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Yaish MW. Isolation and Identification of Growth-Promoting Bacteria from Plants Growing Under Abiotic Stresses. Methods Mol Biol 2024; 2832:241-256. [PMID: 38869801 DOI: 10.1007/978-1-0716-3973-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Identification and isolation of plant growth-promoting bacteria (PGPB) are critical steps toward understanding the role of these bacteria in stress tolerance in plants. This procedure also provides essential knowledge about the microbes needed to formulate effective biofertilizers. This chapter describes culture-dependent and culture-independent strategies to identify and isolate PGPB. The culture-dependent strategy commonly involves growing PGPB on general and selective media. However, the culture-independent strategy involves next-generation sequencing technologies. A combination of both strategies would identify the structure of the bacterial communities and isolate bacteria from their environments. Therefore, this chapter describes a comprehensive strategy where the methods are sequentially applied to identify and isolate epiphytic and endophytic PGPB from a particular environmental sample. However, a single procedure can also be employed to identify and isolate a specific type of PGPB.
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Affiliation(s)
- Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
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2
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Park JW, Braswell WE, Kunta M. Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease. PLANTS (BASEL, SWITZERLAND) 2023; 13:80. [PMID: 38202388 PMCID: PMC10781011 DOI: 10.3390/plants13010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.
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Affiliation(s)
- Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostic Laboratory, USDA APHIS PPQ S&T, Edinburg, TX 78541, USA
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [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: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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Singh S, Aghdam SA, Lahowetz RM, Brown AMV. Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions. ENVIRONMENTAL MICROBIOME 2023; 18:36. [PMID: 37085932 PMCID: PMC10120106 DOI: 10.1186/s40793-023-00493-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microbiomes are critical to plants, promoting growth, elevating stress tolerance, and expanding the plant's metabolic repertoire with novel defense pathways. However, generally microbiomes within plant tissues, which intimately interact with their hosts, remain poorly characterized. These endospheres have become a focus in banana (Musa spp.)-an important plant for study of microbiome-based disease protection. Banana is important to global food security, while also being critically threatened by pandemic diseases. Domestication and clonal propagation are thought to have depleted protective microbiomes, whereas wild relatives may hold promise for new microbiome-based biological controls. The goal was to compare metapangenomes enriched from 7 Musa genotypes, including wild and cultivated varieties grown in sympatry, to assess the host associations with root and leaf endosphere functional profiles. RESULTS Density gradients successfully generated culture-free microbial enrichment, dominated by bacteria, with all together 24,325 species or strains distinguished, and 1.7 million metagenomic scaffolds harboring 559,108 predicted gene clusters. About 20% of sequence reads did not match any taxon databases and ~ 62% of gene clusters could not be annotated to function. Most taxa and gene clusters were unshared between Musa genotypes. Root and corm tissues had significantly richer endosphere communities that were significantly different from leaf communities. Agrobacterium and Rhizobium were the most abundant in all samples while Chitinophagia and Actinomycetia were more abundant in roots and Flavobacteria in leaves. At the bacterial strain level, there were > 2000 taxa unique to each of M. acuminata (AAA genotype) and M. balbisiana (B-genotype), with the latter 'wild' relatives having richer taxa and functions. Gene ontology functional enrichment showed core beneficial functions aligned with those of other plants but also many specialized prospective beneficial functions not reported previously. Some gene clusters with plant-protective functions showed signatures of phylosymbiosis, suggesting long-standing associations or heritable microbiomes in Musa. CONCLUSIONS Metapangenomics revealed key taxa and protective functions that appeared to be driven by genotype, perhaps contributing to host resistance differences. The recovery of rich novel taxa and gene clusters provides a baseline dataset for future experiments in planta or in vivo bacterization or engineering of wild host endophytes.
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Affiliation(s)
- Simrandeep Singh
- Department of Microbiology, University of Illinois, Urbana, IL USA
| | - Shiva A. Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
| | - Rachel M. Lahowetz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Amanda M. V. Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
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Ayilara MS, Adeleke BS, Babalola OO. Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria. MICROBIAL ECOLOGY 2023; 85:1113-1135. [PMID: 36319743 PMCID: PMC10156819 DOI: 10.1007/s00248-022-02136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.
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Affiliation(s)
- Modupe Stella Ayilara
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Bartholomew Saanu Adeleke
- Department of Biological Sciences, Microbiology Unit, Faculty of Science, Olusegun Agagu University of Science and Technology, PMB 353, Okitipupa, Nigeria
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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Yang S, Lee J, Mahmood M, Min D, Im J. Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples. J Microbiol Methods 2023; 206:106677. [PMID: 36716930 DOI: 10.1016/j.mimet.2023.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
Analysis of microbial communities in the epiphytic phyllosphere can be challenging, especially when applying sequencing-based techniques, owing to the interference of plant-derived biomolecules such as nucleic acids. A review of recent studies on the epiphytic microbiome revealed that both mechanical and enzymatic lysis methods are widely used. Here, we evaluated the effects of the two lysis methods on DNA extraction yield, purity, integrity, and microbial 16S rRNA gene copy number per ng of template genomic DNA under different extraction conditions. Furthermore, the effect on bacterial community composition, diversity, and reproducibility was examined using 16S rRNA gene amplicon sequencing. The enzymatic lysis method yielded one to two orders of magnitude more DNA, but the DNA quality was suboptimal. Conversely, the samples prepared using the mechanical method showed high DNA purity albeit lower yield. Unexpectedly, mechanical lysis showed a higher DNA integrity number (DIN) than enzymatic lysis. The 16S rRNA amplicon sequencing results demonstrated that the samples prepared via mechanical disruption exhibited reproducibly similar microbial community compositions regardless of the extraction conditions. In contrast, the enzymatic lysis method resulted in inconsistent taxonomic compositions under different extraction conditions. This study demonstrates that mechanical DNA disruption is more suitable for epiphytic phyllosphere samples than enzymatic disruption.
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Affiliation(s)
- Seongmin Yang
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Jaejin Lee
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - Maheen Mahmood
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Jeongdae Im
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA.
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Zhang S, Sun C, Liu X, Liang Y. Enriching the endophytic bacterial microbiota of Ginkgo roots. Front Microbiol 2023; 14:1163488. [PMID: 37138610 PMCID: PMC10150934 DOI: 10.3389/fmicb.2023.1163488] [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: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 05/05/2023] Open
Abstract
Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.
