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Marx HE, Carboni M, Douzet R, Perrier C, Delbart F, Thuiller W, Lavergne S, Tank DC. Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed. Ecol Evol 2021; 11:12075-12091. [PMID: 34522362 PMCID: PMC8427620 DOI: 10.1002/ece3.7973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/28/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy-to-measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes-functional genomic diversity (FGD)-to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA-seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien-native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro-ecosystems.
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Affiliation(s)
- Hannah E. Marx
- Department of Biology & Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | | | - Rolland Douzet
- CNRSLautaretJardin du LautaretUniversité Grenoble AlpesGrenobleFrance
| | | | - Franck Delbart
- CNRSLautaretJardin du LautaretUniversité Grenoble AlpesGrenobleFrance
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - David C. Tank
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
- Stillinger HerbariumUniversity of IdahoMoscowIdahoUSA
- Present address:
Department of Botany and Rocky Mountain HerbariumUniversity of WyomingLaramieWY82072‐3165USA
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Hoffman AM, Avolio ML, Knapp AK, Smith MD. Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PeerJ 2018; 6:e4394. [PMID: 29473008 PMCID: PMC5816582 DOI: 10.7717/peerj.4394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extremes in climate, such as heat waves and drought, are expected to become more frequent and intense with forecasted climate change. Plant species will almost certainly differ in their responses to these stressors. We experimentally imposed a heat wave and drought in the tallgrass prairie ecosystem near Manhattan, Kansas, USA to assess transcriptional responses of two ecologically important C4 grass species, Andropogon gerardii and Sorghastrum nutans. Based on previous research, we expected that S. nutans would regulate more genes, particularly those related to stress response, under high heat and drought. Across all treatments, S. nutans showed greater expression of negative regulatory and catabolism genes while A. gerardii upregulated cellular and protein metabolism. As predicted, S. nutans showed greater sensitivity to water stress, particularly with downregulation of non-coding RNAs and upregulation of water stress and catabolism genes. A. gerardii was less sensitive to drought, although A. gerardii tended to respond with upregulation in response to drought versus S. nutans which downregulated more genes under drier conditions. Surprisingly, A. gerardii only showed minimal gene expression response to increased temperature, while S. nutans showed no response. Gene functional annotation suggested that these two species may respond to stress via different mechanisms. Specifically, A. gerardii tends to maintain molecular function while S. nutans prioritizes avoidance. Sorghastrum nutans may strategize abscisic acid response and catabolism to respond rapidly to stress. These results have important implications for success of these two important grass species under a more variable and extreme climate forecast for the future.
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Affiliation(s)
- Ava M. Hoffman
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
| | - Meghan L. Avolio
- Department of Earth & Planetary Sciences, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Alan K. Knapp
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
| | - Melinda D. Smith
- Department of Biology, Colorado State University, Fort Collins, CO, United States of America
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States of America
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Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Muños S, Niebel A, Raffaele S, Roux F. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:747-770. [PMID: 29232012 DOI: 10.1111/tpj.13799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
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Affiliation(s)
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Etienne-Pascal Journet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Jean-Benoît Morel
- BGPI, INRA, CIRAD, SupAgro, Université de Montpellier, Montpellier, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Smith MD, Hoffman AM, Avolio ML. Gene expression patterns of two dominant tallgrass prairie species differ in response to warming and altered precipitation. Sci Rep 2016; 6:25522. [PMID: 27174156 PMCID: PMC4865957 DOI: 10.1038/srep25522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/15/2016] [Indexed: 11/09/2022] Open
Abstract
To better understand the mechanisms underlying plant species responses to climate change, we compared transcriptional profiles of the co-dominant C4 grasses, Andropogon gerardii Vitman and Sorghastrum nutans (L.) Nash, in response to increased temperatures and more variable precipitation regimes in a long-term field experiment in native tallgrass prairie. We used microarray probing of a closely related model species (Zea mays) to assess correlations in leaf temperature (Tleaf) and leaf water potential (LWP) and abundance changes of ~10,000 transcripts in leaf tissue collected from individuals of both species. A greater number of transcripts were found to significantly change in abundance levels with Tleaf and LWP in S. nutans than in A. gerardii. S. nutans also was more responsive to short-term drought recovery than A. gerardii. Water flow regulating transcripts associated with stress avoidance (e.g., aquaporins), as well as those involved in the prevention and repair of damage (e.g., antioxidant enzymes, HSPs), were uniquely more abundant in response to increasing Tleaf in S. nutans. The differential transcriptomic responses of the co-dominant C4 grasses suggest that these species may cope with and respond to temperature and water stress at the molecular level in distinct ways, with implications for tallgrass prairie ecosystem function.
