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Sordo Z, Andeer P, Sethian J, Northen T, Ushizima D. RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs. Sci Rep 2024; 14:12907. [PMID: 38839814 PMCID: PMC11153571 DOI: 10.1038/s41598-024-63497-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Flatbed scanners are commonly used for root analysis, but typical manual segmentation methods are time-consuming and prone to errors, especially in large-scale, multi-plant studies. Furthermore, the complex nature of root structures combined with noisy backgrounds in images complicates automated analysis. Addressing these challenges, this article introduces RhizoNet, a deep learning-based workflow to semantically segment plant root scans. Utilizing a sophisticated Residual U-Net architecture, RhizoNet enhances prediction accuracy and employs a convex hull operation for delineation of the primary root component. Its main objective is to accurately segment root biomass and monitor its growth over time. RhizoNet processes color scans of plants grown in a hydroponic system known as EcoFAB, subjected to specific nutritional treatments. The root detection model using RhizoNet demonstrates strong generalization in the validation tests of all experiments despite variable treatments. The main contributions are the standardization of root segmentation and phenotyping, systematic and accelerated analysis of thousands of images, significantly aiding in the precise assessment of root growth dynamics under varying plant conditions, and offering a path toward self-driving labs.
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Affiliation(s)
- Zineb Sordo
- Computing Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94760, USA
| | - Peter Andeer
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94760, USA
| | - James Sethian
- Computing Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94760, USA
- Department of Mathematics, University of California, Berkeley, CA, 94720, USA
| | - Trent Northen
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94760, USA
| | - Daniela Ushizima
- Computing Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94760, USA.
- Berkeley Institute for Data Science, University of California, Berkeley, CA, 94760, USA.
- Bakar Institute, University of California, San Francisco, CA, 94143, USA.
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2
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Chai L, Shank EA, Zaburdaev V. Where bacteria and eukaryotes meet. J Bacteriol 2024; 206:e0004923. [PMID: 38289062 PMCID: PMC10882991 DOI: 10.1128/jb.00049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.
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Affiliation(s)
- Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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3
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Novak V, Andeer PF, Bowen BP, Ding Y, Zhalnina K, Hofmockel KS, Tomaka C, Harwood TV, van Winden MCM, Golini AN, Kosina SM, Northen TR. Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation. SCIENCE ADVANCES 2024; 10:eadg7888. [PMID: 38170767 PMCID: PMC10776018 DOI: 10.1126/sciadv.adg7888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography-tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0's low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.
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Affiliation(s)
- Vlastimil Novak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter F. Andeer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yezhang Ding
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Connor Tomaka
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas V. Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Amber N. Golini
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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McNair MC, Cocioba SC, Pietrzyk P, Rife TW. Toward an open-source 3D-printable laboratory. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11562. [PMID: 38369980 PMCID: PMC10873812 DOI: 10.1002/aps3.11562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 02/20/2024]
Abstract
Premise Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research. Methods We developed a modular system of 3D-printable designs called COBLE (Collection of Bespoke Laboratory Equipment), including novel and remixed 3D-printable lab equipment that can be inexpensively printed, assembled, and repaired for a fraction of the cost of retail equivalents. Results Here we present novel tools that utilize 3D printing to enable a wide range of scientific experiments. We include additional resources for scientists and labs that are interested in utilizing 3D printing for their research. Discussion By describing the broad potential that 3D-printed designs can have in the biological sciences, we hope to inspire others to implement and improve upon these designs, improving accessibility and enabling science for all.