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Affiliation(s)
- Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, Hunan, China
- *Correspondence: Yili Liang
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Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-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: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
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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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In Vivo Evidence of Single 13C and 15N Isotope-Labeled Methanotrophic Nitrogen-Fixing Bacterial Cells in Rice Roots. mBio 2022; 13:e0125522. [PMID: 35608299 PMCID: PMC9239180 DOI: 10.1128/mbio.01255-22] [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] [Indexed: 11/20/2022] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an ecological role in methane and nitrogen fluxes because they are capable of nitrogen fixation and methane oxidation, as indicated by genomic and cultivation-dependent studies. However, the chemical relationships between methanotrophy and diazotrophy and aerobic and anaerobic reactions, respectively, in methanotrophs remain unclear. No study has demonstrated the cooccurrence of both bioactivities in a single methanotroph bacterium in its natural environment. Here, we demonstrate that both bioactivities in type II methanotrophs occur at the single-cell level in the root tissues of paddy rice (Oryza sativa L. cv. Nipponbare). We first verified that difluoromethane, an inhibitor of methane monooxygenase, affected methane oxidation in rice roots. The results indicated that methane assimilation in the roots mostly occurred due to oxygen-dependent processes. Moreover, the results indicated that methane oxidation-dependent and methane oxidation-independent nitrogen fixation concurrently occurred in bulk root tissues. Subsequently, we performed fluorescence in situ hybridization and NanoSIMS analyses, which revealed that single cells of type II methanotrophs (involving six amplicon sequence variants) in paddy rice roots simultaneously and logarithmically fixed stable isotope gases 15N2 and 13CH4 during incubation periods of 0, 23, and 42 h, providing in vivo functional evidence of nitrogen fixation in methanotrophic cells. Furthermore, 15N enrichment in type II methanotrophs at 42 h varied among cells with an increase in 13C accumulation, suggesting that either the release of fixed nitrogen into root systems or methanotroph metabolic specialization is dependent on different microenvironmental niches in the root.
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HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS Genet 2022; 18:e1009776. [PMID: 35286304 PMCID: PMC8947609 DOI: 10.1371/journal.pgen.1009776] [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: 08/10/2021] [Revised: 03/24/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. ENVIRONMENTAL MICROBIOME 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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Choi B, Jeong S, Kim E. Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species,
Capsella bursa‐pastoris. Ecol Evol 2022; 12:e8683. [PMID: 35309752 PMCID: PMC8901890 DOI: 10.1002/ece3.8683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 12/26/2022] Open
Affiliation(s)
- Byungwook Choi
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
| | - Seorin Jeong
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
| | - Eunsuk Kim
- School of Earth Sciences and Environmental Engineering Gwangju Institute of Science and Technology Gwangju South Korea
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Jia J, Ford E, Hobbs SM, Baird SM, Lu SE. Occidiofungin Is the Key Metabolite for Antifungal Activity of the Endophytic Bacterium Burkholderia sp. MS455 Against Aspergillus flavus. PHYTOPATHOLOGY 2022; 112:481-491. [PMID: 34433293 DOI: 10.1094/phyto-06-21-0225-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aflatoxin is a secondary metabolite produced by Aspergillus fungi and presents a major food safety concern globally. Among the available methods for prevention and control of aflatoxin, the application of antifungal bacteria has gained favor in recent years. An endophytic bacterium MS455, isolated from soybean, exhibited broad-spectrum antifungal activity against economically important pathogens, including Aspergillus flavus. MS455 was identified as a strain of Burkholderia based on genomic analysis. Random and site-specific mutations were used in discovery of the genes that share high homology to the ocf gene cluster of Burkholderia contaminans strain MS14, which is responsible for production of the antifungal compound occidiofungin. RNA sequencing analysis demonstrated that ORF1, a homolog to the ambR1 LuxR-type regulatory gene, regulates occidiofungin biosynthesis in MS455. Additionally, 284 differentially expressed genes, including 138 upregulated and 146 downregulated genes, suggesting that, in addition to its role in occidiofungin production, ORF1 is involved in expression of multiple genes, especially those involved in ornibactin biosynthesis. Plate bioassays showed the growth of A. flavus was significantly inhibited by the wild-type strain MS455 as compared with the ORF1 mutant. Similarly, corn kernel assays showed that growth of A. flavus and aflatoxin production were reduced significantly by MS455 as compared with buffer control and the ORF1 mutant. Collectively, the results demonstrated that production of occidiofungin is essential for antifungal activity of the endophytic bacterium MS455. This research has provided insights about antifungal mechanisms of MS455 and development of biological approaches to prevent aflatoxin contamination in plant production.
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Affiliation(s)
- Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Emerald Ford
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Sarah M Hobbs
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Sonya M Baird
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
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15
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Feng H, Guo J, Ma X, Han M, Kneeshaw D, Sun H, Malghani S, Chen H, Wang W. Methane emissions may be driven by hydrogenotrophic methanogens inhabiting the stem tissues of poplar. THE NEW PHYTOLOGIST 2022; 233:182-193. [PMID: 34617594 DOI: 10.1111/nph.17778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Living trees in forests emit methane (CH4 ) from their stems. However, the magnitudes, patterns, drivers, origins, and biogeochemical pathways of these emissions remain poorly understood. We measured in situ CH4 fluxes in poplar stems and soils using static chambers and investigated the microbial communities of heartwood and sapwood by sequencing bacterial 16S, archaeal 16S, and fungal ITS rRNA genes. Methane emissions from poplar stems occurred throughout the sampling period. The mean CH4 emission rate was 2.7 mg m-2 stem d-1 . Stem CH4 emission rate increased significantly with air temperature, humidity, soil water content, and soil CH4 fluxes, but decreased with increasing sampling height. The CO2 reduction and methylotrophic methanogenesis were the major methanogenic pathways in wood tissues. The dominant methanogen groups detected in stem tissues were Methanobacterium, Methanobrevibacter, Rice Cluster I, Methanosarcina, Methanomassiliicoccus, Methanoculleus, and Methanomethylophilaceae. In addition, three methanotrophic genera were identified in the heartwood and sapwood - Methylocystis, Methylobacterium, and Paracoccus. Overall, stem CH4 emissions can originate directly from the internal tissues or co-occur from soils and stems. The co-existence of methanogens and methanotrophs within heartwood and sapwood highlights a need for future research in the microbial mechanisms underlying stem CH4 exchange with the atmosphere.
