1
|
Qiao M, Sun R, Wang Z, Dumack K, Xie X, Dai C, Wang E, Zhou J, Sun B, Peng X, Bonkowski M, Chen Y. Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification. Nat Commun 2024; 15:2924. [PMID: 38575565 PMCID: PMC10995168 DOI: 10.1038/s41467-024-47159-x] [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: 04/06/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.
Collapse
Affiliation(s)
- Mengjie Qiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibo Sun
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Zixuan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- College of Land Resource and Environment, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chuanchao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xinhua Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
2
|
Galindo-Castañeda T, Hartmann M, Lynch JP. Location: root architecture structures rhizosphere microbial associations. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:594-604. [PMID: 37882632 PMCID: PMC10773995 DOI: 10.1093/jxb/erad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
Root architectural phenotypes are promising targets for crop breeding, but root architectural effects on microbial associations in agricultural fields are not well understood. Architecture determines the location of microbial associations within root systems, which, when integrated with soil vertical gradients, determines the functions and the metabolic capability of rhizosphere microbial communities. We argue that variation in root architecture in crops has important implications for root exudation, microbial recruitment and function, and the decomposition and fate of root tissues and exudates. Recent research has shown that the root microbiome changes along root axes and among root classes, that root tips have a unique microbiome, and that root exudates change within the root system depending on soil physicochemical conditions. Although fresh exudates are produced in larger amounts in root tips, the rhizosphere of mature root segments also plays a role in influencing soil vertical gradients. We argue that more research is needed to understand specific root phenotypes that structure microbial associations and discuss candidate root phenotypes that may determine the location of microbial hotspots within root systems with relevance to agricultural systems.
Collapse
Affiliation(s)
| | - Martin Hartmann
- Department of Environmental Systems Service, ETH Zürich, 8092 Zurich, Switzerland
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
3
|
Becker MF, Klueken AM, Knief C. Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings. ENVIRONMENTAL MICROBIOME 2023; 18:43. [PMID: 37245023 DOI: 10.1186/s40793-023-00502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota. RESULTS The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant. CONCLUSIONS Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.
Collapse
Affiliation(s)
- Maximilian Fernando Becker
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany
| | - A Michael Klueken
- Crop Science Division, Disease Control Biology, Bayer AG, Alfred-Nobel-Str. 50, 40789, Monheim am Rhein, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Fox A, Widmer F, Lüscher A. Soil microbial community structures are shaped by agricultural systems revealing little temporal variation. ENVIRONMENTAL RESEARCH 2022; 214:113915. [PMID: 35940233 PMCID: PMC9492858 DOI: 10.1016/j.envres.2022.113915] [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: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.
Collapse
Affiliation(s)
- A Fox
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland; Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - F Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - A Lüscher
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
| |
Collapse
|
6
|
Appidi MR, Bible AN, Carper DL, Jawdy SS, Giannone RJ, Hettich RL, Morrell-Falvey J, Abraham PE. Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:639-649. [PMID: 35349304 DOI: 10.1094/mpmi-01-22-0011-ta] [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] [Indexed: 06/14/2023]
Abstract
Plant-microbe interactions in the rhizosphere play a vital role in plant health and productivity. The composition and function of root-associated microbiomes is strongly influenced by their surrounding environment, which is often customized by their host. How microbiomes change with respect to space and time across plant roots remains poorly understood, and methodologies that facilitate spatiotemporal metaproteomic studies of root-associated microbiomes are yet to be realized. Here, we developed a method that provides spatially resolved metaproteome measurements along plant roots embedded in agar-plate culture systems, which have long been used to study plants. Spatially defined agar "plugs" of interest were excised and subsequently processed using a novel peptide extraction method prior to metaproteomics, which was used to infer both microbial community composition and function. As a proof-of-principle, a previously studied 10-member community constructed from a Populus root system was grown in an agar plate with a 3-week-old Populus trichocarpa plant. Metaproteomics was performed across two time points (24 and 48 h) for three distinct locations (root base, root tip, and a region distant from the root). The spatial resolution of these measurements provides evidence that microbiome composition and expression changes across the plant root interface. Interrogation of the individual microbial proteomes revealed functional profiles related to their behavioral associations with the plant root, in which chemotaxis and augmented metabolism likely supported predominance of the most abundant member. This study demonstrated a novel peptide extraction method for studying plant agar-plate culture systems, which was previously unsuitable for (meta)proteomic measurements.
Collapse
Affiliation(s)
- Manasa R Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | | | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| |
Collapse
|
7
|
Becker MF, Hellmann M, Knief C. Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees. ENVIRONMENTAL MICROBIOME 2022; 17:31. [PMID: 35715810 PMCID: PMC9205072 DOI: 10.1186/s40793-022-00427-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees. RESULTS The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R2-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R2-values of 0.454 and 0.371, respectively). CONCLUSIONS The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.
