHB severity in susceptible varieties under drought. The number of differentially expressed genes (DEGs) and strength of transcriptomic regulation reflected the concentrations of physiological stress markers such as abscisic acid or fungal DNA contents. Infection-related gene expression was associated with susceptibility rather than resistance. Weighted gene co-expression network analysis revealed 18 modules of co-expressed genes that reflected the pathogen- or drought-response in the three varieties. A generally infection-related module contained co-expressed genes for defence, programmed cell death, and mycotoxin detoxification, indicating that the diverse genotypes used a similar defence strategy towards FHB, albeit with different degrees of success. Further, DEGs showed co-expression in drought- or genotype-associated modules that correlated with measured phytohormones or the osmolyte proline. The combination of drought stress with infection led to the highest numbers of DEGs and resulted in a modular composition of the single-stress responses rather than a specific transcriptional output.
PMID: 37668551
J Exp Bot , IF:6.992 , 2023 Nov , V74 (21) : P6396-6398 doi: 10.1093/jxb/erad378
Solving the puzzle of climacteric fruit ripening: EMB1444-like and its regulatory function.
Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.; Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
This article comments on: Zhao W, Wang S, Li W, Shan X, Naeem M, Zhang L, Zhao L. 2023. The transcription factor EMB1444-like affects tomato fruit ripening by regulating YELLOW-FRUITED TOMATO 1, a core component of ethylene signaling transduction. Journal of Experimental Botany 74, 6563-6574.
PMID: 37988177
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
Plant J , IF:6.417 , 2023 Nov doi: 10.1111/tpj.16548
Dynamic transcriptome landscape of maize pericarp development.
State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China.; Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, P. R. China.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China.
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome-wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA-seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non-seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp-specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene-related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
PMID: 37970738
Plant J , IF:6.417 , 2023 Nov , V116 (3) : P887-902 doi: 10.1111/tpj.16416
Organ-enriched gene expression during floral morphogenesis in wild barley.
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.; Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.; Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China.
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
PMID: 37548103
Front Plant Sci , IF:5.753 , 2023 , V14 : P1277585 doi: 10.3389/fpls.2023.1277585
Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach.
Department of Plant Pathology, The Ohio State University, Wooster, OH, United States.; Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States.; Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH, United States.; Translational Plant Sciences Graduate Program, The Ohio State University, Columbus, OH, United States.; Department of Biology, Brandon University, Brandon, Manitoba, MB, Canada.; Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States.
Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad x Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.
PMID: 38023885
Front Plant Sci , IF:5.753 , 2023 , V14 : P1261754 doi: 10.3389/fpls.2023.1261754
Confronting stresses affecting olive cultivation from the holobiont perspective.
Departamento de Microbiologia del Suelo y la Planta, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas (CSIC), Granada, Spain.
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
PMID: 38023867
J Agric Food Chem , IF:5.279 , 2023 Nov , V71 (43) : P15895-15907 doi: 10.1021/acs.jafc.3c03560
Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation.
Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.; Huangshan Institute of Product Quality Inspection, Huangshan 242700, China.; Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Ningbo 315000, China.
Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.
PMID: 37862148
Plant Sci , IF:4.729 , 2023 Nov , V336 : P111855 doi: 10.1016/j.plantsci.2023.111855
Involvement of plant signaling network and cell metabolic homeostasis in nitrogen deficiency-induced early leaf senescence.
Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China.; Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, China. Electronic address: chengfm@zju.edu.cn.
