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Lear L, Hesse E, Buckling A. Disturbances can facilitate prior invasions more than subsequent invasions in microbial communities. Ecol Lett 2024; 27:e14493. [PMID: 39140430 DOI: 10.1111/ele.14493] [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: 01/16/2024] [Revised: 07/02/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024]
Abstract
Invasions are commonly found to benefit from disturbance events. However, the importance of the relative timing of the invasion and disturbance for invader success and impact on community composition remains uncertain. Here, we experimentally test this by invading a five-species bacterial community on eight separate occasions-four before a disturbance and four after. Invader success and impact on community composition was greatest when the invasion immediately followed the disturbance. However, the subsequent invasions had negligible success or impact. Pre-disturbance, invader success and impact was greatest when the invader was added just before the disturbance. Importantly, however, the first three pre-disturbance invasion events had significantly greater success than the last three post-disturbance invasions. Moreover, these findings were consistent across a range of propagule pressures. Overall, we demonstrate that timing is highly important for both the success and impact on community composition of an invader, with both being lower as time since disturbance progresses.
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Affiliation(s)
- Luke Lear
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Elze Hesse
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, UK
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Wang X, Lu T, Yang B, Cao J, Li M. Exposure to resorcinol bis (diphenyl phosphate) induces colonization of alien microorganisms with potential impacts on the gut microbiota and metabolic disruption in male zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172892. [PMID: 38719053 DOI: 10.1016/j.scitotenv.2024.172892] [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: 02/27/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
Organophosphate esters (OPEs) have been demonstrated to induce various forms of toxicity in aquatic organisms. However, a scarcity of evidence impedes the conclusive determination of whether OPEs manifest sex-dependent toxic effects. Here, we investigated the effects of tris (1-chloro-2-propyl) phosphate (TCPP) and resorcinol bis (diphenyl phosphate) (RDP) on the intestines of both female and male zebrafish. The results indicated that, in comparison to TCPP, RDP induced more pronounced intestinal microstructural damage and oxidative stress, particularly in male zebrafish. 16S rRNA sequencing and metabolomics revealed significant alterations in the species richness and oxidative stress-related metabolites in the intestinal microbiota of zebrafish under exposure to both TCPP and RDP, manifesting gender-specific effects. Based on differential species analysis, we defined invasive species and applied invasion theory to analyze the reasons for changes in the male fish intestinal community. Correlation analysis demonstrated that alien species may have potential effects on metabolism. Overall, this study reveals a pronounced gender-dependent impact on both the intestinal microbiota and metabolic disruptions of zebrafish due to OPEs exposure and offers a novel perspective on the influence of pollutants on intestinal microbial communities and metabolism.
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Affiliation(s)
- Xinwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ting Lu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Jiangsu Environmental Engineering Technology Co. Ltd, Nanjing, Jiangsu 210019, China
| | - Bin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jing Cao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Cao Z, Wang L, Huang D, Wu G, Li X, Yue Y, Yu Y, Yu R, Fan Y. Identification and functional analysis of floral terpene synthase genes in Curcuma alismatifolia. PLANTA 2024; 260:26. [PMID: 38861179 DOI: 10.1007/s00425-024-04440-z] [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: 12/13/2023] [Accepted: 05/12/2024] [Indexed: 06/12/2024]
Abstract
MAIN CONCLUSION CaTPS2 and CaTPS3 were significantly expressed in flowers of Curcuma alismatifolia 'Shadow' and demonstrated bifunctional enzyme activity, CaTPS2 generated linalool and nerolidol as products, and CaTPS3 catalyzed β-myrcene and β-farnesene formation. This study presents the discovery and functional characterization of floral terpene synthase (TPS) genes in Curcuma alismatifolia 'Shadow', a cultivar renowned for its unique fragrance. Addressing the gap in understanding the genetic basis of floral scent in this species, we identified eight TPS genes through comprehensive transcriptome sequencing. Among these, CaTPS2 and CaTPS3 were significantly expressed in floral tissues and demonstrated bifunctional enzyme activity corresponding to the major volatile compounds detected in 'Shadow'. Functional analyses, including in vitro assays complemented with rigorous controls and alternative identification methods, elucidated the roles of these TPS genes in terpenoid biosynthesis. In vitro studies were conducted via heterologous expression in E. coli, followed by purification of the recombinant protein using affinity chromatography, enzyme assays were performed with GPP/FPP as the substrate, and volatile products were inserted into the GC-MS for analysis. Partially purified recombinant protein of CaTPS2 catalyzed GPP and FPP to produce linalool and nerolidol, respectively, while partially purified recombinant protein of CaTPS3 generated β-myrcene and β-farnesene with GPP and FPP as substrates, respectively. Real-time quantitative PCR further validated the expression patterns of these genes, correlating with terpenoid accumulation in different plant tissues. Our findings illuminate the molecular mechanisms underpinning floral fragrance in C. alismatifolia and provide a foundation for future genetic enhancements of floral scent in ornamental plants. This study, therefore, contributes to the broader understanding of terpenoid biosynthesis in plant fragrances, paving the way for biotechnological applications in horticulture plant breeding.