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Affiliation(s)
- Huili Feng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Jiahuan Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Xuehong Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Menghua Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Daniel Kneeshaw
- Department of Biological Sciences, University of Quebec at Montreal, Montreal, QC, H3C 3P8, Canada
| | - Hui Sun
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Saadatullah Malghani
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Weifeng Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
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16
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Kihara S, Yamamoto K, Hisatomi A, Shiwa Y, Chu CC, Takada K, Ouyabe M, Pachakkil B, Kikuno H, Tanaka N, Shiwachi H. Bacterial Community of Water Yam (<i>Dioscorea alata</i> L.) cv. A-19. Microbes Environ 2022; 37. [PMID: 35527002 PMCID: PMC9530735 DOI: 10.1264/jsme2.me21062] [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] [Indexed: 11/16/2022] Open
Abstract
The bacterial community of water yam (Dioscorea alata L.) cv. A-19 is vital because it may promote plant growth without the need for fertilization. However, the influence of fertilization practices on the composition and proportion of the bacterial community of water yam cv. A-19 has not yet been extensively examined. Therefore, we herein investigated the diversity and composition of the bacterial community of water yam cv. A-19 cultivated with and without chemical fertilization using amplicon community profiling based on 16S rRNA gene sequences. No significant difference was detected in the growth of plants cultivated with or without chemical fertilization. Alpha diversity indices were significantly dependent on each compartment, and a decrease was observed in indices from the belowground (rhizosphere and root) to aboveground compartments (stem and leaf). The bacterial composition of each compartment was clustered into three groups: bulk soil, rhizosphere and root, and stem and leaf. Chemical fertilization did not significantly influence the diversity or composition of the water yam cv. A-19 bacterial community. It remained robust in plants cultivated with chemical fertilization. The amplicon community profiling of bacterial communities also revealed the dominance of two bacterial clades, the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade and Burkholderia-Caballeronia-Paraburkholderia clade, with and without chemical fertilization. This is the first study to characterize the bacterial community of water yam cv. A-19 cultivated with and without chemical fertilization.
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Affiliation(s)
- Shunta Kihara
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
| | - Kosuke Yamamoto
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Atsushi Hisatomi
- Department of Ecological Symbiotic Science, Graduate school of Agriculture, Tokyo University of Agriculture
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Chia-Cheng Chu
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
| | - Kanako Takada
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
| | - Michel Ouyabe
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
| | - Babil Pachakkil
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
| | - Hidehiko Kikuno
- Miyako Subtropical Training and Research Farm, Tokyo University of Agriculture
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Hironobu Shiwachi
- Department of International Agricultural Development, Graduate School of International Food and Agricultural Studies, Tokyo University of Agriculture
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17
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He YH, Adkar-Purushothama CR, Ito T, Shirakawa A, Yamamoto H, Kashiwagi A, Tatewaki A, Fujibayashi M, Sugiyama S, Yaginuma K, Akahira T, Yamamoto S, Tsushima S, Matsushita Y, Sano T. Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged "Natural Farming" Practices. Microorganisms 2021; 9:microorganisms9102056. [PMID: 34683377 PMCID: PMC8540600 DOI: 10.3390/microorganisms9102056] [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: 08/26/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/03/2022] Open
Abstract
Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard.
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Affiliation(s)
- Ying-Hong He
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Charith Raj Adkar-Purushothama
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
- RNA Group/Groupe ARN, Département de Biochimie, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Tsutae Ito
- Division of Apple Research, Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Morioka 020-0123, Japan; (T.I.); (K.Y.)
| | - Asuka Shirakawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Hideki Yamamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
- Correspondence: (A.K.); (T.S.)
| | - Ayumu Tatewaki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Misato Fujibayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Shuichi Sugiyama
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
| | - Katsuhiko Yaginuma
- Division of Apple Research, Institute of Fruit Tree and Tea Science (NIFTS), National Agriculture and Food Research Organization (NARO), Morioka 020-0123, Japan; (T.I.); (K.Y.)
| | - Tomoya Akahira
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center, Kuroishi 036-0332, Japan; (T.A.); (S.Y.)
| | - Shingen Yamamoto
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center, Kuroishi 036-0332, Japan; (T.A.); (S.Y.)
- Japan Fisheries Research and Education Agency, Fisheries Technology Institute, Fisheries Engineering Division, Kamisu 314-0408, Japan
| | - Seiya Tsushima
- National Agro-Environment Research Institute, Tsukuba 305-0856, Japan; (S.T.); (Y.M.)
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi 243-0034, Japan
| | - Yuko Matsushita
- National Agro-Environment Research Institute, Tsukuba 305-0856, Japan; (S.T.); (Y.M.)
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan; (Y.-H.H.); (C.R.A.-P.); (A.S.); (H.Y.); (A.T.); (M.F.); (S.S.)
- Correspondence: (A.K.); (T.S.)
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18
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Saldierna Guzmán JP, Reyes-Prieto M, Hart SC. Characterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting Endophyte. Front Microbiol 2021; 12:687971. [PMID: 34512566 PMCID: PMC8425249 DOI: 10.3389/fmicb.2021.687971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022] Open
Abstract
The rapidly increasing global population and anthropogenic climate change have created intense pressure on agricultural systems to produce increasingly more food under steadily challenging environmental conditions. Simultaneously, industrial agriculture is negatively affecting natural and agricultural ecosystems because of intensive irrigation and fertilization to fully utilize the potential of high-yielding cultivars. Growth-promoting microbes that increase stress tolerance and crop yield could be a useful tool for helping mitigate these problems. We investigated if commercially grown almonds might be a resource for plant colonizing bacteria with growth promotional traits that could be used to foster more productive and sustainable agricultural ecosystems. We isolated an endophytic bacterium from almond leaves that promotes growth of the model plant Arabidopsis thaliana. Genome sequencing revealed a novel Erwinia gerundensis strain (A4) that exhibits the ability to increase access to plant nutrients and to produce the stress-mitigating polyamine spermidine. Because E. gerundensis is known to be able to colonize diverse plant species including cereals and fruit trees, A4 may have the potential to be applied to a wide variety of crop systems.
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Affiliation(s)
- J Paola Saldierna Guzmán
- Quantitative and Systems Biology, University of California, Merced, Merced, CA, United States.,Sierra Nevada Research Institute, University of California, Merced, Merced, CA, United States
| | - Mariana Reyes-Prieto
- Evolutionary Systems Biology of Symbionts, Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council (CSIC), Valencia, Spain.,Sequencing and Bioinformatics Service of the Foundation for the Promotion of Health and Biomedical Research of the Valencia Region (FISABIO), Valencia, Spain
| | - Stephen C Hart
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA, United States.,Department of Life and Environmental Sciences, University of California, Merced, Merced, CA, United States
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19
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Jia J, Ford E, Baird SM, Lu SE. Complete Genome Sequence Resource for the Endophytic Burkholderia sp. Strain MS389 Isolated from a Healthy Soybean Growing Adjacent to Charcoal Rot Disease Patch. PLANT DISEASE 2021; 105:2704-2707. [PMID: 33876648 DOI: 10.1094/pdis-02-21-0377-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Burkholderia sp. strain MS389, an endophytic bacterium, was isolated from a healthy soybean plant growing adjacent to a patch of plants affected by charcoal rot disease, caused by the fungal pathogen Macrophomina phaseolina. Preliminary studies demonstrated that strain MS389 possesses antimicrobial activities against multiple plant pathogens. Burkholderia sp. strain MS389 was found to have three circular chromosomes of 3,563,380 bp, 3,002,449 bp, and 1,180,421 bp in size, respectively. The 7,746,250-bp genome, with 66.73% G+C content, harbors 6,756 protein coding genes in the predicted 6,985 genes. In total, 18 rRNAs, 68 tRNAs, and four ncRNAs were identified and 139 pseudogenes were annotated as well. The findings of this study will provide valuable data to explore the antimicrobial mechanisms of the endophytic bacterial strain.
