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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [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: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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2
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Tan J, Wei N, Turcotte MM. Trophic interactions in microbiomes influence plant host population size and ecosystem function. Proc Biol Sci 2024; 291:20240612. [PMID: 38772419 DOI: 10.1098/rspb.2024.0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/23/2024] Open
Abstract
Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.
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Affiliation(s)
- Jiaqi Tan
- Department of Biological Sciences, Louisianan State University, Baton Rouge, LA 70803, USA
| | - Na Wei
- The Holden Arboretum, Kirtland, OH 44094, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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3
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Smith GP, Cohen H, Zorn JF, McFrederick QS, Ponisio LC. Plant-pollinator network architecture does not impact intraspecific microbiome variability. Mol Ecol 2024; 33:e17306. [PMID: 38414303 DOI: 10.1111/mec.17306] [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: 05/02/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Variation in how individuals interact with food resources can directly impact, and be affected by, their microbial interactions due to the potential for transmission. The degree to which this transmission occurs, however, may depend on the structure of forager networks, which determine the community-scale transmission opportunities. In particular, how the community-scale opportunity for transfer balances individual-scale barriers to transmission is unclear. Examining the bee-flower and bee-microbial interactions of over 1000 individual bees, we tested (1) the degree to which individual floral visits predicted microbiome composition and (2) whether plant-bee networks with increased opportunity for microbial transmission homogenized the microbiomes of bees within that network. The pollen community composition carried by bees was associated with microbiome composition at some sites, suggesting that microbial transmission at flowers occurred. Contrary to our predictions, however, microbiome variability did not differ based on transfer opportunity: bee microbiomes in asymmetric networks with high opportunity for microbial transfer were similarly variable compared to microbiomes in networks with more evenly distributed links. These findings suggest that microbial transmission at flowers is frequent enough to be observed at the community level, but that community network structure did not substantially change the dynamics of this transmission, perhaps due to filtering processes in host guts.
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Affiliation(s)
- Gordon P Smith
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hamutahl Cohen
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- University of California Cooperative Extension Ventura County, University of California Agriculture and Natural Resources, Ventura, California, USA
| | - Jocelyn F Zorn
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Lauren C Ponisio
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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4
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Christian N, Perlin MH. Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes. Mycologia 2024; 116:227-250. [PMID: 38380970 DOI: 10.1080/00275514.2023.2299658] [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: 05/10/2023] [Accepted: 12/22/2023] [Indexed: 02/22/2024]
Abstract
Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
| | - Michael H Perlin
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
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5
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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6
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Ban S, Cheng W, Wang X, Niu J, Wu Q, Xu Y. Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making. mSystems 2024; 9:e0058623. [PMID: 38206013 PMCID: PMC10878095 DOI: 10.1128/msystems.00586-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Microbial inoculation is an effective way to improve the quality of fermented foods via affecting the microbiota structure. However, it is unclear how the inoculation regulates the microbiota structure, and it is still difficult to directionally control the microbiota function via the inoculation. In this work, using the spontaneous fermentation of the starter (Daqu) for Chinese liquor fermentation as a case, we inoculated different microbiota groups at different time points in Daqu fermentation, and analyzed the effect of the inoculation on the final metabolic profile of Daqu. The inoculated microbiota and inoculated time points both significantly affected the final metabolites via regulating the microbial succession (P < 0.001), and multiple inoculations can promote deterministic assembly. Twenty-seven genera were identified to be related to microbial succession, and drove the variation of 121 metabolites. We then constructed an elastic network model to predict the profile of these 121 metabolites based on the abundances of 27 succession-related genera in Daqu fermentation. Procrustes analysis showed that the model could accurately predict the metabolic abundances (average Spearman correlation coefficients >0.3). This work revealed the effect of inoculation on the microbiota succession and the metabolic profile. The established predicted model of metabolic profile would be beneficial for directionally improving the food quality.IMPORTANCEThis work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.
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Affiliation(s)
- Shibo Ban
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Cheng
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Xi Wang
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Jiao Niu
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
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7
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Van Nuland ME, Daws SC, Bailey JK, Schweitzer JA, Busby PE, Peay KG. Above- and belowground fungal biodiversity of Populus trees on a continental scale. Nat Microbiol 2023; 8:2406-2419. [PMID: 37973868 DOI: 10.1038/s41564-023-01514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023]
Abstract
Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.
