Article
Agronomy
G. S. Ortiz-Barbosa, L. Torres-Martinez, J. Rothschild, J. L. Sachs
Summary: Legumes have the ability to optimize growth by discriminating between fixed nitrogen from rhizobia and nitrogen in the soil. However, the recognition and regulation of symbiotically fixed nitrogen remain poorly understood. This study manipulated the molecular form and concentration of nitrogen available to investigate the adaptability of Lotus japonicus plants in downregulating investment into symbiosis when exposed to different nitrogen sources. The results suggest that L. japonicus can selectively downregulate symbiosis when exposed to certain nitrogen sources, but fails to do so in the presence of aspartic acid, indicating that aspartic acid may interfere with the main signal used by L. japonicus to detect nitrogen fixation.
Article
Agronomy
Satu Ramula, Seyed Abdollah Mousavi, Aino Kalske
Summary: In this study, the relative effectiveness of different strains of rhizobia on the invasive legume Lupinus polyphyllus was examined. The results showed that the differences in nodulation and plant growth promotion among different strains of the genus Bradyrhizobium were more pronounced in the greenhouse than in the common garden.
Article
Agronomy
Kenjiro W. Quides, Hagop S. Atamian
Summary: Rhizobia have long been recognized as effective biofertilizers for legume crops, but the issue of rhizobial competition has hindered their growth benefits. Microbiome engineering has emerged as a potential solution to this problem, focusing on unraveling the complexities of symbiosis.
Article
Biology
Julia A. Boyle, Anna K. Simonsen, Megan E. Frederickson, John R. Stinchcombe
Summary: Priority effects occur when the order of species arrival affects the final community structure. In the case of mutualists interacting with hosts in different orders, the outcome can be influenced by the interaction order, with hosts receiving high-quality mutualists early better tolerating low-quality symbionts later.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yong Feng, Ping Wu, Chao Liu, Liwei Peng, Tao Wang, Chao Wang, Qian Tan, Bixuan Li, Yajuan Ou, Hui Zhu, Songli Yuan, Renliang Huang, Gary Stacey, Zhongming Zhang, Yangrong Cao
Summary: The study found that in Lotus japonicus, SymRK is required for rhizobial suppression of plant innate immunity, while LjBAK1 plays a negative role in rhizobial infection. The protein complex formed by SymRK and LjBAK1 serves as an intersection point between rhizobial symbiotic signaling pathways and innate immunity pathways.
Article
Multidisciplinary Sciences
Rafael E. Venado, Lucas E. Wange, Defeng Shen, Fabienne Pinnau, Tonni Grube Andersen, Wolfgang Enard, Macarena Marin
Summary: This study provides genetic evidence for the formation of the nodule oxygen diffusion barrier in legumes, which is crucial for nitrogen fixation in root nodules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Microbiology
Katy D. Heath, Rebecca T. Batstone, Mario Ceron Romero, John G. McMullen
Summary: In this study, genomics was used to investigate the diversity of mobile genetic elements carrying symbiosis genes in natural populations of Bradyrhizobium. The findings provide insights into the novel mechanisms for generating and maintaining diversity in these ecologically and economically important mutualisms.
Article
Plant Sciences
Meng Liu, Hiromu Kameoka, Akiko Oda, Taro Maeda, Takashi Goto, Koji Yano, Takashi Soyano, Masayoshi Kawaguchi
Summary: Legumes form root nodules in association with rhizobia to overcome nitrogen deficiency. ERN1 is a crucial transcription factor involved in the establishment of root nodule symbiosis, regulating processes such as cell wall remodeling and signal transduction. RNA sequencing revealed 234 genes associated with ERN1, involved in cell wall remodeling, signal transduction, hormone metabolism, and transcription regulation, expanding our understanding of the role of ERN1 in root nodule symbiosis.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yanping Wang, Wenqing Zhou, Jiandong Wu, Kailing Xie, Xiaoyu Li
Summary: This study identified the ammonium transporter LjAMT2;2 in Lotus japonicus as an important player in the arbuscular mycorrhizal symbiosis process, facilitating ammonium transfer and promoting nitrogen absorption. Overexpression of LjAMT2;2 increased nitrogen content, alleviating nitrogen stress and enhancing plant growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Alexandra J. Weisberg, Marilyn Miller, Walt Ream, Niklaus J. Grunwald, Jeff H. Chang
Summary: Members of the agrobacteria-rhizobia complex have multiple and diverse plasmids, which interact with each other and shape the evolution of genomes. This study reveals the interactions and evolutionary histories of oncogenic virulence plasmids, including the discovery of a novel mosaic plasmid.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Microbiology
Ravinder K. K. Goyal, Jemaneh Z. Z. Habtewold
Summary: Plants face unfavorable conditions and microbial pathogens that can cause damage to their growth and survival. Maintaining a healthy and stress-free host plant is crucial for a successful symbiotic relationship with rhizobia. The rhizobia not only assist with nitrogen fixation but also enhance the plant's defense mechanisms against stress and provide disease protection.