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Affiliation(s)
- Zihan Cao
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Lan Wang
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Di Huang
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guilan Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xinyue Li
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yuechong Yue
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yunyi Yu
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Kaur R, Kaur S, Dwibedi V, Kaur C, Akhtar N, Alzahrani A. Development and characterization of rice bran-gum Arabic based encapsulated biofertilizer for enhanced shelf life and controlled bacterial release. Front Microbiol 2023; 14:1267730. [PMID: 37822736 PMCID: PMC10563852 DOI: 10.3389/fmicb.2023.1267730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Currently, microbe-based approaches are being tested to address nutrient deficiencies and enhance nutrient use efficiency in crops. However, these bioinoculants have been unsuccessful at the commercial level due to differences in field and in-vivo conditions. Thus, to enhance bacterial stability, microbial formulations are considered, which will provide an appropriate microenvironment and protection to the bacteria ensuring better rhizospheric-colonization. Methods The present study aimed to develop a phosphobacterium-based encapsulated biofertilizer using the ion-chelation method, wherein a bacterial strain, Myroid gitamensis was mixed with a composite solution containing rice bran (RB), gum Arabic (GA), tricalcium phosphate, and alginate to develop low-cost and slow-release microbeads. The developed microbead was studied for encapsulation efficiency, shape, size, external morphology, shelf-life, soil release behavior, and biodegradability and characterized using SEM, FTIR, and XRD. Further, the wheat growth-promoting potential of microbeads was studied. Results The developed microbeads showed an encapsulation efficiency of 94.11%. The air-dried beads stored at 4°C were favorable for bacterial survival for upto 6 months. Microbeads showed 99.75% degradation within 110 days of incubation showing the bio-sustainable nature of the beads. The application of dried formulations to the pot-grown wheat seedlings resulted in a higher germination rate, shoot length, root length, fresh weight, dry weight of the seedlings, and higher potassium and phosphorus uptake in wheat. Discussion This study, for the first time, provides evidence that compared to liquid biofertilizers, the RB-GA encapsulated bacteria have better potential of enhancing wheat growth and can be foreseen as a future fertilizer option for wheat.