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Affiliation(s)
- Michael E Van Nuland
- Department of Biology, Stanford University, Stanford, CA, USA.
- Society for the Protection of Underground Networks, SPUN, Dover, DE, USA.
| | - S Caroline Daws
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joseph K Bailey
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Jennifer A Schweitzer
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Earth System Science, Stanford University, Stanford, CA, USA
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8
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Francis JS, Mueller TG, Vannette RL. Intraspecific variation in realized dispersal probability and host quality shape nectar microbiomes. THE NEW PHYTOLOGIST 2023; 240:1233-1245. [PMID: 37614102 DOI: 10.1111/nph.19195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/16/2023] [Indexed: 08/25/2023]
Abstract
Epiphytic microbes frequently affect plant phenotype and fitness, but their effects depend on microbe abundance and community composition. Filtering by plant traits and deterministic dispersal-mediated processes can affect microbiome assembly, yet their relative contribution to predictable variation in microbiome is poorly understood. We compared the effects of host-plant filtering and dispersal on nectar microbiome presence, abundance, and composition. We inoculated representative bacteria and yeast into 30 plants across four phenotypically distinct cultivars of Epilobium canum. We compared the growth of inoculated communities to openly visited flowers from a subset of the same plants. There was clear evidence of host selection when we inoculated flowers with synthetic communities. However, plants with the highest microbial densities when inoculated did not have the highest microbial densities when openly visited. Instead, plants predictably varied in the presence of bacteria, which was correlated with pollen receipt and floral traits, suggesting a role for deterministic dispersal. These findings suggest that host filtering could drive plant microbiome assembly in tissues where species pools are large and dispersal is high. However, deterministic differences in microbial dispersal to hosts may be equally or more important when microbes rely on an animal vector, dispersal is low, or arrival order is important.
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Affiliation(s)
- Jacob S Francis
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Tobias G Mueller
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Rachel L Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
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9
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Lv H, Li X, He D, Chen X, Liu M, Lan Y, Zhao J, Wang H, Yan Z. Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza. MICROBIAL ECOLOGY 2023; 86:2934-2948. [PMID: 37667132 DOI: 10.1007/s00248-023-02295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.
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Affiliation(s)
- Hongyang Lv
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyu Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Liu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yin Lan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Chengdu, China.
- Institute of Chinese Medical Sciences, University of Macau, Taipa, China.
| | - Hai Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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10
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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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11
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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12
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Andreo-Jimenez B, Te Beest DE, Kruijer W, Vannier N, Kadam NN, Melandri G, Jagadish SVK, van der Linden G, Ruyter-Spira C, Vandenkoornhuyse P, Bouwmeester HJ. Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance. RICE (NEW YORK, N.Y.) 2023; 16:26. [PMID: 37212977 DOI: 10.1186/s12284-023-00641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, University of Arizona, Tucson, USA
| | - S V Krishna Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Kansas State University, Manhattan, KS, 66506, USA
| | | | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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13
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Zhang M, Wang Y, Hu Y, Wang H, Liu Y, Zhao B, Zhang J, Fang R, Yan Y. Heterosis in root microbiota inhibits growth of soil-borne fungal pathogens in hybrid rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1059-1076. [PMID: 36426878 DOI: 10.1111/jipb.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
In nature, plants are colonized by various microbes that play essential roles in their growth and health. Heterosis is a natural genetic phenomenon whereby first-generation hybrids exhibit superior phenotypic performance relative to their parents. It remains unclear whether this concept can be extended to the "hybridization" of microbiota from two parents in their descendants and what benefits the hybrid microbiota might convey. Here, we investigated the structure and function of the root microbiota from three hybrid rice varieties and their parents through amplicon sequencing analysis of bacterial 16S ribosomal DNA (rDNA) and fungal internal transcribed spacer (ITS) regions. We show that the bacterial and fungal root microbiota of the varieties are distinct from those of their parental lines and exhibit potential heterosis features in diversity and composition. Moreover, the root bacterial microbiota of hybrid variety LYP9 protects rice against soil-borne fungal pathogens. Systematic analysis of the protective capabilities of individual strains from a 30-member bacterial synthetic community derived from LYP9 roots indicated that community members have additive protective roles. Global transcription profiling analyses suggested that LYP9 root bacterial microbiota activate rice reactive oxygen species production and cell wall biogenesis, contributing to heterosis for protection. In addition, we demonstrate that the protection conferred by the LYP9 root microbiota is transferable to neighboring plants, potentially explaining the observed hybrid-mediated superior effects of mixed planting. Our findings suggest that some hybrids exhibit heterosis in their microbiota composition that promotes plant health, highlighting the potential for microbiota heterosis in breeding hybrid crops.
