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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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52
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Zhao L, Walkowiak S, Fernando WGD. Artificial Intelligence: A Promising Tool in Exploring the Phytomicrobiome in Managing Disease and Promoting Plant Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091852. [PMID: 37176910 PMCID: PMC10180744 DOI: 10.3390/plants12091852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
There is increasing interest in harnessing the microbiome to improve cropping systems. With the availability of high-throughput and low-cost sequencing technologies, gathering microbiome data is becoming more routine. However, the analysis of microbiome data is challenged by the size and complexity of the data, and the incomplete nature of many microbiome databases. Further, to bring microbiome data value, it often needs to be analyzed in conjunction with other complex data that impact on crop health and disease management, such as plant genotype and environmental factors. Artificial intelligence (AI), boosted through deep learning (DL), has achieved significant breakthroughs and is a powerful tool for managing large complex datasets such as the interplay between the microbiome, crop plants, and their environment. In this review, we aim to provide readers with a brief introduction to AI techniques, and we introduce how AI has been applied to areas of microbiome sequencing taxonomy, the functional annotation for microbiome sequences, associating the microbiome community with host traits, designing synthetic communities, genomic selection, field phenotyping, and disease forecasting. At the end of this review, we proposed further efforts that are required to fully exploit the power of AI in studying phytomicrobiomes.
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Affiliation(s)
- Liang Zhao
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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Kaur J, Harder CB, Sharma J. Congeneric temperate orchids recruit similar-yet differentially abundant-endophytic bacterial communities that are uncoupled from soil, but linked to host phenology and population size. AMERICAN JOURNAL OF BOTANY 2023; 110:e16168. [PMID: 37052191 DOI: 10.1002/ajb2.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 05/16/2023]
Abstract
PREMISE Besides the beneficial plant-fungus symbiosis in mycorrhizal plants, bacteria also enhance plant fitness via tripartite interactions. While bacterial associations are presumably just as important for the obligate mycorrhizal family Orchidaceae, little is known about orchid associating bacteria (OAB). METHODS We examined the OAB communities of two, congeneric, terrestrial orchids, Platanthera cooperi and Platanthera praeclara, which represent widely disparate North American ecosystems. We tested whether they recruit distinct OAB communities, and whether variability in OAB communities can be linked to phenology, population size, or habitat soil. Genomic DNAs from roots of seedling, vegetative, and reproductive plants and from soil were subjected to Illumina sequencing of V4 and V5 regions of the 16S rRNA gene. RESULTS We obtained 809 OAB Zero-radius Operational Taxonomic Units (ZOTUs). Despite an overlap of 209 ZOTUs that accounted for >75% relative abundances of their respective OAB communities, the overall community structures of the two orchids were distinct. Within each orchid, distinctions were detected in the OAB communities of large and small populations and the three phenological stages. The OAB ZOTUs were either absent or present with low abundances in soil associated with both orchids. CONCLUSIONS The two orchids exhibited preferential recruitment of known growth-promoting OAB communities from soil. Their OAB communities also showed considerable overlap despite the large environmental and geographical separation of the two host taxa. Our results lend further support to the emerging evidence that not only the fungi, but root-associated bacteria also have functional importance for orchid ecology.
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Affiliation(s)
- Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
- Department of Biology, University of Wisconsin-La Crosse, La Crosse, Wisconsin, USA
| | - Christoffer B Harder
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
- Department of Biology, MEMEG, Lund University, Ekologihuset, Sölvegatan, Sweden
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA
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Zhang J, Liu W, Bu J, Lin Y, Bai Y. Host genetics regulate the plant microbiome. Curr Opin Microbiol 2023; 72:102268. [PMID: 36708613 DOI: 10.1016/j.mib.2023.102268] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weidong Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jingshu Bu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
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Birt HWG, Pattison AB, Skarshewski A, Daniells J, Raghavendra A, Dennis PG. The core fungal microbiome of banana (Musa spp.). Front Microbiol 2023; 14:1127779. [PMID: 37065131 PMCID: PMC10098452 DOI: 10.3389/fmicb.2023.1127779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype – two factors that are likely to differ between farms – on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core ‘candidates’, which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.
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Affiliation(s)
- Henry W. G. Birt
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Anthony B. Pattison
- Department of Agriculture and Fisheries, Centre for Wet Tropics Agriculture, South Johnstone, QLD, Australia
| | - Adam Skarshewski
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeff Daniells
- Department of Agriculture and Fisheries, Centre for Wet Tropics Agriculture, South Johnstone, QLD, Australia
| | - Anil Raghavendra
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Paul G. Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Paul G. Dennis,
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57
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Liu Q, Pang Z, Liu Y, Fallah N, Hu C, Lin W, Yuan Z. Rhizosphere Fungal Dynamics in Sugarcane during Different Growth Stages. Int J Mol Sci 2023; 24:ijms24065701. [PMID: 36982779 PMCID: PMC10052501 DOI: 10.3390/ijms24065701] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Understanding the normal variation of the sugarcane rhizosphere fungal community throughout its life cycle is essential for the development of agricultural practices for fungal and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform for correlation analysis of rhizosphere fungal community time series, covering information from 84 samples in four growth periods. The results revealed that the sugarcane rhizosphere fungi possessed the maximum fungal richness in Tillering. Rhizosphere fungi were closely associated with sugarcane growth, including Ascomycota, Basidiomycota, and Chytridiomycota, which showed high abundance in a stage-specific manner. Through the Manhattan plots, 10 fungal genera showed a decreasing trend throughout the sugarcane growth, and two fungal genera were significantly enriched at three stages of sugarcane growth (p < 0.05) including Pseudallescheria (Microascales, Microascaceae) and Nectriaceae (Hypocreales, Nectriaceae). In addition, soil pH, soil temperature, total nitrogen, and total potassium were critical drivers of fungal community structure at different stages of sugarcane growth. We also found that sugarcane disease status showed a significant and strong negative effect on selected soil properties by using structural equation modeling (SEM), suggesting that poor soil increases the likelihood of sugarcane disease. In addition, the assembly of sugarcane rhizosphere fungal community structure was mainly influenced by stochastic factors, but after the sugarcane root system became stable (Maturity), the stochastic contribution rate decreased to the lowest value. Our work provides a more extensive and solid basis for the biological control of sugarcane potential fungal diseases.
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Affiliation(s)
- Qiang Liu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqin Pang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yueming Liu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nyumah Fallah
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chaohua Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaonian Yuan
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning 530000, China
- Correspondence:
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Sapkota R, Jørgensen LN, Boeglin L, Nicolaisen M. Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic. MICROBIAL ECOLOGY 2023; 85:617-627. [PMID: 35229200 DOI: 10.1007/s00248-022-01985-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.