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Affiliation(s)
- Rajinder Kaur
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Sukhminderjit Kaur
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Vagish Dwibedi
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Charanjit Kaur
- Department of Microbiology, Bhojia Institute of Life Sciences, Baddi, India
| | - Nadeem Akhtar
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Abdulhakeem Alzahrani
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Symanczik S, Lipp C, Mäder P, Thonar C, Kundel D. Limited effectiveness of selected bioeffectors combined with recycling phosphorus fertilizers for maize cultivation under Swiss farming conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1239393. [PMID: 37719227 PMCID: PMC10501308 DOI: 10.3389/fpls.2023.1239393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
The use of plant biostimulants, also known as bioeffectors (BEs), has attracted increasing attention as an environmentally friendly strategy for more sustainable crop production. BEs are substances or microorganisms that are applied to plants or the surrounding soil to stimulate natural processes to enhance nutrient uptake, stress tolerance, and plant growth. Here, we tested the effectiveness of five BEs to enhance maize growth and phosphorus (P) uptake from various recycled P fertilizers in a series of pot and field experiments. First, the impact of two bacterial BEs and one soil-specific plant-based BE on crop performance was assessed in a 4-week screening experiment conducted in two arable, P-deficient soils of differing soil pH (a silty clay loam of pH 7.1 and a silty loam of pH 7.8) amended with recycled P-fertilizers (rock phosphate, biogas digestate, green waste compost, composted dairy manure, and chicken manure pellets). Then, for each soil type, the plant growth-promoting effect of the most promising BE-fertilizer combinations was re-assessed in an 8-week experiment. In addition, over a period of up to 3 years, three field experiments were conducted with maize in which up to two bacterial BEs were used either alone or in combination with a plant-based BE. Our experiments show that while BEs in combination with specific P-fertilizers can promote maize growth within the first weeks of growth under controlled conditions, the observed effects vanished in the long term, both in pots and under field conditions. In a tracing experiment, in which we tested the persistence of one bacterial BE over a period of 5 weeks, we observed a drastic decrease in colony-forming units already 2 weeks after inoculation. As previously shown in other studies, our data indicate that the plant growth-promoting effects of BEs found under controlled conditions are not directly transferable to field conditions. It is suggested that the drastic decline in inoculated bacterial strains in the tracing experiment is the reason for the decline in plant growth effect.
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Affiliation(s)
- Sarah Symanczik
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Carina Lipp
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Paul Mäder
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Cécile Thonar
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium
- Agroecology Lab, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Dominika Kundel
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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Dai Y, Li J, Yang X, Wang S, Zhao X, Wang Y, Zhang D, Luo C, Zhang G. New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131271. [PMID: 36989785 DOI: 10.1016/j.jhazmat.2023.131271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.
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Affiliation(s)
- Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Xiumin Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shuang Wang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
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Piccardi P, Alberti G, Alexander JM, Mitri S. Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves. THE ISME JOURNAL 2022; 16:2644-2652. [PMID: 36104451 PMCID: PMC9666444 DOI: 10.1038/s41396-022-01314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/27/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Predicting whether microbial invaders will colonize an environment is critical for managing natural and engineered ecosystems, and controlling infectious disease. Invaders often face competition by resident microbes. But how invasions play out in communities dominated by facilitative interactions is less clear. We previously showed that growth medium toxicity can promote facilitation between four bacterial species, as species that cannot grow alone rely on others to survive. Following the same logic, here we allowed other bacterial species to invade the four-species community and found that invaders could more easily colonize a toxic medium when the community was present. In a more benign environment instead, invasive species that could survive alone colonized more successfully when the residents were absent. Next, we asked whether early colonists could exclude future ones through a priority effect, by inoculating the invaders into the resident community only after its members had co-evolved for 44 weeks. Compared to the ancestral community, the co-evolved resident community was more competitive toward invaders and less affected by them. Our experiments show how communities may assemble by facilitating one another in harsh, sterile environments, but that arriving after community members have co-evolved can limit invasion success.
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Affiliation(s)
- Philippe Piccardi
- grid.9851.50000 0001 2165 4204Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland
| | - Géraldine Alberti
- grid.9851.50000 0001 2165 4204Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland
| | - Jake M. Alexander
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, ETH Zurich, Zürich, Switzerland
| | - Sara Mitri
- grid.9851.50000 0001 2165 4204Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Magliozzi C, Artois M, Bertaccini A, Candresse T, Tsiamis K, D'Amico F, Deriu I, Gervasini E, Cardoso AC. European primary datasets of alien bacteria and viruses. Sci Data 2022; 9:403. [PMID: 35831307 PMCID: PMC9279316 DOI: 10.1038/s41597-022-01485-1] [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: 01/20/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022] Open
Abstract
Bacteria and viruses are a natural component of Earth biodiversity and play an essential role in biochemical and geological cycles. They may also pose problems outside their native range, where they can negatively impact on natural resources, wildlife, and human health. To address these challenges and develop sustainable conservation strategies, a thorough understanding of their invasion related- factors is needed: origin, country and year of introduction, and pathways dynamics. Yet, alien bacteria and viruses are underrepresented in invasion ecology studies, which limits our ability to quantify their impacts and address future introductions. This study provides primary datasets of alien bacteria and viruses of plants and animals present in the European environment. The datasets contain expert-revised data on 446 taxa and their invasion related- factors across terrestrial and aquatic environments. Taxa information are complemented with spatial occurrences. The datasets provide a basis for collaborative initiatives to improve the collection of alien bacteria and viruses' data, and a starting point for data-driven conservation practices.