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Affiliation(s)
- Mengting Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinyue Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Huacai Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yawen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongsheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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14
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Jones KR, Hughey MC, Belden LK. Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles. Proc Biol Sci 2023; 290:20230308. [PMID: 36946107 PMCID: PMC10031419 DOI: 10.1098/rspb.2023.0308] [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: 02/06/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.
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Affiliation(s)
- Korin Rex Jones
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
| | - Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061-0131, USA
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15
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Faist H, Trognitz F, Antonielli L, Symanczik S, White PJ, Sessitsch A. Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation. ENVIRONMENTAL MICROBIOME 2023; 18:18. [PMID: 36918963 PMCID: PMC10012461 DOI: 10.1186/s40793-023-00469-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure. RESULTS The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desirée, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desirée, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner. CONCLUSION Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.
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Affiliation(s)
- Hanna Faist
- Bioresources Unit, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Friederike Trognitz
- Bioresources Unit, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Livio Antonielli
- Bioresources Unit, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Sarah Symanczik
- Soil Science Department, Research Institute of Organic Agriculture (FiBL), Ackerstraße 113, 5070 Frick, Switzerland
| | | | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
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16
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Anguita-Maeso M, Navas-Cortés JA, Landa BB. Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees. PLANTS (BASEL, SWITZERLAND) 2023; 12:912. [PMID: 36840260 PMCID: PMC9967459 DOI: 10.3390/plants12040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.
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17
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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18
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Vita F, Sabbatini L, Sillo F, Ghignone S, Vergine M, Guidi Nissim W, Fortunato S, Salzano AM, Scaloni A, Luvisi A, Balestrini R, De Bellis L, Mancuso S. Salt stress in olive tree shapes resident endophytic microbiota. FRONTIERS IN PLANT SCIENCE 2022; 13:992395. [PMID: 36247634 PMCID: PMC9556989 DOI: 10.3389/fpls.2022.992395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Olea europaea L. is a glycophyte representing one of the most important plants in the Mediterranean area, both from an economic and agricultural point of view. Its adaptability to different environmental conditions enables its cultivation in numerous agricultural scenarios, even on marginal areas, characterized by soils unsuitable for other crops. Salt stress represents one current major threats to crop production, including olive tree. In order to overcome this constraint, several cultivars have been evaluated over the years using biochemical and physiological methods to select the most suitable ones for cultivation in harsh environments. Thus the development of novel methodologies have provided useful tools for evaluating the adaptive capacity of cultivars, among which the evaluation of the plant-microbiota ratio, which is important for the maintenance of plant homeostasis. In the present study, four olive tree cultivars (two traditional and two for intensive cultivation) were subjected to saline stress using two concentrations of salt, 100 mM and 200 mM. The effects of stress on diverse cultivars were assessed by using biochemical analyses (i.e., proline, carotenoid and chlorophyll content), showing a cultivar-dependent response. Additionally, the olive tree response to stress was correlated with the leaf endophytic bacterial community. Results of the metabarcoding analyses showed a significant shift in the resident microbiome for plants subjected to moderate salt stress, which did not occur under extreme salt-stress conditions. In the whole, these results showed that the integration of stress markers and endophytic community represents a suitable approach to evaluate the adaptation of cultivars to environmental stresses.
