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Chai YN, Qi Y, Goren E, Chiniquy D, Sheflin AM, Tringe SG, Prenni JE, Liu P, Schachtman DP. Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 2024; 9:e0119023. [PMID: 38132569 PMCID: PMC10804983 DOI: 10.1128/msystems.01190-23] [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: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.
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Affiliation(s)
- Yen Ning Chai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yunhui Qi
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Emily Goren
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Dawn Chiniquy
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amy M. Sheflin
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Susannah G. Tringe
- Environmental Genomics and System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jessica E. Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Colorado State University, Fort Collins, Colorado, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Brozel VS. Special Issue "Microbial Interactions in Soil": Editorial. Microorganisms 2023; 11:1260. [PMID: 37317234 DOI: 10.3390/microorganisms11051260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Soils are home to a wide variety of microorganisms [...].
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Affiliation(s)
- Volker S Brozel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [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: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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Qiao Z, Barnes E, Tringe S, Schachtman DP, Liu P. Poisson hurdle model-based method for clustering microbiome features. Bioinformatics 2022; 39:6873739. [PMID: 36469352 PMCID: PMC9825753 DOI: 10.1093/bioinformatics/btac782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 10/13/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. RESULTS We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation-maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. AVAILABILITY AND IMPLEMENTATION R package is freely available for download at https://cran.r-project.org/package=PHclust. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhili Qiao
- To whom correspondence should be addressed. or
| | - Elle Barnes
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Susannah Tringe
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Peng Liu
- To whom correspondence should be addressed. or
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Response of root endosphere bacterial communities of typical rice cultivars to nitrogen fertilizer reduction at the jointing stage. Arch Microbiol 2022; 204:722. [DOI: 10.1007/s00203-022-03334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/16/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022]
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Lu GH, Zheng K, Cao R, Fazal A, Na Z, Wang Y, Yang Y, Sun B, Yang H, Na ZY, Zhao X. Root-associated fungal microbiota of the perennial sweet sorghum cultivar under field growth. Front Microbiol 2022; 13:1026339. [PMID: 36386674 PMCID: PMC9643593 DOI: 10.3389/fmicb.2022.1026339] [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: 08/23/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022] Open
Abstract
Root-associated fungal microbiota, which inhabit the rhizosphere, rhizoplane and endosphere, have a profound impact on plant growth and development. Sorghum bicolor (L.) Moench, also called broomcorn or sweet sorghum, is a multipurpose crop. The comparison between annual and perennial sweet sorghum cultivars in terms of plant growth, as well as their interactions with belowground fungal microbiota, is still poorly understood, although there has been growing interest in the mutualism between annual sweet sorghum and soil bacteria or bacterial endophytes. In this study, the perennial sweet sorghum cultivar N778 (N778 simply) and its control lines TP213 and TP60 were designed to grow under natural field conditions. Bulk soil, rhizosphere soil and sorghum roots were collected at the blooming and maturity stages, and then the fungal microbiota of those samples were characterized by high-throughput sequencing of the fungal ITS1 amplicon. Our results revealed that the alpha diversity of the fungal microbiota in rhizosphere soil and root samples was significantly different between N778 and the two control lines TP213 and TP60 at the blooming or maturity stage. Moreover, beta diversity in rhizosphere soil of N778 was distinct from those of TP213 and TP60, while beta diversity in root samples of N778 was distinct from those of TP213 but not TP60 by PCoA based on Bray–Curtis and WUF distance metrics. Furthermore, linear discriminant analysis (LDA) and multiple group comparisons revealed that OTU4372, a completely unclassified taxon but with symbiotroph mode, was enriched in sorghum roots, especially in N778 aerial roots at the blooming stage. Our results indicate that Cladosporium and Alternaria, two fungal genera in the rhizosphere soil, may also be dominant indicators of sorghum yield and protein content in addition to Fusarium at the maturity stage and imply that the perennial sweet sorghum N778 can primarily recruit dominant psychrotolerant bacterial taxa but not dominant cold-tolerant fungal taxa into its rhizosphere to support its survival below the freezing point.
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Affiliation(s)
- Gui-Hua Lu
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Gui-Hua Lu,
| | - Kezhi Zheng
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Rui Cao
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhiye Na
- Yunnan Eco-Agriculture Research Institute, Kunming, China
| | - Yuanyuan Wang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Bo Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hongjun Yang
- Yunnan Eco-Agriculture Research Institute, Kunming, China
| | - Zhong-Yuan Na
- Yunnan Eco-Agriculture Research Institute, Kunming, China
- Zhong-Yuan Na,
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Xiangxiang Zhao,
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Chai YN, Futrell S, Schachtman DP. Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops. Front Microbiol 2022; 13:791110. [PMID: 35154049 PMCID: PMC8826558 DOI: 10.3389/fmicb.2022.791110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.
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Affiliation(s)
- Yen Ning Chai
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, United States
| | - Stephanie Futrell
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, United States
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture and Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, United States
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