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Affiliation(s)
- Rumakanta Sapkota
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Laure Boeglin
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
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Sarker PK, Karmoker D, Shohan MUS, Saha AK, Rima FS, Begum RA, Islam MR, Seraj ZI. Effects of multiple halotolerant rhizobacteria on the tolerance, growth, and yield of rice plants under salt stress. Folia Microbiol (Praha) 2023; 68:55-72. [PMID: 35913659 DOI: 10.1007/s12223-022-00997-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Halotolerant bacteria get adapted to a saline environment through modified physiological/structural characteristics and may provide stress tolerance along with enhanced growth to the host plants by different direct and indirect mechanisms. This study reports on multiple halotolerant plant growth-promoting rhizobacteria isolated from the coastal soils in Bangladesh, in fields where the halophytic wild rice Oryza coarctata is endemic. The aim was to find halotolerant bacteria for potential use as biofertilizer under normal/salt-stressed conditions. In this study, eight different strains were selected from a total of 20 rhizobacterial isolates from the saline-prone regions of Debhata and Satkhira based on their higher salt tolerance. 16S rRNA gene sequencing results of the rhizobacterial strains revealed that they belonged to Halobacillus, Bacillus, Acinetobactor, and Enterobactor genera. A total of ten halotolerant rhizobacteria (the other 2 bacteria were previously isolated and already reported as beneficial for rice growth) were used as both single inoculants and in combinations and applied to rice growing in pots. To investigate their capability to improve rice growth, physiological parameters such as shoot and root length and weight, chlorophyll content at the seedling stage as well as survival and yield at the reproductive stage were measured in the absence or presence (in concentration 40 or 80 mmol/L) of NaCl and in the absence or presence of the rhizobacteria. At the reproductive stage, only 50% of the uninoculated plants survived without setting any grains in 80 mmol/L NaCl in contrast to 100% survival of the rice plants inoculated with a combination of the rhizobacteria. The combined halotolerant rhizobacterial inoculations showed significantly higher chlorophyll retention as well as yield under the maximum NaCl concentration applied compared to application of single species. Thus, the use of a combination of halotolerant rhizobacteria as bioinoculants for rice plants under moderate salinity can synergistically alleviate the effects of stress and promote rice growth and yield.
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Affiliation(s)
- Protup Kumer Sarker
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Dola Karmoker
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Umer Sharif Shohan
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Anik Kumar Saha
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Fahmida Sultana Rima
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
| | - Rifat Ara Begum
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Rakibul Islam
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Zeba Islam Seraj
- Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
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Zhang YL, Guo XJ, Huang X, Guo RJ, Lu XH, Li SD, Zhang H. The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease. BIOLOGY 2023; 12:biology12020143. [PMID: 36829422 PMCID: PMC9952826 DOI: 10.3390/biology12020143] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The root microbiota contributes to the plant's defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08-61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.
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Affiliation(s)
- Yu-Lu Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiao-Jing Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Rong-Jun Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
| | - Xiao-Hong Lu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
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Li Q, Wei Y, Zhang T, Che F, Yao S, Wang C, Shi D, Tang H, Song B. Predictive models and early postoperative recurrence evaluation for hepatocellular carcinoma based on gadoxetic acid-enhanced MR imaging. Insights Imaging 2023; 14:4. [PMID: 36617581 PMCID: PMC9826770 DOI: 10.1186/s13244-022-01359-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/17/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The prognosis of hepatocellular carcinoma (HCC) is still poor largely due to the high incidence of recurrence. We aimed to develop and validate predictive models of early postoperative recurrence for HCC using clinical and gadoxetic acid-enhanced magnetic resonance (MR) imaging-based findings. METHODS In this retrospective case-control study, 209 HCC patients, who underwent gadoxetic acid-enhanced MR imaging before curative-intent resection, were enrolled. Boruta algorithm and backward stepwise selection with Akaike information criterion (AIC) were used for variables selection Random forest, Gradient-Boosted decision tree and logistic regression model analysis were used for model development. The area under the receiver operating characteristic curve (AUC), calibration plots, and decision curve analysis were used to evaluate model's performance. RESULTS One random forest model with Boruta algorithm (RF-Boruta) was developed consisting of preoperative serum ALT and AFP levels and six MRI findings, while preoperative serum AST and AFP levels and four MRI findings were included in one logistic regression model with backward stepwise selection method (Logistic-AIC).The two predictive models demonstrated good discrimination performance in both the training set (RF-Boruta: AUC, 0.820; Logistic-AIC: AUC, 0.853), internal validation set (RF-Boruta: AUC, 0.857, Logistic-AIC: AUC, 0.812) and external validation set(RF-Boruta: AUC, 0.805, Logistic-AIC: AUC, 0.789). Besides, in both the internal validation and external validation sets, the RF-Boruta model outperformed Barcelona Clinic Liver Cancer (BCLC) stage (p < 0.05). CONCLUSIONS The RF-Boruta and Logistic-AIC models with good prediction performance for early postoperative recurrence may lead to optimal and comprehensive treatment approaches, and further improve the prognosis of HCC after resection.
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Affiliation(s)
- Qian Li
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Yi Wei
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Tong Zhang
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Feng Che
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Shan Yao
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Cong Wang
- grid.414011.10000 0004 1808 090XDepartment of Radiology, Henan Provincial People’s Hospital, Zhengzhou, Henan Province People’s Republic of China
| | - Dandan Shi
- grid.414011.10000 0004 1808 090XDepartment of Radiology, Henan Provincial People’s Hospital, Zhengzhou, Henan Province People’s Republic of China
| | - Hehan Tang
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China
| | - Bin Song
- grid.412901.f0000 0004 1770 1022Department of Radiology, Sichuan University, West China Hospital, No. 37, GUOXUE Alley, Chengdu, 610041 Sichuan Province People’s Republic of China ,Department of Radiology, Sanya People’s Hospital, Sanya, 572000 People’s Republic of China
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Arnault G, Mony C, Vandenkoornhuyse P. Plant microbiota dysbiosis and the Anna Karenina Principle. TRENDS IN PLANT SCIENCE 2023; 28:18-30. [PMID: 36127241 DOI: 10.1016/j.tplants.2022.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.
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Affiliation(s)
- Gontran Arnault
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
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Chaudhari HG, Prajapati S, Wardah ZH, Raol G, Prajapati V, Patel R, Shati AA, Alfaifi MY, Elbehairi SEI, Sayyed RZ. Decoding the microbial universe with metagenomics: a brief insight. Front Genet 2023; 14:1119740. [PMID: 37197021 PMCID: PMC10183756 DOI: 10.3389/fgene.2023.1119740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.
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Affiliation(s)
- Hiral G. Chaudhari
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Shobha Prajapati
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Zuhour Hussein Wardah
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Gopal Raol
- Shri R. P. Arts, Shri K.B. Commerce, and Smt. BCJ Science College, Khambhat, Gujarat, India
| | - Vimalkumar Prajapati
- Division of Microbial and Environmental Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat, India
- *Correspondence: Vimalkumar Prajapati,
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | | | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal's S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, India
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Liu K, Wang Q, Sun M, Gao S, Liu Q, Shan L, Guo J, Bian J. Soil bacterial communities of paddy are dependent on root compartment niches but independent of growth stages from Mollisols of Northeast China. Front Microbiol 2023; 14:1170611. [PMID: 37125155 PMCID: PMC10140518 DOI: 10.3389/fmicb.2023.1170611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Deep insights into adhering soil of root zones (rhizosphere and rhizoplane) microbial community could provide a better understanding of the plant-microbe relationship. To better understand the dynamics of these microbial assemblies over the plant life cycle in rhizodeposition along rice roots. Methods Here, we investigated bacterial distribution in bulk, rhizosphere, and rhizoplane soils at tillering, heading, and mature stage, from rice (Oryza sativa) fields of the Northeast China. Results and Discussion Our results revealed that soil bacterial α-diversity and community composition were significantly affected by root compartment niches but not by temporal change. Compared to rhizoplane soils in the same period, bulk in the heading and rhizosphere in the mature had the largest increase in Shannon's index, with 11.02 and 14.49% increases, respectively. Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria are predominant across all soil samples, bulk soil had more phyla increased across the growing season than that of root related-compartments. Deterministic mechanisms had a stronger impact on the bacterial community in the compartments connected to the roots, with the relative importance of the bulk soil, rhizoplane and rhizosphere at 83, 100, and 56%, respectively. Because of ecological niche drivers, the bacterial networks in bulk soils exhibit more complex networks than rhizosphere and rhizoplane soils, reflected by more nodes, edges, and connections. More module hub and connector were observed in bulk (6) and rhizoplane (5) networks than in rhizosphere (2). We also detected shifts from bulk to rhizoplane soils in some functional guilds of bacteria, which changed from sulfur and nitrogen utilization to more carbon and iron cycling processes. Taken together, our results suggest distinct bacterial network structure and distribution patterns among rhizosphere, rhizoplane, and bulk soils, which could possibly result in potential functional differentiation. And the potential functional differentiation may be influenced by plant root secretions, which still needs to be further explored.