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Affiliation(s)
- Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Emerald Ford
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Sonya M Baird
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
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20
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Okazaki K, Tsurumaru H, Hashimoto M, Takahashi H, Okubo T, Ohwada T, Minamisawa K, Ikeda S. Community Analysis-based Screening of Plant Growth-promoting Bacteria for Sugar Beet. Microbes Environ 2021; 36. [PMID: 33907063 PMCID: PMC8209457 DOI: 10.1264/jsme2.me20137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.
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Affiliation(s)
- Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | | | - Hiroyuki Takahashi
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine
| | | | - Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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21
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Wassermann B, Rybakova D, Adam E, Zachow C, Bernhard M, Müller M, Mancinelli R, Berg G. Studying Seed Microbiomes. Methods Mol Biol 2021; 2232:1-21. [PMID: 33161534 DOI: 10.1007/978-1-0716-1040-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recent studies indicate that seed microbiomes affect germination and plant performance. However, the interplay between seed microbiota and plant health is still poorly understood. To get a complete picture of the system, a comprehensive analysis is required, comprising culture-dependent and culture-independent techniques. In this chapter, we provide a combination of methods that are established and optimized for the analysis of the seed microbiome. These include methods to: (1) activate and cultivate dormant seed microbiota, (2) analyze microbiota in germinated seeds (with and without substrate), (3) quantify microbial DNA via real-time PCR, (4) deplete host DNA for amplicon and metagenome analysis, and (5) visualize seed endophytes in microtomed sections using fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). A deep understanding of the seed microbiome and its functions can help in developing new seed treatments and breeding strategies for sustainable agriculture.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Eveline Adam
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Maria Bernhard
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Maria Müller
- Department of Plant Sciences, Institute of Biology, NAWI Graz, University of Graz, Graz, Austria
| | - Riccardo Mancinelli
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
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22
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Tveit AT, Kiss A, Winkel M, Horn F, Hájek T, Svenning MM, Wagner D, Liebner S. Environmental patterns of brown moss- and Sphagnum-associated microbial communities. Sci Rep 2020; 10:22412. [PMID: 33376244 PMCID: PMC7772339 DOI: 10.1038/s41598-020-79773-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022] Open
Abstract
Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (< 1% of all operational taxonomic units (OTUs)) but strikingly abundant (up to 65% of relative abundance) OTUs. This core community overlapped by one third with the Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.
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Affiliation(s)
- Alexander Tøsdal Tveit
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | - Andrea Kiss
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Tomáš Hájek
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Mette Marianne Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | - Dirk Wagner
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany
- University of Potsdam, Institute of Geosciences, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Center for Geosciences, Section Geomicrobiology, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany.
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23
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Garcias-Bonet N, Eguíluz VM, Díaz-Rúa R, Duarte CM. Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environ Microbiol 2020; 23:2021-2034. [PMID: 33225561 DOI: 10.1111/1462-2920.15334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, E-07122, Spain
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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24
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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25
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Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 2020; 366:606-612. [PMID: 31672892 DOI: 10.1126/science.aaw9285] [Citation(s) in RCA: 435] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/21/2019] [Accepted: 09/17/2019] [Indexed: 01/20/2023]
Abstract
Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
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Affiliation(s)
- Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Juan Perez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,PECET, University of Antioquia, Medellín, Antioquia 050010, Colombia
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Daniel Ruiz-Buck
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Wilfred F J van Ijcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, 3025 CN Rotterdam, Netherlands
| | - Ruth Gomez-Exposito
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Somayah S Elsayed
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Adini Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340, Km 127.5, 13820-000 Jaguariúna, Brazil
| | - Gilles P van Wezel
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands.
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands. .,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
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26
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Johnston‐Monje D, Lopez Mejia J. Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11334. [PMID: 32351795 PMCID: PMC7186905 DOI: 10.1002/aps3.11334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/28/2020] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.
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Affiliation(s)
- David Johnston‐Monje
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
- Max Planck Institute for Plant Breeding ResearchDepartment of Plant Microbe InteractionsCarl-von-Linne-Weg 10D-50829CologneGermany
| | - Jessica Lopez Mejia
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
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27
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Matthews A, Pierce S, Hipperson H, Raymond B. Rhizobacterial Community Assembly Patterns Vary Between Crop Species. Front Microbiol 2019; 10:581. [PMID: 31019492 PMCID: PMC6458290 DOI: 10.3389/fmicb.2019.00581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/06/2019] [Indexed: 02/01/2023] Open
Abstract
Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.
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Affiliation(s)
- Andrew Matthews
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Sarah Pierce
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom.,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Helen Hipperson
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom.,Department of Animal and Plant Sciences, P3 Institute for Plant and Soil Biology, The University of Sheffield, Sheffield, United Kingdom
| | - Ben Raymond
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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28
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Barba J, Bradford MA, Brewer PE, Bruhn D, Covey K, van Haren J, Megonigal JP, Mikkelsen TN, Pangala SR, Pihlatie M, Poulter B, Rivas-Ubach A, Schadt CW, Terazawa K, Warner DL, Zhang Z, Vargas R. Methane emissions from tree stems: a new frontier in the global carbon cycle. THE NEW PHYTOLOGIST 2019; 222:18-28. [PMID: 30394559 DOI: 10.1111/nph.15582] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4 ). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH4 emissions and trace their potential origin. We identified the need: (1) for both long-term, high-frequency measurements of stem CH4 emissions to understand the fine-scale processes, alongside rapid large-scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (3) to develop a mechanistic model including passive and active transport of CH4 from the soil-tree-atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH4 emissions, and allow for the integration of pathways and mechanisms of CH4 production and emissions into process-based models. These advances will facilitate the upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local to global CH4 budget.