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Affiliation(s)
- Mason C. McNair
- Plant and Environmental Sciences, Pee Dee Research and Education CenterClemson University2200 Pocket RoadFlorenceSouth Carolina29506USA
| | - Sebastian C. Cocioba
- Binomica Labs4301 22nd Street, Floor 3, Studio 342, Long Island CityNew York11101USA
| | - Peter Pietrzyk
- Department of Plant BiologyUniversity of Georgia120 Carlton StreetAthensGeorgia30602USA
| | - Trevor W. Rife
- Plant and Environmental Sciences, Pee Dee Research and Education CenterClemson University2200 Pocket RoadFlorenceSouth Carolina29506USA
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5
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Kim J, Lu LC, Gao X, Hofmockel KS, Masiello CA, Silberg JJ. Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium. ACS Synth Biol 2023; 12:3743-3753. [PMID: 37991716 DOI: 10.1021/acssynbio.3c00559] [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: 11/23/2023]
Abstract
Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five-membered MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that V. beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally relevant hydration conditions. We find that methyl halide production can report on an MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC responds to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.
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Affiliation(s)
- Jiwoo Kim
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Caroline A Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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6
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Candry P, Abrahamson B, Stahl DA, Winkler MKH. Microbially mediated climate feedbacks from wetland ecosystems. GLOBAL CHANGE BIOLOGY 2023; 29:5169-5183. [PMID: 37386740 DOI: 10.1111/gcb.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%-30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change.
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Affiliation(s)
- Pieter Candry
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Britt Abrahamson
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - David Allan Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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7
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Acharya SM, Yee MO, Diamond S, Andeer PF, Baig NF, Aladesanmi OT, Northen TR, Banfield JF, Chakraborty R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUNICATIONS 2023; 3:54. [PMID: 37280433 PMCID: PMC10244434 DOI: 10.1038/s43705-023-00265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
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Affiliation(s)
- Shwetha M Acharya
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mon Oo Yee
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nameera F Baig
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Omolara T Aladesanmi
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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8
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Kaiser CF, Perilli A, Grossmann G, Meroz Y. Studying root-environment interactions in structured microdevices. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad122. [PMID: 37042515 PMCID: PMC10353529 DOI: 10.1093/jxb/erad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 06/19/2023]
Abstract
In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.
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Affiliation(s)
- Christian-Frederic Kaiser
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alessia Perilli
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Yasmine Meroz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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9
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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: 0] [Impact Index Per Article: 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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10
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Hasterok R, Catalan P, Hazen SP, Roulin AC, Vogel JP, Wang K, Mur LAJ. Brachypodium: 20 years as a grass biology model system; the way forward? TRENDS IN PLANT SCIENCE 2022; 27:1002-1016. [PMID: 35644781 DOI: 10.1016/j.tplants.2022.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.
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Affiliation(s)
- Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
| | - Pilar Catalan
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca 22071, Spain; Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
| | - Samuel P Hazen
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8008, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Berkeley, CA 94720, USA; University California, Berkeley, Berkeley, CA 94720, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Edward Llwyd Building, Aberystwyth SY23 3DA, UK; College of Agronomy, Shanxi Agricultural University, Taiyuan 030801, Shanxi, China.
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11
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Kuang W, Sanow S, Kelm JM, Müller Linow M, Andeer P, Kohlheyer D, Northen T, Vogel JP, Watt M, Arsova B. N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5306-5321. [PMID: 35512445 PMCID: PMC9440436 DOI: 10.1093/jxb/erac184] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25-30 plants h-1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH4NO3 the benefit appears through N fixation, while at 0.5 mM NH4NO3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.
