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Koch H, Sessitsch A. The microbial-driven nitrogen cycle and its relevance for plant nutrition. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5547-5556. [PMID: 38900822 DOI: 10.1093/jxb/erae274] [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: 09/15/2023] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.
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Affiliation(s)
- Hanna Koch
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-3430 Tulln, Austria
| | - Angela Sessitsch
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, A-3430 Tulln, Austria
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2
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Rose SA, Robicheau BM, Tolman J, Fonseca-Batista D, Rowland E, Desai D, Ratten JM, Kantor EJH, Comeau AM, Langille MG, Jerlström-Hultqvist J, Devred E, Sarthou G, Bertrand EM, LaRoche J. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni. SCIENCE ADVANCES 2024; 10:eadn1476. [PMID: 39083619 PMCID: PMC11290528 DOI: 10.1126/sciadv.adn1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.
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Affiliation(s)
- Sonja A. Rose
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Debany Fonseca-Batista
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ella Joy H. Kantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M. Comeau
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G.I. Langille
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Emmanuel Devred
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Halifax, Nova Scotia, Canada
| | | | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Rabbee MF, Ali MS, Islam MN, Rahman MM, Hasan MM, Baek KH. Endophyte mediated biocontrol mechanisms of phytopathogens in agriculture. Res Microbiol 2024:104229. [PMID: 38992820 DOI: 10.1016/j.resmic.2024.104229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The global human population is growing and demand for food is increasing. Global agriculture faces numerous challenges, including excessive application of synthetic pesticides, emergence of herbicide-and pesticide-resistant pathogenic microbes, and more frequent natural disasters associated with global warming. Searches for valuable endophytes have increased, with the aim of making agriculture more sustainable and environmentally friendly. Endophytic microbes are known to have a variety of beneficial effects on plants. They can effectively transfer nutrients from the soil into plants, promote plant growth and development, increase disease resistance, increase stress tolerance, prevent herbivore feeding, reduce the virulence of pathogens, and inhibit the growth of rival plant species. Endophytic microbes can considerably minimize the need for agrochemicals, such as fertilizers, fungicides, bactericides, insecticides, and herbicides in the cultivation of crop plants. This review summarizes current knowledge on the roles of endophytes focusing on their mechanisms of disease control against phytopathogens through the secretion of antimicrobial substances and volatile organic compounds, and the induction of systemic resistance in plants. Additionally, the beneficial roles of these endophytes and their metabolites in the control of postharvest diseases in plants have been summarized.
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Affiliation(s)
- Muhammad Fazle Rabbee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, South Korea.
| | - Md Sarafat Ali
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj 8100, Bangladesh
| | - Md Nurul Islam
- Soil Resource Development Institute, Regional Office, Rajshahai 6000, Bangladesh
| | - Mohammed M Rahman
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Md Mohidul Hasan
- Department of Plant Pathology, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh.
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, South Korea.
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Guiry E, Kennedy JR, Malcom C, Miller M, Hall O, Buckley M, Szpak P. Archaeological evidence for long-term human impacts on sea turtle foraging behaviour. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240120. [PMID: 39021767 PMCID: PMC11253035 DOI: 10.1098/rsos.240120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/18/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Early conservation efforts to prevent the loss of green sea turtles (Chelonia mydas) from the Caribbean Sea jumpstarted marine habitat and biodiversity protection. However, even there, limitations on historical observations of turtle ecology have hampered efforts to contextualize foraging behaviours for conservation management. We integrate isotopic and zooarchaeological evidence from green sea turtles harvested at the Miskito Cays (Nicaragua) to assess foraging behaviour before and after a step change in harvesting intensity. Highly structured isotopic evidence shows greater foraging adaptability in earlier populations. This provides a counterpoint to recent synthesis, suggesting the ecological non-exchangeability of sea turtles, which complicates conservation planning focused on genetic-stock-based repopulation. In contrast, our results suggest future populations would have a capacity for higher degrees of ecological exchangeability than current perspectives allow. This highlights a need to consider the kinds of longer term perspectives, such as those offered by archaeological materials, when planning for future sea turtle recovery.
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Affiliation(s)
- Eric Guiry
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, OntarioK9L 0G2, Canada
- School of Archaeology and Ancient History, University of Leicester, Mayor’s Walk, LeicesterLE1 7RH, UK
| | - J. Ryan Kennedy
- Department of Anthropology, Indiana University Bloomington, 701 East Kirkwood Avenue, Bloomington, IN47405, USA
| | - Corey Malcom
- Florida Keys History Center, 700 Fleming Street, Key West, FL33040, USA
| | - Mariah Miller
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, OntarioK9L 0G2, Canada
| | - Olivia Hall
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, OntarioK9L 0G2, Canada
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, ManchesterM17 DN, UK
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, OntarioK9L 0G2, Canada
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5
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Younker IT, Molnar N, Scorza K, Weed R, Light SH, Pfister CA. Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13270. [PMID: 38778582 PMCID: PMC11112141 DOI: 10.1111/1758-2229.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/06/2024] [Indexed: 05/25/2024]
Abstract
In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.
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Affiliation(s)
- Isaac T. Younker
- Committee on MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | - Nichos Molnar
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Kaylie Scorza
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Roo Weed
- The Graduate Program in Biophysical SciencesThe University of ChicagoChicagoIllinoisUSA
| | - Samuel H. Light
- Department of MicrobiologyThe University of ChicagoChicagoIllinoisUSA
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Zehr JP, Capone DG. Unsolved mysteries in marine nitrogen fixation. Trends Microbiol 2024; 32:532-545. [PMID: 37658011 DOI: 10.1016/j.tim.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.
