Crit Rev Biotechnol , IF:8.429 , 2023 Dec , V43 (5) : P716-733 doi: 10.1080/07388551.2022.2058460
Systems seed biology to understand and manipulate rice grain quality and nutrition.
Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines.; Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
PMID: 35723584
Sci Total Environ , IF:7.963 , 2023 Oct , 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 Nov , V900 : P165800 doi: 10.1016/j.scitotenv.2023.165800
Designing an automatic pollen monitoring network for direct usage of observations to reconstruct the concentration fields.
Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland. Electronic address: Mikhail.sofiev@fmi.fi.; Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center, Munich, Germany.; Federal Office of Meteorology and Climatology MeteoSwiss, Chemin de l'Aerologie 1, 1530 Payerne, Switzerland.; Finnish Meteorological Institute, Erik Palmenin Aukio 1, 00560 Helsinki, Finland.; Faculty of Geography and Earth Sciences, University of Latvia, Rainis bvld 19, Riga LV-1586, Latvia.; University of Worcester, UK.; Institute of Allergology, Charite - Universitatsmedizin Berlin, Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.; Department of Biology and Environmental Sciences, University of Gothenburg, Box 461, S-405 30 Gothenburg, Sweden.; Deutscher Wetterdienst, Berlin, Germany.; National Laboratory of Health, Environment and Food, Slovenia.; School of Chemical Sciences, Dublin City University, Ireland.; Department of Botany, Ecology and Plant Physiology, Agrifood Campus of International Excellence CeiA3, University of Cordoba, Rabanales Campus, Celestino Mutis Building, E-14071 Cordoba, Spain; Andalusian Inter-University Institute for Earth System IISTA, University of Cordoba, Spain.; Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Pole of the Faculty of Sciences, University of Porto, Portugal.; German Pollen Information Service Foundation (PID), Berlin, Germany.
We consider several approaches to a design of a regional-to-continent-scale automatic pollen monitoring network in Europe. Practical challenges related to the arrangement of such a network limit the range of possible solutions. A hierarchical network is discussed, highlighting the necessity of a few reference sites that follow an extended observations protocol and have corresponding capabilities. Several theoretically rigorous approaches to a network design have been developed so far. However, before starting the process, a network purpose, a criterion of its performance, and a concept of the data usage should be formalized. For atmospheric composition monitoring, developments follow one of the two concepts: a network for direct representation of concentration fields and a network for model-based data assimilation, inverse problem solution, and forecasting. The current paper demonstrates the first approach, whereas the inverse problems are considered in a follow-up paper. We discuss the approaches for the network design from theoretical and practical standpoints, formulate criteria for the network optimality, and consider practical constraints for an automatic pollen network. An application of the methodology is demonstrated for a prominent example of Germany's pollen monitoring network. The multi-step method includes (i) the network representativeness and (ii) redundancy evaluation followed by (iii) fidelity evaluation and improvement using synthetic data.
PMID: 37595925
Sci Total Environ , IF:7.963 , 2023 Nov , V897 : P165441 doi: 10.1016/j.scitotenv.2023.165441
Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers.
The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.; The National Key Laboratory of Water Disaster Prevention, Dayu College, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China. Electronic address: envly@hhu.edu.cn.
In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.
PMID: 37437635
Sci Total Environ , IF:7.963 , 2023 Oct , V896 : P165249 doi: 10.1016/j.scitotenv.2023.165249
Response of heavy-metal and antibiotic resistance genes and their related microbe in rice paddy irrigated with treated municipal wastewaters.
China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China.; China National Rice Research Institute, Hangzhou 310006, PR China; Rice Product Quality Inspection and Supervision Testing Center of Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, PR China. Electronic address: qyan2005@hotmail.com.
Paddy irrigation with secondary effluents from municipal wastewater treatment plants (MWTPs) is a well-established practice to alleviate water scarcity. However, the reuse might lead to more complicated contamination caused by interactions between residual antibiotics in effluents and heavy metals in paddy soil. To date, no information is available for the potential effects of dual stress of heavy metals and antibiotics on heavy-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Here, this study investigated the response of heavy metal and antibiotic resistance genes, and related microorganisms to the dual threat of antibiotics and heavy metals under the long-term MWTP effluent irrigation for rice paddy using metagenome. The results showed that there was not a negative effect on rice consumption if MWTP effluent was used to irrigate rice for a long time. The concentration of antibiotics could reshape the ARGs and MRG profiles in rice paddy soil. The findings revealed the co-occurrence of ARGs and MRGs in rice paddy soils, thus highlighting the need for simultaneous elimination of antibiotics and heavy metals to effectively reduce ARGs and MRGs. Acn and sul1 genes encoding Iron and sulfonamides resistance mechanisms are the most abundant MRG and ARG, respectively. Network analysis revealed the possibility that IntI1 plays a role in the co-transmission of MRG and ARG to host microbes, and that Proteobacteria are the most dominant hosts for MRG, ARG, and integrons. The presence of antibiotics in irrigated MWTP effluents has been found to stimulate the proliferation of heavy metal and antibiotic resistances by altering soil microbial communities. This study will enhance our comprehension of the co-selection between ARGs and MRGs, as well as reveal the concealed environmental impacts of combined pollution. The obtained results have important implications for food safety and human health in rice.
