Trends Plant Sci , IF:18.313 , 2024 Oct doi: 10.1016/j.tplants.2024.10.008
Single same-cell multiome for dissecting key plant traits.
Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh 201314, India; Centre of Excellence in Epigenetics, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh 201314, India.; BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China.; Translational Genomics and Systems Biology Laboratory, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Electronic address: mjain@jnu.ac.in.
Understanding molecular dynamics at the single cell level is crucial to understand plant traits. Recently, Liu et al. and Cui et al. reported multiome analysis in the same cell/nucleus to dissect the key plant traits (osmotic stress response and pod development). Their results provide novel insights into pathways and regulatory networks at a single cell resolution.
PMID: 39487081
Microbiome , IF:14.65 , 2024 Nov , V12 (1) : P236 doi: 10.1186/s40168-024-01959-x
Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation.
Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.; College of Ecology, Taiyuan University of Technology, Taiyuan, 030024, People's Republic of China.; Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China. yfeng@zju.edu.cn.
BACKGROUND: Although numerous endophytic bacteria have been isolated and characterized from cadmium (Cd) hyperaccumulators, the contribution and potential application of the core endophytic microbiomes on facilitating phytoremediation were still lack of intensive recognition. Therefore, a 2-year field sampling in different location were firstly conducted to identify the unique core microbiome in Cd hyperaccumulators, among which the representative cultivable bacteria of different genera were then selected to construct synthetic communities (SynComs). Finally, the effects and mechanisms of the optimized SynCom in regulating Cd accumulation in different ecotypes of Sedum alfredii were studied to declare the potential application of the bacterial agents based on core microbiome. RESULTS: Through an innovative network analysis workflow, 97 core bacterial taxa unique to hyperaccumulator Sedum was identified based on a 2-year field 16S rRNA sequencing data. A SynCom comprising 13 selected strains belonging to 6 different genera was then constructed. Under the combined selection pressure of the plant and Cd contamination, Alcaligenes sp. exhibited antagonistic relationships with other genera and plant Cd concentration. Five representative strains of the other five genera were further conducted genome resequencing and developed six SynComs, whose effects on Cd phytoremediation were compared with single strains by hydroponic experiments. The results showed that SynCom-NS comprising four strains (including Leifsonia shinshuensis, Novosphingobium lindaniclasticum, Ochrobactrum anthropi, and Pseudomonas izuensis) had the greatest potential to enhance Cd phytoremediation. After inoculation with SynCom-NS, genes related to Cd transport, antioxidative defense, and phytohormone signaling pathways were significantly upregulated in both ecotypes of S. alfredii, so as to promote plant growth, Cd uptake, and translocation. CONCLUSION: In this study, we designed an innovative network analysis workflow to identify the core endophytic microbiome in hyperaccumulator. Based on the cultivable core bacteria, an optimized SynCom-NS was constructed and verified to have great potential in enhancing phytoremediation. This work not only provided a framework for identifying core microbiomes associated with specific features but also paved the way for the construction of functional synthetic communities derived from core microbiomes to develop high efficient agricultural agents. Video Abstract.
PMID: 39543675
Glob Chang Biol , IF:10.863 , 2024 Nov , V30 (11) : Pe17583 doi: 10.1111/gcb.17583
A Proposed Coupling Framework of Biological Invasions: Quantifying the Management Prioritization in Mealybugs Invasion.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.; Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.; Institute of Plant Protection, Fujian Academy of Agriculture Sciences, Fuzhou, China.; CSIRO Health & Biosecurity, Canberra, Australian Capital Territory, Australia.