Collapse
Affiliation(s)
- Maximilian Fernando Becker
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany
| | - Manfred Hellmann
- Dienstleistungszentrum Ländlicher Raum (DLR) Rheinpfalz, Kompetenzzentrum Gartenbau Klein-Altendorf, 53359, Rheinbach, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany.
| |
Collapse
|
8
|
Huang YH, Liu Y, Geng J, Lü H, Zhao HM, Xiang L, Li H, Mo CH, Li YW, Cai QY. Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128280. [PMID: 35093749 DOI: 10.1016/j.jhazmat.2022.128280] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution.
Collapse
Affiliation(s)
- Yu-Hong Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yue Liu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jun Geng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huixiong Lü
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
9
|
Gardner CM, Gerhard WA, Redfern LK, Gunsch CK. Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35319433 DOI: 10.1099/mic.0.001155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r S≥0.70 or r S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.
Collapse
Affiliation(s)
- Courtney M Gardner
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Washington State University, Civil and Environmental Engineering, 405 Spokane St., PO Box 642910, Pullman, WA 99164, USA
| | - William A Gerhard
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA
| | - Lauren K Redfern
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Florida Gulf Coast University, Environmental and Civil Engineering, 10501 FGCU Blvd. South, Ft. Myers, FL 33965, USA
| | - Claudia K Gunsch
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Duke University, Durham, NC 27708, USA
| |
Collapse
|
10
|
Laschke L, Schütz V, Schackow O, Sicker D, Hennig L, Hofmann D, Dörmann P, Schulz M. Survival of Plants During Short-Term BOA-OH Exposure: ROS Related Gene Expression and Detoxification Reactions Are Accompanied With Fast Membrane Lipid Repair in Root Tips. J Chem Ecol 2022; 48:219-239. [PMID: 34988771 PMCID: PMC8881443 DOI: 10.1007/s10886-021-01337-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022]
Abstract
For the characterization of BOA-OH insensitive plants, we studied the time-dependent effects of the benzoxazolinone-4/5/6/7-OH isomers on maize roots. Exposure of Zea mays seedlings to 0.5 mM BOA-OH elicits root zone-specific reactions by the formation of dark rings and spots in the zone of lateral roots, high catalase activity on root hairs, and no visible defense reaction at the root tip. We studied BOA-6-OH- short-term effects on membrane lipids and fatty acids in maize root tips in comparison to the benzoxazinone-free species Abutilon theophrasti Medik. Decreased contents of phosphatidylinositol in A. theophrasti and phosphatidylcholine in maize were found after 10-30 min. In the youngest tissue, α-linoleic acid (18:2), decreased considerably in both species and recovered within one hr. Disturbances in membrane phospholipid contents were balanced in both species within 30-60 min. Triacylglycerols (TAGs) were also affected, but levels of maize diacylglycerols (DAGs) were almost unchanged, suggesting a release of fatty acids for membrane lipid regeneration from TAGs while resulting DAGs are buildings blocks for phospholipid reconstitution, concomitant with BOA-6-OH glucosylation. Expression of superoxide dismutase (SOD2) and of ER-bound oleoyl desaturase (FAD2-2) genes were contemporaneously up regulated in contrast to the catalase CAT1, while CAT3 was arguably involved at a later stage of the detoxification process. Immuno-responses were not elicited in short-terms, since the expression of NPR1, POX12 were barely affected, PR4 after 6 h with BOA-4/7-OH and PR1 after 24 h with BOA-5/6-OH. The rapid membrane recovery, reactive oxygen species, and allelochemical detoxification may be characteristic for BOA-OH insensitive plants.
Collapse
Affiliation(s)
- Laura Laschke
- IMBIO Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten Str. 13, 53115, Bonn, Germany
| | - Vadim Schütz
- IMBIO Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten Str. 13, 53115, Bonn, Germany
| | - Oliver Schackow
- Institute of Organic Chemistry, Institut Für Organische Chemie, Universität Leipzig, Johannisallee 29, 04103, Leipzig, Germany
| | - Dieter Sicker
- Institute of Organic Chemistry, Institut Für Organische Chemie, Universität Leipzig, Johannisallee 29, 04103, Leipzig, Germany
| | - Lothar Hennig
- Institute of Organic Chemistry, Institut Für Organische Chemie, Universität Leipzig, Johannisallee 29, 04103, Leipzig, Germany
| | - Diana Hofmann
- IBG-3: Agrosphäre, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peter Dörmann
- IMBIO Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten Str. 13, 53115, Bonn, Germany
| | - Margot Schulz
- IMBIO Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Karlrobert-Kreiten Str. 13, 53115, Bonn, Germany.
| |
Collapse
|
11
|
Yoshiura CA, Venturini AM, Braga LPP, da França AG, de Lyra MDCCP, Tsai SM, Rodrigues JLM. Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production. FRONTIERS IN PLANT SCIENCE 2021; 12:683658. [PMID: 34276734 PMCID: PMC8278312 DOI: 10.3389/fpls.2021.683658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.
Collapse
Affiliation(s)
- Caio Augusto Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Lucas Palma Perez Braga
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Aline Giovana da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | |
Collapse
|