PMID: 37406708
Sci Total Environ , IF:7.963 , 2023 Oct , V895 : P165099 doi: 10.1016/j.scitotenv.2023.165099
Spatial and molecular variations in forest topsoil dissolved organic matter as revealed by FT-ICR mass spectrometry.
Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: liucongqiang@tju.edu.cn.; School of Environment Studies, China University of Geosciences, Wuhan 430074, China.; LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.; Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China. Electronic address: fupingqing@tju.edu.cn.
Forest soils cover about 30 % of the Earth's land surface and play a fundamental role in the global cycle of organic matter. Dissolved organic matter (DOM), the largest active pool of terrestrial carbon, is essential for soil development, microbial metabolism and nutrient cycling. However, forest soil DOM is a highly complex mixture of tens of thousands of individual compounds, which is largely composed of organic matter from primary producers, residues from microbial process and the corresponding chemical reactions. Therefore, we need a detailed picture of molecular composition in forest soil, especially the pattern of large-scale spatial distribution, which can help us understand the role of DOM in the carbon cycle. To explore the spatial and molecular variations of DOM in forest soil, we choose six major forest reserves located in different latitudes ranging in China, which were investigated by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). Results show that aromatic-like molecules are preferentially enriched in DOM at high latitude forest soils, while aliphatic/peptide-like, carbohydrate-like, and unsaturated hydrocarbon molecules are preferentially enriched in DOM at low latitude forest soils, besides, lignin-like compounds account for the highest proportion in all forest soil DOM. High latitude forest soils have higher aromatic equivalents and aromatic indices than low latitude forest soils, which suggest that organic matter at higher latitude forest soils preferentially contain plant-derived ingredients and are refractory to degradation while microbially derived carbon is dominant in organic matter at low latitudes. Besides, we found that CHO and CHON compounds make up the majority in all forest soil samples. Finally, we visualized the complexity and diversity of soil organic matter molecules through network analysis. Our study provides a molecular-level understanding of forest soil organic matter at large scales, which may contribute to the conservation and utilization of forest resources.
PMID: 37379928
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V76 : P102474 doi: 10.1016/j.pbi.2023.102474
How to utilize comparative transcriptomics to dissect morphological diversity in plants.
Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.; Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo Bunkyo-ku Tokyo, 113-0033, Japan.; Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA. Electronic address: nrsinha@ucdavis.edu.
Comparative transcriptomics has emerged as a powerful approach that allows us to unravel the genetic basis of organ morphogenesis and its diversification processes during evolution. However, the application of comparative transcriptomics in studying plant morphological diversity addresses challenges such as identifying homologous gene pairs, selecting appropriate developmental stages for comparison, and extracting biologically meaningful networks. Methods such as phylostratigraphy, clustering, and gene co-expression networks are explored to identify functionally equivalent genes, align developmental stages, and uncover gene regulatory relationships. In the current review, we highlight the importance of these approaches in overcoming the complexity of plant genomes, the impact of heterochrony on stage alignment, and the integration of gene networks with additional data for a comprehensive understanding of morphological evolution.
PMID: 37804608
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
Environ Res , IF:6.498 , 2023 Oct , V234 : P116499 doi: 10.1016/j.envres.2023.116499
Community recovery of benthic macroinvertebrates in a stream influenced by mining activity: Importance of microhabitat monitoring.
Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: mjbae@nnibr.re.kr.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea.; Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, South Korea. Electronic address: ejkim@nnibr.re.kr.