Prioritizing potential invasive alien species, introduction pathways, and likely places susceptible to biological invasions is collectively critical for developing the targeting of management strategies at pre-border, border, and post-border. A framework for prioritizing the invasion management that considered all these elements in combination is lacking, particularly in the context of potential coinvasion scenarios of multispecies. Here, for the first time, we have constructed a coupling framework of biological invasions to evaluate and prioritize multiple invasion risks of 35 invasive alien mealybugs (IAMs) that posed a significant threat to the agri-horticultural crops in China. We found that the imported tropical fruits from free trade areas of the Association of Southeast Asian Nations to entry ports of southern China were the primary introduction pathway for IAMs, vectored on various fruit commodities. There was also a high probability for cointroductions of potential multi-IAMs with a single imported tropical fruit. The potential distribution of such IAMs with dissimilar net relatedness were mainly located in southern China. These distributions, however, are likely to expand to the higher latitudes of northern China under future climate and land use/land cover changes. Temperature and anthropogenic factors were both independently and collectively determining factors for the diversity and distribution patterns of imported IAMs under near-current climate conditions. Our findings highlight that these multiple components of global change have and will continue to facilitate the introduction and establishment risks of IAMs in southern China, as well as the spread risk into northern China. Additionally, our findings, for the first time, demonstrated management prioritization across the continuous invasion stages of 35 IAMs in China, and provide additional insights into the development of targeting of their biosecurity and management decisions.
PMID: 39555767
New Phytol , IF:10.151 , 2024 Nov , V244 (3) : P1057-1073 doi: 10.1111/nph.20059
Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots.
Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, 330045, China.; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10x platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.
PMID: 39140996
Bioresour Technol , IF:9.642 , 2024 Dec , V413 : P131484 doi: 10.1016/j.biortech.2024.131484
Microbial community dynamics in different floc size aggregates during nitrogen removal process upgrading in a full-scale landfill leachate treatment plant.
School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: shengbb@gdpu.edu.cn.; School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, PR China. Electronic address: rxzhang@gdpu.edu.cn.
Upgrading processes to reduce biodegradable organic substance addition is crucial for treating landfill leachate with high pollutant concentrations, aiding carbon emission reduction. Aggregate size in activated sludge processes impacts pollutant removal and sludge/water separation. This study investigated microbial community succession and driving mechanisms in different floc-size aggregates during nitrogen removal progress upgrade from conventional to partial nitrification-denitrification in a full-scale landfill leachate treatment plant (LLTP) using 16S rRNA gene sequencing. The upgrade and floc sizes significantly influenced microbial diversity and composition. After upgrading, ammonia-oxidizing bacteria were enriched while nitrite-oxidizing bacteria suppressed in small flocs with homogeneity and high mass transfer efficiency. Larger flocs enriched Defluviicoccus, Thauera, and Truepera, while smaller flocs enriched Nitrosomonas, suggesting their potential as biomarkers. Multi-network analyses revealed microbial interactions. A deep learning model with convolutional neural networks predicted nitrogen removal efficiency. These findings guide optimizing LLTP processes and understanding microbial community dynamics based on floc size.
PMID: 39277056
Crit Rev Biotechnol , IF:8.429 , 2024 Dec , V44 (8) : P1478-1494 doi: 10.1080/07388551.2024.2336529
Chromatin modifications and memory in regulation of stress-related polyphenols: finding new ways to control flavonoid biosynthesis.
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
The influence of epigenetic factors on plant defense responses and the balance between growth and defense is becoming a central area in plant biology. It is believed that the biosynthesis of secondary metabolites can be regulated by epigenetic factors, but this is not associated with the formation of a "memory" to the previous biosynthetic status. This review shows that some epigenetic effects can result in epigenetic memory, which opens up new areas of research in secondary metabolites, in particular flavonoids. Plant-controlled chromatin modifications can lead to the generation of stress memory, a phenomenon through which information regarding past stress cues is retained, resulting in a modified response to recurring stress. How deeply are the mechanisms of chromatin modification and memory generation involved in the control of flavonoid biosynthesis? This article collects available information from the literature and interactome databases to address this issue. Visualization of the interaction of chromatin-modifying proteins with the flavonoid biosynthetic machinery is presented. Chromatin modifiers and "bookmarks" that may be involved in the regulation of flavonoid biosynthesis through memory have been identified. Through different mechanisms of chromatin modification, plants can harmonize flavonoid metabolism with: stress responses, developmental programs, light-dependent processes, flowering, and longevity programs. The available information points to the possibility of developing chromatin-modifying technologies to control flavonoid biosynthesis.