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Affiliation(s)
- Kai Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiuju Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Minglong Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shiwei Gao
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Qing Liu
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Lili Shan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junxiang Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Jingyang Bian
- Daqing Branches of Heilongjiang Academy of Agricultural Sciences, Daqing, China
- *Correspondence: Jingyang Bian,
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Fujiwara F, Miyazawa K, Nihei N, Ichihashi Y. Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data. Biosci Biotechnol Biochem 2022; 87:21-27. [PMID: 36416843 DOI: 10.1093/bbb/zbac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022]
Abstract
In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.
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Affiliation(s)
- Fuki Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Kae Miyazawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, Japan
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Wicaksono WA, Egamberdieva D, Berg C, Mora M, Kusstatscher P, Cernava T, Berg G. Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea. mSystems 2022; 7:e0073922. [PMID: 36377901 PMCID: PMC9765073 DOI: 10.1128/msystems.00739-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022] Open
Abstract
The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches. IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Maximilian Mora
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Bai D, Li D, Zhao C, Wang Z, Shao M, Guo B, Liu Y, Wang Q, Li J, Guo S, Wang R, Li YH, Qiu LJ, Jin X. Estimation of soybean yield parameters under lodging conditions using RGB information from unmanned aerial vehicles. FRONTIERS IN PLANT SCIENCE 2022; 13:1012293. [PMID: 36589058 PMCID: PMC9795850 DOI: 10.3389/fpls.2022.1012293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/28/2022] [Indexed: 06/15/2023]
Abstract
The estimation of yield parameters based on early data is helpful for agricultural policymakers and food security. Developments in unmanned aerial vehicle (UAV) platforms and sensor technology help to estimate yields efficiency. Previous studies have been based on less cultivars (<10) and ideal experimental environments, it is not available in practical production. Therefore, the objective of this study was to estimate the yield parameters of soybean (Glycine max (L.) Merr.) under lodging conditions using RGB information. In this study, 17 time point data throughout the soybean growing season in Nanchang, Jiangxi Province, China, were collected, and the vegetation index, texture information, canopy cover, and crop height were obtained by UAV-image processing. After that, partial least squares regression (PLSR), logistic regression (Logistic), random forest regression (RFR), support vector machine regression (SVM), and deep learning neural network (DNN) were used to estimate the yield parameters. The results can be summarized as follows: (1) The most suitable time point to estimate the yield was flowering stage (48 days), which was when most of the soybean cultivars flowered. (2) The multiple data fusion improved the accuracy of estimating the yield parameters, and the texture information has a high potential to contribute to the estimation of yields, and (3) The DNN model showed the best accuracy of training (R2=0.66 rRMSE=32.62%) and validation (R2=0.50, rRMSE=43.71%) datasets. In conclusion, these results provide insights into both best estimate period selection and early yield estimation under lodging condition when using remote sensing.
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Affiliation(s)
- Dong Bai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaosen Zhao
- Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Zixu Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingchao Shao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingfu Guo
- Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yadong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jindong Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Shiyu Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Ruizhen Wang
- Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ying-hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li-juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuliang Jin
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:1028153. [PMID: 36518495 PMCID: PMC9742542 DOI: 10.3389/fpls.2022.1028153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.
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Affiliation(s)
- Davide Francioli
- Institute of Crop Science, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Wang S, Jiao C, Zhao D, Zeng J, Xing P, Liu Y, Wu QL. Disentangling the assembly mechanisms of bacterial communities in a transition zone between the alpine steppe and alpine meadow ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157446. [PMID: 35863578 DOI: 10.1016/j.scitotenv.2022.157446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Alpine meadows and alpine steppes are two major grassland types distributed on the Tibetan Plateau. Due in large part to the differences in hydrothermal and nutrient conditions following the thawing of lakeshore permafrost, alpine meadows and alpine steppes which are characterized by disparate above- and below-ground biomass, could emerge together in the grassland transition zone between meadows and steppes of the Tibetan Plateau. Bacterial communities are essential components of alpine grassland ecosystems and respond rapidly to environmental changes. Despite their ecological significance, it remains poorly elucidated whether and how the assembly patterns of bacterial communities differed between alpine meadows and alpine steppes. Here, to disentangle the assembly mechanisms of bacterial communities from alpine meadows and alpine steppes, we collected samples from three diverse habitats (i.e., sediments, rhizosphere soils and bulk soils) in both alpine meadow and steppe ecosystems on the Tibetan Plateau. Our results indicated that in both meadows and steppes, rhizosphere bacterial communities exhibited higher alpha-diversity but lower beta-diversity compared to the bacterial communities in sediments and bulk soils. However, the close relationships of bacterial communities between different habitats weakened from meadows to steppes. Null model analysis indicated that the importance of environmental selection shaping bacterial community assemblages in all habitats decreased from meadows to steppes, whereas the role of dispersal limitation showed an opposite pattern. Moreover, pH was the primary driver of phylogenetic turnover of bacterial communities in the steppes across all habitats, whereas the dominant drivers of phylogenetic turnover of bacterial communities in meadows varied with habitat types. Overall, our findings provide novel insights into understanding the differences in microbial communities between meadows and steppes in the grassland transition zone on the Tibetan Plateau.
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Affiliation(s)
- Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China.
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, China.; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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Singh A, Kumar M, Chakdar H, Pandiyan K, Kumar SC, Zeyad MT, Singh BN, Ravikiran KT, Mahto A, Srivastava AK, Saxena AK. Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion. Front Microbiol 2022; 13:1033158. [PMID: 36452918 PMCID: PMC9702084 DOI: 10.3389/fmicb.2022.1033158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 08/29/2023] Open
Abstract
Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Kuppusamy Pandiyan
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- Ginning Training Center, ICAR-Central Institute for Research on Cotton Technology, Nagpur, India
| | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | | | - K. T. Ravikiran
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
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71
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Li X, Zhao Y, Chai F, Yu H, Sun X, Liu D. Phytoplankton Community Structure Dynamics in Relation to Water Environmental Factors in Zhalong Wetland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14996. [PMID: 36429711 PMCID: PMC9690911 DOI: 10.3390/ijerph192214996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Phytoplankton, as the primary producer of the wetland water ecosystem's food chain, are very sensitive to environmental changes. In order to explore the significance of phytoplankton in protecting ecosystem integrity, the wetland ecosystem in Zhalong wetland, one of the most important international wetlands, was selected as the research area. For the study, 81 sampling sites were set up in the whole wetland, and phytoplankton samples and water quality environmental factors were measured in spring, summer, and autumn of 2019. The phytoplankton community structure and water environmental factors were evaluated by canonical correspondence analysis (CCA). The main research findings are as follows: a total of 292 species and variants of phytoplankton belonging to 8 phyla and 110 genera were identified within Zhalong wetland in spring, summer, and autumn 2019. The total phytoplankton abundance and biomass in summer were higher than in spring and autumn, and Cyclotella meneghiniana was the most dominant species in three seasons and three areas. The results of random forest are generally consistent with the results of CCA in spring, when the main environmental factors affecting phytoplankton were NTU and WT; the result in summer and autumn agreed with those of CCA, which awaits further study. In addition, the phytoplankton is mainly affected by WT, depth, and DO in the lake area, TP, DO, and NTU in the river area, and WT in the wetland area.