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Affiliation(s)
| | - Marc Artois
- LISAE (Lorraine investigation in animal and environmental health), Lagney, France
| | | | | | | | - Fabio D'Amico
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Ivan Deriu
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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Lechón-Alonso P, Clegg T, Cook J, Smith TP, Pawar S. The role of competition versus cooperation in microbial community coalescence. PLoS Comput Biol 2021; 17:e1009584. [PMID: 34748540 PMCID: PMC8601617 DOI: 10.1371/journal.pcbi.1009584] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/18/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023] Open
Abstract
New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed "community coalescence". Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.
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Affiliation(s)
- Pablo Lechón-Alonso
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Tom Clegg
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Jacob Cook
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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Hu J, Yang T, Friman VP, Kowalchuk GA, Hautier Y, Li M, Wei Z, Xu Y, Shen Q, Jousset A. Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome. Proc Biol Sci 2021; 288:20211396. [PMID: 34641724 PMCID: PMC8511750 DOI: 10.1098/rspb.2021.1396] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.
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Affiliation(s)
- Jie Hu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Yann Hautier
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Mei Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant immunity, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, Utrecht 3584CH, The Netherlands
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11
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Smith TP, Clegg T, Bell T, Pawar S. Systematic variation in the temperature dependence of bacterial carbon use efficiency. Ecol Lett 2021; 24:2123-2133. [PMID: 34240797 DOI: 10.1111/ele.13840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
Abstract
Carbon use efficiency (CUE) is a key characteristic of microbial physiology and underlies community-level responses to changing environments. Yet, we currently lack general empirical insights into variation in microbial CUE at the level of individual taxa. Here, through experiments with 29 strains of environmentally isolated bacteria, we find that bacterial CUE typically responds either positively to temperature, or has no discernible response, within biologically meaningful temperature ranges. Using a global data synthesis, we show that these results are generalisable across most culturable groups of bacteria. This variation in the thermal responses of bacterial CUE is taxonomically structured, and stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide new insights into microbial physiology, and a basis for more accurately modelling the effects of thermal fluctuations on complex microbial communities.
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Affiliation(s)
- Thomas P Smith
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Tom Clegg
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Samrāt Pawar
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
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12
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He X, Yang Y, Wei H, Yuan Z. Soil microbiome-mediated salinity tolerance in poplar plantlets is source-dependent. CHEMOSPHERE 2021; 272:129600. [PMID: 33482522 DOI: 10.1016/j.chemosphere.2021.129600] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Soil salinization is a global environmental problem and one of the most common land degradation processes. To effectively utilize saline lands, it is crucial to improve plant growth and stress tolerance, particularly through the microbiome intervention strategy. However, less is known about the interactions of microbes with trees than those with crops or herbaceous plants. Here, we examined how natural soil microbes affected the performance of salt-sensitive Populus deltoides × P. euramericana 'Nanlin895' (NL895) under salt stress. Gnotobiotic NL895 plantlets were inoculated with soil microbiome extracted from no-salt (NS; soluble salt: 0.71 g/kg), low-salt (LS; 5.14 g/kg), and high-salt (HS; 23.07 g/kg) lands, and then exposed to salt treatments. Compared to control, 33.8%, 18.0%, and 29.9% of the aboveground biomass was increased by NS, LS, and HS inoculation, respectively. The salt injury index was lower in LS and HS than in NS treatments. Rhizosphere microbial communities of all treatments were taxonomically and functionally different across multiple stages, while the variation extent was larger in bacterial than in fungal communities. FUNGuild and PICRUSt2 analysis demonstrated the changes of fungal trophic modes and bacterial metabolic pathways, respectively. In summary, our findings revealed the stronger potential of NS than LS and HS inoculants in growth promotion, while weaker strength than LS and HS inoculants in enhancing salt tolerance of NL895 plantlets. This source-dependent effect should be considered in future microbiome engineering, aiming at harnessing soil microbes to create predictable plant phenotypes.