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Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Douglas G Capone
- Marine and Environmental Biology Section of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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Zhao B, Jia X, Yu N, Murray JD, Yi K, Wang E. Microbe-dependent and independent nitrogen and phosphate acquisition and regulation in plants. THE NEW PHYTOLOGIST 2024; 242:1507-1522. [PMID: 37715479 DOI: 10.1111/nph.19263] [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: 06/30/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023]
Abstract
Nitrogen (N) and phosphorus (P) are the most important macronutrients required for plant growth and development. To cope with the limited and uneven distribution of N and P in complicated soil environments, plants have evolved intricate molecular strategies to improve nutrient acquisition that involve adaptive root development, production of root exudates, and the assistance of microbes. Recently, great advances have been made in understanding the regulation of N and P uptake and utilization and how plants balance the direct uptake of nutrients from the soil with the nutrient acquisition from beneficial microbes such as arbuscular mycorrhiza. Here, we summarize the major advances in these areas and highlight plant responses to changes in nutrient availability in the external environment through local and systemic signals.
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Affiliation(s)
- Boyu Zhao
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xianqing Jia
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Keke Yi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
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8
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Brodersen KE, Mosshammer M, Bittner MJ, Hallstrøm S, Santner J, Riemann L, Kühl M. Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs. Microbiol Spectr 2024; 12:e0333523. [PMID: 38426746 PMCID: PMC10986515 DOI: 10.1128/spectrum.03335-23] [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: 09/11/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations. IMPORTANCE Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.
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Affiliation(s)
| | - Maria Mosshammer
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Meriel J. Bittner
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jakob Santner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln an der Donau, Austria
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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McGrath AH, Lema K, Egan S, Wood G, Gonzalez SV, Kjelleberg S, Steinberg PD, Marzinelli EM. Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont. NPJ Biofilms Microbiomes 2024; 10:33. [PMID: 38553475 PMCID: PMC10980776 DOI: 10.1038/s41522-024-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.
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Affiliation(s)
- Alexander Harry McGrath
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia.
- Sydney Institute of Marine Science, Mosman, NSW, Australia.
| | - Kimberley Lema
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Georgina Wood
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- UWA Oceans Institute & School of Biological Sciences, Indian Ocean Marine Research Centre, The University of Western Australia, Sydney, Australia
| | - Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
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10
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Berlinghof J, Montilla LM, Peiffer F, Quero GM, Marzocchi U, Meador TB, Margiotta F, Abagnale M, Wild C, Cardini U. Accelerated nitrogen cycling on Mediterranean seagrass leaves at volcanic CO 2 vents. Commun Biol 2024; 7:341. [PMID: 38503855 PMCID: PMC11254932 DOI: 10.1038/s42003-024-06011-0] [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: 06/02/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO2 vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N2 fixation contributes to 35% of the plant's N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N2 production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.
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Affiliation(s)
- Johanna Berlinghof
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.
- Department of Marine Ecology, University of Bremen, Bremen, Germany.
- Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genova, Italy.
| | - Luis M Montilla
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Friederike Peiffer
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Grazia M Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (CNR), Ancona, Italy
| | - Ugo Marzocchi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Center for water technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Travis B Meador
- Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Francesca Margiotta
- Department of Research Infrastructures for marine biological resources, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Maria Abagnale
- Department of Research Infrastructures for marine biological resources, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Christian Wild
- Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Ulisse Cardini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.
- Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genova, Italy.
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11
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Ma X, Vanneste S, Chang J, Ambrosino L, Barry K, Bayer T, Bobrov AA, Boston L, Campbell JE, Chen H, Chiusano ML, Dattolo E, Grimwood J, He G, Jenkins J, Khachaturyan M, Marín-Guirao L, Mesterházy A, Muhd DD, Pazzaglia J, Plott C, Rajasekar S, Rombauts S, Ruocco M, Scott A, Tan MP, Van de Velde J, Vanholme B, Webber J, Wong LL, Yan M, Sung YY, Novikova P, Schmutz J, Reusch TBH, Procaccini G, Olsen JL, Van de Peer Y. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. NATURE PLANTS 2024; 10:240-255. [PMID: 38278954 PMCID: PMC7615686 DOI: 10.1038/s41477-023-01608-5] [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: 03/31/2023] [Accepted: 12/05/2023] [Indexed: 01/28/2024]
Abstract
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.
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Affiliation(s)
- Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiyang Chang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Luca Ambrosino
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Justin E Campbell
- Coastlines and Oceans Division, Institute of Environment, Florida International University-Biscayne Bay Campus, Miami, FL, USA
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria Luisa Chiusano
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agricultural Sciences, University Federico II of Naples, Naples, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Guifen He
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Lázaro Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Attila Mesterházy
- Centre for Ecological Research, Wetland Ecology Research Group, Debrecen, Hungary
| | - Danish-Daniel Muhd
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Min Pau Tan
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jozefien Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Li Lian Wong
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Mi Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yeong Yik Sung
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Polina Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
- National Biodiversity Future Centre, Palermo, Italy.