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Affiliation(s)
- Weiqi Kuang
- College of Life and Environmental Sciences, Hunan University of Arts and Science, 415000 Changde, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Innovation Academy for Seed Design, Chinese Academy of Sciences, 410125 Changsha, China
| | - Stefan Sanow
- IBG-2 Plant Sciences, Institut für Bio- und Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Jana M Kelm
- IBG-2 Plant Sciences, Institut für Bio- und Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Mark Müller Linow
- IBG-2 Plant Sciences, Institut für Bio- und Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Peter Andeer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dietrich Kohlheyer
- IBG-1 Biotechnology, Institut für Bio- und Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Trent Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John P Vogel
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michelle Watt
- IBG-2 Plant Sciences, Institut für Bio- und Geowissenschaften, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty of Science, The University of Melbourne, Melbourne, Australia
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12
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Manzoor A, Dippold MA, Loeppmann S, Blagodatskaya E. Two-Phase Conceptual Framework of Phosphatase Activity and Phosphorus Bioavailability. FRONTIERS IN PLANT SCIENCE 2022; 13:935829. [PMID: 35928705 PMCID: PMC9343760 DOI: 10.3389/fpls.2022.935829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/15/2022] [Indexed: 06/02/2023]
Abstract
The activity of extracellular phosphatases is a dynamic process controlled by both plant roots and microorganisms, which is responsible for the mineralization of soil phosphorus (P). Plants regulate the availability of soil P through the release of root mucilage and the exudation of low-molecular weight organic acids (LMWOAs). Mucilage increases soil hydraulic conductivity as well as pore connectivity, both of which are associated with increased phosphatase activity. The LMWOAs, in turn, stimulate the mineralization of soil P through their synergistic effects of acidification, chelation, and exchange reactions. This article reviews the catalytic properties of extracellular phosphatases and their interactions with the rhizosphere interfaces. We observed a biphasic effect of root metabolic products on extracellular phosphatases, which notably altered their catalytic mechanism. In accordance with the proposed conceptual framework, soil P is acquired by both plants and microorganisms in a coupled manner that is characterized by the exudation of their metabolic products. Due to inactive or reduced root exudation, plants recycle P through adsorption on the soil matrix, thereby reducing the rhizosphere phosphatase activity. The two-phase conceptual framework might assist in understanding P-acquisition (substrate turnover) and P-restoration (phosphatase adsorption by soil) in various terrestrial ecosystems.
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Affiliation(s)
- Aamir Manzoor
- Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
| | - Michaela A. Dippold
- Geo-Biosphere Interactions, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Sebastian Loeppmann
- Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
- Institute of Plant Nutrition and Soil Science, Christian–Albrechts University, Kiel, Germany
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13
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de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R, Northen TR. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol 2022; 13:855331. [PMID: 35694313 PMCID: PMC9174792 DOI: 10.3389/fmicb.2022.855331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
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Affiliation(s)
- Markus de Raad
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Yifan V. Li
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Peter F. Andeer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Suzanne M. Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Andrew Hendrickson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Nicholas R. Saichek
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Amber N. Golini
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - La Zhen Han
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Ying Wang
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Trent R. Northen,
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14
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Suwanchaikasem P, Idnurm A, Selby-Pham J, Walker R, Boughton BA. Root-TRAPR: a modular plant growth device to visualize root development and monitor growth parameters, as applied to an elicitor response of Cannabis sativa. PLANT METHODS 2022; 18:46. [PMID: 35397608 PMCID: PMC8994333 DOI: 10.1186/s13007-022-00875-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/14/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant growth devices, for example, rhizoponics, rhizoboxes, and ecosystem fabrication (EcoFAB), have been developed to facilitate studies of plant root morphology and plant-microbe interactions in controlled laboratory settings. However, several of these designs are suitable only for studying small model plants such as Arabidopsis thaliana and Brachypodium distachyon and therefore require modification to be extended to larger plant species like crop plants. In addition, specific tools and technical skills needed for fabricating these devices may not be available to researchers. Hence, this study aimed to establish an alternative protocol to generate a larger, modular and reusable plant growth device based on different available resources. RESULTS Root-TRAPR (Root-Transparent, Reusable, Affordable three-dimensional Printed Rhizo-hydroponic) system was successfully developed. It consists of two main parts, an internal root growth chamber and an external structural frame. The internal root growth chamber comprises a polydimethylsiloxane (PDMS) gasket, microscope slide and acrylic sheet, while the external frame is printed from a three-dimensional (3D) printer and secured with nylon screws. To test the efficiency and applicability of the system, industrial hemp (Cannabis sativa) was grown with or without exposure to chitosan, a well-known plant elicitor used for stimulating plant defense. Plant root morphology was detected in the system, and plant tissues were easily collected and processed to examine plant biological responses. Upon chitosan treatment, chitinase and peroxidase activities increased in root tissues (1.7- and 2.3-fold, respectively) and exudates (7.2- and 21.6-fold, respectively). In addition, root to shoot ratio of phytohormone contents were increased in response to chitosan. Within 2 weeks of observation, hemp plants exhibited dwarf growth in the Root-TRAPR system, easing plant handling and allowing increased replication under limited growing space. CONCLUSION The Root-TRAPR system facilitates the exploration of root morphology and root exudate of C. sativa under controlled conditions and at a smaller scale. The device is easy to fabricate and applicable for investigating plant responses toward elicitor challenge. In addition, this fabrication protocol is adaptable to study other plants and can be applied to investigate plant physiology in different biological contexts, such as plant responses against biotic and abiotic stresses.