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Affiliation(s)
- Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China; Nanjing Forestry University, Nanjing, 210037, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Yuzhan Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Huanshen Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China; Nanjing Forestry University, Nanjing, 210037, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
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13
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Sierocinski P, Soria Pascual J, Padfield D, Salter M, Buckling A. The impact of propagule pressure on whole community invasions in biomethane-producing communities. iScience 2021; 24:102659. [PMID: 34151242 PMCID: PMC8192723 DOI: 10.1016/j.isci.2021.102659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings. Complex communities can successfully invade other communities Invasions change the community composition independently of propagule pressure Number of taxa invading increases with increased propagule pressure Larger propagule pressure impacts both the community structure and function
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Affiliation(s)
- Pawel Sierocinski
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Jesica Soria Pascual
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Daniel Padfield
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | | | - Angus Buckling
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
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14
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Mitter EK, Tosi M, Obregón D, Dunfield KE, Germida JJ. Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606815] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.
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15
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Albright MBN, Sevanto S, Gallegos-Graves LV, Dunbar J. Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. mBio 2020; 11:e02089-20. [PMID: 33109758 PMCID: PMC7593967 DOI: 10.1128/mbio.02089-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/07/2020] [Indexed: 01/08/2023] Open
Abstract
Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context-propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)-is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering.IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).
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Affiliation(s)
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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16
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Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice. Microorganisms 2020; 8:microorganisms8111657. [PMID: 33114532 PMCID: PMC7693704 DOI: 10.3390/microorganisms8111657] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023] Open
Abstract
Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.
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17
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Räsänen E, Lindström L, Ketola T. Environmental Fluctuations Drive Species' Competitive Success in Experimental Invasions. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Emmi Räsänen
- Department of Biological and Environmental Science, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Leena Lindström
- Department of Biological and Environmental Science, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Tarmo Ketola
- Department of Biological and Environmental Science, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
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18
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Castledine M, Sierocinski P, Padfield D, Buckling A. Community coalescence: an eco-evolutionary perspective. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190252. [PMID: 32200752 PMCID: PMC7133537 DOI: 10.1098/rstb.2019.0252] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Meaghan Castledine
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
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19
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Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors. Sci Rep 2020; 10:2316. [PMID: 32047185 PMCID: PMC7012823 DOI: 10.1038/s41598-020-59048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 12/23/2022] Open
Abstract
Interactions between bacteria govern the progression of respiratory infections; however, the mechanisms underpinning these interactions are still unclear. Understanding how a bacterial species comes to dominate infectious communities associated with respiratory infections has direct relevance to treatment. In this study, Burkholderia, Pseudomonas, and Staphylococcus species were isolated from the sputum of an individual with Cystic Fibrosis and assembled in a fully factorial design to create simple microcosms. Measurements of growth and habitat modification were recorded over time, the later using proton Nuclear Magnetic Resonance spectra. The results showed interactions between the bacteria became increasingly neutral over time. Concurrently, the bacteria significantly altered their ability to modify the environment, with Pseudomonas able to utilise secondary metabolites produced by the other two isolates, whereas the reverse was not observed. This study indicates the importance of including data about the habitat modification of a community, to better elucidate the mechanisms of bacterial interactions.
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20
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Smith TP, Thomas TJH, García-Carreras B, Sal S, Yvon-Durocher G, Bell T, Pawar S. Community-level respiration of prokaryotic microbes may rise with global warming. Nat Commun 2019; 10:5124. [PMID: 31719536 PMCID: PMC6851113 DOI: 10.1038/s41467-019-13109-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/18/2019] [Indexed: 11/22/2022] Open
Abstract
Understanding how the metabolic rates of prokaryotes respond to temperature is fundamental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima [Formula: see text]C), but not thermophiles ([Formula: see text]C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Because climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, biomass-specific CO[Formula: see text] production, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.
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Affiliation(s)
- Thomas P Smith
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.
| | - Thomas J H Thomas
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
| | - Bernardo García-Carreras
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
| | - Sofía Sal
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
| | - Gabriel Yvon-Durocher
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9EZ, UK
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
| | - Samrāt Pawar
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.