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Affiliation(s)
- Melinda D. Smith
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Ava M. Hoffman
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Meghan L. Avolio
- National Socio-Environmental Synthesis Center, Annapolis, MD, 21401, USA
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Schenkel D, Lemfack MC, Piechulla B, Splivallo R. A meta-analysis approach for assessing the diversity and specificity of belowground root and microbial volatiles. FRONTIERS IN PLANT SCIENCE 2015; 6:707. [PMID: 26442022 PMCID: PMC4568395 DOI: 10.3389/fpls.2015.00707] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 05/20/2023]
Abstract
Volatile organic compounds are secondary metabolites emitted by all organisms, especially by plants and microbes. Their role as aboveground signals has been established for decades. Recent evidence suggests that they might have a non-negligible role belowground and might be involved in root-root and root-microbial/pest interactions. Our aim here was to make a comprehensive review of belowground volatile diversity using a meta-analysis approach. At first we synthesized current literature knowledge on plant root volatiles and classified them in terms of chemical diversity. In a second step, relying on the mVOC database of microbial volatiles, we classified volatiles based on their emitters (bacteria vs. fungi) and their specific ecological niche (i.e., rhizosphere, soil). Our results highlight similarities and differences among root and microbial volatiles and also suggest that some might be niche specific. We further explored the possibility that volatiles might be involved in intra- and inter-specific root-root communication and discuss the ecological implications of such scenario. Overall this work synthesizes current knowledge on the belowground volatilome and the potential signaling role of its constituents. It also highlights that the total diversity of belowground volatiles might be orders of magnitude larger that the few hundreds of compounds described to date.
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Affiliation(s)
- Denis Schenkel
- Institute for Molecular Biosciences, Goethe University FrankfurtFrankfurt, Germany
- Integrative Fungal Research ClusterFrankfurt, Germany
| | - Marie C. Lemfack
- Institute for Biological Sciences, University of RostockRostock, Germany
| | - Birgit Piechulla
- Institute for Biological Sciences, University of RostockRostock, Germany
| | - Richard Splivallo
- Institute for Molecular Biosciences, Goethe University FrankfurtFrankfurt, Germany
- Integrative Fungal Research ClusterFrankfurt, Germany
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Depuydt S. Arguments for and against self and non-self root recognition in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:614. [PMID: 25414719 PMCID: PMC4222137 DOI: 10.3389/fpls.2014.00614] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 05/22/2023]
Abstract
Root-root interaction research gained more and more attention over the past few years. Roots are pivotal for plant survival because they ensure uptake of water and nutrients. Therefore, detection of adjacent roots might lead to competitive advantages. Several lines of experimental evidence suggest that roots have ways to discriminate non-related roots, kin, and-importantly-that they can sense self/non-self roots to avoid intra-plant competition. In this mini-review, the existence of self/non-self recognition in plant roots will be discussed and the current knowledge on the mechanisms that could be involved will be summarized. Although the process of identity recognition is still not completely understood, interesting data are available and emerging new technologies will certainly aid to better understand this research field that can have an important biological, ecological, and agricultural impact.
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Affiliation(s)
- Stephen Depuydt
- Ghent University Global Campus, Incheon, South Korea
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent, Belgium
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D'Abrosca B, Scognamiglio M, Fiumano V, Esposito A, Choi YH, Verpoorte R, Fiorentino A. Plant bioassay to assess the effects of allelochemicals on the metabolome of the target species Aegilops geniculata by an NMR-based approach. PHYTOCHEMISTRY 2013; 93:27-40. [PMID: 23628625 DOI: 10.1016/j.phytochem.2013.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/20/2013] [Accepted: 03/21/2013] [Indexed: 06/02/2023]
Abstract
A metabolomic-based approach for the study of allelopathic interactions in the Mediterranean area is proposed using Aegilops geniculata Roth (Poaceae), a Mediterranean herbaceous plant, as test species. Its metabolome has been elucidated by 1D and 2D NMR experiments. Hydroponic plant cultures of A. geniculata were treated with specific compounds of known allelopathic potential: catechol, coumarin, p-coumaric acid, p-hydroxybenzoic acid, ferulic acid and juglone. The metabolic variations due to the presence of allelochemicals have been analyzed and measured. All of the compounds showed the strongest effects at the highest concentration, with coumarin and juglone as the most active compounds, causing an increase of several metabolites. The metabolome changes in test plants confirmed the allelochemicals' reported modes of action. The results demonstrated that the proposed method is a promising tool. It can be applied to plant extracts, making it possible to evidence the metabolites responsible for the activity, as well as their mechanisms of action.
