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Ben zineb A, Barkaoui K, Karray F, Mhiri N, Sayadi S, Mliki A, Gargouri M. Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions. Front Microbiol 2022; 13:977797. [PMID: 36386625 PMCID: PMC9650424 DOI: 10.3389/fmicb.2022.977797] [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: 06/24/2022] [Accepted: 10/06/2022] [Indexed: 09/08/2024] Open
Abstract
Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes' rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.
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Affiliation(s)
- Ameni Ben zineb
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Karim Barkaoui
- CIRAD, UMR ABSys, Montpellier, France
- ABSys, Univ Montpellier, CIHEAM-IAMM, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Sami Sayadi
- Biotechnology Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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2
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Garcias-Bonet N, Eguíluz VM, Díaz-Rúa R, Duarte CM. Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environ Microbiol 2020; 23:2021-2034. [PMID: 33225561 DOI: 10.1111/1462-2920.15334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, E-07122, Spain
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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3
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Zhang X, Zhao C, Yu S, Jiang Z, Liu S, Wu Y, Huang X. Rhizosphere Microbial Community Structure Is Selected by Habitat but Not Plant Species in Two Tropical Seagrass Beds. Front Microbiol 2020; 11:161. [PMID: 32194512 PMCID: PMC7065525 DOI: 10.3389/fmicb.2020.00161] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 11/19/2022] Open
Abstract
Rhizosphere bacterial community structures and their determining drivers have been studied in a variety of marine and freshwater ecosystems for a range of plant species. However, there is still limited information about the influence of habitat on microbial communities in seagrass beds. This study aimed to determine which factors (habitat and plant species) have crucial roles on the rhizospheric bacteria associated with two tropical seagrass species (Thalassia hemprichii and Enhalus acoroides) that are dominant at Xincun Bay and Tanmen Harbor in Hainan Island, South China. Using Illumina HiSeq sequencing, we observed substantial differences in the bacterial richness, diversity, and relative abundances of taxa between the two habitats, which were characterized differently in sediment type and nutrient status. Rhizospheric bacteria from sandy sediment at the eutrophic Xincun Bay were dominated by Desulfobacteraceae and Helicobacteraceae, which are primarily involved in sulfate cycling, whereas rhizosphere microbes from the reef flat at oligotrophic Tanmen Harbor were dominated by Vibrionaceae and Woeseiaceae, which may play important roles in nitrogen and carbon fixing. Additionally, we speculated that host-specific effects of these two seagrass species may be covered under nutrient-rich conditions and in mixed community patches, emphasizing the importance of the nutrient status of the sediment and vegetation composition of the patches. In addition, our study confirmed that Proteobacteria was more adapted to the rhizosphere environment than to low-carbon conditions that occurred in bulk sediment, which was primarily dominated by well-known fermentative bacteria in the phylum Firmicutes.
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Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Shuo Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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4
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Brodersen KE, Siboni N, Nielsen DA, Pernice M, Ralph PJ, Seymour J, Kühl M. Seagrass rhizosphere microenvironment alters plant-associated microbial community composition. Environ Microbiol 2018; 20:2854-2864. [PMID: 29687545 DOI: 10.1111/1462-2920.14245] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 11/26/2022]
Abstract
The seagrass rhizosphere harbors dynamic microenvironments, where plant-driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass-mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2 S and pH occurred. Significantly higher relative abundances of sulphate-reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide-oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2 S re-oxidation here were similar to those observed in a pre-sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant-microbe interactions potentially affecting seagrass health.
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Affiliation(s)
- Kasper Elgetti Brodersen
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia.,Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Daniel A Nielsen
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Peter J Ralph
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Justin Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Michael Kühl
- Climate Change Cluster, Faculty of Science, University of Technology Sydney (UTS), Sydney, NSW, Australia.,Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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5
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Schrameyer V, York PH, Chartrand K, Ralph PJ, Kühl M, Brodersen KE, Rasheed MA. Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef). MARINE ENVIRONMENTAL RESEARCH 2018; 136:38-47. [PMID: 29472034 DOI: 10.1016/j.marenvres.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/11/2018] [Indexed: 06/08/2023]
Abstract
Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.
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Affiliation(s)
- Verena Schrameyer
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Paul H York
- Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
| | - Kathryn Chartrand
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
| | - Peter J Ralph
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Michael Kühl
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Kasper Elgetti Brodersen
- Climate Change Cluster, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia; Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
| | - Michael A Rasheed
- Centre for Tropical Water & Aquatic Ecosystem Research, James Cook University, Cairns, QLD, Australia
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Cúcio C, Engelen AH, Costa R, Muyzer G. Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific. Front Microbiol 2016; 7:440. [PMID: 27065991 PMCID: PMC4815253 DOI: 10.3389/fmicb.2016.00440] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.
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Affiliation(s)
- Catarina Cúcio
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Aschwin H. Engelen
- Marine Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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