PMID: 38697923
Environ Pollut , IF:8.071 , 2024 Nov , V361 : P124849 doi: 10.1016/j.envpol.2024.124849
One-year monitoring of grass-type architectural waterscapes with long-term operation: Water quality and microorganism.
Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China; School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China. Electronic address: tmmdh2@163.com.; Shenzhen Jianyan Testing Co., Ltd., 518031 Shenzhen, Guangdong, China.; Shenzhen Institute of Building Research Co., Ltd., 518049 Shenzhen, Guangdong, China.; School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), 518055 Shenzhen, Guangdong, China.
Grass-type architectural waterscapes (GAWs) utilize submerged plants to enhance self-purification ability and maintain a clear-water state. However, knowledge about their long-term water quality and microbial community dynamics remains limited. This study monitored the water quality, microbial community composition, and networks in two GAWs. GAW1 consisted solely Hydrilla verticillata with a water depth of 0.70 m, while GAW2 primarily contained Vallisneria natans, Microsorum pteropus, and Aquarius grisebachii with a water depth of 0.30 m. Results show that both water depth and submerged plant species play crucial roles in GAW establishment. The water depth of 0.7 m enabled Hydrilla verticillata to thrive underwater despite temperature variations, which demonstrated excellent nutrient uptake capacity. Thus, GAW1 exhibited superior self-purification ability, consistently meeting Class III standard for surface water in China. In contrast, GAW2 had a shallow water depth and contained ornamental plants, only meeting Class V standard. Furthermore, microbial communities were shaped by water quality, with distinct enriched genera serving as potential "microbial indicators". Enrichment of the hgcI clade and Sporichthyaceae_unclassified indicated superior water quality in GAW1, while prevalence of Comamonadaceae_unclassified, Flavobacterium, Rhodoluna, and Pseudarcicella suggested poor water quality in GAW2. Additionally, highly complex and connected microbial networks suggested elevated pollutant levels in GAWs. This study emphasized the significance of submerged plant species and water depth in GAWs construction and highlighted microbial communities and networks as potential indicators of water quality.
PMID: 39214442
mBio , IF:7.867 , 2024 Nov : Pe0303024 doi: 10.1128/mbio.03030-24
Transcription factor-dependent regulatory networks of sexual reproduction in Fusarium graminearum.
Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea.; Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA.; Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA.; Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
Transcription factors (TFs) involved in sexual reproduction in filamentous fungi have been characterized. However, we have little understanding of how these TFs synergize within regulatory networks resulting in sexual development. We investigated 13 TFs in Fusarium graminearum, whose knockouts exhibited abortive or arrested phenotypes during sexual development to elucidate the transcriptional regulatory cascade underlying the development of the sexual fruiting bodies. A Bayesian network of the TFs was inferred based on transcriptomic data from key stages of sexual development. We evaluated in silico knockout impacts to the networks of the developmental phenotypes among the TFs and guided knockout transcriptomics experiments to properly assess regulatory roles of genes with same developmental phenotypes. Additional transcriptome data were collected for the TF knockouts guided by the stage at which their phenotypes appeared and by the cognate in silico prediction. Global TF networks revealed that TFs within the mating-type locus (MAT genes) trigger a transcriptional cascade involving TFs that affected early stages of sexual development. Notably, PNA1, whose knockout mutants produced exceptionally small protoperithecia, was shown to be an upstream activator for MAT genes and several TFs essential for ascospore production. In addition, knockout mutants of SUB1 produced excessive numbers of protoperithecia, wherein MAT genes and pheromone-related genes exhibited dysregulated expression. We conclude that PNA1 and SUB1 play central and suppressive roles in initiating sexual reproduction, respectively. This comprehensive investigation contributes to our understanding of the transcriptional framework governing the multicellular body plan during sexual reproduction in F. graminearum.IMPORTANCEUnderstanding transcriptional regulation of sexual development is crucial to the elucidation of the complex reproductive biology in Fusarium graminearum. We performed gene knockouts on 13 transcription factors (TFs), demonstrating knockout phenotypes affecting distinct stages of sexual development. Using transcriptomic data across stages of sexual development, we inferred a Bayesian network of these TFs that guided experiments to assess the robustness of gene interactions using a systems biology approach. We discovered that the mating-type locus (MAT genes) initiates a transcriptional cascade, with PNA1 identified as an upstream activator essential for early sexual development and ascospore production. Conversely, SUB1 was found to play a suppressive role, with knockout mutants exhibiting excessive protoperithecia due to abnormally high expression of MAT and pheromone-related genes. These findings highlight the central roles of PNA1 and SUB1 in regulating other gene activity related to sexual reproduction, contributing to a deeper understanding of the mechanisms of the multiple TFs that regulate sexual development.