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Affiliation(s)
- Brigida D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, via Vivaldi 43, I-81100 Caserta, Italy
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Schmid C, Bauer S, Müller B, Bartelheimer M. Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress. FRONTIERS IN PLANT SCIENCE 2013; 4:296. [PMID: 23967000 PMCID: PMC3743015 DOI: 10.3389/fpls.2013.00296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/16/2013] [Indexed: 05/23/2023]
Abstract
Root-root interactions are much more sophisticated than previously thought, yet the mechanisms of belowground neighbor perception remain largely obscure. Genome-wide transcriptome analyses allow detailed insight into plant reactions to environmental cues. A root interaction trial was set up to explore both morphological and whole genome transcriptional responses in roots of Arabidopsis thaliana in the presence or absence of an inferior competitor, Hieracium pilosella. Neighbor perception was indicated by Arabidopsis roots predominantly growing away from the neighbor (segregation), while solitary plants placed more roots toward the middle of the pot. Total biomass remained unaffected. Database comparisons in transcriptome analysis revealed considerable similarity between Arabidopsis root reactions to neighbors and reactions to pathogens. Detailed analyses of the functional category "biotic stress" using MapMan tools found the sub-category "pathogenesis-related proteins" highly significantly induced. A comparison to a study on intraspecific competition brought forward a core of genes consistently involved in reactions to neighbor roots. We conclude that beyond resource depletion roots perceive neighboring roots or their associated microorganisms by a relatively uniform mechanism that involves the strong induction of pathogenesis-related proteins. In an ecological context the findings reveal that belowground neighbor detection may occur independently of resource depletion, allowing for a time advantage for the root to prepare for potential interactions.
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Affiliation(s)
- Christoph Schmid
- Faculty of Biology and Preclinical Medicine, Institute of Botany, University of RegensburgRegensburg, Germany
| | - Sibylle Bauer
- Faculty of Biology and Preclinical Medicine, Institute of Botany, University of RegensburgRegensburg, Germany
| | - Benedikt Müller
- Faculty of Biology and Preclinical Medicine, Institute of Botany, University of RegensburgRegensburg, Germany
- Faculty of Biology and Preclinical Medicine, Cell Biology and Plant Biochemistry, University of RegensburgRegensburg, Germany
| | - Maik Bartelheimer
- Faculty of Biology and Preclinical Medicine, Institute of Botany, University of RegensburgRegensburg, Germany
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Broz AK, Broeckling CD, De-la-Peña C, Lewis MR, Greene E, Callaway RM, Sumner LW, Vivanco JM. Plant neighbor identity influences plant biochemistry and physiology related to defense. BMC PLANT BIOLOGY 2010; 10:115. [PMID: 20565801 PMCID: PMC3095278 DOI: 10.1186/1471-2229-10-115] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 06/17/2010] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors. RESULTS In the greenhouse, C. maculosa individuals were paired with either conspecific (C. maculosa) or heterospecific (Festuca idahoensis) plant neighbors and elicited with the plant defense signaling molecule methyl jasmonate to mimic insect herbivory. We found that elicited C. maculosa plants grown with conspecific neighbors exhibited increased levels of total phenolics, whereas those grown with heterospecific neighbors allocated more resources towards growth. To further investigate these results in the field, we conducted a metabolomics analysis to explore chemical differences between individuals of C. maculosa growing in naturally occurring conspecific and heterospecific field stands. Similar to the greenhouse results, C. maculosa individuals accumulated higher levels of defense-related secondary metabolites and lower levels of primary metabolites when growing in conspecific versus heterospecific field stands. Leaf herbivory was similar in both stand types; however, a separate field study positively correlated specialist herbivore load with higher densities of C. maculosa conspecifics. CONCLUSIONS Our results suggest that an individual C. maculosa plant can change its defensive strategy based on the identity of its plant neighbors. This is likely to have important consequences for individual and community success.
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Affiliation(s)
- Amanda K Broz
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Clelia De-la-Peña
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Matthew R Lewis
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Erick Greene
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ragan M Callaway
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Plant Biology, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
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