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Affiliation(s)
- Josep Barba
- Plant and Soil Sciences Department, University of Delaware, Newark, DE, 19711, USA
| | - Mark A Bradford
- School of Forestry and Environmental Studies, Yale University, New Haven, CT, 06511, USA
| | - Paul E Brewer
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Dan Bruhn
- Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg, Denmark
| | - Kristofer Covey
- School of Forestry and Environmental Studies, Yale University, New Haven, CT, 06511, USA
- Environmental Studies and Sciences Program, Skidmore College, NY, 12866, USA
- Skidmore College, Dana Science Center, Saratoga Springs, NY, 12866, USA
| | - Joost van Haren
- Biosphere 2 and Honors College, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Teis Nørgaard Mikkelsen
- Department of Environmental Engineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Sunitha R Pangala
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster, LA1 4YQ, UK
| | - Mari Pihlatie
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, 00014, Helsinki, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, 00560, Helsinki, Finland
| | - Ben Poulter
- Biospheric Sciences Laboratory, NASA GSFC, Greenbelt, MD, 20771, USA
| | - Albert Rivas-Ubach
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Kazuhiko Terazawa
- Department of Northern Biosphere Agriculture, Tokyo University of Agriculture, 099-2493, Abashiri, Japan
| | - Daniel L Warner
- Plant and Soil Sciences Department, University of Delaware, Newark, DE, 19711, USA
| | - Zhen Zhang
- Department of Geographical Sciences, University of Maryland, College Park, MD, 20740, USA
| | - Rodrigo Vargas
- Plant and Soil Sciences Department, University of Delaware, Newark, DE, 19711, USA
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29
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Hara S, Morikawa T, Wasai S, Kasahara Y, Koshiba T, Yamazaki K, Fujiwara T, Tokunaga T, Minamisawa K. Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses. Front Microbiol 2019; 10:407. [PMID: 30915047 PMCID: PMC6422874 DOI: 10.3389/fmicb.2019.00407] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/15/2019] [Indexed: 02/04/2023] Open
Abstract
Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using “omics” approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9–3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.
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Affiliation(s)
- Shintaro Hara
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takashi Morikawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sawa Wasai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | | | - Kiyoshi Yamazaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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30
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Cordovez V, Schop S, Hordijk K, Dupré de Boulois H, Coppens F, Hanssen I, Raaijmakers JM, Carrión VJ. Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp. Appl Environ Microbiol 2018; 84:e01865-18. [PMID: 30194105 PMCID: PMC6210106 DOI: 10.1128/aem.01865-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/04/2018] [Indexed: 12/23/2022] Open
Abstract
Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here, we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only briefly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific; that is, exposure of roots to volatiles from EC8 led to an increase in plant biomass, whereas shoot exposure resulted in no or less growth promotion. Gas chromatography-quadrupole time of flight mass spectometry (GC-QTOF-MS) analysis revealed that EC8 produces a wide array of sulfur-containing compounds, as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent, with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed upregulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion, most likely via modulation of sulfur and nitrogen metabolism.IMPORTANCE In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance the growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction or root colonization and survival of the microbial inoculant.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Sharella Schop
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Kees Hordijk
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Hervé Dupré de Boulois
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
- R&D Department, DCM nv, Grobbendonk, Belgium
| | - Filip Coppens
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
| | - Inge Hanssen
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
- R&D Department, DCM nv, Grobbendonk, Belgium
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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31
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Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China. Syst Appl Microbiol 2018; 41:516-527. [PMID: 29934111 DOI: 10.1016/j.syapm.2018.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/24/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Actinobacteria from special habitats are of interest due to their producing of bioactive compounds and diverse ecological functions. However, little is known of the diversity and functional traits of actinobacteria inhabiting coastal salt marsh soils. We assessed actinobacterial diversity from eight coastal salt marsh rhizosphere soils from Jiangsu Province, China, using culture-based and 16S rRNA gene high throughput sequencing (HTS) methods, in addition to evaluating their plant growth-promoting (PGP) traits of isolates. Actinobacterial sequences represented 2.8%-43.0% of rhizosphere bacterial communities, as determined by HTS technique. The actinobacteria community comprised 34 families and 79 genera. In addition, 196 actinobacterial isolates were obtained, of which 92 representative isolates were selected for further 16S rRNA gene sequencing and phylogenetic analysis. The 92 strains comprised seven suborders, 12 families, and 20 genera that included several potential novel species. All representative strains were tested for their ability of producing indole acetic acid (IAA), siderophores, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), hydrolytic enzymes, and phosphate solubilization. Based on the presence of multiple PGP traits, two strains, Streptomyces sp. KLBMP S0051 and Micromonospora sp. KLBMP S0019 were selected for inoculation of wheat seeds grown under salt stress. Both strains promoted seed germination, and KLBMP S0019 significantly enhanced seedling growth under NaCl stress. Our study demonstrates that coastal salt marsh rhizosphere soils harbor a diverse reservoir of actinobacteria that are potential resources for the discovery of novel species and functions. Moreover, several of the isolates identified here are good candidates as PGP bacteria that may contribute to plant adaptions to saline soils.
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32
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Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET. Core microbiomes for sustainable agroecosystems. NATURE PLANTS 2018; 4:247-257. [PMID: 29725101 DOI: 10.1038/s41477-018-0139-4] [Citation(s) in RCA: 370] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/23/2018] [Indexed: 05/18/2023]
Abstract
In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Masato Yamamichi
- Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan
| | - Kazuhiko Narisawa
- Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Kei Hiruma
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinji Fukuda
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shinji Nakaoka
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Yoshida
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
- Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China
| | - Ryo Sugiura
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan
| | - Yasunori Ichihashi
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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Dos-Santos CM, de Souza DG, Balsanelli E, Cruz LM, de Souza EM, Baldani JI, Schwab S. A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization. MICROBIAL ECOLOGY 2017; 74:453-465. [PMID: 28160057 DOI: 10.1007/s00248-017-0941-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/19/2017] [Indexed: 05/16/2023]
Abstract
Bacterial endophytes constitute a very diverse community and they confer important benefits which help to improve agricultural yield. Some of these benefits remain underexplored or little understood, mainly due to the bottlenecks associated with the plant feature, a low number of endophytic bacterial cells in relation to the plant, and difficulties in accessing these bacteria using cultivation-independent methods. Enriching endophytic bacterial cells from plant tissues, based on a non-biased, cultivation-independent physical enrichment method, may help to circumvent those problems, especially in the case of sugarcane stems, which have a high degree of interfering factors, such as polysaccharides, phenolic compounds, nucleases, and fibers. In the present study, an enrichment approach for endophytic bacterial cells from sugarcane lower stems is described. The results demonstrate that the enriched bacterial cells are suitable for endophytic community characterization. A community analysis revealed the presence of previously well-described but also novel endophytic bacteria in sugarcane tissues which may exert functions such as plant growth promotion and biological control, with a predominance of the Proteobacterial phylum, but also Actinobacteria, Bacteroidetes, and Firmicutes, among others. In addition, by comparing the present and literature data, it was possible to list the most frequently detected bacterial endophyte genera in sugarcane tissues. The presented enrichment approach paves the way for improved future research toward the assessment of endophytic bacterial community in sugarcane and other biofuel crops.