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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12
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Inoue T, Kohzu A, Akaji Y, Miura S, Baba S. Diazotrophic nitrogen fixation through aerial roots occurs in Avicennia marina: implications for adaptation of mangrove plant growth to low-nitrogen tidal flats. THE NEW PHYTOLOGIST 2024; 241:1464-1475. [PMID: 38013587 DOI: 10.1111/nph.19442] [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: 10/03/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Nitrogen limitation of primary production is common in coastal ecosystems. Mangrove trees maintain high levels of nitrogen fixation around their roots. The interior aerial space of mangrove roots, in which atmospheric gas is supplied through lenticels, could be efficient sites for nitrogen fixation. We measured tidal variations of partial pressure of N2 in root aerenchyma and conducted field experiments using 15 N2 as a tracer to track N2 movement through aerial roots of Avicennia marina. We used the acetylene reduction assay to identify the root parts harboring diazotrophs. The nitrogenase activity and estimated nitrogen fixation through aerenchyma were higher in pneumatophores and absorbing roots than in cable roots. Positive correlations between root nitrogen contents and turnover rates of root nitrogen derived from N2 through aerenchyma suggested that the internal supply of N2 to diazotrophs could be the main source for nitrogen assimilation by A. marina roots. Our results confirmed that N2 is supplied to diazotrophs through aerial roots and that nitrogen fixation occurs in A. marina roots. The aerial root structures, which occur across families of mangrove plants, could be an adaptation to survival in not only low-oxygen environments but also tidal flats with little plant-available nitrogen.
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Affiliation(s)
- Tomomi Inoue
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yasuaki Akaji
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shingo Miura
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shigeyuki Baba
- International Society for Mangrove Ecosystems, University of the Ryukyus, Nishihara, Okinawa, 903-0129, Japan
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13
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Graham OJ, Adamczyk EM, Schenk S, Dawkins P, Burke S, Chei E, Cisz K, Dayal S, Elstner J, Hausner ALP, Hughes T, Manglani O, McDonald M, Mikles C, Poslednik A, Vinton A, Wegener Parfrey L, Harvell CD. Manipulation of the seagrass-associated microbiome reduces disease severity. Environ Microbiol 2024; 26:e16582. [PMID: 38195072 DOI: 10.1111/1462-2920.16582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.
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Affiliation(s)
- Olivia J Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily M Adamczyk
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siobhan Schenk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phoebe Dawkins
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Samantha Burke
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily Chei
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kaitlyn Cisz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Sukanya Dayal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jack Elstner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Taylor Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Omisha Manglani
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Miles McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Chloe Mikles
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Anna Poslednik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Audrey Vinton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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14
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Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
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Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
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15
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Shen L, Feng J. NIN-at the heart of NItrogen-fixing Nodule symbiosis. FRONTIERS IN PLANT SCIENCE 2024; 14:1284720. [PMID: 38283980 PMCID: PMC10810997 DOI: 10.3389/fpls.2023.1284720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Legumes and actinorhizal plants establish symbiotic relationships with nitrogen-fixing bacteria, resulting in the formation of nodules. Nodules create an ideal environment for nitrogenase to convert atmospheric nitrogen into biological available ammonia. NODULE INCEPTION (NIN) is an indispensable transcription factor for all aspects of nodule symbiosis. Moreover, NIN is consistently lost in non-nodulating species over evolutions. Here we focus on recent advances in the signaling mechanisms of NIN during nodulation and discuss the role of NIN in the evolution of nitrogen-fixing nodule symbiosis.
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Affiliation(s)
- Lisha Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jian Feng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- CAS−JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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16
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Zheng J, Huang L, Yi H, Yan Y, Zhang X, Akresi J, Yin Y. Carbohydrate-active enzyme annotation in microbiomes using dbCAN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575125. [PMID: 38260309 PMCID: PMC10802576 DOI: 10.1101/2024.01.10.575125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
CAZymes or carbohydrate-active enzymes are critically important for human gut health, lignocellulose degradation, global carbon recycling, soil health, and plant disease. We developed dbCAN as a web server in 2012 and actively maintain it for automated CAZyme annotation. Considering data privacy and scalability, we provide run_dbcan as a standalone software package since 2018 to allow users perform more secure and scalable CAZyme annotation on their local servers. Here, we offer a comprehensive computational protocol on automated CAZyme annotation of microbiome sequencing data, covering everything from short read pre-processing to data visualization of CAZyme and glycan substrate occurrence and abundance in multiple samples. Using a real-world metagenomic sequencing dataset, this protocol describes commands for dataset and software preparation, metagenome assembly, gene prediction, CAZyme prediction, CAZyme gene cluster (CGC) prediction, glycan substrate prediction, and data visualization. The expected results include publication-quality plots for the abundance of CAZymes, CGCs, and substrates from multiple CAZyme annotation routes (individual sample assembly, co-assembly, and assembly-free). For the individual sample assembly route, this protocol takes ∼33h on a Linux computer with 40 CPUs, while other routes will be faster. This protocol does not require programming experience from users, but it does assume a familiarity with the Linux command-line interface and the ability to run Python scripts in the terminal. The target audience includes the tens of thousands of microbiome researchers who routinely use our web server. This protocol will encourage them to perform more secure, rapid, and scalable CAZyme annotation on their local computer servers.