PMID: 39589130
Food Chem , IF:7.514 , 2024 Dec , V460 (Pt 3) : P140771 doi: 10.1016/j.foodchem.2024.140771
Transcriptome and metabolome analyses provide insights into the fruit softening disorder of papaya fruit under postharvest heat stress.
Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.; Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China. Electronic address: xiaoyang_zhu@scau.edu.cn.
Heat stress in summer causes softening disorder in papaya but the molecular mechanism is not clear. In this study, papaya fruit stored at 35 degrees C showed a softening disorder termed rubbery texture. Analysis of the transcriptome and metabolome identified numerous differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) between the fruit stored at 25 degrees C and 35 degrees C. The DEGs and DAMs related to lignin biosynthesis were upregulated, while those related to ethylene biosynthesis, sucrose metabolism, and cell wall degradation were downregulated under heat stress. Co-expression network analysis highlighted the correlation between the DEGs and metabolites associated with lignin biosynthesis, ethylene biosynthesis, and cell wall degradation under heat stress. Finally, the correlation analysis identified the key factors regulating softening disorder under heat stress. The study's findings reveal that heat stress inhibited papaya cell wall degradation and ethylene production, delaying fruit ripening and softening and ultimately resulting in a rubbery texture.
PMID: 39128369
J Environ Manage , IF:6.789 , 2024 Nov , V370 : P122726 doi: 10.1016/j.jenvman.2024.122726
Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure.
Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: nh1263179511@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany. Electronic address: cli5104@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: zhjia2018@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: xuef0117@gmail.com.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: liuxinswc@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: lqq77@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: chenmeiling@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: dingyong252027@163.com.; Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037, China. Electronic address: zhangjc8811@gmail.com.
Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.
PMID: 39366236
J Environ Manage , IF:6.789 , 2024 Nov , V370 : P122428 doi: 10.1016/j.jenvman.2024.122428
Opposite effects of soil pH on bacteria and fungi beta diversity in forests at a continental scale.
Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China.; Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, 200030, China.; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.; Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China.; Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS), CSIC, Sevilla, Spain.; Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China. Electronic address: xhzhou@des.ecnu.edu.cn.
Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial beta diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal beta diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with beta diversity but not for fungal diversity. Soil fungi exhibited higher beta diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal beta diversity, and significant positive correlations were found between fungal beta diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with beta-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial beta diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.
PMID: 39260281
Front Plant Sci , IF:5.753 , 2024 , V15 : P1463300 doi: 10.3389/fpls.2024.1463300
Integrated eQTL mapping approach reveals genomic regions regulating candidate genes of the E8-r3 locus in soybean.
Soybean Breeding and Genetics Lab, Centre de recherche sur les grains (CEROM) Inc., St-Mathieu-de-Beloeil, QC, Canada.; Department of Plant Science, McGill University, Montreal, QC, Canada.