Nitrogen (N) is a basic building block that plays an essential role in the maintenance of normal plant growth and its metabolic functions through complex regulatory networks. Such the N metabolic network comprises a series of transcription factors (TFs), with the coordinated actions of phytohormone and sugar signaling to sustain cell homeostasis. The fluctuating N concentration in plant tissues alters the sensitivity of several signaling pathways to stressful environments and regulates the senescent-associated changes in cellular structure and metabolic process. Here, we review recent advances in the interaction between N assimilation and carbon metabolism in response to N deficiency and its regulation to the nutrient remobilization from source to sink during leaf senescence. The regulatory networks of N and sugar signaling for N deficiency-induced leaf senescence is further discussed to explain the effects of N deficiency on chloroplast disassembly, reactive oxygen species (ROS) burst, asparagine metabolism, sugar transport, autophagy process, Ca(2+) signaling, circadian clock response, brassinazole-resistant 1 (BZRI), and other stress cell signaling. A comprehensive understanding for the metabolic mechanism and regulatory network underlying N deficiency-induced leaf senescence may provide a theoretical guide to optimize the source-sink relationship during grain filling for the achievement of high yield by a selection of crop cultivars with the properly prolonged lifespan of functional leaves and/or by appropriate agronomic managements.
PMID: 37678563
Plant Physiol Biochem , IF:4.27 , 2023 Nov , V204 : P108131 doi: 10.1016/j.plaphy.2023.108131
WRKY transcription factors in Arachis hypogaea and its donors: From identification to function prediction.
Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China. Electronic address: biosonghui@outlook.com.; Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.; Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.; Shandong Peanut Research Institute, Qingdao, 266000, China.
WRKY transcription factors (TFs) play important roles in plant growth and development and responses to abiotic and biotic stresses. Since the initial isolation of a WRKY TF in Ipomoea batatas in 1994, WRKY TFs have been identified in plants, protozoa, and fungi. Peanut (Arachis hypogaea) is a key oil and protein crop for humans and a forage source for animal consumption. Several Arachis genomes have been sequenced and genome-wide WRKY TFs have been identified. In this review, we summarized WRKY TFs and their functions in A. hypogaea and its donors. We also standardized the nomenclature for Arachis WRKY TFs to ensure uniformity. We determined the evolutionary relationships between Arachis and Arabidopsis thaliana WRKY (AtWRKY) TFs using a phylogenetic analysis. Biological functions and regulatory networks of Arachis WRKY TFs were predicted using AtWRKY TFs. Thus, this review paves the way for studies of Arachis WRKY TFs.
PMID: 37897893
Environ Sci Pollut Res Int , IF:4.223 , 2023 Nov , V30 (53) : P113747-113757 doi: 10.1007/s11356-023-30196-2
Native forests transformed into cash crops reduced soil multi-functionality by modifying the microbial community composition and keystone species' abundance in the Jianghuai Hilly Region.
School of Geographic Information and Tourism, Chuzhou University, Chuzhou, 239000, China.; Hunan University of Humanities, Science and Technology, Loudi, 417000, China.; College of Tobacco Science, Yunnan Agricultural University, Kunming, 650000, China. chengganghe63@163.com.
Conversion of native forest to cash crops is the predominant form of land use change in the Jianghuai Hilly Region. However, how plantations with different cash crops affect the soil multi-functionality is not well documented. In this study, we collected three kinds of cash crops soils (vegetable, orchard, and tea) and forest soil, to systematically review the relationship between soil microbial communities and soil multi-functionality. Soil multi-functionality had decreased in vegetable and orchard as compared to native forest, whereas tea plantation had no significant effects on soil multi-functionality. The results also showed that cash crop plantations decreased soil multi-functionality by shifting keystone species' abundance, for forest, vegetable, and orchard, the keystone species that were classified as module hubs in the bacterial co-occurrence network significantly negatively contributed to soil multi-functionality, but the keystone species categorized as module hubs in fungal co-occurrence network positively affected soil multi-functionality. Multiple soil properties were the drivers of the soil microbial community; thus, indicating that the altered soil properties under cash crop plantations were vital in determining microbial composition and biological processes. These results identified that sustainable management strategy in cash crop plantation needed to be developed for improving soil multi-functionality.
PMID: 37851254
BMC Plant Biol , IF:4.215 , 2023 Nov , V23 (1) : P573 doi: 10.1186/s12870-023-04600-5
Regulation of an endophytic nitrogen-fixing bacteria GXS16 promoting drought tolerance in sugarcane.
Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, Guangxi, China.; Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pest, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.; Institute of Biological Science, Sage University Indore, Bhopal, Madhya Pradesh, India.; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland.; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, Guangxi, China. liyr@gxaas.net.; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, Guangxi, China. lcn560@126.com.
BACKGROUND: Drought limits crop growth and is an important issue in commercial sugarcane (Saccharum officinarum) production. Drought tolerance in sugarcane induced by endophytic nitrogen-fixing bacteria is a complex biological process that ranges from altered gene expression and cellular metabolism to changes in growth and productivity. RESULTS: In this study, changes in physiological features and transcriptome related to drought tolerance in sugarcane conferred by the Burkholderia endophytic nitrogen-fixing bacterial strain GXS16 were investigated. Sugarcane samples inoculated with GXS16 exhibited significantly higher leaf relative water content than those without GXS16 inoculation during the drought stages. Sugarcane treated with GXS16 had lower levels of H(2)O(2) and higher levels of abscisic acid than sugarcane not treated with GXS16 in the non-watering groups. Transcriptomic analysis of sugarcane roots identified multiple differentially expressed genes between adjacent stages under different treatments. Moreover, both trend and weighted correlation network analyses revealed that carotenoid biosynthesis, terpenoid backbone biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction strongly contributed to the drought-tolerant phenotype of sugarcane induced by GXS16 treatment. Accordingly, a gene regulatory network including four differentially regulated genes from carotenoid biosynthesis (crtB, crtZ, ZEP and CYP707A) and three genes from terpenoid backbone biosynthesis (dxs, dxr, and PCME) was constructed. CONCLUSIONS: This study provides insights into the molecular mechanisms underlying the application of GXS16 treatment to enhance drought tolerance in sugarcane, which will lay the foundation for crop development and improve productivity.
PMID: 37978424
Tree Physiol , IF:4.196 , 2023 Oct doi: 10.1093/treephys/tpad133
Transcriptome and Photosynthetic Analyses Provide New Insight into the Molecular Mechanisms Underlying Heat Stress Tolerance in Rhodo-dendron x pulchrum Sweet.
Jiyang college, Zhejiang A&F University, Zhuji, 311800, China.; Hangzhou Animation & Game College, Hangzhou Vocational & Technical College, Hangzhou 310018, China.; College of life science and health, Huzhou College, Huzhou, 313000, China.
Rhododendron species provide excellent ornamental use worldwide, yet heat stress (HS) is one of the major threats to their cultivation. However, the intricate mechanisms underlying the photochemical and transcriptional regulations associated with the heat stress response (HSR) in Rhododendron remain relatively unexplored. In this study, the analyses of morphological characteristics and chlorophyll fluorescence (ChlF) kinetics showed that HS (40 degrees C/35 degrees C) had a notable impact on both the donor and acceptor sides of photosystem II (PSII), resulting in reduced PSII activity and electron transfer capacity. While the gradual recovery of plants observed following a 5-day period of culture under normal conditions, indicating the reversible nature of the HS impact on R. x pulchrum. Analysis of transcriptome data unveiled noteworthy trends: four genes associated with photosynthesis-antenna protein synthesis (LHCb1, LHCb2, LHCb3) and the antioxidant system (GCL) experienced significant down-regulation in the leaves of R. x pulchrum during HS. Conversely, APX and GSTU8 demonstrated an up-regulated pattern. Furthermore, six down-regulated genes (PPC4, SBPASE, RPI2, HCEF1, BGLU32, and SS2) and two up-regulated genes (BGLU2 and UGP2) implicated in photosynthetic carbon fixation and starch/sucrose metabolism were identified during the recovery process. To augment these insights, a weighted gene co-expression network analysis (WGCNA) yielded a co-expression network, pinpointing hub genes correlated with ChlF dynamics' variation trends. The cumulative results showed that HS inhibited the synthesis of photosynthesis-antenna proteins in R. x pulchrum leaves. This disruption subsequently led to diminished photochemical activities in both PSII and PSI, albeit with PSI exhibiting heightened thermostability. Depending on the regulation of the reactive oxygen species (ROS) scavenging system and heat dissipation, photoprotection sustained the recoverability of R. x pulchrum to HS.