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17
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Raut Y, Barr CR, Paris ER, Kapili BJ, Dekas AE, Capone DG. Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments. Front Microbiol 2024; 14:1312843. [PMID: 38249476 PMCID: PMC10796445 DOI: 10.3389/fmicb.2023.1312843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Macroalgae, commonly known as seaweed, are foundational species in coastal ecosystems and contribute significantly to coastal primary production globally. However, the impact of macroalgal decomposition on benthic biological nitrogen fixation (BNF) after deposition to the seafloor remains largely unexplored. In this study, we measure BNF rates at three different sites at the Big Fisherman's Cove on Santa Catalina Island, CA, USA, which is representative of globally distributed rocky bottom macroalgal habitats. Unamended BNF rates varied among sites (0.001-0.05 nmol N g-1 h -1) and were generally within the lower end of previously reported ranges. We hypothesized that the differences in BNF between sites were linked to the availability of organic matter. Indeed, additions of glucose, a labile carbon source, resulted in 2-3 orders of magnitude stimulation of BNF rates in bottle incubations of sediment from all sites. To assess the impact of complex, autochthonous organic matter, we simulated macroalgal deposition and remineralization with additions of brown (i.e., Macrocystis pyrifera and Dictyopteris), green (i.e., Codium fragile), and red (i.e., Asparagopsis taxiformis) macroalgae. While brown and green macroalgal amendments resulted in 53- to 520-fold stimulation of BNF rates-comparable to the labile carbon addition-red alga was found to significantly inhibit BNF rates. Finally, we employed nifH sequencing to characterize the diazotrophic community associated with macroalgal decomposition. We observed a distinct community shift in potential diazotrophs from primarily Gammaproteobacteria in the early stages of remineralization to a community dominated by Deltaproteobacteria (e.g., sulfate reducers), Bacteroidia, and Spirochaeta toward the latter phase of decomposition of brown, green, and red macroalgae. Notably, the nifH-containing community associated with red macroalgal detritus was distinct from that of brown and green macroalgae. Our study suggests coastal benthic diazotrophs are limited by organic carbon and demonstrates a significant and phylum-specific effect of macroalgal loading on benthic microbial communities.
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Affiliation(s)
- Yubin Raut
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Emily R. Paris
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Bennett J. Kapili
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Anne E. Dekas
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Douglas G. Capone
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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18
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Zhou W, Ling J, Shen X, Xu Z, Yang Q, Yue W, Liu H, Suo A, Dong J. Inoculation with plant growth-promoting rhizobacteria improves seagrass Thalassia hemprichii photosynthesis performance and shifts rhizosphere microbiome. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106260. [PMID: 38061311 DOI: 10.1016/j.marenvres.2023.106260] [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: 08/18/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 01/02/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) inoculation is a crucial strategy for maintaining the sustainability of agriculture and presents a promising solution for seagrass ecological restoration in the face of disturbances. However, the possible roles and functions of PGPRs in the seagrass rhizosphere remain unclear. Here, we isolated rhizosphere bacterial strains from both reef and coastal regions and screened two PGPR isolates regarding their in vivo functional traits. Subsequently, we conducted microcosm experiments to elucidate how PGPR inoculation affected seagrass photosynthesis and shape within each rhizosphere microbiome. Both screened PGPR strains, Raoultella terrigena NXT28 and Bacillus aryabhattai XT37, excelled at expressing a specific subset of plant-beneficial functions and increased the photosynthetic rates of the seagrass host. PGPR inoculation not only decreased the abundance of sulfur-cycling bacteria, it also improved the abundance of putative iron-cycling bacteria in the seagrass rhizosphere. Strain XT37 successfully colonized the seagrass rhizosphere and displayed a leading role in microbial network structure. As a nitrogen-fixing bacteria, NXT28 showed potential to change the microbial nitrogen cycle with denitrification in the rhizosphere and alter dissimilatory and assimilatory nitrate reduction in bulk sediment. These findings have implications for the development of eco-friendly strategies aimed at exploiting microbial communities to confer sulfide tolerance in coastal seagrass ecosystem.
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Affiliation(s)
- Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Juan Ling
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, China
| | - Xiaomei Shen
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Zhimeng Xu
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qingsong Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, China
| | - Weizhong Yue
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Hongbin Liu
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Anning Suo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Junde Dong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, China.
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19
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Pfister CA, Cardini U, Mirasole A, Montilla LM, Veseli I, Gattuso JP, Teixido N. Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification. Sci Rep 2023; 13:19996. [PMID: 37968499 PMCID: PMC10651887 DOI: 10.1038/s41598-023-47126-4] [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: 04/29/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6-17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.