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21
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Vila JCC, Jones ML, Patel M, Bell T, Rosindell J. Uncovering the rules of microbial community invasions. Nat Ecol Evol 2019; 3:1162-1171. [PMID: 31358951 DOI: 10.1038/s41559-019-0952-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/24/2019] [Indexed: 12/30/2022]
Abstract
Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion.
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Affiliation(s)
- Jean C C Vila
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK. .,Microbial Sciences Institute, West Campus, Yale University, West Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| | - Matt L Jones
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
| | - Matishalin Patel
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Tom Bell
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
| | - James Rosindell
- Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK
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22
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Giard-Laliberté C, Azarbad H, Tremblay J, Bainard L, Yergeau É. A water stress-adapted inoculum affects rhizosphere fungi, but not bacteria nor wheat. FEMS Microbiol Ecol 2019; 95:5499018. [DOI: 10.1093/femsec/fiz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Charlotte Giard-Laliberté
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hamed Azarbad
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, 6100 avenue Royalmount, Montreal, QC, H4P 2R2, Canada
| | - Luke Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport road, Swift Current, SK, S9H 3X2, Canada
| | - Étienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
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23
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Zhao Z, Hui C, Plant RE, Su M, Carpenter T, Papadopoulos N, Li Z, Carey JR. Life table invasion models: spatial progression and species-specific partitioning. Ecology 2019; 100:e02682. [PMID: 31018019 DOI: 10.1002/ecy.2682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 02/04/2019] [Indexed: 01/04/2023]
Abstract
Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units, we here conceptualize the invasion process as the transition from pristine to invaded spatial units. We use California cities as the spatial units and a long-term database of invasive tropical tephritids to characterize the invasion patterns. A new life-table method based on insect demography, including the progression model of invasion stage transition and the species-specific partitioning model of multispecies invasions, was developed to analyze the invasion patterns. The progression model allows us to estimate the probability and rate of transition for individual cities from pristine to infested stages and subsequently differentiate the first year of detection from detection recurrences. Importantly, we show that the interval of invasive tephritid recurrence in a city declines with increasing invasion stages of the city. The species-specific partitioning model revealed profound differences in invasion outcome depending on which tephritid species was first detected (and then locally eradicated) in the early stage of invasion. Taken together, we discuss how these two life-table invasion models can cast new light on existing invasion concepts; in particular, on formulating invasion dynamics as the state transition of cities and partitioning species-specific roles during multispecies invasions. These models provide a new set of tools for predicting the spatiotemporal progression of invasion and providing early warnings of recurrent invasions for efficient management.
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Affiliation(s)
- Zihua Zhao
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland, 7602, South Africa.,Mathematical and Physical Biosciences, African Institute for Mathematical Sciences, Muizenberg, 7945, South Africa
| | - Richard E Plant
- Departments of Plant Sciences and Biological and Agricultural Engineering, University of California, Davis, Davis, California, 95616, USA
| | - Min Su
- School of Mathematics, Hefei University of Technology, Hefei, 230009, China
| | - Tim Carpenter
- School of Veterinary Medicine, University of California, Davis, Davis, California, 95616, USA
| | - Nikos Papadopoulos
- Laboratory of Entomology and Agricultural Zoology, School of Agricultural Sciences, University of Thessaly, Thessaly, 38446, Greece
| | - Zhihong Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - James R Carey
- Department of Entomology, University of California, Davis, California, 95616, USA.,Center for the Economic and Demography of Aging, University of California, Berkeley, California, 94720, USA
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24
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Kaminsky LM, Trexler RV, Malik RJ, Hockett KL, Bell TH. The Inherent Conflicts in Developing Soil Microbial Inoculants. Trends Biotechnol 2019; 37:140-151. [DOI: 10.1016/j.tibtech.2018.11.011] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 11/30/2022]
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25
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Bell T. Next-generation experiments linking community structure and ecosystem functioning. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:20-22. [PMID: 30474920 DOI: 10.1111/1758-2229.12711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 05/28/2023]
Affiliation(s)
- Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
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26