Deciphering the gene regulatory networks of critical quantitative trait loci associated with early maturity provides information for breeders to unlock soybean's (Glycine max (L.) Merr.) northern potential and expand its cultivation range. The E8-r3 locus is a genomic region regulating the number of days to maturity under constant short-day photoperiodic conditions in two early-maturing soybean populations (QS15524(F2:F3) and QS15544(RIL)) belonging to maturity groups MG00 and MG000. In this study, we developed a combinatorial expression quantitative trait loci mapping approach using three algorithms (ICIM, IM, and GCIM) to identify the regions that regulate three candidate genes of the E8-r3 locus (Glyma.04G167900/GmLHCA4a, Glyma.04G166300/GmPRR1a, and Glyma.04G159300/GmMDE04). Using this approach, a total of 2,218 trans (2,061 genes)/7 cis (7 genes) and 4,073 trans (2,842 genes)/3,083 cis (2,418 genes) interactions were mapped in the QS15524(F2:F3) and QS15544(RIL) populations, respectively. From these interactions, we successfully identified two hotspots (F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386) and three minor regions (RIL_GM04:17,227,512-20,251,662, RIL_GM04:31,408,946-31,525,671 and RIL_GM13:37,289,785-38,620,690) regulating the candidate genes of E8-r3 and several of their homologs. Based on co-expression network and single nucleotide variant analyses, we identified ALTERED PHLOEM DEVELOPMENT (Glyma.15G263700) and DOMAIN-CONTAINING PROTEIN 21 (Glyma.18G025600) as the best candidates for the F2_GM15:49,385,092-49,442,237 and F2_GM18:1,434,182-1,935,386 hotspots. These findings demonstrate that a few key regions are involved in the regulation of the E8-r3 candidates GmLHCA4a, GmPRR1a, and GmMDE04.
PMID: 39600900
J Anim Ecol , IF:5.091 , 2024 Nov , V93 (11) : P1758-1770 doi: 10.1111/1365-2656.14189
Plant metabolites modulate social networks and lifespan in a sawfly.
Chemical Ecology, Bielefeld University, Bielefeld, Germany.; Theoretical Biology, Bielefeld University, Bielefeld, Germany.
Social interactions influence disease spread, information flow and resource allocation across species, yet heterogeneity in social interaction frequency and its fitness consequences are still poorly understood. Additionally, the role of exogenous chemicals, such as non-nutritive plant metabolites that are utilised by several animal species, in shaping social networks remains unclear. Here, we investigated how non-nutritive plant metabolites impact social interactions and the lifespan of the turnip sawfly, Athalia rosae. Adult sawflies acquire neo-clerodane diterpenoids ('clerodanoids') from non-food plants and this can serve as a defence against predation and increase mating success. We found intraspecific variation in clerodanoids in natural populations and laboratory-reared individuals. Clerodanoids could also be acquired from conspecifics that had prior access to the plant metabolites, which led to increased agonistic social interactions. Network analysis indicated increased social interactions in sawfly groups where some or all individuals had prior access to clerodanoids, while groups with no prior access had fewer interactions. The frequency of social interactions was influenced by the clerodanoid status of the focal individual and that of other conspecifics. Finally, we observed a shorter lifespan in adults with prior clerodanoid access when grouped with individuals without prior access, suggesting that social interactions to obtain clerodanoids have fitness costs. Our findings highlight the role of intraspecific variation in the acquisition of non-nutritional plant metabolites in shaping social networks. This variation influences individual fitness and social interactions, thereby shaping the individualised social niche.
PMID: 39307977
Plant Cell Physiol , IF:4.927 , 2024 Nov , V65 (10) : P1601-1607 doi: 10.1093/pcp/pcae037
Multiple Roles of Brassinosteroid Signaling in Vascular Development.
College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, 525-8577 Japan.; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, 560-0043 Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan.; Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe, 657-8501 Japan.
Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for transporting water and nutrients throughout the plant body, initially establishes a tissue pattern during primary development and then dramatically increases the number of vascular cells during secondary development. This complex developmental process is properly regulated by a network consisting of various hormonal signaling pathways. Genetic studies have revealed that mutants that are defective in BR biosynthesis or the BR signaling cascade exhibit a multifaceted vascular development phenotype. Furthermore, BR crosstalk with other plant hormones, including peptide hormones, coordinately regulates vascular development. Recently, the involvement of BR in vascular development, especially in xylem differentiation, has also been suggested in plant species other than the model plant Arabidopsis thaliana. In this review, we briefly summarize the recent findings on the roles of BR in primary and secondary vascular development in Arabidopsis and other species.