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Affiliation(s)
- Catherine A Pfister
- The Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Alice Mirasole
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Luis M Montilla
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, USA
| | - Jean-Pierre Gattuso
- CNRS, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
- Institute for Sustainable Development and International Relations, Sciences Po, 27 Rue Saint Guillaume, 75007, Paris, France
| | - Nuria Teixido
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- CNRS, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
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20
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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21
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Zhang J, Yang Q, Yue W, Yang B, Zhou W, Chen L, Huang X, Zhang W, Dong J, Ling J. Seagrass Thalassia hemprichii and associated bacteria co-response to the synergistic stress of ocean warming and ocean acidification. ENVIRONMENTAL RESEARCH 2023; 236:116658. [PMID: 37454799 DOI: 10.1016/j.envres.2023.116658] [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: 03/11/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Seagrass meadows play vital ecological roles in the marine ecosystem. Global climate change poses considerable threats to seagrass survival. However, it is unclear how seagrass and its associated bacteria will respond under future complex climate change scenarios. This study explored the effects of ocean warming (+2 °C) and ocean acidification (-0.4 units) on seagrass physiological indexes and bacterial communities (sediment and rhizosphere bacteria) of the seagrass Thalassia hemprichii during an experimental exposure of 30 days. Results demonstrated that the synergistic effect of ocean warming and ocean acidification differed from that of one single factor on seagrass and the associated bacterial community. The seagrass showed a weak resistance to ocean warming and ocean acidification, which manifested through the increase in the activity of typical oxidoreductase enzymes. Moreover, the synergistic effect of ocean warming and ocean acidification caused a significant decrease in seagrass's chlorophyll content. Although the bacterial community diversity exhibited higher resistance to ocean warming and ocean acidification, further bacterial functional analysis revealed the synergistic effect of ocean warming and ocean acidification led to significant increases in SOX-related genes abundance which potentially supported the seagrass in resisting climate stress by producing sulfates and oxidizing hydrogen sulfide. More stable bacterial communities were detected in the seagrass rhizosphere under combined ocean warming and ocean acidification. While for one single environmental stress, simpler networks were detected in the rhizosphere. In addition, the observed significant correlations between several modules of the bacterial community and the physiological indexes of the seagrass indicate the possible intimate interaction between seagrass and bacteria under ocean warming and ocean acidification. This study extends our understanding regarding the role of seagrass associated bacterial communities and sheds light on both the prediction and preservation of the seagrass meadow ecosystems in response to global climate change.
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Affiliation(s)
- Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Weizhong Yue
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Bing Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Luxiang Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenqian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China.
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China.
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22
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Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. THE NEW PHYTOLOGIST 2023; 240:439-451. [PMID: 37381111 PMCID: PMC10962543 DOI: 10.1111/nph.19112] [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: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bacteria colonize plant roots and engage in reciprocal interactions with their hosts. However, the contribution of individual taxa or groups of bacteria to plant nutrition and fitness is not well characterized due to a lack of in situ evidence of bacterial activity. To address this knowledge gap, we developed an analytical approach that combines the identification and localization of individual bacteria on root surfaces via gold-based in situ hybridization with correlative NanoSIMS imaging of incorporated stable isotopes, indicative of metabolic activity. We incubated Kosakonia strain DS-1-associated, gnotobiotically grown rice plants with 15 N-N2 gas to detect in situ N2 fixation activity. Bacterial cells along the rhizoplane showed heterogeneous patterns of 15 N enrichment, ranging from the natural isotope abundance levels up to 12.07 at% 15 N (average and median of 3.36 and 2.85 at% 15 N, respectively, n = 697 cells). The presented correlative optical and chemical imaging analysis is applicable to a broad range of studies investigating plant-microbe interactions. For example, it enables verification of the in situ metabolic activity of host-associated commercialized strains or plant growth-promoting bacteria, thereby disentangling their role in plant nutrition. Such data facilitate the design of plant-microbe combinations for improvement of crop management.
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Affiliation(s)
- Hannes Schmidt
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Stefan Gorka
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Doctoral School in Microbiology and Environmental ScienceUniversity of ViennaVienna1030Austria
| | - David Seki
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
- Large‐Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems ScienceUniversity of ViennaVienna1030Austria
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23
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Abstract
Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.
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Affiliation(s)
- Peng Xu
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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24
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Xia Y, He R, Xu W, Zhang J. The Zoige pioneer plant Leymus secalinus has different endophytic bacterial community structures to adapt to environmental conditions. PeerJ 2023; 11:e15363. [PMID: 37220526 PMCID: PMC10200098 DOI: 10.7717/peerj.15363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/16/2023] [Indexed: 05/25/2023] Open
Abstract
Background Leymus secalinus is a pioneer plant grown in the Zoige desertified alpine grassland and it is also one of the dominant plant species used for environmental remediation. L. secalinus plays a large role in vegetation reconstruction in sandy land, but the abundance and diversity of its endophytes have not yet been investigated. Objectives This study was performed to investigate the changes in the endophytic bacterial community structure of L. secalinus under different ecological environments and to analyze the effects of environmental changes and different plant tissues on the L. secalinus endophytic bacteria. Methods Leaf, stem, and root tissue samples of L. secalinus were collected from Zoige Glassland (Alpine sandy land) and an open field nursery (Control). DNA was extracted and the 16S ribosomal DNA was amplified. The sequence library was sequenced on an Illumina MiSeq platform and clustered by operational taxonomic units (OTUs). α-diversity and β-diversity analyses, species diversity analyses, functional prediction, and redundancy (RDA) analyses for the soil physicochemical properties were conducted. Results α-diversity and β-diversity analyses showed that the endophytic bacteria in L. secalinus varied in different areas and tissues. The abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, which is related to nitrogen fixation, increased significantly in the L. secalinus found in the Zoige Grassland.Moreover, the abundance of nutrition metabolism and anti-stress abilities increased in functional prediction in the desert samples. The soil physicochemical properties had an insignificant influence on bacterial diversity. Conclusion The changes in the endophytic bacterial community structure in L. secalinus were significant and were caused by environmental alterations and plant choice. The endophytic bacteria in L. secalinus grown in alpine sandy land may have greater anti-stress properties and the ability to fix nitrogen, which has potential value in environmental remediation and agricultural production.