Article
Biochemistry & Molecular Biology
Akihiro Yamazaki, Kai Battenberg, Yoshikazu Shimoda, Makoto Hayashi
Summary: LysM-like receptor kinases play important roles in both plant immunity and symbiosis, particularly in signal perception and activation of downstream signal cascades. The study revealed that NHL13 interacts with NFR1 and SymRK, suggesting its involvement in both plant immunity and symbiosis.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Agronomy
Niall Millar, Jonah Piovia-Scott, Stephanie S. Porter
Summary: This study compared the symbiosis traits between domesticated and wild legume cultivars in response to varying nitrogen levels. The results showed that there are differences in mutualistic outcomes between domesticated and wild chickpea and soybean, but not lentil, pea, or peanut.
Article
Plant Sciences
Jesus Montiel, Dugald Reid, Thomas H. Gronbaek, Caroline M. Benfeldt, Euan K. James, Thomas Ott, Franck A. Ditengou, Marcin Nadzieja, Simon Kelly, Jens Stougaard
Summary: This study reports intercellular infection of the model legume Lotus japonicus by the IRBG74 strain and reveals the genetic requirements and differences in the pathways governing this process compared to intracellular infection. The results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry, highlighting distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.
Article
Microbiology
Yuanhui Liu, Bin Ma, Wenfeng Chen, Klaus Schlaeppi, Matthias Erb, Erinne Stirling, Lingfei Hu, Entao Wang, Yunzeng Zhang, Kankan Zhao, Zhijiang Lu, Shudi Ye, Jianming Xu
Summary: Root-microbiome interactions play a crucial role in plant performance and yield, particularly in legumes which engage in symbiosis with N-2-fixing rhizobia. The rhizobial symbiotic capacity was found to significantly alter root-associated microbiomes by impacting diversity, co-occurrence interactions, and microbial depletion in the rhizosphere and rhizoplane. Root exudates and soil physiochemical properties were closely correlated with microbial community shifts in response to different rhizobial treatments.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alexandra J. Weisberg, Charles G. Kramer, Raghavendhar R. Kotha, Devanand L. Luthria, Jeff H. Chang, Christopher R. Clarke
Summary: Even within the same species-level group of Streptomyces strains, there can be variations in aggressiveness and pathogenicity, despite the presence of the same virulence genes. The necessary genomic context for bacteria to cause common scab symptoms in tuber and root crops is not fully characterized.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2021)
Article
Ecology
Gabriel S. Ortiz-Barbosa, Lorena Torres-Martinez, Angela Manci, Sierra Neal, Tarek Soubra, Fizzah Khairi, Jerry Trinh, Paola Cardenas, Joel L. Sachs
Summary: Modern agriculture tends to focus on the aboveground structures of plants and overlooks the belowground features that influence microbiota. The domestication process in crops, along with drift, inbreeding, and relaxed selection for symbiosis, may lead to degradation of plant mechanisms that support beneficial microbes. However, domesticated cowpea does not show evidence of degradation in symbiosis unlike other crops.
Article
Microbiology
Hien P. Nguyen, Alexandra J. Weisberg, Jeff H. Chang, Christopher R. Clarke
Summary: Fourteen strains of Streptomyces isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. The strains have unique characteristics and susceptibilities to certain antibiotics. Although their 16S rRNA gene sequences are identical to other Streptomyces species, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that they belong to a new species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maureen C. Onyeziri, Ramya Natarajan, Gail G. Hardy, Jing Xu, Ian P. Reynolds, Jinwoo Kim, Peter M. Merritt, Thomas Danhorn, Michael E. Hibbing, Alexandra J. Weisberg, Jeff H. Chang, Clay Fuqua
Summary: Agrobacterium tumefaciens, a type of bacteria that infects plants and associates with various surfaces, produces a polysaccharide called UPP in two distinct forms, each requiring a specific polymerase. These findings have important implications for understanding polysaccharide biosynthesis mechanisms.
MOLECULAR MICROBIOLOGY
(2022)
Article
Ecology
Camille E. Wendlandt, Kelsey A. Gano-Cohen, Peter J. N. Stokes, Basava N. R. Jonnala, Avissa J. Zomorrodian, Khadija Al-Moussawi, Joel L. Sachs
Summary: The effects of nitrogen enrichment on plants and soil microbial communities mainly depend on the differences among plant lines rather than soil nitrogen levels. Despite elevated soil nitrogen levels, plant populations still impose strong selection on rhizobial nitrogen fixation, suggesting that host control traits are stable under long-term nutrient enrichment.