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Affiliation(s)
- Carlos M Dos-Santos
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23897-000, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Daniel G de Souza
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
- Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - José I Baldani
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil.
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Minami T, Anda M, Mitsui H, Sugawara M, Kaneko T, Sato S, Ikeda S, Okubo T, Tsurumaru H, Minamisawa K. Metagenomic Analysis Revealed Methylamine and Ureide Utilization of Soybean-Associated Methylobacterium. Microbes Environ 2016; 31:268-78. [PMID: 27431374 PMCID: PMC5017803 DOI: 10.1264/jsme2.me16035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 01/29/2023] Open
Abstract
Methylobacterium inhabits the phyllosphere of a large number of plants. We herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in Tohoku University (Kashimadai, Miyagi, Japan). Methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. We classified plant-derived Methylobacterium species into Groups I, II, and III based on 16S rRNA gene sequences, and found that Group I members (phylogenetically close to M. extorquens) were dominant in soybean-associated Methylobacterium. By comparing 29 genomes, we found that all Group I members possessed a complete set of genes for the N-methylglutamate pathway for methylamine utilization, and genes for urea degradation (urea carboxylase, urea amidolyase, and conventional urease). Only Group I members and soybean methylobacterial isolates grew in a culture supplemented with methylamine as the sole carbon source. They utilized urea or allantoin (a urea-related compound in legumes) as the sole nitrogen source; however, group III also utilized these compounds. The utilization of allantoin may be crucial in soybean-bacterial interactions because allantoin is a transported form of fixed nitrogen in legume plants. Soybean-derived Group I strain AMS5 colonized the model legume Lotus japonicus well. A comparison among the 29 genomes of plant-derived and other strains suggested that several candidate genes are involved in plant colonization such as csgG (curli fimbriae). Genes for the N-methylglutamate pathway and curli fimbriae were more abundant in soybean microbiomes than in rice microbiomes in the field. Based on these results, we discuss the lifestyle of Methylobacterium in the legume phyllosphere.
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Affiliation(s)
- Tomoyuki Minami
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Misue Anda
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Takakazu Kaneko
- Kazusa DNA Research Institute2–6–7 Kazusa-kamatari, Kisarazu, Chiba 292–0818Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
- Kazusa DNA Research Institute2–6–7 Kazusa-kamatari, Kisarazu, Chiba 292–0818Japan
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Takashi Okubo
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Hirohito Tsurumaru
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai 980–85577Japan
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Utturkar SM, Cude WN, Robeson MS, Yang ZK, Klingeman DM, Land ML, Allman SL, Lu TYS, Brown SD, Schadt CW, Podar M, Doktycz MJ, Pelletier DA. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis. Appl Environ Microbiol 2016; 82:5698-708. [PMID: 27422831 PMCID: PMC5007785 DOI: 10.1128/aem.01285-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria. IMPORTANCE Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses of genomes of uncultured bacteria to provide genomics information that will facilitate future cultivation attempts.
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Affiliation(s)
- Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - W Nathan Cude
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin K Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steve L Allman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture. Biotechnol Adv 2016; 34:1245-1259. [PMID: 27587331 DOI: 10.1016/j.biotechadv.2016.08.005] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/15/2023]
Abstract
Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions.
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Law AD, Fisher C, Jack A, Moe LA. Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community. MICROBIAL ECOLOGY 2016; 72:120-129. [PMID: 27023797 DOI: 10.1007/s00248-016-0754-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
Tobacco-specific nitrosamines are carcinogenic N-nitrosamine compounds present at very low levels in freshly harvested tobacco leaves that accumulate during leaf curing. Formation of N-nitrosamine compounds is associated with high nitrate levels in the leaf at harvest, and nitrate is presumed to be the source from which the N-nitrosation species originates. More specifically, nitrite is considered to be a direct precursor, and nitrite is linked with N-nitrosation in many environmental matrices where it occurs via microbial nitrate reduction. Here, we initiate work exploring the role of leaf microbial communities in formation of tobacco-specific nitrosamines. Leaves from burley tobacco line TN90H were air cured under various temperature and relative humidity levels, and 22 cured tobacco samples were analyzed for their microbial communities and leaf chemistry. Analysis of nitrate, nitrite, and total tobacco-specific nitrosamine levels revealed a strong positive correlation between the three variables, as well as a strong positive correlation with increasing relative humidity during cure conditions. 16S rRNA gene amplicon sequencing was used to assess microbial communities in each of the samples. In most samples, Proteobacteria predominated at the phylum level, accounting for >90 % of the OTUs. However, a distinct shift was noted among members of the high tobacco-specific nitrosamine group, with increases in Firmicutes and Actinobacteria. Several OTUs were identified that correlate strongly (positive and negative) with tobacco-specific nitrosamine content. Copy number of bacterial nitrate reductase genes, obtained using quantitative PCR, did not correlate strongly with tobacco-specific nitrosamine content. Incomplete denitrification is potentially implicated in tobacco-specific nitrosamine levels.
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Affiliation(s)
- Audrey D Law
- Department of Plant & Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Colin Fisher
- Kentucky Tobacco Research & Development Center, University of Kentucky, Lexington, KY, 40546-0236, USA
| | - Anne Jack
- Kentucky Tobacco Research & Development Center, University of Kentucky, Lexington, KY, 40546-0236, USA
| | - Luke A Moe
- Department of Plant & Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA.
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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Saleem M, Law AD, Moe LA. Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes. MICROBIAL ECOLOGY 2016; 71:469-72. [PMID: 26391804 DOI: 10.1007/s00248-015-0672-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 05/06/2023]
Abstract
Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community.
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Affiliation(s)
- Muhammad Saleem
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA.
| | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA.
| | - Luke A Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA.