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Affiliation(s)
- Federico Vita
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Leonardo Sabbatini
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Fabiano Sillo
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Stefano Ghignone
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Werther Guidi Nissim
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | | | - Anna Maria Salzano
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, National Research Council of Italy, Institute for the Animal Production System in the Mediterranean Environment (CNR-ISPAAM), Portici, Italy
| | - Andrea Scaloni
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, National Research Council of Italy, Institute for the Animal Production System in the Mediterranean Environment (CNR-ISPAAM), Portici, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Raffaella Balestrini
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Stefano Mancuso
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
- Fondazione per il futuro delle città (FFC), Florence, Italy
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19
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Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa. Commun Biol 2022; 5:959. [PMID: 36104398 PMCID: PMC9474469 DOI: 10.1038/s42003-022-03860-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/18/2022] [Indexed: 01/03/2023] Open
Abstract
AbstractMicrobial experimental systems provide a platform to observe how networks of groups emerge to impact plant development. We applied selection pressure for microbiome enhancement of Brassica rapa biomass to examine adaptive bacterial group dynamics under soil nitrogen limitation. In the 9th and final generation of the experiment, selection pressure enhanced B. rapa seed yield and nitrogen use efficiency compared to our control treatment, with no effect between the random selection and control treatments. Aboveground biomass increased for both the high biomass selection and random selection plants. Soil bacterial diversity declined under high B. rapa biomass selection, suggesting a possible ecological filtering mechanism to remove bacterial taxa. Distinct sub-groups of interactions emerged among bacterial phyla such as Proteobacteria and Bacteroidetes in response to selection. Extended Local Similarity Analysis and NetShift indicated greater connectivity of the bacterial community, with more edges, shorter path lengths, and altered modularity through the course of selection for enhanced plant biomass. In contrast, bacterial communities under random selection and no selection showed less complex interaction profiles of bacterial taxa. These results suggest that group-level bacterial interactions could be modified to collectively shift microbiome functions impacting the growth of the host plant under soil nitrogen limitation.
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20
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Busby PE, Newcombe G, Neat AS, Averill C. Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:337-356. [PMID: 35584884 DOI: 10.1146/annurev-phyto-021320-010717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States (n = 0-876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.
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Affiliation(s)
- Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, Idaho, USA
| | - Abigail S Neat
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Colin Averill
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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21
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Zhimo VY, Kumar A, Biasi A, Abdelfattah A, Sharma VK, Salim S, Feygenberg O, Bartuv R, Freilich S, Whitehead SR, Wisniewski M, Droby S. Assembly and dynamics of the apple carposphere microbiome during fruit development and storage. Front Microbiol 2022; 13:928888. [PMID: 36016781 PMCID: PMC9395710 DOI: 10.3389/fmicb.2022.928888] [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: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.
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Affiliation(s)
- V. Yeka Zhimo
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ajay Kumar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Antonio Biasi
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee, Potsdam, Germany
| | - Vijay Kumar Sharma
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Rotem Bartuv
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
| | - Susan R. Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Samir Droby
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
- *Correspondence: Samir Droby,
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22
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Bergmann GE, Leveau JHJ. A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds. Front Microbiol 2022; 13:877519. [PMID: 35935241 PMCID: PMC9355165 DOI: 10.3389/fmicb.2022.877519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.
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23
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Whitaker BK, Giauque H, Timmerman C, Birk N, Hawkes CV. Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass. MICROBIAL ECOLOGY 2022; 84:122-130. [PMID: 34405252 DOI: 10.1007/s00248-021-01836-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.
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Affiliation(s)
- Briana K Whitaker
- Department of Plant and Microbial Biology, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention & Applied Microbiology Unit, 1815 N University St, Peoria, IL, 61604, USA
| | - Hannah Giauque
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Corey Timmerman
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Nicolas Birk
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA.
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24
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Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis. Curr Biol 2022; 32:2719-2729.e5. [DOI: 10.1016/j.cub.2022.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/14/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023]
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25
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Burr AA, Woods KD, Cassidy ST, Wood CW. Priority effects alter the colonization success of a host-associated parasite and mutualist. Ecology 2022; 103:e3720. [PMID: 35396706 DOI: 10.1002/ecy.3720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
Priority effects shape the assembly of free-living communities and host-associated communities. However, the current literature does not fully incorporate two features of host-symbiont interactions-correlated host responses to multiple symbionts and ontogenetic changes in host responses to symbionts-leading to an incomplete picture of the role of priority effects in host-associated communities. We factorially manipulated the inoculation timing of two plant symbionts (mutualistic rhizobia bacteria and parasitic root-knot nematodes) and tested how host age at arrival, arrival order, and arrival synchrony affected symbiont colonization success in the model legume Medicago truncatula. We found that host age, arrival order, and arrival synchrony significantly affected colonization of one or both symbionts. Host age at arrival only affected nematodes but not rhizobia: younger plants were more heavily infected than older plants. By contrast, arrival order only affected rhizobia but not nematodes: plants formed more rhizobia nodules when rhizobia arrived before nematodes. Finally, synchronous arrival decreased colonization both symbionts, an effect that depended on host age. Our results demonstrate that priority effects compromise the host's ability to control colonization by two major symbionts, and suggest that the role of correlated host responses and host ontogeny in the assembly of host-associated communities deserve further attention.