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Affiliation(s)
- Yue Xia
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ruipeng He
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Wanru Xu
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jie Zhang
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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25
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Wilkinson H, Coppock A, Richmond BL, Lagunas B, Gifford ML. Plant-Environment Response Pathway Regulation Uncovered by Investigating Non-Typical Legume Symbiosis and Nodulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:1964. [PMID: 37653881 PMCID: PMC10223263 DOI: 10.3390/plants12101964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Nitrogen is an essential element needed for plants to survive, and legumes are well known to recruit rhizobia to fix atmospheric nitrogen. In this widely studied symbiosis, legumes develop specific structures on the roots to host specific symbionts. This review explores alternate nodule structures and their functions outside of the more widely studied legume-rhizobial symbiosis, as well as discussing other unusual aspects of nodulation. This includes actinorhizal-Frankia, cycad-cyanobacteria, and the non-legume Parasponia andersonii-rhizobia symbioses. Nodules are also not restricted to the roots, either, with examples found within stems and leaves. Recent research has shown that legume-rhizobia nodulation brings a great many other benefits, some direct and some indirect. Rhizobial symbiosis can lead to modifications in other pathways, including the priming of defence responses, and to modulated or enhanced resistance to biotic and abiotic stress. With so many avenues to explore, this review discusses recent discoveries and highlights future directions in the study of nodulation.
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Affiliation(s)
- Helen Wilkinson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alice Coppock
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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26
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Pang Z, Mao X, Zhou S, Yu S, Liu G, Lu C, Wan J, Hu L, Xu P. Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage. MICROBIOME 2023; 11:85. [PMID: 37085934 PMCID: PMC10120241 DOI: 10.1186/s40168-023-01525-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis. RESULTS Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat. Metabolite and microbiota profiling showed that the aerial root mucilage is enriched in carbohydrates and diazotrophic bacteria. Nitrogen isotope-labeling experiments, 15N natural abundance, and gene expression analysis indicated that the aerial root-mucilage microbiota could fix atmospheric nitrogen to support plant growth. While the aerial root mucilage is a hotspot of nutrients, we did not observe high abundance of other environmental and pathogenic microbes inside. We further identified a fungus isolate in mucilage that has shown broad-spectrum antimicrobial activities, but solely allows the growth of diazotrophic bacteria. This "friendly" fungus may be the key driver to maintain nitrogen fixation function in the mucilage microhabitat. Video Abstract CONCLUSION: The discovery of new biological function and mucilage-habitat friendly fungi provides insights into microbial homeostasis maintenance of microenvironmental function and rhizosphere ecology.
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Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shaoqun Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sheng Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guizhou Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Chengkai Lu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jinpeng Wan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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27
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Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY. An agroecological structure model of compost-soil-plant interactions for sustainable organic farming. ISME COMMUNICATIONS 2023; 3:28. [PMID: 37002405 PMCID: PMC10066230 DOI: 10.1038/s43705-023-00233-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan.
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan.
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan.
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan.
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | | | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunya Taguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Teruo Matsushita
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshiaki Ito
- Keiyo Gas Energy Solution Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Sankichi Horiuchi
- Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa, Chiba, 277-8567, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kenichi Mori
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Miroku Co., Ltd., Kitsuki, Oita, 873-0021, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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28
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Miyamoto H, Kawachi N, Kurotani A, Moriya S, Suda W, Suzuki K, Matsuura M, Tsuji N, Nakaguma T, Ishii C, Tsuboi A, Shindo C, Kato T, Udagawa M, Satoh T, Wada S, Masuya H, Miyamoto H, Ohno H, Kikuchi J. Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture. ENVIRONMENTAL RESEARCH 2023; 219:115130. [PMID: 36563976 DOI: 10.1016/j.envres.2022.115130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 05/02/2023]
Abstract
Coastal seagrass meadows are essential in blue carbon and aquatic ecosystem services. However, this ecosystem has suffered severe eutrophication and destruction due to the expansion of aquaculture. Therefore, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found near the shore downstream of the onshore aquaculture facility. To evaluate the characteristics of the sediment for growing seagrass, physicochemical properties and bacterial ecological evaluations of the sediment were conducted. Evaluation of chemical properties in seagrass sediments confirmed a significant increase in total carbon and a decrease in zinc content. Association analysis and linear discriminant analysis refined bacterial candidates specified in seagrass overgrown- and nonovergrown-sediment. Energy landscape analysis indicated that the symbiotic bacterial groups of seagrass sediment were strongly affected by the distance close to the seagrass-growing aquaculture facility despite their bacterial population appearing to fluctuate seasonally. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal sediment symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the sediment symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan.