Article
Biology
Alexandra J. Weisberg, Marilyn Miller, Walt Ream, Niklaus J. Grunwald, Jeff H. Chang
Summary: Members of the agrobacteria-rhizobia complex have multiple and diverse plasmids, which interact with each other and shape the evolution of genomes. This study reveals the interactions and evolutionary histories of oncogenic virulence plasmids, including the discovery of a novel mosaic plasmid.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Alexandra J. Weisberg, Joel L. Sachs, Jeff H. Chang
Summary: The chromosome architecture of Bradyrhizobium bacteria is largely conserved despite variations in genome composition and location of attachment sites recognized by integrases of symICEs. Simulated nonnative chromosome-symICE combinations are predicted to result in lethal deletions or disruptions to architecture. The findings suggest compatibility between chromosomes and symICEs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Review
Ecology
David C. Fronk, Joel L. Sachs
Summary: Diverse organisms have evolved specialized structures to interact with beneficial microbes, forming symbiotic organs that play crucial roles in shaping microbial genomes. Future research should consider the emergent forces that shape these symbiotic organs.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Microbiology
Alexandra J. Weisberg, Arafat Rahman, Dakota Backus, Parinita Tyavanagimatt, Jeff H. Chang, Joel L. Sachs
Summary: Genetic variation in symbiotic nitrogen fixation is maintained through a modular system that allows for flexibility and reshuffling of genes. This results in variation in the services provided by symbionts and can lead to the evolution of uncooperative genotypes. However, the overall symbiosis between legume hosts and Bradyrhizobium bacteria is evolutionarily stable.
Article
Agronomy
M. Manci, O. G. Mercado, R. X. Camantigue, T. Nguyen, J. Rothschild, F. Khairi, S. Neal, W. F. Farsamin, M. T. Lampe, I. A. Perez, T. H. Le, G. S. Ortiz-Barbosa, L. Torres-Martinez, J. L. Sachs
Summary: This study investigated the benefits that cowpeas receive from microbiota, depending on plant genotype, domestication status, and soil source. The results showed that the variation in root nodulation and growth benefits to the host were observed among different soil sites, with soil microbiota being the predominant factor shaping plant performance.
Article
Agronomy
G. S. Ortiz-Barbosa, L. Torres-Martinez, J. Rothschild, J. L. Sachs
Summary: Legumes have the ability to optimize growth by discriminating between fixed nitrogen from rhizobia and nitrogen in the soil. However, the recognition and regulation of symbiotically fixed nitrogen remain poorly understood. This study manipulated the molecular form and concentration of nitrogen available to investigate the adaptability of Lotus japonicus plants in downregulating investment into symbiosis when exposed to different nitrogen sources. The results suggest that L. japonicus can selectively downregulate symbiosis when exposed to certain nitrogen sources, but fails to do so in the presence of aspartic acid, indicating that aspartic acid may interfere with the main signal used by L. japonicus to detect nitrogen fixation.
Article
Biochemistry & Molecular Biology
Arafat Rahman, Max Manci, Cassandra Nadon, Ivan A. Perez, Warisha F. Farsamin, Matthew T. Lampe, Tram H. Le, Lorena Torres Martinez, Alexandra J. Weisberg, Jeff H. Chang, Joel L. Sachs
Summary: The capacity of beneficial microbes to compete for host infection and the ability of hosts to discriminate among them introduce evolutionary conflict that may destabilize mutualism. This study investigates the fitness outcomes in associations between legumes and their symbiotic rhizobia, and finds that microbial competition has an impact on fitness. The findings suggest that inter-strain competition favors fast-growing, minimally beneficial rhizobia strains, and that competition traits are polygenic and linked with inter-strain allelopathic interactions in the rhizosphere.
Article
Microbiology
Lucas Waldburger, Mitchell G. Thompson, Alexandra J. Weisberg, Namil Lee, Jeff H. H. Chang, Jay D. Keasling, Patrick M. M. Shih
Summary: Transcription start sites (TSSs) play a fundamental role in understanding gene expression and regulation. Agrobacteria are prokaryotes widely used in plant biotechnology due to their ability to transfer DNA into host plant genomes. However, the genome-wide transcriptional regulation of agrobacteria, especially in less-studied lineages, remains poorly understood. A study using differential RNA-seq and an optimized algorithm has successfully identified thousands of TSSs with nucleotide resolution for representatives of each lineage, providing a framework for understanding the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The importance of parameter optimization in genome-wide TSS identification and genomics is also highlighted by the optimized algorithm.