PMID: 38590039
Plant Physiol Biochem , IF:4.27 , 2024 Nov , V216 : P109176 doi: 10.1016/j.plaphy.2024.109176
Regulatory network analysis reveals gene-metabolite relationships in pear fruit treated with methyl jasmonate.
Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: slzhang@njau.edu.cn.; Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: wuxiao@njau.edu.cn.
The economic value of pear is determined by its intrinsic qualities, which are influenced by metabolites produced during the ripening process. Methyl jasmonate (MeJA), a hormone, plays an important role in plant metabolism. To date, few studies have investigated the molecular mechanism underlying the changes in metabolic pathways related to the internal quality of pear fruit after MeJA treatment. In this study, ultrahigh-performance liquid chromatography‒Q Exactive Orbitrap mass spectrometry (UHPLC‒QE‒MS) was used to determine the changes in metabolite contents in pear after MeJA treatment. MeJA treatment primarily activated carbohydrate metabolism and amino acid metabolism pathways. Through combined analysis of UHPLC‒QE‒MS data and whole-transcriptome data, the abovementioned pathways and each metabolite were analysed separately, and competitive endogenous RNA (ceRNA) and microRNA-transcription factor-target (miRNA-TF-target) regulatory networks were constructed. The core nodes of three genes (PEA, Pbr022732.1; GAA, Pbr035655.1; and miR8033-x) and two genes (SDS, Pbr031708.1; and novel-m6796-3p) were associated with the carbohydrate metabolism and amino acid metabolism pathways, respectively. The core mRNA nodes TCONS_00048038 and Pbr019584.1, the core miRNA node miR4993-x, the core lncRNA node TCONS_0004356, the core circRNA node novel_circ_001967 and the core transcription factor node TSO1 (Pbr025407.1) were identified via separate metabolite analyses. These findings elucidate the changes in metabolites related to fruit quality in 'Nanguo' pear and the relationships between the metabolites and genes, reveal the molecular mechanism underlying the response of MeJA treatment in pear fruit, and provide a theoretical basis for improving the internal quality of 'Nanguo' pear.
PMID: 39378644
Tree Physiol , IF:4.196 , 2024 Nov , V44 (11) doi: 10.1093/treephys/tpae139
The circadian clock participates in seasonal growth in Norway spruce (Picea abies).
Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea SE-901 87, Sweden.; Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, Umea SE-901 83, Sweden.
The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.
PMID: 39488796
Plants (Basel) , IF:3.935 , 2024 Oct , V13 (21) doi: 10.3390/plants13213072
Identification of Target Gene and Interacting Protein of Two LaSCL6 Alternative Splicing Variants Provides Novel Insights into Larch Somatic Embryogenesis.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.; College of Horticulture, Shanxi Agricultural University, Jinzhong, 030801, China.
Somatic embryogenesis is valuable for clonal propagation and genetic improvement, and it also serves as an ideal system for studying plant development mechanisms. In Larix kaempferi, microRNA171 and its target gene L. kaempferi SCARECROW-LIKE6 (LaSCL6), which has two alternative splicing variants, can regulate somatic embryogenesis; however, the underlying molecular mechanism is still unknown. In this study, we overexpressed these two LaSCL6 variants in Oryza sativa and Arabidopsis thaliana and then used the RNA-Seq method to screen genes from O. sativa and A. thaliana, whose expression patterns are related to those of LaSCL6 variants. The screened genes were then used to search L. kaempferi proteins to identify the candidate target genes of LaSCL6. After yeast one-hybrid and dual- luciferase transcriptional activity assays, cytochrome P450, family 89, subfamily A, polypeptide 5 (CYP89A5), and wall-associated receptor kinase-like 20 (WAKL20) were confirmed to be the target genes of LaSCL6-var1; in addition, WAKL20 and UDP-glycosyltransferase 85A3 (UGT85A3) were confirmed to be the target genes of LaSCL6-var2. Moreover, APETALA2-like protein 2, a transcription factor from the AP2/ERF family, was shown to interact with LaSCL6-var1 and LaSCL6-var2. Taken together, our results suggest a regulatory network of miR171-LaSCL6. The findings presented here not only provide novel insights into the regulation of the miR171-LaSCL6 module but also explain the mechanism underlying larch somatic embryogenesis and other biological processes.