The decrease in freshwater biodiversity owing to anthropogenic disturbances such as mining activity is a global challenge; hence, there is an urgent need for systematic approaches to continuously monitor such disturbances and/or the recovery of biodiversity in freshwater habitats. The Hwangjicheon Stream is the source of South Korea's longest river and has been subjected to runoff from coal mining. We investigated changes in the diversity of the benthic macroinvertebrate community in various microhabitats, including riffle, run, and pool, to monitor the recovery of biodiversity in the stream following the improvement of a mining water treatment plant in 2019. The dataset comprised 111 samples obtained from four types of microhabitats (riffle, run, pool, and riparian) over a four-year period from 2018 to 2021. The mining-affected sites had lower macroinvertebrate community complexities according to a network analysis, and grouped into the same cluster based on self-organizing map (SOM) analysis. Moreover, 51 taxa selected as indicator species represented each cluster obtained through the SOM analysis. Among them, only Limnodrilus gotoi and Radix auricularia were included as indicator species at the mining-affected sites. However, after 2020, the benthic macroinvertebrate community complexity increased, and some of the microhabitats at the mining-affected sites were included in the same cluster as the reference sites in the SOM analysis, indicating that the recovery of benthic macroinvertebrate communities had initiated in certain microhabitats (e.g., riparian). Further analysis confirmed that the macroinvertebrate community clearly differed according to the survey year, even in different microhabitats at the same sites. This suggests that more acute microhabitat monitoring may be necessary to quickly confirm biodiversity restoration when assessing the degree of the recovery in river biodiversity from anthropogenic disturbances.
PMID: 37429394
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
J Agric Food Chem , IF:5.279 , 2023 Oct 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
FEMS Microbiol Ecol , IF:4.194 , 2023 Oct , V99 (11) doi: 10.1093/femsec/fiad118
Bacterial community structure and assembly dynamics hinge on plant litter quality.
Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China.; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.; Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, USA.
Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.
PMID: 37771081
BMC Genomics , IF:3.969 , 2023 Oct , V24 (1) : P607 doi: 10.1186/s12864-023-09628-3
Tissue-specific transcriptome and metabolome analyses reveal candidate genes for lignan biosynthesis in the medicinal plant Schisandra sphenanthera.
College of Life Science, Northwest A & F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China.; College of Life Science, Northeast Forestry University, Harbin, 150040, China.; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.; College of Life Science, Northwest A & F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China. xnzzy@nwsuaf.edu.cn.; College of Life Science, Northwest A & F University, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China. mapengda@163.com.
Schisandra sphenanthera is an extremely important medicinal plant, and its main medicinal component is bioactive lignans. The S. sphenanthera fruit is preferred by the majority of consumers, and the root, stem, and leaf are not fully used. To better understand the lignan metabolic pathway, transcriptome and metabolome analyses were performed on the four major tissues of S. sphenanthera. A total of 167,972,229 transcripts and 91,215,760 unigenes with an average length of 752 bp were identified. Tissue-specific gene analysis revealed that the root had the highest abundance of unique unigenes (9703), and the leaves had the lowest (189). Transcription factor analysis showed that MYB-, bHLH- and ERF-transcription factors, which played important roles in the regulation of secondary metabolism, showed rich expression patterns and may be involved in the regulation of processes involved in lignan metabolism. In different tissues, lignans were preferentially enriched in fruit and roots by gene expression profiles related to lignan metabolism and relative lignan compound content. Furthermore, schisandrin B is an important compound in S. sphenanthera. According to weighted gene co-expression network analysis, PAL1, C4H-2, CAD1, CYB8, OMT27, OMT57, MYB18, bHLH3, and bHLH5 can be related to the accumulation of lignans in S. sphenanthera fruit, CCR5, SDH4, CYP8, CYP20, and ERF7 can be related to the accumulation of lignans in S. sphenanthera roots. In this study, transcriptome sequencing and targeted metabolic analysis of lignans will lay a foundation for the further study of their biosynthetic genes.
PMID: 37821824
BMC Genomics , IF:3.969 , 2023 Oct , V24 (1) : P620 doi: 10.1186/s12864-023-09714-6
Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response.
Department of Electrical & Computer Engineering, North Carolina State University, Raleigh, USA.; Department of Biosciences, Rice University, Houston, USA.; Life Sciences Customer Advisory, SAS Institute Inc, Cary, USA.; Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA.; Department of Electrical & Computer Engineering, North Carolina State University, Raleigh, USA. cmwilli5@ncsu.edu.
BACKGROUND: Plants respond to stress through highly tuned regulatory networks. While prior works identified master regulators of iron deficiency responses in A. thaliana from whole-root data, identifying regulators that act at the cellular level is critical to a more comprehensive understanding of iron homeostasis. Within the root epidermis complex molecular mechanisms that facilitate iron reduction and uptake from the rhizosphere are known to be regulated by bHLH transcriptional regulators. However, many questions remain about the regulatory mechanisms that control these responses, and how they may integrate with developmental processes within the epidermis. Here, we use transcriptional profiling to gain insight into root epidermis-specific regulatory processes. RESULTS: Set comparisons of differentially expressed genes (DEGs) between whole root and epidermis transcript measurements identified differences in magnitude and timing of organ-level vs. epidermis-specific responses. Utilizing a unique sampling method combined with a mutual information metric across time-lagged and non-time-lagged windows, we identified relationships between clusters of functionally relevant differentially expressed genes suggesting that developmental regulatory processes may act upstream of well-known Fe-specific responses. By integrating static data (DNA motif information) with time-series transcriptomic data and employing machine learning approaches, specifically logistic regression models with LASSO, we also identified putative motifs that served as crucial features for predicting differentially expressed genes. Twenty-eight transcription factors (TFs) known to bind to these motifs were not differentially expressed, indicating that these TFs may be regulated post-transcriptionally or post-translationally. Notably, many of these TFs also play a role in root development and general stress response. CONCLUSIONS: This work uncovered key differences in -Fe response identified using whole root data vs. cell-specific root epidermal data. Machine learning approaches combined with additional static data identified putative regulators of -Fe response that would not have been identified solely through transcriptomic profiles and reveal how developmental and general stress responses within the epidermis may act upstream of more specialized -Fe responses for Fe uptake.