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40
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Kanno M, Constant P, Tamaki H, Kamagata Y. Detection and isolation of plant-associated bacteria scavenging atmospheric molecular hydrogen. Environ Microbiol 2016; 18:2495-506. [PMID: 26636257 DOI: 10.1111/1462-2920.13162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/21/2015] [Accepted: 11/27/2015] [Indexed: 11/28/2022]
Abstract
High-affinity hydrogen (H2 )-oxidizing bacteria possessing group 5 [NiFe]-hydrogenase genes are important contributors to atmospheric H2 uptake in soil environments. Although previous studies reported the occurrence of a significant H2 uptake activity in vegetation, there has been no report on the identification and diversity of the responsible microorganisms. Here, we show the existence of plant-associated bacteria with the ability to consume atmospheric H2 that may be a potential energy source required for their persistence in plants. Detection of the gene hhyL - encoding the large subunit of group 5 [NiFe]-hydrogenase - in plant tissues showed that plant-associated high-affinity H2 -oxidizing bacteria are widely distributed in herbaceous plants. Among a collection of 145 endophytic isolates, seven Streptomyces strains were shown to possess hhyL gene and exhibit high- or intermediate-affinity H2 uptake activity. Inoculation of Arabidopsis thaliana (thale cress) and Oryza sativa (rice) seedlings with selected isolates resulted in an internalization of the bacteria in plant tissues. H2 uptake activity per bacterial cells was comparable between plant and soil, demonstrating that both environments are favourable for the H2 uptake activity of streptomycetes. This study first demonstrated the occurrence of plant-associated high-affinity H2 -oxidizing bacteria and proposed their potential contribution as atmospheric H2 sink.
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Affiliation(s)
- Manabu Kanno
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
| | - Philippe Constant
- Centre INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, QC, Canada, H7V 1B7
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8562, Japan
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Kobayashi A, Kobayashi YO, Someya N, Ikeda S. Community Analysis of Root- and Tuber-Associated Bacteria in Field-Grown Potato Plants Harboring Different Resistance Levels against Common Scab. Microbes Environ 2015; 30:301-9. [PMID: 26657303 PMCID: PMC4676553 DOI: 10.1264/jsme2.me15109] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eight genotypes of potato plants with different resistance levels against common scab were grown in a field infested with Streptomyces turgidiscabies. DNA was extracted from the roots, tubers, and rhizosphere soils of each of the eight genotypes at the flowering stage, and the quantity of S. turgidiscabies genomic DNA was assessed by real-time PCR using a TaqMan probe. The results obtained showed that the different potato genotypes had significant impacts on the population levels of S. turgidiscabies between resistant and susceptible genotypes in the tubers, but not in the roots or rhizosphere soils. Clone analyses of 16S rRNA gene libraries from the eight potato genotypes identified three phyla (Proteobacteria, Firmicutes, and Actinobacteria) as dominant taxa in root and tuber clone libraries, while a clustering analysis identified 391 operational taxonomic units (OTUs) at the species level. Eleven OTUs closely related to Aquicella siphonis, Arthrobacter nicotinovorans, Streptomyces rishiriensis, Rhodococcus baikonurensis, Rhizobium radiobacter, Rhizobium etli, Phyllobacterium myrsinacearum, Paenibacillus pabuli, Paenibacillus alginolyticus, and Bacillus halmapalus were detected in the root or tuber libraries of all the potato genotypes examined. Furthermore, an abundance of OTUs related to Aquicella and Rhodococcus was observed in the rhizospheres of resistant and susceptible potato genotypes, respectively. Based on this ecological information, an efficient survey may be conducted for biological agents from the potato rhizosphere.
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Affiliation(s)
- Akira Kobayashi
- National Agricultural Research Center for Hokkaido Region, National Agriculture and Food Research Organization
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Ikenaga M, Tabuchi M, Oyama T, Akagi I, Sakai M. Development of LNA oligonucleotide-PCR clamping technique in investigating the community structures of plant-associated bacteria. Biosci Biotechnol Biochem 2015; 79:1556-66. [PMID: 25943373 DOI: 10.1080/09168451.2015.1038213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is major limitation in investigating the community structures of plant-associated bacteria. Although locked nucleic acid (LNA) oligonucleotides was designed to selectively amplify the bacterial small subunit rRNA genes by applying the PCR clamping technique, those for plastids were applicable only for particular plants, while those for mitochondria were available throughout most plants. To widen the applicable range, new LNA oligonucleotides specific for plastids were designed, and the efficacy was investigated. PCR without LNA oligonucleotides predominantly amplified the organelle genes, while bacterial genes were predominantly observed in having applied the LNA oligonucleotides. Denaturing gradient gel electrophoresis (DGGE) analysis displayed additional bacterial DGGE bands, the amplicons of which were prepared using the LNA oligonucleotides. Thus, new designed LNA oligonucleotides specific for plastids were effective and have widened the scope in investigating the community structures of plant-associated bacteria.
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Affiliation(s)
- Makoto Ikenaga
- a Faculty of Agriculture , Kagoshima University , Kagoshima , Japan
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Okubo T, Liu D, Tsurumaru H, Ikeda S, Asakawa S, Tokida T, Tago K, Hayatsu M, Aoki N, Ishimaru K, Ujiie K, Usui Y, Nakamura H, Sakai H, Hayashi K, Hasegawa T, Minamisawa K. Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria. Front Microbiol 2015; 6:136. [PMID: 25750640 PMCID: PMC4335179 DOI: 10.3389/fmicb.2015.00136] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/05/2015] [Indexed: 11/13/2022] Open
Abstract
A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 μmol.mol(-1)) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.
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Affiliation(s)
- Takashi Okubo
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
| | - Dongyan Liu
- Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan
| | - Hirohito Tsurumaru
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
| | - Seishi Ikeda
- Large-scale Farming Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research OrganizationHokkaido, Japan
| | - Susumu Asakawa
- Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan
| | - Takeshi Tokida
- Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Naohiro Aoki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
| | - Ken Ishimaru
- Division of Plant Sciences, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Kazuhiro Ujiie
- Division of Plant Sciences, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Yasuhiro Usui
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | | | - Hidemitsu Sakai
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kentaro Hayashi
- Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Toshihiro Hasegawa
- Agro-Meteorology Division, National Institute for Agro-Environmental SciencesTsukuba, Japan
| | - Kiwamu Minamisawa
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku UniversitySendai, Japan
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Tsurumaru H, Okubo T, Okazaki K, Hashimoto M, Kakizaki K, Hanzawa E, Takahashi H, Asanome N, Tanaka F, Sekiyama Y, Ikeda S, Minamisawa K. Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 2015; 30:63-9. [PMID: 25740621 PMCID: PMC4356465 DOI: 10.1264/jsme2.me14109] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.