PMID: 39519988
Gene , IF:3.688 , 2025 Jan , V933 : P148994 doi: 10.1016/j.gene.2024.148994
Genome‑wide identification of circular RNAs and MAPKs reveals the regulatory networks in response to green peach aphid infestation in peach (Prunus persica).
School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, 453003, PR China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, PR China. Electronic address: wangxianyou@hist.edu.cn.; School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, 453003, PR China; Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, PR China.
The green peach aphid (GPA), Myzus persicae (Sulzer), is a serious agricultural pest with a worldwide distribution and a vector of over 100 plant viruses. Various pathways, such as the mitogen-activated protein kinase (MAPK) cascades, play pivotal roles in signaling plant defense against pest attack, and circular RNAs (circRNAs) regulate the expression of mRNAs in response to pest attack. However, the mechanism underlying peach (Prunus persica) response to GPA attack remains unclear. The present study initially identified and characterized 316 circRNAs and 18 PpMAPKs from healthy and GPA-infested peach leaves by whole-transcriptome sequencing and predicted the differentially expressed circRNAs (DECs) after GPA infestation. PCR and Sanger sequencing confirmed the presence of six DECs in peach samples. Besides, RNA sequencing analysis detected 13 DECs, including 5 upregulated and 8 downregulated ones, in peach in response to the GPA attack. Gene ontology (GO) enrichment analysis indicated that specific DECs play crucial roles in the MAPK signaling pathway, and qRT-PCR revealed that GPA infestation altered the expression patterns of PpMAPKs. Finally, five circRNAs, three microRNA (miRNAs), and two MAPK target genes were identified to interact as a network and perform critical roles in modulating the MAPK pathway in the peach during GPA infestation.
PMID: 39395730
Gene , IF:3.688 , 2024 Dec , V931 : P148899 doi: 10.1016/j.gene.2024.148899
Multiple functions and regulatory networks of WRKY33 and its orthologs.
School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China. Electronic address: chenyh@ntu.edu.cn.; School of Life Sciences, Nantong University, Nantong, China; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong, China.
Arabidopsis thaliana WRKY33 is currently one of the most studied members of the Group I WRKY transcription factor family. Research has confirmed that WRKY33 is involved in the regulation of various biological and abiotic stresses and occupies a central position in the regulatory network. The functional studies of orthologous genes of WRKY33 from other species are also receiving increasing attention. In this article, we summarized thirty-eight orthologous genes of AtWKRY33 from twenty-five different species. Their phylogenetic relationship and conserved WRKY domain were analyzed and compared. Similar to AtWKRY33, the well-studied orthologous gene members from rice and tomato also have multiple functions. In addition to playing important regulatory roles in responding to their specific pathogens, they are also involved in regulating various abiotic stresses and development. AtWKRY33 exerts its multiple functions through a complex regulatory network. Upstream transcription factors or other regulatory factors activate or inhibit the expression of AtWKRY33 at the chromatin and transcriptional levels. Interacting proteins affect the transcriptional activity of AtWKRY33 through phosphorylation, ubiquitination, SUMOylation, competition, or cooperation. The downstream genes are diverse and include three major categories: transcription factors, synthesis, metabolism, and signal transduction of various hormones, and disease resistance genes. In the regulatory network of AtWRKY33 orthologs, many conserved regulatory characteristics have been discovered, such as self-activation and phosphorylation by MAP kinases. This can provide a comparative reference for further studying the functions of other orthologous genes of AtWKRY33.