| | | | - Atsushi Kurotani
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Wataru Suda
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Suzuki
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan
| | - Chie Shindo
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Udagawa
- Keiyo Gas Energy Solution Co. Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0329, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Hiroshi Masuya
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan; Miroku Co.Ltd.: Kitsuki, Oita, 873-0021, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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29
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Yu Z, Peng X, Liu L, Yang JR, Zhai X, Xue Y, Mo Y, Yang J. Microbial one‑carbon and nitrogen metabolisms are beneficial to the reservoir recovery after cyanobacterial bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159004. [PMID: 36155037 DOI: 10.1016/j.scitotenv.2022.159004] [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: 07/06/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacterial blooms have profound effects on the structure and function of plankton communities in inland waters, but few studies have focused on the effects of microbial-based processes in one‑carbon and nitrogen cycling on water quality improvement following the bloom. Here, we compared the structure and function of the bacterial community, focusing on microbial one‑carbon and nitrogen metabolisms during and after a cyanobacterial Microcystis bloom in a deep subtropical reservoir. Our data showed that microbial one‑carbon and nitrogen cycles were closely related to different periods of the bloom, and the changes of functional genes in microbial carbon and nitrogen cycling showed the same consistent trend as that of Methylomonas sp. With the receding of the bloom, the abundance of Methylomonas as well as the functional genes of microbial one‑carbon and nitrogen cycling reached the peak and then recovered. Our results indicate that microbial one‑carbon and nitrogen metabolisms were beneficial to the recovery of water quality from the cyanobacterial bloom. This study lays a foundation for a deep understanding of the cyanobacterial decomposition mediated by microbes in one‑carbon and nitrogen cycles in inland freshwaters.
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Affiliation(s)
- Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xuan Peng
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jun R Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xingyu Zhai
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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30
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Conte C, Apostolaki ET, Vizzini S, Migliore L. A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations. PLANTS (BASEL, SWITZERLAND) 2023; 12:350. [PMID: 36679063 PMCID: PMC9863530 DOI: 10.3390/plants12020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.
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Affiliation(s)
- Chiara Conte
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- CoNISMa, National Interuniversity Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Roma, Italy
| | - Luciana Migliore
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, Via Isimbardi 10, 22060 Novedrate (CO), Italy
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31
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Miyamoto H, Kikuchi J. An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach. Comput Struct Biotechnol J 2023; 21:869-878. [PMID: 36698969 PMCID: PMC9860287 DOI: 10.1016/j.csbj.2023.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba, Chiba 260-0034, Japan
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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32
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
- Nancy A Eckardt
- Senior Features Editor, The Plant Cell, American Society of Plant Biologists, USA
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Huang X, Zeng Z, Chen Z, Tong X, Jiang J, He C, Xiang T. Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway. Front Microbiol 2022; 13:1035167. [PMID: 36406393 PMCID: PMC9671153 DOI: 10.3389/fmicb.2022.1035167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 09/24/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic Rhizobium sp. WYJ-E13 strain from the roots of Curcuma wenyujin Y.H. Chen et C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that Rhizobium sp. WYJ-E13 possesses the collinear region among three species: Rhizobium acidisoli FH23, Rhizobium gallicum R602 and Rhizobium phaseoli R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (nifU, gltA, gltB, gltD, glnA, glnD), hormone production (trp ABCDEFS), sulfur metabolism (cysD, cysE, cysK, cysN), phosphate metabolism (pstA, pstC, phoB, phoH, phoU), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for Rhizobium sp. WYJ-E13 associated with C. wenyujin. WYJ-E13 strain has a high potential to be used as Curcuma biofertilizer for sustainable agriculture.
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Affiliation(s)
- Xiaoping Huang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Zhehao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
| | - Xiaxiu Tong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jie Jiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenjing He
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Taihe Xiang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, China
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34
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Abstract
Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.
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35
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Investigating plant-microbe interactions within the root. Arch Microbiol 2022; 204:639. [PMID: 36136275 DOI: 10.1007/s00203-022-03257-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants' control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant-microbe interaction.
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36
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Unsworth RKF, Cullen-Unsworth LC, Jones BLH, Lilley RJ. The planetary role of seagrass conservation. Science 2022; 377:609-613. [PMID: 35926055 DOI: 10.1126/science.abq6923] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Seagrasses are remarkable plants that have adapted to live in a marine environment. They form extensive meadows found globally that bioengineer their local environments and preserve the coastal seascape. With the increasing realization of the planetary emergency that we face, there is growing interest in using seagrasses as a nature-based solution for greenhouse gas mitigation. However, seagrass sensitivity to stressors is acute, and in many places, the risk of loss and degradation persists. If the ecological state of seagrasses remains compromised, then their ability to contribute to nature-based solutions for the climate emergency and biodiversity crisis remains in doubt. We examine the major ecological role that seagrasses play and how rethinking their conservation is critical to understanding their part in fighting our planetary emergency.
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Affiliation(s)
- Richard K F Unsworth
- Seagrass Ecosystem Research Group, Faculty of Science and Engineering, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK.,Project Seagrass, The Yard, Bridgend Industrial Estate, Bridgend CF31 3EB, Wales, UK
| | - Leanne C Cullen-Unsworth
- Seagrass Ecosystem Research Group, Faculty of Science and Engineering, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK.,Project Seagrass, The Yard, Bridgend Industrial Estate, Bridgend CF31 3EB, Wales, UK
| | - Benjamin L H Jones
- Project Seagrass, The Yard, Bridgend Industrial Estate, Bridgend CF31 3EB, Wales, UK.,Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Richard J Lilley
- Project Seagrass, The Yard, Bridgend Industrial Estate, Bridgend CF31 3EB, Wales, UK
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37
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Sogin EM, Michellod D, Gruber-Vodicka HR, Bourceau P, Geier B, Meier DV, Seidel M, Ahmerkamp S, Schorn S, D'Angelo G, Procaccini G, Dubilier N, Liebeke M. Sugars dominate the seagrass rhizosphere. Nat Ecol Evol 2022; 6:866-877. [PMID: 35501482 PMCID: PMC9262712 DOI: 10.1038/s41559-022-01740-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/21/2022] [Indexed: 12/14/2022]
Abstract
Seagrasses are among the most efficient sinks of carbon dioxide on Earth. While carbon sequestration in terrestrial plants is linked to the microorganisms living in their soils, the interactions of seagrasses with their rhizospheres are poorly understood. Here, we show that the seagrass, Posidonia oceanica excretes sugars, mainly sucrose, into its rhizosphere. These sugars accumulate to µM concentrations-nearly 80 times higher than previously observed in marine environments. This finding is unexpected as sugars are readily consumed by microorganisms. Our experiments indicated that under low oxygen conditions, phenolic compounds from P. oceanica inhibited microbial consumption of sucrose. Analyses of the rhizosphere community revealed that many microbes had the genes for degrading sucrose but these were only expressed by a few taxa that also expressed genes for degrading phenolics. Given that we observed high sucrose concentrations underneath three other species of marine plants, we predict that the presence of plant-produced phenolics under low oxygen conditions allows the accumulation of labile molecules across aquatic rhizospheres.