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Affiliation(s)
- Xiaoyu Li
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yuxi Zhao
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Fangying Chai
- School of Management, Heilongjiang University of Science and Technology, Harbin 150020, China
| | - Hongxian Yu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Xu Sun
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Di Liu
- Heilongjiang Provincial Water Conservancy and Hydroelectric Power Investigation Design and Research Institute, Harbin 150080, China
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72
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Yang M, Liu N, Wang B, Li Y, Li J, Liu CQ. Archaeal contribution to carbon-functional composition and abundance in China's coastal wetlands: Not to be underestimated. Front Microbiol 2022; 13:1013408. [PMID: 36439847 PMCID: PMC9685420 DOI: 10.3389/fmicb.2022.1013408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/27/2022] [Indexed: 01/16/2024] Open
Abstract
Microbial diversity, together with carbon function, plays a key role in driving the wetland carbon cycle; however, the composition, driving factors of carbon-functional genes and the relationship with microbial community have not been well characterized in coastal wetlands. To understand these concerns, microbes, carbon-functional genes, and related environmental factors were investigated in twenty wetlands along China's coast. The results indicate that carbon-functional gene composition is dominated by archaeal rather than bacterial community and that Nanoarchaeaeota is the dominant archaeal phylum associated with carbon cycling in anoxic sediments. Compared with microbes, carbon-functional composition was more stable because they showed the highest Shannon diversity and archaeal functional redundancy. Deterministic processes dominated microbial community, and stochastic processes were more important for carbon-functional genes. Labile Fe governed archaeal and carbon-functional composition by coupling with nitrogen and carbon biogeochemical cycles, while bacterial community was affected by NH4-N and SOC/SON. This study highlights the predominant contributions of archaea to carbon-functional genes and to the stability of carbon-functional composition, thus providing new insights into the microbial dominance of the carbon cycle and the evaluation of carbon function in coastal wetlands.
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Affiliation(s)
- Meiling Yang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Na Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Baoli Wang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
| | - Yajun Li
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Jianfeng Li
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Cong-Qiang Liu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
- Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin, China
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73
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Ma Y, Wang D, Guo X, Zhu YG, Delgado-Baquerizo M, Chu H. Root stoichiometry explains wheat endophytes and their link with crop production after four decades of fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157407. [PMID: 35850352 DOI: 10.1016/j.scitotenv.2022.157407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/24/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Fertilization can impact root endophytic microbiomes and food production. However, the impacts of decades of continued fertilization on root microbiomes, and their link with ongoing crop production, remain poorly understood. Here, we used a four decade-long fertilization experiment, including contrasting types of organic and inorganic fertilization, to investigate the effects of long-term fertilization on multi-kingdom root endophytic microbiomes, including keystone species (modules within microbial networks), and their indirect associations with the production of wheat, which is one of the most important crops worldwide. We found that long-term inorganic (nitrogen, phosphorus, potassium (NPK)) and organic (NPK with straw (NPKS) and NPK with cow manure (NPKM)) fertilization had significant impacts on the community composition of endophytic arbuscular mycorrhizal fungi (AMF), bacteria, and non-mycorrhizal fungi. In addition, compared with NPK fertilization, NPKS and NPKM amendments significantly decreased the microbial network complexity, which was associated with changes in the root iron content. Finally, we identified an important subset of keystone root endophyte species within the microbial network (Module #2), which was positively correlated with wheat yield, and affected by changes in root carbon to phosphorus ratio. This study provides evidence that long-term fertilization can affect keystone root endophytic species in the root microbiome, with implications for food security in an over-fertilized world.
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Affiliation(s)
- Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei 230031, China
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei 230031, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012 Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain.
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Aoki W, Kogawa M, Matsuda S, Matsubara K, Hirata S, Nishikawa Y, Hosokawa M, Takeyama H, Matoh T, Ueda M. Massively parallel single-cell genomics of microbiomes in rice paddies. Front Microbiol 2022; 13:1024640. [PMID: 36406415 PMCID: PMC9669790 DOI: 10.3389/fmicb.2022.1024640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.
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Affiliation(s)
- Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | | | | | | | - Yohei Nishikawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Hosokawa
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Toru Matoh
- Kyoto Agriculture Research Institute KARI, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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75
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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76
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Luo X, Ye X, Wang W, Chen Y, Li Z, Wang Y, Huang Y, Ran W, Cao H, Cui Z. Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice. Front Microbiol 2022; 13:1016547. [PMID: 36312965 PMCID: PMC9606772 DOI: 10.3389/fmicb.2022.1016547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022] Open
Abstract
Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R2 ≥ 0.959, p < 0.001), followed by growth period (R2 ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.
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Affiliation(s)
- Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
| | - Wenhui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yang Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wei Ran
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Science, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhongli Cui, , ; Xianfeng Ye,
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Carper DL, Appidi MR, Mudbhari S, Shrestha HK, Hettich RL, Abraham PE. The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont. Microorganisms 2022; 10:microorganisms10102013. [PMID: 36296289 PMCID: PMC9609723 DOI: 10.3390/microorganisms10102013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Sameer Mudbhari
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence:
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Wang C, Ma H, Feng Z, Yan Z, Song B, Wang J, Zheng Y, Hao W, Zhang W, Yao M, Wang Y. Integrated organic and inorganic fertilization and reduced irrigation altered prokaryotic microbial community and diversity in different compartments of wheat root zone contributing to improved nitrogen uptake and wheat yield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156952. [PMID: 35752240 DOI: 10.1016/j.scitotenv.2022.156952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The effect of long-term water and integrated fertilization on prokaryotic microorganisms and their regulation for crop nutrient uptake remains unknown. Therefore, the impact of soil water and integrated fertilization after eight years on prokaryotic microbial communities in different compartments of root zone and their association with wheat nitrogen (N) absorption and yield were investigated. The results showed that compared with fertilization treatments (F), water regimes (W) more drastically modulated the prokaryotic microbial community structure and diversity in bulk soil, rhizosphere and endosphere. The increase of irrigation improved the prokaryotic diversity in the rhizosphere and endosphere while decreased the diversity in the bulk soil. Application of organic fertilizers significantly improved soil organic matter (SOM) and nutrient contents, increased rhizosphere and endophytic prokaryotic microbial diversity, and elevated the relative abundance of aerobic ammonia oxidation and nitrification-related functional microorganisms in rhizosphere and endosphere. Increasing irrigation elevated the relative abundance of functional microorganisms related to aerobic ammonia oxidation and nitrification in the rhizosphere and endosphere. Soil water content (SWC) and NH4+-N as well as NO3--N were key predictors of prokaryotic microbial community composition under W and F treatments, respectively. Appropriate application of irrigation and organic fertilizers increased the relative abundance of some beneficial bacteria such as Flavobacterium. Water and fertilization treatments regulated the prokaryotic microbial communities of bulk soil, rhizosphere and endosphere by altering SWC and SOM, and provided evidence for the modulation of prokaryotic microorganisms to promote nitrogen uptake and wheat yield under long-term irrigation and fertilization. Conclusively, the addition of organic manure (50 %) with inorganic fertilizers (50 %) and reduced amount of irrigation (pre-sowing and jointing-period irrigation) decreased the application amount of chemical fertilizers and water, while increased SOM and nutrient content, improved prokaryotic diversity, and changed prokaryotic microbial community structure in the wheat root zone, resulting in enhanced nutrient uptake and wheat yield.
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Affiliation(s)
- Chao Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Ma
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Tropical Crops Nutrition of Hainan Province, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Zhihan Feng
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenxing Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bolong Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialong Wang
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuyin Zheng
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiping Hao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenying Zhang
- Institute of Dryland Farming, Hebei Academy of Agriculture and Forestry Sciences, Hengshui 053000, China.
| | - Minjie Yao
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yaosheng Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wu Y, Sun J, Yu P, Zhang W, Lin Y, Ma D. The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil. BMC Microbiol 2022; 22:232. [PMID: 36180838 PMCID: PMC9523940 DOI: 10.1186/s12866-022-02648-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Background Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study. Results In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice. Conclusions Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02648-1.