PMID: 37930230
FEMS Microbiol Ecol , IF:4.194 , 2023 Nov , V99 (12) doi: 10.1093/femsec/fiad130
Maintaining beneficial alga-associated bacterial communities under heat stress: insights from controlled co-culture experiments using antibiotic-resistant bacterial strains.
Integrative Biology of Marine Models, Sorbonne Universite/CNRS, UMR8227, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France.
Brown algae, like many eukaryotes, possess diverse microbial communities. Ectocarpus-a model brown alga-relies on these communities for essential processes, such as growth development. Controlled laboratory systems are needed for functional studies of these algal-bacterial interactions. We selected bacterial strains based on their metabolic networks to provide optimal completion of the algal metabolism, rendered them resistant to two antibiotics, and inoculate them to establish controlled co-cultures with Ectocarpus under continuous antibiotic treatment. We then monitored the stability of the resulting associations under control conditions and heat stress using 16S metabarcoding. Antibiotics strongly reduced bacterial diversity both in terms of taxonomy and predicted metabolic functions. In the inoculated sample, 63%-69% of reads corresponded to the inoculated strains, and the communities remained stable during temperature stress. They also partially restored the predicted metabolic functions of the natural community. Overall, the development of antibiotic-resistant helper cultures offers a promising route to fully controlled laboratory experiments with algae and microbiota and thus represents an important step towards generating experimental evidence for specific host-microbe interactions in the systems studied. Further work will be required to achieve full control and progressively expand our repertoire of helper strains including those currently 'unculturable'.
PMID: 37833238
Photochem Photobiol Sci , IF:3.982 , 2023 Nov , V22 (11) : P2635-2650 doi: 10.1007/s43630-023-00478-2
Metabolomic response to high light from pgrl1 and pgr5 mutants of Chlamydomonas reinhardtii.
Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.; The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion, 8499000, Beersheba, Israel.; National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.; Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India. srgsl@uohyd.ernet.in.
Chlamydomonas (C.) reinhardtii metabolomic changes in cyclic electron flow-dependent mutants are still unknown. Here, we used mass spectrometric analysis to monitor the changes in metabolite levels in wild-type, cyclic electron-deficient mutants pgrl1 and pgr5 grown under high-light stress. A total of 55 metabolites were detected using GC-MS analysis. High-light stress-induced selective anaplerotic amino acids in pgr5. In addition, pgr5 showed enhancement in carbohydrate, polyamine, and polyol metabolism by 2.5-fold under high light. In response to high light, pgr5 triggers an increase in several metabolites involved in regulating osmotic pressure. Among these metabolites are glycerol pathway compounds such as glycerol-3-phosphate and glyceryl-glycoside, which increase significantly by 1.55 and 3.07 times, respectively. In addition, pgr5 also enhanced proline and putrescine levels by 2.6- and 1.36-fold under high light. On the other hand, pgrl1-induced metabolites, such as alanine and serine, are crucial for photorespiration when subjected to high-light stress. We also observed a significant increase in levels of polyols and glycerol by 1.37- and 2.97-fold in pgrl1 under high-light stress. Both correlation network studies and KEGG pathway enrichment analysis revealed that metabolites related to several biological pathways, such as amino acid, carbohydrate, TCA cycle, and fatty acid metabolism, were positively correlated in pgrl1 and pgr5 under high-light stress conditions. The relative mRNA expression levels of genes related to the TCA cycle, including PDC3, ACH1, OGD2, OGD3, IDH3, and MDH4, were significantly upregulated in pgrl1 and pgr5 under HL. In pgr5, the MDH1 level was significantly increased, while ACS1, ACS3, IDH2, and IDH3 levels were reduced considerably in pgrl1 under high-light stress. The current study demonstrates both pgr5 and prgl1 showed a differential defense response to high-light stress at the primary metabolites and mRNA expression level, which can be added to the existing knowledge to explore molecular regulatory responses of prg5 and pgrl1 to high-light stress.
PMID: 37751074