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Affiliation(s)
- Audrey A Burr
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kamron D Woods
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven T Cassidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Corlett W Wood
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Romeralo C, Martín-García J, Martínez-Álvarez P, Muñoz-Adalia EJ, Gonçalves DR, Torres E, Witzell J, Diez JJ. Pine species determine fungal microbiome composition in a common garden experiment. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2021.101137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Redondo MA, Oliva J, Elfstrand M, Boberg J, Capador-Barreto HD, Karlsson B, Berlin A. Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce. Environ Microbiol 2022; 24:3640-3654. [PMID: 35315253 PMCID: PMC9544151 DOI: 10.1111/1462-2920.15974] [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: 12/14/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/28/2022]
Abstract
The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
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Affiliation(s)
- Miguel A Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Jonàs Oliva
- Department of Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, Lleida, 25198, Spain.,Joint Research Unit CTFC-AGROTECNIO, Alcalde Rovira Roure 191, Lleida, 25198, Spain
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Johanna Boberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Hernán D Capador-Barreto
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Bo Karlsson
- Skogforsk, Svalöv, Ekebo 2250, 268 90, Sweden
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
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28
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Barge EG, Leopold DR, Rojas A, Vilgalys R, Busby PE. Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism. Mol Ecol 2022; 31:3018-3030. [DOI: 10.1111/mec.16436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Edward G. Barge
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Devin R. Leopold
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology University of Arkansas Fayetteville AR 72701 USA
| | - Rytas Vilgalys
- Department of Biology Duke University Durham NC 27708 USA
| | - Posy E. Busby
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
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29
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Malacrinò A, Mosca S, Li Destri Nicosia MG, Agosteo GE, Schena L. Plant Genotype Shapes the Bacterial Microbiome of Fruits, Leaves, and Soil in Olive Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050613. [PMID: 35270082 PMCID: PMC8912820 DOI: 10.3390/plants11050613] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 06/02/2023]
Abstract
The plant microbiome plays an important role in plant biology, ecology, and evolution. While recent technological developments enabled the characterization of plant-associated microbiota, we still know little about the impact of different biotic and abiotic factors on the diversity and structures of these microbial communities. Here, we characterized the structure of bacterial microbiomes of fruits, leaves, and soil collected from two olive genotypes (Sinopolese and Ottobratica), testing the hypothesis that plant genotype would impact each compartment with a different magnitude. Results show that plant genotype differently influenced the diversity, structure, composition, and co-occurence network at each compartment (fruits, leaves, soil), with a stronger effect on fruits compared to leaves and soil. Thus, plant genotype seems to be an important factor in shaping the structure of plant microbiomes in our system, and can be further explored to gain functional insights leading to improvements in plant productivity, nutrition, and defenses.
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Wolfe ER, Dove R, Webster C, Ballhorn DJ. Culturable fungal endophyte communities of primary successional plants on Mount St. Helens, WA, USA. BMC Ecol Evol 2022; 22:18. [PMID: 35168544 PMCID: PMC8845407 DOI: 10.1186/s12862-022-01974-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 02/09/2022] [Indexed: 12/03/2022] Open
Abstract
Background While a considerable amount of research has explored plant community composition in primary successional systems, little is known about the microbial communities inhabiting these pioneer plant species. Fungal endophytes are ubiquitous within plants, and may play major roles in early successional ecosystems. Specifically, endophytes have been shown to affect successional processes, as well as alter host stress tolerance and litter decomposition dynamics—both of which are important components in harsh environments where soil organic matter is still scarce. Results To determine possible contributions of fungal endophytes to plant colonization patterns, we surveyed six of the most common woody species on the Pumice Plain of Mount St. Helens (WA, USA; Lawetlat'la in the Cowlitz language; created during the 1980 eruption)—a model primary successional ecosystem—and found low colonization rates (< 15%), low species richness, and low diversity. Furthermore, while endophyte community composition did differ among woody species, we found only marginal evidence of temporal changes in community composition over a single field season (July–September). Conclusions Our results indicate that even after a post-eruption period of 40 years, foliar endophyte communities still seem to be in the early stages of community development, and that the dominant pioneer riparian species Sitka alder (Alnus viridis ssp. sinuata) and Sitka willow (Salix sitchensis) may be serving as important microbial reservoirs for incoming plant colonizers. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01974-2.