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Affiliation(s)
- Yue Wu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Pengcheng Yu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Weiliang Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Youze Lin
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
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80
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Zeng F, Zhu Y, Zhang D, Zhao Z, Li Q, Ma P, Zhang G, Wang Y, Wu S, Guo S, Sun G. Metagenomic analysis of the soil microbial composition and salt tolerance mechanism in Yuncheng Salt Lake, Shanxi Province. Front Microbiol 2022; 13:1004556. [PMID: 36225369 PMCID: PMC9549588 DOI: 10.3389/fmicb.2022.1004556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
The soil in Yuncheng Salt Lake has serious salinization and the biogeographic environment affects the composition and distribution of special halophilic and salt-tolerant microbial communities in this area. Therefore, this study collected soils at distances of 15, 30, and 45 m from the Salt Lake and used non-saline soil (60 m) as a control to explore the microbial composition and salt tolerance mechanisms using metagenomics technology. The results showed that the dominant species and abundance of salt-tolerant microorganisms changed gradually with distance from Salt Lake. The salt-tolerant microorganisms can increase the expression of the Na+/H+ antiporter by upregulating the Na+/H+ antiporter subunit mnhA-G to respond to salt stress, simultaneously upregulating the genes in the betaine/proline transport system to promote the conversion of choline into betaine, while also upregulating the trehalose/maltose transport system encode genes to promote the synthesis of trehalose to resist a high salt environment.
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Affiliation(s)
- Feifeng Zeng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonghong Zhu
- Cotton Research Institute, Shanxi Agricultural University, Shanxi, China
| | - Dongling Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengqiang Zhao
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Quansheng Li
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Panpan Ma
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Guoli Zhang
- Xinjiang Academy of Agricultural and Reclamation, Xinjiang, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenjie Wu
- Cotton Research Institute, Shanxi Agricultural University, Shanxi, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Guoqing Sun,
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81
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Birt HWG, Tharp CL, Custer GF, Dini-Andreote F. Root phenotypes as modulators of microbial microhabitats. FRONTIERS IN PLANT SCIENCE 2022; 13:1003868. [PMID: 36212354 PMCID: PMC9539067 DOI: 10.3389/fpls.2022.1003868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/08/2022] [Indexed: 06/09/2023]
Abstract
Plant roots are colonized by a multitude of microbial taxa that dynamically influence plant health. Plant-microbe interactions at the root-soil interface occur at the micro-scale and are affected by variation in root phenotypes. Different root phenotypes can have distinct impacts on physical and chemical gradients at the root-soil interface, leading to heterogeneous microhabitats for microbial colonization. Microbes that influence plant physiology will establish across these heterogeneous microhabitats, and, therefore, exploiting variation in root phenotypes can allow for targeted manipulation of plant-associated microbes. In this mini-review, we discuss how changes in root anatomy and architecture can influence resource availability and the spatial configuration of microbial microhabitats. We then propose research priorities that integrate root phenotypes and microbial microhabitats for advancing the manipulation of root-associated microbiomes. We foresee the yet-unexplored potential to harness diverse root phenotypes as a new level of precision in microbiome management in plant-root systems.
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82
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Liu L, Ma L, Feng J, Lu X. Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants. Appl Environ Microbiol 2022; 88:e0100322. [PMID: 36036572 PMCID: PMC9499033 DOI: 10.1128/aem.01003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.
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Affiliation(s)
- Lixue Liu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Luyao Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Jinsong Feng
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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83
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Sugars and Jasmonic Acid Concentration in Root Exudates Affect Maize Rhizosphere Bacterial Communities. Appl Environ Microbiol 2022; 88:e0097122. [PMID: 36073926 PMCID: PMC9499034 DOI: 10.1128/aem.00971-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Root exudates contribute to shaping the root-associated microbiomes, but it is unclear which of the many exudate compounds are important in this process. Here, we focused on understanding the influence of sugars and jasmonic acid (JA) concentrations in maize root exudates on the rhizobacterial communities. Twelve maize genotypes were identified with variable concentrations of sugars and JA based on a screening of 240 maize genotypes grown in a semihydroponic system. These twelve maize genotypes were grown in a replicated field experiment in which samples were collected at three maize developmental stages. The 16S rRNA gene (V4 region) was amplified and sequenced. Sugars and JA concentrations from rhizosphere soils were also quantified. The results indicated that the maize genotypic variability in sugars and JA concentration in root exudates, measured in the semihydroponic system, significantly affected the rhizosphere bacterial community composition at multiple stages plant development. In contrast, the root endosphere and bulk soil bacterial communities were only affected at specific growth stages. Sugars and JA concentration as quantified in rhizosphere soil samples confirmed that these two compounds affected the rhizobacterial communities at all developmental stages analyzed. The effects of specific sugars on the composition of the rhizobacterial communities were also measured, with larger effects of sucrose at earlier developmental stages and trehalose at later developmental stages. Our results indicate that JA and sugars are important root exudate compounds that influence the composition of the maize rhizobacterial communities. IMPORTANCE Roots secrete exudates that are important in interactions with soil microbes that promote plant growth and health. However, the exact chemical compounds in root exudates that participate in these interactions are not fully known. Here, we investigated whether sugars and the phytohormone jasmonic acid influence the composition of the rhizobacterial communities of maize, which is an important crop for food, feed, and energy. Our results revealed that both compounds contribute to the assemblage of rhizobacterial communities at different maize developmental stages. Knowledge about the specific compounds in root exudates that contribute to shape the rhizobiome will be important for future strategies to develop sustainable agricultural practices that are less dependent on agrochemicals.
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84
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Su A, Xu Y, Xu M, Ding S, Li M, Zhang Y. Resilience of the wheat root-associated microbiome to the disturbance of phenanthrene. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156487. [PMID: 35667431 DOI: 10.1016/j.scitotenv.2022.156487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The microbial communities are of high importance to the restoration of ecological function and plant health, while little information about the influence of exogenous pollutants on the resilience and temporal dynamics of root microbial communities is available. In this study, a greenhouse experiment was conducted to investigate the effects of exogenous phenanthrene in terms of time and pollution disturbance on the wheat root-associated microbial communities. It was found that a high phenanthrene degradation rate of 86 % was achieved in the rhizosphere of wheat after the first-week planting. Compared to phenanthrene pollution, temporal changes had more significant impacts on the wheat root microbial communities. Obvious change of microbes influenced by PHE had been revealed at the initial three-week planting even most of PHE has been degraded, and the enriched microbes in the rhizosphere were affiliated to Altererythrobacter, Massilia, Mycobacterium, Ramlibacter, Sphingobium, Novosphingobium and Romboutsia. However, at the later stage after four-week incubation, the wheat root-associated microbial communities gradually recovered to the state without pollution. The results of this study were helpful to deepen the understanding of the response of root-associated microbial resilience to the exogenous phenanthrene pollution, and would benefit the stability and balance of agricultural ecology facing exogenous organic pollutants.