PMID: 37853316
Plants (Basel) , IF:3.935 , 2023 Sep , V12 (19) doi: 10.3390/plants12193449
Comparative Root Transcriptome Profiling and Gene Regulatory Network Analysis between Eastern and Western Carrot (Daucus carota L.) Cultivars Reveals Candidate Genes for Vascular Tissue Patterning.
Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India.; Kittur Rani Chennamma College of Horticulture, Arabhavi, Gokak 591218, Belgaum Dt., Karnataka, India.; University of Horticultural Sciences, Bagalkot 587103, Karnataka, India.; Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase-I, Bengaluru 560100, Karnataka, India.; Department of Soil Amelioration, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia.; Indian Institute of Rice Research, Hyderabad 500030, Telangana, India.
Carrot (Daucus carota L.) is a highly consumed vegetable rich in carotenoids, known for their potent antioxidant, anti-inflammatory, and immune-protecting properties. While genetic and molecular studies have largely focused on wild and Western carrot cultivars (cvs), little is known about the evolutionary interactions between closely related Eastern and Western cvs. In this study, we conducted comparative transcriptome profiling of root tissues from Eastern (UHSBC-23-1) and Western (UHSBC-100) carrot cv. to better understand differentially expressed genes (DEGs) associated with storage root development and vascular cambium (VC) tissue patterning. Through reference-guided TopHat mapping, we achieved an average mapping rate of 73.87% and identified a total of 3544 DEGs (p < 0.05). Functional annotation and gene ontology classification revealed 97 functional categories, including 33 biological processes, 19 cellular components, 45 metabolic processes, and 26 KEGG pathways. Notably, Eastern cv. exhibited enrichment in cell wall, plant-pathogen interaction, and signal transduction terms, while Western cv. showed dominance in photosynthesis, metabolic process, and carbon metabolism terms. Moreover, constructed gene regulatory network (GRN) for both cvs. obtained orthologs with 1222 VC-responsive genes of Arabidopsis thaliana. In Western cv, GRN revealed VC-responsive gene clusters primarily associated with photosynthetic processes and carbon metabolism. In contrast, Eastern cv. exhibited a higher number of stress-responsive genes, and transcription factors (e.g., MYB15, WRKY46, AP2/ERF TF connected via signaling pathways with NAC036) were identified as master regulators of xylem vessel differentiation and secondary cell wall thickening. By elucidating the comparative transcriptome profiles of Eastern and Western cvs. for the first time, our study provides valuable insights into the differentially expressed genes involved in root development and VC tissue patterning. The identification of key regulatory genes and their roles in these processes represents a significant advancement in our understanding of the evolutionary relations and molecular mechanisms underlying secondary growth of carrot and regulation by vascular cambium.
PMID: 37836190
Plant Reprod , IF:3.767 , 2023 Oct doi: 10.1007/s00497-023-00482-7
Evolution of major flowering pathway integrators in Orchidaceae.
Facultad de Ciencias Exactas y Naturales, Instituto de Biologia, Universidad de Antioquia, Medellin, Colombia.; Facultad de Medicina, Centro Nacional de Secuenciacion Genomica, Sede de Investigacion Universitaria, Universidad de Antioquia, Medellin, Colombia.; Facultad de Ciencias Exactas y Naturales, Instituto de Biologia, Universidad de Antioquia, Medellin, Colombia. lucia.pabon@udea.edu.co.
The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.
PMID: 37823912
G3 (Bethesda) , IF:3.154 , 2023 Sep , V13 (10) doi: 10.1093/g3journal/jkad178
Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis.
The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.; The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK.; Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK.; Beebytes Analytics CIC, The Roslin Innovation Centre, University of Edinburgh, The Charnock Bradley Building, Easter Bush, Midlothian EH25 9RG, UK.
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behavior, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination, and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study, we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15) and sought to determine their gene expression signatures. To identify cell-type populations, we examined the cell-to-cell network based on the similarity of the single-cells transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas, and gene ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes, and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single-cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
PMID: 37548242