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Affiliation(s)
- Emily R Wolfe
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97201, USA.
| | - Robyn Dove
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97201, USA
| | - Cassandra Webster
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97201, USA
| | - Daniel J Ballhorn
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97201, USA
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31
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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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Impact of Harvest on Switchgrass Leaf Microbial Communities. Genes (Basel) 2021; 13:genes13010022. [PMID: 35052362 PMCID: PMC8774549 DOI: 10.3390/genes13010022] [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: 10/21/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.
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Sullam KE, Musa T. Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens. PLANTS 2021; 10:plants10122697. [PMID: 34961168 PMCID: PMC8707103 DOI: 10.3390/plants10122697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.
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34
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Bhattacharya M, Chatterjee S, Sharma AR, Agoramoorthy G, Chakraborty C. D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Appl Microbiol Biotechnol 2021; 105:9035-9045. [PMID: 34755213 PMCID: PMC8578012 DOI: 10.1007/s00253-021-11676-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
Abstract
The progression of the COVID-19 pandemic has generated numerous emerging variants of SARS-CoV-2 on a global scale. These variants have gained evolutionary advantages, comprising high virulence and serious infectivity due to multiple spike glycoprotein mutations. As a reason, variants are demonstrating significant abilities to escape the immune responses of the host. The D614G mutation in the S-glycoprotein of SARS-CoV-2 variants has shown the most efficient interaction with the ACE2 receptor of the cells. This explicit mutation at amino acid position 614 (aspartic acid-to-glycine substitution) is the prime cause of infection and re-infection. It changes the conformation of RBD and cleavage patterns S-glycoprotein with higher stability, replication fitness, and fusion efficiencies. Therefore, this review aims to provide several crucial pieces of information associated with the D614 mutational occurrence of SARS-CoV-2 variants and their infectivity patterns. This review will also effectively emphasize the mechanism of action of D614G mutant variants, immune escape, and partial vaccine escape of this virus. Furthermore, the viral characteristic changes leading to the current global pandemic condition have been highlighted. Here, we have tried to illustrate a novel direction for future researchers to develop effective therapeutic approaches and counterweight strategies to minimize the spread of COVID-19.Key points• D614G mutation arises within the S-glycoprotein of significant SARS-CoV-2 variants.• The D614G mutation affects infection, re-infection, cleavage patterns of S-glycoprotein, and replication fitness of SARS-CoV-2 variants.• The D614G mutation influences the immunity and partial vaccine escape.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | | | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
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35
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Wagner MR. Prioritizing host phenotype to understand microbiome heritability in plants. THE NEW PHYTOLOGIST 2021; 232:502-509. [PMID: 34287929 DOI: 10.1111/nph.17622] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/02/2021] [Indexed: 05/06/2023]
Abstract
Breeders and evolutionary geneticists have grappled with the complexity of the 'genotype-to-phenotype map' for decades. Now, recent studies highlight the relevance of this concept for understanding heritability of plant microbiomes. Because host phenotype is a more proximate cause of microbiome variation than host genotype, microbiome heritability varies across plant anatomy and development. Fine-scale variation of plant traits within organs suggests that the well-established concept of 'microbiome compartment' should be refined. Additionally, recent work shows that the balance of deterministic processes (including host genetic effects) vs stochastic processes also varies over time and space. Together, these findings suggest that re-centering plant phenotype - both as a predictor and a readout of microbiome function - will accelerate new insights into microbiome heritability.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
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36
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Christian N, Espino Basurto B, Toussaint A, Xu X, Ainsworth EA, Busby PE, Heath KD. Elevated carbon dioxide reduces a common soybean leaf endophyte. GLOBAL CHANGE BIOLOGY 2021; 27:4154-4168. [PMID: 34022078 DOI: 10.1111/gcb.15716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2 ] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2 ] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, KY, USA
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Baldemar Espino Basurto
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Amber Toussaint
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Xinyan Xu
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Elizabeth A Ainsworth
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Katy D Heath
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
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37
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Hawkes CV, Kjøller R, Raaijmakers JM, Riber L, Christensen S, Rasmussen S, Christensen JH, Dahl AB, Westergaard JC, Nielsen M, Brown-Guedira G, Hestbjerg Hansen L. Extension of Plant Phenotypes by the Foliar Microbiome. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:823-846. [PMID: 34143648 DOI: 10.1146/annurev-arplant-080620-114342] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.