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Affiliation(s)
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jamie Selby-Pham
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Nutrifield Pty Ltd, Melbourne, VIC, 3020, Australia
| | - Robert Walker
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Australian National Phenome Centre, Murdoch University, Perth, WA, 6150, Australia
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15
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Aufrecht J, Khalid M, Walton CL, Tate K, Cahill JF, Retterer ST. Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip. LAB ON A CHIP 2022; 22:954-963. [PMID: 35089295 DOI: 10.1039/d1lc00705j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The rhizosphere is a challenging ecosystem to study from a systems biology perspective due to its diverse chemical, physical, and biological characteristics. In the past decade, microfluidic platforms (e.g. plant-on-a-chip) have created an alternative way to study whole rhizosphere organisms, like plants and microorganisms, under reduced-complexity conditions. However, in reducing the complexity of the environment, it is possible to inadvertently alter organism phenotype, which biases laboratory data compared to in situ experiments. To build back some of the complexity of the rhizosphere in a fully-defined, parameterized approach we have developed a rhizosphere-on-a-chip platform that mimics the physical structure of soil. We demonstrate, through computational simulation, how this synthetic soil structure can influence the emergence of molecular "hotspots" and "hotmoments" that arise naturally from the plant's exudation of labile carbon compounds. We establish the amenability of the rhizosphere-on-a-chip for long-term culture of Brachypodium distachyon, and experimentally validate the presence of exudate hotspots within the rhizosphere-on-a-chip pore spaces using liquid microjunction surface sampling probe mass spectrometry.
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Affiliation(s)
- Jayde Aufrecht
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kylee Tate
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott T Retterer
- Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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16
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Liu C, Liu WS, Huot H, Guo MN, Zhu SC, Zheng HX, Morel JL, Tang YT, Qiu RL. Biogeochemical cycles of nutrients, rare earth elements (REEs) and Al in soil-plant system in ion-adsorption REE mine tailings remediated with amendment and ramie (Boehmeria nivea L.). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152075. [PMID: 34890651 DOI: 10.1016/j.scitotenv.2021.152075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
The exploitation of ion-adsorption rare earth element (REE) deposits in South China has left large areas of mine tailings. However, limited remediation practices on these tailings have been reported, and how the remediation strategies and economic plants cultivation affect the biogeochemical cycles of nutrients, REEs and Al remains unclear. The aim of the present study was to investigate the effects of the combination of the addition of soil amendment and the root development and activity of a fiber plant ramie (Boehmeria nivea L.) on the availability and distribution of nutrients, as well as of REEs and other potentially toxic elements (e.g. Al) in the soil-plant system. The results showed that the application of organic amendment and ramie planting induced a significant increase in soil pH, total carbon (C), nitrogen (N), and other nutrient (e.g. P and Ca) concentrations, while led to a decrease of 80-90% and 60-90% in soil extractable REE and Al concentrations respectively. Matrices of correlation showed that soil pH, total C, N, and P concentrations were among the most important factors controlling the availability of soil REEs and Al, and root characteristics (e.g. fine root length). The total C, N, P and extractable nutrient concentrations, and electrical conductivity were higher in the rhizosphere soils of ramie than those in the bulk soils. Moreover, more than 60% of the quantity of REE and Al in the whole ramie plant was stored within the thick roots. These results showed that, in addition to amendment, the effects induced by the roots of ramie could further improve soil properties through C input, nutrient mobilization and toxic element stabilization. Our study concludes that ramie planting with organic amendment is a promising phytostabilization strategy for the remediation of REE mine tailings in South China.