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Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- University of California at Merced, Merced, CA, USA.
| | - Dolma Michellod
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences of the University of Bremen, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dimitri V Meier
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Michael Seidel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | | | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Grace D'Angelo
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM-Center for Marine Environmental Sciences of the University of Bremen, Bremen, Germany.
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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38
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Jiang Z, Liu S, Cui L, He J, Fang Y, Premarathne C, Li L, Wu Y, Huang X, Kumar M. Sand supplementation favors tropical seagrass Thalassia hemprichii in eutrophic bay: implications for seagrass restoration and management. BMC PLANT BIOLOGY 2022; 22:296. [PMID: 35710355 PMCID: PMC9205049 DOI: 10.1186/s12870-022-03647-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sediment is crucial for the unique marine angiosperm seagrass growth and successful restoration. Sediment modification induced by eutrophication also exacerbates seagrass decline and reduces plantation and transplantation survival rates. However, we lack information regarding the influence of sediment on seagrass photosynthesis and the metabolics, especially regarding the key secondary metabolic flavone. Meanwhile, sulfation of flavonoids in seagrass may mitigate sulfide intrusion, but limited evidence is available. RESULTS We cultured the seagrass Thalassia hemprichii under controlled laboratory conditions in three sediment types by combining different ratios of in-situ eutrophic sediment and coarse beach sand. We examined the effects of beach sand mixed with natural eutrophic sediments on seagrass using photobiology, metabolomics and isotope labelling approaches. Seagrasses grown in eutrophic sediments mixed with beach sand exhibited significantly higher photosynthetic activity, with a larger relative maximum electron transport rate and minimum saturating irradiance. Simultaneously, considerably greater belowground amino acid and flavonoid concentrations were observed to counteract anoxic stress in eutrophic sediments without mixed beach sand. This led to more positive belowground stable sulfur isotope ratios in eutrophic sediments with a lower Eh. CONCLUSIONS These results indicated that coarse beach sand indirectly enhanced photosynthesis in T. hemprichii by reducing sulfide intrusion with lower amino acid and flavonoid concentrations. This could explain why T. hemprichii often grows better on coarse sand substrates. Therefore, it is imperative to consider adding beach sand to sediments to improve the environmental conditions for seagrass and restore seagrass in eutrophic ecosystems.
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Affiliation(s)
- Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
- Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jialu He
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chanaka Premarathne
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Linglan Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
- University of Chinese Academy of Sciences, Beijing, 100049, PR China.
- Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Manoj Kumar
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
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Capó-Bauçà S, Iñiguez C, Aguiló-Nicolau P, Galmés J. Correlative adaptation between Rubisco and CO 2-concentrating mechanisms in seagrasses. NATURE PLANTS 2022; 8:706-716. [PMID: 35729266 DOI: 10.1038/s41477-022-01171-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/13/2022] [Indexed: 05/19/2023]
Abstract
Submerged angiosperms sustain some of the most productive and diverse ecosystems worldwide. However, their carbon acquisition and assimilation mechanisms remain poorly explored, missing an important step in the evolution of photosynthesis during the colonization of aquatic environments by angiosperms. Here we reveal a convergent kinetic adaptation of Rubisco in phylogenetically distant seagrass species that share catalytic efficiencies and CO2 and O2 affinities up to three times lower than those observed in phylogenetically closer angiosperms from terrestrial, freshwater and brackish-water habitats. This Rubisco kinetic convergence was found to correlate with the effectiveness of seagrass CO2-concentrating mechanisms (CCMs), which probably evolved in response to the constant CO2 limitation in marine environments. The observed Rubisco kinetic adaptation in seagrasses more closely resembles that seen in eukaryotic algae operating CCMs rather than that reported in terrestrial C4 plants. Our results thus demonstrate a general pattern of co-evolution between Rubisco function and biophysical CCM effectiveness that traverses distantly related aquatic lineages.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain.
| | - Pere Aguiló-Nicolau
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Spain
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The marine nitrogen cycle: new developments and global change. Nat Rev Microbiol 2022; 20:401-414. [PMID: 35132241 DOI: 10.1038/s41579-022-00687-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/25/2022]
Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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41
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A seagrass harbours a nitrogen-fixing bacterial partner. Nature 2021. [DOI: 10.1038/d41586-021-02956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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