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Affiliation(s)
- Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Jesper Cairo Westergaard
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service and Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
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38
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Gong T, Xin XF. Phyllosphere microbiota: Community dynamics and its interaction with plant hosts. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:297-304. [PMID: 33369158 DOI: 10.1111/jipb.13060] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/17/2020] [Indexed: 05/22/2023]
Abstract
Plants are colonized by various microorganisms in natural environments. While many studies have demonstrated key roles of the rhizosphere microbiota in regulating biological processes such as nutrient acquisition and resistance against abiotic and biotic challenges, less is known about the role of the phyllosphere microbiota and how it is established and maintained. This review provides an update on current understanding of phyllosphere community assembly and the mechanisms by which plants and microbes establish the phyllosphere microbiota for plant health.
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Affiliation(s)
- Tianyu Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial Sciences, Shanghai, 200032, China
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39
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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40
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Plett JM, Solomon J, Snijders F, Marlow-Conway J, Plett KL, Bithell SL. Order of microbial succession affects rhizobia-mediated biocontrol efforts against Phytophthora root rot. Microbiol Res 2020; 242:126628. [PMID: 33153885 DOI: 10.1016/j.micres.2020.126628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023]
Abstract
The management of soilborne root diseases in pulse crops is challenged by a limited range of resistance sources and often a complete absence of in-crop management options. Therefore, alternative management strategies need to be developed. We evaluated disease limiting interactions between the rhizobia species Mesorhizobium ciceri, and the oomycete pathogen Phytophthora medicaginis, which causes Phytophthora root rot (PRR) of chickpea (Cicer arietinum). For the PRR susceptible var. Sonali plants, post-pathogen M. ciceri inoculation significantly improved probability of plant survival when compared to P. medicaginis infected plants only pre-inoculated with M. ciceri (75 % versus 35 %, respectively). Potential mechanisms for these effects were investigated: rhizobia inoculation benefits to plant nodulation were not demonstrated, but the highest nodule N-fixation activity of P. medicaginis inoculated plants occurred for the post-pathogen M. ciceri treatment; rhizobia inoculation treatment did not reduce lesion development but certain combinations of microbial inoculation led to significant reduction in root growth. Microcosm studies, however, showed that the presence of M. ciceri reduced growth of P. medicaginis isolates. Putative chickpea disease resistance gene expression was evaluated using qPCR in var. Sonali roots. When var. Sonali plants were treated with M. ciceri post-P. medicaginis inoculation, the gene regulation in the plant host became more similar to PRR moderately resistant var. PBA HatTrick. These results suggest that M. ciceri application post P. medicaginis inoculation may improve plant survival by inducing defense responses similar to a PRR moderately resistant chickpea variety. Altogether, these results indicate that order of microbial succession can significantly affect PRR plant survial in susceptible chickpea under controlled conditions and improved plant survival effects are due to a number of different mechanisms including improved host nutrition, through direct inhibiton of pathogen growth, as well as host defense priming.
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Affiliation(s)
- J M Plett
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia.
| | - J Solomon
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - F Snijders
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - J Marlow-Conway
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - K L Plett
- Hawkesbury Institute for the Environment, University of Western Sydney, Richmond, NSW, 2753, Australia
| | - S L Bithell
- New South Wales Department of Primary Industries, Tamworth, NSW, 2340, Australia
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41
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Oliva J, Ridley M, Redondo MA, Caballol M. Competitive exclusion amongst endophytes determines shoot blight severity on pine. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13692] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonàs Oliva
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
- Joint Research Unit CTFC‐AGROTECNIO Lleida Spain
| | - Maia Ridley
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
| | - Miguel A. Redondo
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Maria Caballol
- Department of Crop and Forest Sciences University of Lleida Lleida Spain
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