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Affiliation(s)
- Chang Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Laboratoire Sols et Environnement, INRAE-Université de Lorraine, F-54518 Vandoeuvre-lès-Nancy, France
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Hermine Huot
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
| | - Mei-Na Guo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Laboratoire Sols et Environnement, INRAE-Université de Lorraine, F-54518 Vandoeuvre-lès-Nancy, France
| | - Shi-Chen Zhu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Hong-Xiang Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jean Louis Morel
- Laboratoire Sols et Environnement, INRAE-Université de Lorraine, F-54518 Vandoeuvre-lès-Nancy, France
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Rong-Liang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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17
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Exploring the roles of microbes in facilitating plant adaptation to climate change. Biochem J 2022; 479:327-335. [PMID: 35119455 PMCID: PMC8883484 DOI: 10.1042/bcj20210793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant-microbe-environment interactions. In this perspective, we highlight some of the key factors influencing plant-microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant-microbe-environment interactions under a changing climate.
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18
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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19
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. THE NEW PHYTOLOGIST 2021. [PMID: 34608637 DOI: 10.1111/nph.17572.hal-03379708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T Freschet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
| | - Loïc Pagès
- UR 1115 PSH, Centre PACA, site Agroparc, INRAE, 84914, Avignon cedex 9, France
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Louise H Comas
- USDA-ARS Water Management Research Unit, 2150 Centre Avenue, Bldg D, Suite 320, Fort Collins, CO, 80526, USA
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Catherine Roumet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany CAS, Dukelska 135, 37901, Trebon, Czech Republic
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johannes A Postma
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Thomas S Adams
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - A Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee,, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee,, DD1 4HN, UK
| | - Elison B Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Johannes H C Cornelissen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eric Garnier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Arthur Gessler
- Forest Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Ina C Meier
- Functional Forest Ecology, University of Hamburg, Haidkrugsweg 1, 22885, Barsbütel, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | | | - Laura Rose
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Peter Ryser
- Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, 2300 RA, the Netherlands
| | - Alexia Stokes
- INRAE, AMAP, CIRAD, IRD, CNRS, University of Montpellier, Montpellier, 34000, France
| | - Tao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, Leipzig, 04103, Germany
| | - Nina Wurzburger
- Odum School of Ecology, University of Georgia, 140 E. Green Street, Athens, GA, 30602, USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds, LS2 9JT, UK
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Moemy Gomes de Moraes
- Department of Botany, Institute of Biological Sciences, Federal University of Goiás, 19, 74690-900, Goiânia, Goiás, Brazil
| | - Štěpán Janeček
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Crawley (Perth), WA, Australia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - M Luke McCormack
- Center for Tree Science, Morton Arboretum, 4100 Illinois Rt. 53, Lisle, IL, 60532, USA
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20
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Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere. mSystems 2021; 6:e0076521. [PMID: 34519527 PMCID: PMC8547458 DOI: 10.1128/msystems.00765-21] [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] [Indexed: 12/05/2022] Open
Abstract
Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget. Exploring and understanding the molecular mechanisms governing ecosystem responses via rhizosphere interactions allow the rational and sustainable design of future ecosystems. However, visualizing the plant root system architecture with spatially resolved root exudate and microbiome profiles along the root in its native state remains an ambitious grand challenge in rhizosphere biology. To address this challenge, we developed a three-dimensional (3D) root cartography platform to accurately visualize molecular and microbial constituents and their interactions in the root-rhizosphere zone.