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Affiliation(s)
- Aoxue Su
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Yan Xu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China.
| | - Minmin Xu
- Shandong Academy of Environmental Sciences Co., LTD., Jinan 250100, China
| | - Shuang Ding
- China National Institute of Standardization, Beijing, China
| | - Mingyue Li
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Ying Zhang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
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85
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Wang B, Huang S, Li Z, Zhou Z, Huang J, Yu H, Peng T, Song Y, Na X. Factors driving the assembly of prokaryotic communities in bulk soil and rhizosphere of Torreya grandis along a 900-year age gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155573. [PMID: 35504392 DOI: 10.1016/j.scitotenv.2022.155573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/24/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Excessive nutrient inputs imperil the stability of forest ecosystems via modifying the interactions among soil properties, microbes, and plants, particularly in forests composed of cash crops that are under intensive disturbances of agricultural activities, such as Torreya grandis. Understanding the potential drivers of soil microbial community helps scientists develop effective strategies for balancing the protection and productivity of the ancient Torreya forest. Here, we assayed the link between plant and soil parameters and prokaryote communities in bulk soil and T. grandis rhizosphere in 900-year-old stands by detecting plant and soil properties in two independent sites in southeastern China. Our results showed no apparent influence of stand age on the compositions of prokaryote communities in bulk soil and T. grandis rhizosphere. In contrast, soil abiotic factors (i.e., soil pH) overwhelm plant characteristics (i.e., height, plant tissue carbon, nitrogen, and phosphorus content) and contribute most to the shift in prokaryote communities in bulk soil and T. grandis rhizosphere. Soil pH leads to an increase in microbiota alpha diversity in both compartments. With the help of a random forest, we found a critical transition point of pH (pH = 4.9) for the dominance of acidic and near-neutral bacterial groups. Co-occurrence network analysis further revealed a substantially simplified network in plots with a pH of <4.9 versus samples with a pH of ≥4.9, indicating that soil acidification induces biodiversity loss and disrupts potential interactions among soil microbes. Our findings provide empirical evidence that soil abiotic properties nearly completely offset the roles of host plants in the assembly and potential interactions of rhizosphere microorganisms. Hence, reduction in inorganic fertilization and proper liming protocols should be seriously considered by local farmers to protect ancient Torreya forests.
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Affiliation(s)
- Bin Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Shengyi Huang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Zhengcai Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Juying Huang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Hailong Yu
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Tong Peng
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
| | - Yanfang Song
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
| | - Xiaofan Na
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China.
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86
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Kudjordjie EN, Hooshmand K, Sapkota R, Darbani B, Fomsgaard IS, Nicolaisen M. Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots. Microbiol Spectr 2022; 10:e0122622. [PMID: 35766498 PMCID: PMC9430778 DOI: 10.1128/spectrum.01226-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Kourosh Hooshmand
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Behrooz Darbani
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Inge S. Fomsgaard
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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87
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Wei N, Yue X. Distribution of Core Root Microbiota of Tibetan Hulless Barley along an Altitudinal and Geographical Gradient in the Tibetan Plateau. Microorganisms 2022; 10:1737. [PMID: 36144339 PMCID: PMC9504843 DOI: 10.3390/microorganisms10091737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022] Open
Abstract
The Tibetan Plateau is regarded as the third pole of the earth and is one of the least explored places on the planet. Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is the only cereal crop grown widely in the Tibetan Plateau as a staple food. Extensive and long-term cropping of barley may influence the soil’s chemical and biological properties, including microbial communities. However, microbiota associated with hull-less barley is largely unexplored. This study aimed to reveal the composition and diversity of bacterial and fungal communities associated with the hull-less barley at different elevations in the Tibetan Plateau. The core bacterial and fungal taxa of Tibetan hull-less barley were identified, with Bacillaceae, Blastocatellaceae, Comamonadaceae, Gemmatimonadaceae, Planococcaceae, Pyrinomonadaceae, Sphingomonadaceae, and Nitrospiraceae being the most abundant bacterial taxa and Ceratobasidiaceae, Chaetomiaceae, Cladosporiaceae, Didymellaceae, Entolomataceae, Microascaceae, Mortierellaceae, and Nectriaceae being the most abundant fungal taxa (relative abundance > 1%). Both bacterial and fungal diversities of hull-less barley were affected by altitude and soil properties such as total carbon, total nitrogen, and available phosphorus and potassium. Both bacterial and fungal diversities showed a significant negative correlation with altitude, indicating that the lower elevations provide a conducive environment for the survival and maintenance of hull-less barley-associated microbiota. Our results also suggest that the high altitude-specific microbial taxa may play an important role in the adaptation of the hull-less barley to the earth’s third pole.
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Affiliation(s)
- Na Wei
- Institutions of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850032, China
| | - Xiaofeng Yue
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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88
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. FRONTIERS IN PLANT SCIENCE 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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Xie Y, Wang Z, Cheng X, Qiu R, Hamoud YA, Hong C, Zong X, Wang Y, Agathokleous E, Guo X. Dissecting the combined effects of cultivar, fertilization, and irrigation on rhizosphere bacterial communities and nitrogen productivity in rice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155534. [PMID: 35489484 DOI: 10.1016/j.scitotenv.2022.155534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Rice cultivars, fertilizer types, and irrigation modes can affect soil bacterial communities and thus influence nitrogen utilization by soil microorganisms and plants. However, the combined effects of these three factors on soil bacterial communities and nitrogen productivity in rice plants remain unknown. Here, we examined the response of rhizosphere bacteria and nitrogen productivity to different combinations of cultivar (japonica or indica), fertilization (organic plus chemical or chemical), and irrigation (controlled or shallow-frequent). The results demonstrated the interactive effects of cultivars with fertilizers and irrigation on rhizosphere bacterial communities, nitrogen accumulation, and grain yield. These significant interactive effects were related to differences in the response to soil environment (soil inorganic nitrogen concentration and moisture condition) between diverse rhizosphere bacteria recruited by indica and japonica. We found that rhizosphere bacterial communities recruited by indica were more active in soil fertilized with organic plus chemical nitrogen, while those recruited by japonica were suitable for living in soil fertilized with chemical nitrogen. Rhizosphere bacteria diversity positively correlated with soluble inorganic nitrogen in soil, suggesting that more diverse bacterial communities and greater contents of NH4+-N might favor nitrogen accumulation in rice plants under shallow-frequent irrigation. The combinations of cultivars, fertilizer types, and irrigation greatly affected rhizosphere bacterial communities, thus triggering a significant difference in soil inorganic nitrogen content, which could play an essential role in affecting nitrogen productivity.
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Affiliation(s)
- Yi Xie
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Zhenchang Wang
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China.
| | - Xinxin Cheng
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Rangjian Qiu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Yousef Alhaj Hamoud
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China; Department of Soil and Land Reclamation, Aleppo University, Aleppo 1319, Syria
| | - Cheng Hong
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Xingyu Zong
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Yaosheng Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Evgenios Agathokleous
- School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xiangping Guo
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
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90
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Crop Root Responses to Drought Stress: Molecular Mechanisms, Nutrient Regulations, and Interactions with Microorganisms in the Rhizosphere. Int J Mol Sci 2022; 23:ijms23169310. [PMID: 36012575 PMCID: PMC9409098 DOI: 10.3390/ijms23169310] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Roots play important roles in determining crop development under drought. Under such conditions, the molecular mechanisms underlying key responses and interactions with the rhizosphere in crop roots remain limited compared with model species such as Arabidopsis. This article reviews the molecular mechanisms of the morphological, physiological, and metabolic responses to drought stress in typical crop roots, along with the regulation of soil nutrients and microorganisms to these responses. Firstly, we summarize how root growth and architecture are regulated by essential genes and metabolic processes under water-deficit conditions. Secondly, the functions of the fundamental plant hormone, abscisic acid, on regulating crop root growth under drought are highlighted. Moreover, we discuss how the responses of crop roots to altered water status are impacted by nutrients, and vice versa. Finally, this article explores current knowledge of the feedback between plant and soil microbial responses to drought and the manipulation of rhizosphere microbes for improving the resilience of crop production to water stress. Through these insights, we conclude that to gain a more comprehensive understanding of drought adaption mechanisms in crop roots, future studies should have a network view, linking key responses of roots with environmental factors.