PMID: 39209179
Ecol Evol , IF:2.912 , 2024 Nov , V14 (11) : Pe70537 doi: 10.1002/ece3.70537
Evolution of Duplicated Glutathione Metabolic Pathway in Gossypium hirsutum and Its Response to UV-B Stress.
School of Life Sciences Qufu Normal University Qufu Shandong China.
Increasing levels of UV-B radiation caused by the greenhouse effect has become an emerging threat to crop health and yield. The glutathione (GSH) metabolic pathway is generally involved in plant stress responses through scavenging accumulated reactive oxygen species, and is therefore believed to play an essential role in enhancing plant tolerance to UV-B stress. However, the complex evolutionary details of this pathway in polyploid plants, especially under UV-B stress, remain largely unknown. Here, using the important allotetraploid crop, Gossypium hirsutum, as an example, we comprehensively investigated the composition and phylogenetic relationships of genes encoding 12 key structural enzymes in this pathway, and compared the expression changes of all the relevant genes under UV-B stress (16 kJ m(-2) d(-1)) based on six leaf transcriptomes. Consequently, we identified 205 structural genes by genome-wide searching and predicted 98 potential regulatory genes under multiple stress conditions by co-expression network analysis. Furthermore, we revealed that 19 structural genes including 5 homoeologous pairs and 96 regulatory genes possessing 25 homoeologous pairs were reticulately correlated without homoeologous selection preference under UV-B stress. This result suggests a complex rewiring and reassignment between structural genes and their regulatory networks in the duplicated metabolic pathways of polyploid cotton. This study extends our understanding of the molecular dynamics of the GSH metabolic pathway in response to UV-B stress in G. hirsutum and, more broadly, in polyploid plants.
PMID: 39563703
J Ethnobiol Ethnomed , IF:2.733 , 2024 Nov , V20 (1) : P96 doi: 10.1186/s13002-024-00739-z
Core-periphery structure of a medicinal botanical system in Uruguay.
Departamento de Ecologia y Gestion Ambiental, Centro Universitario Regional Este, Universidad de la Republica, Maldonado, Uruguay. elencasti@gmail.com.; Departamento de Biologia Vegetal, Facultad de Agronomia, Universidad de la Republica, Montevideo, Uruguay. elencasti@gmail.com.; Laboratorio de Etnobotanica y Botanica Aplicada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Buenos Aires, Argentina. elencasti@gmail.com.; Departamento de Ecologia y Gestion Ambiental, Centro Universitario Regional Este, Universidad de la Republica, Maldonado, Uruguay.
BACKGROUND: Human evolution has granted upon an individual's cognitive mechanisms necessary for remembering experiences, vital for both survival and reproduction. These experiences manifest into cultural traits, influencing human culture, particularly in healthcare and maintenance. Studies regarding medicinal plants and treatments are integral to the study of the medical botanical system. Pharmacopeias highlight the prevalence of specific species widely used, aligning with the "consensus within diversity theory" in evolutionary ethnobiology. Within the framework of this theory, we reflect on the results we've achieved in a priority area recognized by UNESCO for its biocultural significance, both locally and regionally. METHODS: This study integrated network analysis and qualitative methods to examine the botanical medical system of "Parque Regional Quebradas del Norte" in Rivera, Uruguay. RESULTS: Study results demonstrate a core-periphery structure, with a strongly interconnected core resistant to fragmentation, ensuring structural stability. Additionally, the presence of peripheral nodes throughout the system was identified, enhancing the resilience of the botanical medicinal system against potential disturbances. CONCLUSION: The core species renowned for their versatility and multiple medicinal uses, treating less severe ailments effectively. Additionally, core plants serve as prototypes for innovations. Their extinction poses a threat to the system's resilience. Conversely, peripheral plants, though vulnerable, offer possibilities for therapeutic innovations. In the face of environmental change, conservation efforts should prioritize species that are vulnerable to extinction, particularly within the core. Simultaneously, preserving knowledge associated with peripheral plants presents a bicultural conservation strategy, ensuring the botanical system's robustness among evolving ecological conditions.
PMID: 39501258