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21
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Bajić D, Rebolleda-Gómez M, Muñoz MM, Sánchez Á. The Macroevolutionary Consequences of Niche Construction in Microbial Metabolism. Front Microbiol 2021; 12:718082. [PMID: 34671327 PMCID: PMC8522508 DOI: 10.3389/fmicb.2021.718082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 12/01/2022] Open
Abstract
Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g., horizontal gene transfer or de novo evolution of enzymes and pathways. This process is governed by a combination of environmental factors, selective pressures, and the constraints imposed by the genetic architecture of metabolic networks. In addition, many independent results hint that the process of niche construction, by which organisms actively modify their own and each other’s niches and selective pressures, could play a major role in microbial innovation and diversification. Yet, the general principles by which niche construction shapes microbial macroevolutionary patterns remain largely unexplored. Here, we discuss several new hypotheses and directions, and suggest metabolic modeling methods that could allow us to explore large-scale empirical genotype-phenotype-(G-P)-environment spaces in order to study the macroevolutionary effects of niche construction. We hope that this short piece will further stimulate a systematic and quantitative characterization of macroevolutionary patterns and processes in microbial metabolism.
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Affiliation(s)
- Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.,Microbial Sciences Institute, Yale University, West Haven, CT, United States
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22
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Jabusch LK, Kim PW, Chiniquy D, Zhao Z, Wang B, Bowen B, Kang AJ, Yoshikuni Y, Deutschbauer AM, Singh AK, Northen TR. Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant-Microbe Interactions. Int J Mol Sci 2021; 22:7880. [PMID: 34360661 PMCID: PMC8348081 DOI: 10.3390/ijms22157880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022] Open
Abstract
Fabricated ecosystems (EcoFABs) offer an innovative approach to in situ examination of microbial establishment patterns around plant roots using nondestructive, high-resolution microscopy. Previously high-resolution imaging was challenging because the roots were not constrained to a fixed distance from the objective. Here, we describe a new 'Imaging EcoFAB' and the use of this device to image the entire root system of growing Brachypodium distachyon at high resolutions (20×, 40×) over a 3-week period. The device is capable of investigating root-microbe interactions of multimember communities. We examined nine strains of Pseudomonas simiae with different fluorescent constructs to B. distachyon and individual cells on root hairs were visible. Succession in the rhizosphere using two different strains of P. simiae was examined, where the second addition was shown to be able to establish in the root tissue. The device was suitable for imaging with different solid media at high magnification, allowing for the imaging of fungal establishment in the rhizosphere. Overall, the Imaging EcoFAB could improve our ability to investigate the spatiotemporal dynamics of the rhizosphere, including studies of fluorescently-tagged, multimember, synthetic communities.
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Affiliation(s)
- Lauren K. Jabusch
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (L.K.J.); (D.C.); (A.J.K.); (A.M.D.)
| | - Peter W. Kim
- CBRN Defense and Energy Technologies, Sandia National Laboratory, Livermore, CA 94550, USA
| | - Dawn Chiniquy
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (L.K.J.); (D.C.); (A.J.K.); (A.M.D.)
| | - Zhiying Zhao
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (Z.Z.); (B.W.); (B.B.); (Y.Y.)
| | - Bing Wang
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (Z.Z.); (B.W.); (B.B.); (Y.Y.)
| | - Benjamin Bowen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (Z.Z.); (B.W.); (B.B.); (Y.Y.)
| | - Ashley J. Kang
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (L.K.J.); (D.C.); (A.J.K.); (A.M.D.)
| | - Yasuo Yoshikuni
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (Z.Z.); (B.W.); (B.B.); (Y.Y.)