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91
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Zhang X, Huang Z, Zhong Z, Li Q, Bian F, Gao G, Yang C, Wen X. Evaluating the Rhizosphere and Endophytic Microbiomes of a Bamboo Plant in Response to the Long-Term Application of Heavy Organic Amendment. PLANTS (BASEL, SWITZERLAND) 2022; 11:2129. [PMID: 36015431 PMCID: PMC9412275 DOI: 10.3390/plants11162129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Root-associated bacteria play a major role in plant health and productivity. However, how organic amendment influences root-associated bacteria is uncertain in Lei bamboo (Phyllostachys praecox) plantations. Here, we compared the rhizosphere and endophytic microbiomes in two Lei bamboo plantations with (IMS) and without (TMS) the application of organic amendment for 16 years. The results showed IMS significantly increased (p < 0.05) the relative abundance of Proteobacteria and significantly decreased (p < 0.05) the relative abundance of Acidobacteria, Bacteroidetes, and Verrucomicrobiota. The root endophytic Proteobacteria and Acidobacteria were significantly higher in abundance (p < 0.05) in the IMS than in the TMS, while Actinobacteria and Firmicutes were significantly lower in abundance. Five taxa were assigned to Proteobacteria and Acidobacteria, which were identified as keystones in the rhizosphere soil microbiome, while two species taxonomically affiliated with Proteobacteria were identified as keystones in the root endophytic microbiota, indicating this phylum can be an indicator for a root-associated microbiome in response to IMS. The soil pH, soil total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and TOC:TP ratio were significantly correlated (p < 0.05) with the bacterial community composition of both rhizosphere soils and root endophytes. TMS increased the microbial network complexity of root endophytes but decreased the microbial network complexity of rhizosphere soil. Our results suggest IMS shapes the rhizosphere and endophytic bacterial community compositions and their interactions differently, which should be paid attention to when designing management practices for the sustainable development of forest ecosystems.
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Affiliation(s)
- Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
- Engineering Research Center of Biochar of Zhejiang Province, Hangzhou 310021, China
| | - Zhiyuan Huang
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Zheke Zhong
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Qiaoling Li
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Fangyuan Bian
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Guibin Gao
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Chuanbao Yang
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Xing Wen
- China National Bamboo Research Center, Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, Hangzhou 310012, China
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
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92
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Li Y, He X, Yuan H, Lv G. Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum. Microorganisms 2022; 10:microorganisms10081644. [PMID: 36014066 PMCID: PMC9414475 DOI: 10.3390/microorganisms10081644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 01/02/2023] Open
Abstract
Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.
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Affiliation(s)
- Yan Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Xuemin He
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Hongfei Yuan
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
- Correspondence:
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93
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Wang L, Qu F, Zhu Z, Zhao Y, Chen X, Shi M, Wei Z. The important role of tricarboxylic acid cycle metabolism pathways and core bacterial communities in carbon sequestration during chicken manure composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 150:20-29. [PMID: 35785624 DOI: 10.1016/j.wasman.2022.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/11/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
As a kind of livestock manure, chicken manure (CM) was rich in organic matter and microorganisms. However, a large amount of foul gas discharged by its random stacking not only threatened the environment, but also caused harm to human health. In view of the serious carbon loss and the unclear action mechanism of microbial community on carbon metabolism during CM composting, the effect of adding regulators on the sequestration of organic carbon was explored. Therefore, the purpose of this study was to explore the regulation mechanism of adding tricarboxylic acid cycle (TCA cycle) regulators on the core carbon metabolism pathway during CM composting. The results showed that the adenosine triphosphate (ATP) and malonic acid (MA) slowed down organic carbon degradation, resulting in lower carbon loss rate, which were 64.99% (CK), 62.35% (MA), and 61.26% (ATP) in each treatment. By comparing the abundance and structure of the carbon-related bacterial communities in different treatments, it was found that adding ATP and MA not only reduced the bacterial community abundance, but also tended to be similar in bacterial community composition. Moreover, the microbial specificity related to carbon metabolism pathway was enhanced, while the related gene expression and gene abundance were weakened. The regulation of TCA cycle metabolism pathway was confirmed to be the main way to improve organic carbon content. These findings revealed the positive effects of ATP and MA on carbon fixation from the perspective of gene metabolism.
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Affiliation(s)
- Liqin Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Fengting Qu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zechen Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaomeng Chen
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingzi Shi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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94
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Kim H, Jeon J, Lee KK, Lee YH. Longitudinal transmission of bacterial and fungal communities from seed to seed in rice. Commun Biol 2022; 5:772. [PMID: 35915150 PMCID: PMC9343636 DOI: 10.1038/s42003-022-03726-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/14/2022] [Indexed: 12/22/2022] Open
Abstract
Vertical transmission of microbes is crucial for the persistence of host-associated microbial communities. Although vertical transmission of seed microbes has been reported from diverse plants, ecological mechanisms and dynamics of microbial communities from parent to progeny remain scarce. Here we reveal the veiled ecological mechanism governing transmission of bacterial and fungal communities in rice across two consecutive seasons. We identify 29 bacterial and 34 fungal members transmitted across generations. Abundance-based regression models allow to classify colonization types of the microbes. We find that they are late colonizers dominating each community at the ripening stage. Ecological models further show that the observed temporal colonization patterns are affected by niche change and neutrality. Source-sink modeling reveals that parental seeds and stem endosphere are major origins of progeny seed microbial communities. This study gives empirical evidence for ecological mechanism and dynamics of bacterial and fungal communities as an ecological continuum during seed-to-seed transmission.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Kiseok Kieth Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Plant Microbiome Research, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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95
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Barro M, Wonni I, Simonin M, Kassankogno AI, Klonowska A, Moulin L, Béna G, Somda I, Brunel C, Tollenaere C. The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso. FEMS Microbiol Ecol 2022; 98:6648705. [PMID: 35867879 DOI: 10.1093/femsec/fiac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs. rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.
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Affiliation(s)
- Mariam Barro
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.,Univ Nazi Boni, Institut du Développement rural, Laboratoire des Systèmes naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Marie Simonin
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Abalo Itolou Kassankogno
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.,INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gilles Béna
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Irénée Somda
- Univ Nazi Boni, Institut du Développement rural, Laboratoire des Systèmes naturels, Agrosystèmes et Ingénierie de l'Environnement (SyNAIE), Bobo-Dioulasso, Burkina Faso
| | - Caroline Brunel
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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96
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Wang J, Cheng X, Zhang J, Liu Z, Cheng F, Yan J, Zhang G. Estimating the time since deposition (TsD) in saliva stains using temporal changes in microbial markers. Forensic Sci Int Genet 2022; 60:102747. [PMID: 35870433 DOI: 10.1016/j.fsigen.2022.102747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 06/07/2022] [Accepted: 07/14/2022] [Indexed: 11/04/2022]
Abstract
Determining the time since deposition (TsD) of traces could be helpful in the investigation of criminal offenses. However, there are no reliable markers and models available for the inference of short-term TsD. The goal of this study was to investigate the potential of the succession pattern of human salivary microbial communities to serve as an efficiency TsD prediction tool in the resolution of the forensic cases. Saliva stains exposed to indoor conditions up to 20 days were collected and analyzed by 16S rRNA profiling using high-throughput sequencing technique. Noticeable differences in microbial composition were observed between different time points, and the indoor exposure time of saliva stains were inversely correlated with alpha diversity estimates across the measured time period. The sequencing results were used to identify TsD-dependent bacterial indicators to regress a generalized random forest model, resulting in a mean absolute deviation (MAD) of 1.41 days. Furthermore, a simplified TsD predictive model was also developed utilizing Enhydrobacter, Paenisporosarcina, and Janthinobacterium by quantitative PCR (qPCR) with a MAD of 1.32 days, and then forensic practice assessment were also performed by using mock samples with a MAD of 3.53 days. In conclusion, this study revealed significant changes in salivary microbial abundance as the prolongation of TsD. It demonstrated that the microbial biomarkers could be invoked as a "clock" for TsD estimation in human dried saliva stains.