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Castledine M, Buckling A, Padfield D. A shared coevolutionary history does not alter the outcome of coalescence in experimental populations of Pseudomonas fluorescens. J Evol Biol 2019; 32:58-65. [PMID: 30346633 PMCID: PMC7379710 DOI: 10.1111/jeb.13394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/13/2018] [Accepted: 10/08/2018] [Indexed: 11/30/2022]
Abstract
Community coalescence, the mixing of multiple communities, is ubiquitous in natural microbial communities. During coalescence, theory suggests the success of a population will be enhanced by the presence of species it has coevolved with (relative to foreign species), because coevolution will result in greater resource specialization to minimize competition. Thus, more coevolved communities should dominate over less coevolved communities during coalescence events. We test these hypotheses using the bacterium Pseudomonas fluorescens which diversifies into coexisting niche-specialist morphotypes. We first evolved replicate populations for ~40 generations and then isolated evolved genotypes. In a series of competition trials, we determined if using coevolved versus random genotypes affected the relative performance of "communities" of single and multiple genotypes. We found no effect of coevolutionary history on either genotype fitness or community performance, which suggests parallel (co)evolution between communities. However, fitness was enhanced by the presence of other genotypes of the same strain type (wild-type or an isogenic strain with a LacZ marker; the inclusion of the latter necessary to distinguish genotypes during competition), indicative of local adaptation with respect to genetic background. Our results are the first to investigate the effect of (co)evolution on the outcome of coalescence and suggest that when input populations are functionally similar and added at equal mixing ratios, the outcome community may not be asymmetrically dominated by either input population.
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Affiliation(s)
- Meaghan Castledine
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynCornwallUK
| | - Angus Buckling
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynCornwallUK
| | - Daniel Padfield
- Environment and Sustainability InstituteUniversity of ExeterPenrynCornwallUK
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Tao J, Qin C, Feng X, Ma L, Liu X, Yin H, Liang Y, Liu H, Huang C, Zhang Z, Xiao N, Meng D. Traits of Exogenous Species and Indigenous Community Contribute to the Species Colonization and Community Succession. Front Microbiol 2018; 9:3087. [PMID: 30619168 PMCID: PMC6299020 DOI: 10.3389/fmicb.2018.03087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/29/2018] [Indexed: 12/28/2022] Open
Abstract
Introducing exogenous species into an environment is an effective method to strengthen ecological functions. The traits of the exogenous species and the indigenous communities, as well as the resistance and subsequent succession of the community to exogenous species, are not well-understood. Here, three different functional consortia were introduced into two extremely acidic systems, leaching heap (LH) and leaching solution (LS), derived from the Zijin copper mine in China. The results showed that the structures of both LS and LH communities were affected by the three consortia, but not all the structural changes were in line with variations of community function. Among the three consortia, only the complementary sulfur oxidizers greatly enhanced copper extraction efficiency of LS (by 50.42%). This demonstrated that functional niche novelty gave exogenous species an advantage to occupy an ecological niche in a complementary manner, thus leading to successful colonization. The resistance to, and subsequent succession by, exogenous organisms varied between the two indigenous communities. More specifically, the LS community with low community diversity and simple composition was susceptible to exogenous species, and the community structural changes of LS were both divergent and irreversible. In comparison, the LH community with greater community diversity and more complex composition was more resistant to exogenous species, with the community structures showing a convergent trend over time despite different species being introduced. Therefore, we propose that diverse communities compete for resources more intensely with exogenous species and resist their introduction, and that communities with complex composition are able to cope with exogenous disturbances.
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Affiliation(s)
- Jiemeng Tao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Chong Qin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xue Feng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Beijing, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Caoming Huang
- China Nonferrous Metal Mining (Group) Co., Ltd., Beijing, China
| | | | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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28
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Cairns J, Jokela R, Hultman J, Tamminen M, Virta M, Hiltunen T. Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution. Front Genet 2018; 9:312. [PMID: 30154827 PMCID: PMC6102323 DOI: 10.3389/fgene.2018.00312] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/23/2018] [Indexed: 01/21/2023] Open
Abstract
Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.
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Affiliation(s)
- Johannes Cairns
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Roosa Jokela
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Manu Tamminen
- Department of Biology, University of Turku, Turku, Finland
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
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