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (L.K.J.); (D.C.); (A.J.K.); (A.M.D.)
| | - Anup K. Singh
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (L.K.J.); (D.C.); (A.J.K.); (A.M.D.)
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (Z.Z.); (B.W.); (B.B.); (Y.Y.)
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23
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Yee MO, Kim P, Li Y, Singh AK, Northen TR, Chakraborty R. Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front Microbiol 2021; 12:625752. [PMID: 33841353 PMCID: PMC8032546 DOI: 10.3389/fmicb.2021.625752] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.
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Affiliation(s)
- Mon Oo Yee
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Kim
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Yifan Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anup K. Singh
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Trent R. Northen
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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24
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The sum is greater than the parts: exploiting microbial communities to achieve complex functions. Curr Opin Biotechnol 2021; 67:149-157. [PMID: 33561703 DOI: 10.1016/j.copbio.2021.01.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.
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25
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Ecophysiological Study of Paraburkholderia sp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency. Appl Environ Microbiol 2020; 86:AEM.01851-20. [PMID: 33008817 PMCID: PMC7688210 DOI: 10.1128/aem.01851-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, Paraburkholderia sp. strain 1N. The growth of Paraburkholderia sp. 1N was monitored under aerobic conditions in a soil-extracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as Paraburkholderia sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of Paraburkholderia sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression.IMPORTANCE Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here, we show that growth of a bacterial soil isolate, Paraburkholderia sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content are used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with Paraburkholderia sp. 1N, which belongs to a metabolically diverse genus, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.
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26
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Sharma M, Saleh D, Charron JB, Jabaji S. A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium. Front Microbiol 2020; 11:575578. [PMID: 33123106 PMCID: PMC7573104 DOI: 10.3389/fmicb.2020.575578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Dina Saleh
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Suha Jabaji
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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27
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Arsova B, Foster KJ, Shelden MC, Bramley H, Watt M. Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake. THE NEW PHYTOLOGIST 2020; 225:1111-1119. [PMID: 31127613 DOI: 10.1111/nph.15955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/19/2019] [Indexed: 05/12/2023]
Abstract
Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.
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Affiliation(s)
- Borjana Arsova
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
| | - Kylie J Foster
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Megan C Shelden
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
| | - Michelle Watt
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
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28
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Tracy SR, Nagel KA, Postma JA, Fassbender H, Wasson A, Watt M. Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. TRENDS IN PLANT SCIENCE 2020; 25:105-118. [PMID: 31806535 DOI: 10.1016/j.tplants.2019.10.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today's phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems.
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Affiliation(s)
- Saoirse R Tracy
- School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Kerstin A Nagel
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Johannes A Postma
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Heike Fassbender
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Anton Wasson
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michelle Watt
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany.
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29
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Griffiths M. A 3D Print Repository for Plant Phenomics. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:8640215. [PMID: 33575669 PMCID: PMC7870102 DOI: 10.34133/2020/8640215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/10/2020] [Indexed: 05/19/2023]
Affiliation(s)
- M. Griffiths
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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30
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Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods 2019; 16:567-571. [PMID: 31227812 PMCID: PMC6733021 DOI: 10.1038/s41592-019-0465-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, which we term EcoFABs, will provide such model systems for microbiome studies.
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Affiliation(s)
- Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Kirsten Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Scott W Behie
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hans C Bernstein
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- The Norwegian College of Fishery Science and Arctic Centre for Sustainable Energy, UiT-The Arctic University of Norway, Tromsø, Norway
| | - James B Brown
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Centre for Computational Biology, School of Biosciences, University of Birmingham, Birmingham, UK
- Statistics Department, University of California, Berkeley, Berkeley, CA, USA
- Preminon, LLC, Antioch, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Sheri A Floge
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Samuel P Forry
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Scott A Jackson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | | | - Matthew D Wallenstein
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth A Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- DOE Joint Genome Institute, Walnut Creek, CA, USA.
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