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Ikeda S, Tokida T, Nakamura H, Sakai H, Usui Y, Okubo T, Tago K, Hayashi K, Sekiyama Y, Ono H, Tomita S, Hayatsu M, Hasegawa T, Minamisawa K. Characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in CO₂, temperature, and nitrogen levels under field conditions. Microbes Environ 2015; 30:51-62. [PMID: 25740174 PMCID: PMC4356464 DOI: 10.1264/jsme2.me14117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/10/2014] [Indexed: 01/12/2023] Open
Abstract
Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene. Principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by PC1 (61.5%), that was mainly attributed to the high abundance of Planctomycetes in leaf sheaths. Our results also indicated that the community structures of leaf blade-associated bacteria were more sensitive than those of leaf sheath-associated bacteria to the environmental factors examined. Among these environmental factors, LN strongly affected the community structures of leaf blade-associated bacteria by increasing the relative abundance of Bacilli. The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively. The community structures of leaf blade-associated bacteria under the combination of FACE and ET were more similar to those of the control than to those under ET or FACE. Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.
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Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research OrganizationShinsei, Memuro-cho, Kasai-gun, Hokkaido 082–0081Japan
| | - Takeshi Tokida
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | | | - Hidemitsu Sakai
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Yasuhiro Usui
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Takashi Okubo
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577Japan
| | - Kanako Tago
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Kentaro Hayashi
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Yasuyo Sekiyama
- National Food Research Institute, National Agriculture and Food Research Organization2–1–12 Kannondai, Tsukuba, Ibaraki 305–8642Japan
| | - Hiroshi Ono
- National Food Research Institute, National Agriculture and Food Research Organization2–1–12 Kannondai, Tsukuba, Ibaraki 305–8642Japan
| | - Satoru Tomita
- National Food Research Institute, National Agriculture and Food Research Organization2–1–12 Kannondai, Tsukuba, Ibaraki 305–8642Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Toshihiro Hasegawa
- National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577Japan
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Montenegro D, Kalpana K, Chrissian C, Sharma A, Takaoka A, Iacovidou M, Soll CE, Aminova O, Heguy A, Cohen L, Shen S, Kawamura A. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations. Bioorg Med Chem Lett 2015; 25:466-9. [PMID: 25547935 PMCID: PMC4297534 DOI: 10.1016/j.bmcl.2014.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022]
Abstract
Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs.
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Affiliation(s)
- Diego Montenegro
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Kriti Kalpana
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Christine Chrissian
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Ashutosh Sharma
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Anna Takaoka
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Maria Iacovidou
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Clifford E Soll
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
| | - Olga Aminova
- Genome Technology Center, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Adriana Heguy
- Genome Technology Center, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Lisa Cohen
- Genome Technology Center, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Steven Shen
- Genome Technology Center, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, Center for Health Informatics and Bioinformatics, NYU School of Medicine, 227 East 30th Street, New York, NY 10016, USA
| | - Akira Kawamura
- Department of Chemistry, Hunter College of CUNY, 695 Park Avenue, New York, NY 10065, USA
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Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T. Roots shaping their microbiome: global hotspots for microbial activity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:403-24. [PMID: 26243728 DOI: 10.1146/annurev-phyto-082712-102342] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.
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Affiliation(s)
- Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, D-28334 Bremen, Germany; , , , ,
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Tago K, Okubo T, Itoh H, Kikuchi Y, Hori T, Sato Y, Nagayama A, Hayashi K, Ikeda S, Hayatsu M. Insecticide-degrading Burkholderia symbionts of the stinkbug naturally occupy various environments of sugarcane fields in a Southeast island of Japan. Microbes Environ 2014; 30:29-36. [PMID: 25736865 PMCID: PMC4356461 DOI: 10.1264/jsme2.me14124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/11/2014] [Indexed: 11/16/2022] Open
Abstract
The stinkbug Cavelerius saccharivorus, which harbors Burkholderia species capable of degrading the organophosphorus insecticide, fenitrothion, has been identified on a Japanese island in farmers' sugarcane fields that have been exposed to fenitrothion. A clearer understanding of the ecology of the symbiotic fenitrothion degraders of Burkholderia species in a free-living environment is vital for advancing our knowledge on the establishment of degrader-stinkbug symbiosis. In the present study, we analyzed the composition and abundance of degraders in sugarcane fields on the island. Degraders were recovered from field samples without an enrichment culture procedure. Degrader densities in the furrow soil in fields varied due to differences in insecticide treatment histories. Over 99% of the 659 isolated degraders belonged to the genus Burkholderia. The strains related to the stinkbug symbiotic group predominated among the degraders, indicating a selection for this group in response to fenitrothion. Degraders were also isolated from sugarcane stems, leaves, and rhizosphere in fields that were continuously exposed to fenitrothion. Their density was lower in the plant sections than in the rhizosphere. A phylogenetic analysis of 16S rRNA gene sequences demonstrated that most of the degraders from the plants and rhizosphere clustered with the stinkbug symbiotic group, and some were identical to the midgut symbionts of C. saccharivorus collected from the same field. Our results confirmed that plants and the rhizosphere constituted environmental reservoirs for stinkbug symbiotic degraders. To the best of our knowledge, this is the first study to investigate the composition and abundance of the symbiotic fenitrothion degraders of Burkholderia species in farmers' fields.
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Affiliation(s)
- Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Takashi Okubo
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido2–17–2–1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido2–17–2–1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517Japan
| | - Tomoyuki Hori
- Research Institute for Environmental Management Technology, AISTTsukuba, Ibaraki 305–8569Japan
| | - Yuya Sato
- Research Institute for Environmental Management Technology, AISTTsukuba, Ibaraki 305–8569Japan
| | - Atsushi Nagayama
- Okinawa Prefectural Agricultural Research CenterItoman, Okinawa 901–0336Japan
| | - Kentaro Hayashi
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
| | - Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization9–4 Shinsei Minami, Memuro-cho, Kasai-gun, Hokkaido 082–0081Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604Japan
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Draft Genome Sequence of the Betaproteobacterial Endosymbiont Associated with the Fungus Mortierella elongata FMR23-6. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01272-14. [PMID: 25502669 PMCID: PMC4263831 DOI: 10.1128/genomea.01272-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The fungus Mortierella elongata FMR23-6 harbors an endobacterium inside its mycelium. Attempts to isolate the endobacterium from the fungus were not yet successful, but a highly purified bacterial fraction was prepared. Here, we report the draft genome sequence of the endobacterium.
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Okubo T, Ikeda S, Sasaki K, Ohshima K, Hattori M, Sato T, Minamisawa K. Phylogeny and functions of bacterial communities associated with field-grown rice shoots. Microbes Environ 2014; 29:329-32. [PMID: 25130883 PMCID: PMC4159046 DOI: 10.1264/jsme2.me14077] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51–52%), Actinobacteria (11–15%), Gammaproteobacteria (9–10%), and Betaproteobacteria (4–10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant–microbe interactions and biogeochemical metabolism in rice shoots.
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