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Affiliation(s)
- Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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97
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Chen QY, Que SJ, Chen JY, Qing-Zhong, Liu ZY, Wang JB, Lin JX, Lu J, Cao LL, Lin M, Tu RH, Huang ZN, Lin JL, Zheng HL, Xie JW, Zheng CH, Li P, Huang CM. Development and validation of metabolic scoring to individually predict prognosis and monitor recurrence early in gastric cancer: A large-sample analysis. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2022; 48:2149-2158. [PMID: 35864012 DOI: 10.1016/j.ejso.2022.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 05/14/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023]
Abstract
PURPOSE To develop and validate a simple metabolic score (Metabolic score, MS) for use in evaluating the prognosis of gastric cancer (GC) patients and dynamically monitor for early recurrence. METHODS We retrospectively collected general clinicopathological data of patients who underwent radical gastrectomy for GC between September 2012 and December 2017 in the Department of Gastric Surgery of the Fujian Medical University Union Hospital. Using a random forest algorithm to screen preoperative blood indicators into the Least absolute shrinkage and selection operator (LASSO) model, we developed a novel MS to predict prognosis. RESULTS Data of 1974 patients were used to develop and validate the model. Total cholesterol (TCHO), bilirubin (TBIL), direct bilirubin (DBIL), and 15 other metabolic indicators had significant predictive value for the prognosis using the random forest algorithm. In the overall population, 533 patients (27.0%) had high and 1441 (73%) had low MS status. High MS status was related to tumor progression. The KM curves of 3-year OS and RFS for training set patients showed low MS had a better prognosis than high MS (OS: 79.4% vs 59.7%, P < 0.001; RFS: 76.0% vs 56.2%, P < 0.001). CONCLUSIONS We have developed and validated MS to predict the long-term survival of GC patients and allow early monitoring of recurrence. This will provide physicians with simple, economical, and dynamic tumor monitoring information.
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Affiliation(s)
- Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Si-Jin Que
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jun-Yu Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Qing-Zhong
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Zhi-Yu Liu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jun Lu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ru-Hong Tu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ze-Ning Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ju-Li Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Hua-Long Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China; Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China.
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98
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Zhang D, Zhang Y, Zhao Z, Xu S, Cai S, Zhu H, Rengel Z, Kuzyakov Y. Carbon-Phosphorus Coupling Governs Microbial Effects on Nutrient Acquisition Strategies by Four Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:924154. [PMID: 35865291 PMCID: PMC9294595 DOI: 10.3389/fpls.2022.924154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Plants adjust root morphological and/or exudation traits in response to phosphorus (P) mobilization mediated by microorganisms. We hypothesized that straw application coupled with P fertilization would influence microbial P and then root nutrient-acquisition strategies related to crop growth. Root morphological (length and average diameter) and exudation traits (acid phosphatase and carboxylates) of Brassica chinensis, Solanum lycopersicum, Lactuca sativa, and Vigna unguiculata in response to microbial P dynamics were characterized in no-P and P-fertilized soil with/without straw addition. Straw addition increased the growth of fungi and bacteria, stimulating microbial P immobilization at day 24. The high microbial abundance was associated with four tested crops having short roots in straw-amended compared with no-straw soil at day 24. In straw-amended soil, B. chinensis and S. lycopersicum shifted toward root P-acquisition strategies based on fast elongation and strong carboxylate exudation from days 24 to 40. Such effective root P-acquisition strategies together with microbial P release increased shoot P content in S. lycopersicum in straw-amended compared with those without straw at day 40. Conversely, L. sativa and V. unguiculata produced short roots in response to the stable (or even increased) microbial P after straw addition till day 40. In straw-amended soil, high P application stimulated root elongation and carboxylate exudation in L. sativa and V. unguiculata, whereas carboxylate exudation by S. lycopersicum was decreased compared with the straw-amended but non-fertilized treatment at day 40. In summary, root P-acquisition strategies in response to microbial P differed among the tested crop species. Phosphorus fertilization needs to be highlighted when returning straw to enhance P-use efficiency in vegetable cropping systems.
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Affiliation(s)
- Deshan Zhang
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, China
| | - Yuqiang Zhang
- Nicholas School of the Environment, Duke University, Durham, NC, United States
| | - Zheng Zhao
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, China
| | - Sixin Xu
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, China
| | - Shumei Cai
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, China
| | - Haitao Zhu
- Institute of Ecological Environment Protection Research, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, China
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Institute for Adriatic Crops and Karst Reclamation, Split, Croatia
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Göttingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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99
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Jia G, Hu W, Zhang B, Li G, Shen S, Gao Z, Li Y. Assessing impacts of the Ecological Retreat project on water conservation in the Yellow River Basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154483. [PMID: 35283132 DOI: 10.1016/j.scitotenv.2022.154483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The Ecological Retreat (ER) project significantly impacts water conservation functions in the Yellow River Basin (YRB). However, studies on the impact and benefit of different ER modes on ecological water effects still lack systematic and integral disclosure. In our study, CNLUCC (China land use/cover data sets) and the Markov transition matrix were used to simulate land pattern changes from 2000 to 2018. Water yield was chosen as an indicator of water conservation to explore the impact of the ER project by using the water yield module of the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model. After the ER project, the land pattern changed significantly because massive cropland was transformed into forest and grassland. Thus, the total water yields of the YRB increased by 46.32 × 103 hm3 from 2000 to 2018, and the overall water yield benefit was 12.39% larger than the water loss. Forest rehabilitation (FR) showed the highest average water yield capacity, while grassland restoration (GR) exhibited the most incredible total water conservation benefit. Wetland recovery (WLR) manifested a great capacity to improve average water yield, but its total benefit was far less than FR and GR, while waterbody recovery (WBR) showed a negative impact. The results indicate that FR and GR were effective restoration methods, and WLR showed great potential to improve water yield. By using the random forest and principal components analysis, precipitation (PRE), evaporation (AET and ET0), and variation of forest and grassland proved to be the most critical driving indicators affecting water yield changes. Additionally, the correlation and sensitivity between root depth (R_depth) and water yield indicate that increasing R_Depth can also enhance water conservation. The ER project provides a valuable restoration model for water yield and water conservation benefits. The results can provide theoretical support for eco-hydrology and land ecological restoration studies.
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Affiliation(s)
- Guanyu Jia
- Central South University of Forestry and Technology, Changsha 410004, China; Engineering Technology Research Centre of Big Data for Landscape Resources in Nature Protected Areas of Hunan Province, Changsha 410004, China
| | - Wenmin Hu
- Central South University of Forestry and Technology, Changsha 410004, China; Engineering Technology Research Centre of Big Data for Landscape Resources in Nature Protected Areas of Hunan Province, Changsha 410004, China; Research Institute of Forest Resources Information Technique, Chinese Academy of Forestry, Beijing 100001, China.
| | - Bin Zhang
- Huazhong Agricultural University, China.
| | - Guo Li
- Central South University of Forestry and Technology, Changsha 410004, China; Engineering Technology Research Centre of Big Data for Landscape Resources in Nature Protected Areas of Hunan Province, Changsha 410004, China.
| | - Shouyun Shen
- Central South University of Forestry and Technology, Changsha 410004, China; Engineering Technology Research Centre of Big Data for Landscape Resources in Nature Protected Areas of Hunan Province, Changsha 410004, China
| | - Zhihai Gao
- Research Institute of Forest Resources Information Technique, Chinese Academy of Forestry, Beijing 100001, China.
| | - Yi Li
- Hunan Agricultural University, Changsha 410015, China
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100
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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