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Palmer J, Bugnot AB, Filippini G, Gribben PE, Varkey D, Erickson K, Dafforn KA. The influence of bioturbator activity on sediment bacterial structure and function is moderated by environment. MARINE ENVIRONMENTAL RESEARCH 2024; 201:106702. [PMID: 39213892 DOI: 10.1016/j.marenvres.2024.106702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/04/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
Bioturbation in coastal sediments plays a crucial role in biogeochemical cycling. However, a key knowledge gap is the extent to which bioturbation influences bacterial community diversity and ecosystem processes, such as nitrogen cycling. This study paired bacterial diversity, bioturbation activity and in situ flux measurements of oxygen and nitrogen from bioturbated sediments at six estuaries along the East coast of Australia. Bacterial community diversity, composition and predicted functional profiles were similar across burrow and surface sediments but were significantly influenced by bioturbator activity (measured as number of burrows) at sites with higher fine grain content. Sediment oxygen demand increased with bioturbator activity but changes in nitrogen cycling (as measured by fluxes and predicted bacterial functional gene analysis) were more spatially variable and were unrelated to bioturbator activity and bacterial community shifts. This study highlights how bioturbator activity influences bacterial community structure and functioning and what implications this has for biogeochemical cycles in estuarine sediments.
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Affiliation(s)
- Julia Palmer
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
| | - Ana B Bugnot
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia; CSIRO Environment, Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD, 4067, Australia
| | - Giulia Filippini
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia; Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul E Gribben
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Katherine Erickson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Katherine A Dafforn
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia; Sydney Institute of Marine Science, Mosman, New South Wales, Australia
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Yang X, Garuglieri E, Van Goethem MW, Marasco R, Fusi M, Daffonchio D. Mangrovimonas cancribranchiae sp. nov., a novel bacterial species associated with the gills of the fiddler crab Cranuca inversa (Brachyura, Ocypodidae) from Red Sea mangroves. Int J Syst Evol Microbiol 2024; 74:006415. [PMID: 38865172 PMCID: PMC11261673 DOI: 10.1099/ijsem.0.006415] [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: 03/14/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
Two bacteria, UG2_1T and UG2_2, were isolated from the gill tissues of the mangrove fiddler crab Cranuca inversa collected on the east coast of the Red Sea (Thuwal, Saudi Arabia). The cells are Gram-negative, rod-shaped, orange-pigmented, motile by gliding with no flagella, strictly aerobic, and grow at 20-37 °C (optimum, 28-35 °C), at pH 5.0-9.0 (optimum, pH 6.0-7.0), and with 1-11 % (w/v) NaCl (optimum, 2-4 %). They were positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolates UG2_1T and UG2_2 belong to the genus Mangrovimonas, showing the highest similarity to Mangrovimonas spongiae HN-E26T (99.4 %). Phylogenomic analysis based on the whole genomes, independently using 49 and 120 concatenated genes, showed that strains UG2_1T and UG2_2 formed a monophyletic lineage in a different cluster from other type strain species within the genus Mangrovimonas. The genome sizes were 3.08 and 3.07 Mbp for UG2_1T and UG2_2, respectively, with a G+C content of 33.8 mol% for both strains. Values of average nucleotide identity and digital DNA-DNA hybridization between the strains and closely related species were 91.0 and 43.5 %, respectively. Chemotaxonomic analysis indicated that both strains had iso-C15 : 0 and iso-C15 : 1 G as dominant fatty acids, and the primary respiratory quinone was identified as MK-6. The major polar lipids comprised phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid, two unidentified aminolipids, and four unidentified lipids. Based on phylogenetic, phylogenomic, genome relatedness, phenotypic, and chemotaxonomical data, the two isolates represent a novel species within the genus Mangrovimonas, with the proposed name Mangrovimonas cancribranchiae sp. nov., and the type strain UG2_1T (=KCTC 102158T=DSM 117025T).
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Affiliation(s)
- Xinyuan Yang
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marc W. Van Goethem
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Marco Fusi
- Dove Marine Laboratory, School of Natural and Environmental Sciences Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Garuglieri E, Marasco R, Odobel C, Chandra V, Teillet T, Areias C, Sánchez-Román M, Vahrenkamp V, Daffonchio D. Searching for microbial contribution to micritization of shallow marine sediments. Environ Microbiol 2024; 26:e16573. [PMID: 38217094 DOI: 10.1111/1462-2920.16573] [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: 07/25/2023] [Accepted: 12/21/2023] [Indexed: 01/15/2024]
Abstract
Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.
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Affiliation(s)
- Elisa Garuglieri
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ramona Marasco
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Charlene Odobel
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Viswasanthi Chandra
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas Teillet
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Camila Areias
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Mónica Sánchez-Román
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit, Amsterdam, the Netherlands
| | - Volker Vahrenkamp
- Ali I. Al-Naimi Petroleum Engineering Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Division of Biological Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Abd Rahim NH, Cannicci S, Ibrahim YS, Not C, Idris I, Mohd Jani J, Dahdouh-Guebas F, Satyanarayana B. Commercially important mangrove crabs are more susceptible to microplastic contamination than other brachyuran species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166271. [PMID: 37586534 DOI: 10.1016/j.scitotenv.2023.166271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Brachyuran crabs are ecologically and economically important macrofauna in mangrove habitats. However, they are exposed to various contaminants, including plastics, which bioaccumulate in relation to their feeding modes. Setiu Wetlands is a unique place on the east coast of Peninsular Malaysia where different ecosystems such as mangroves, lagoon, beaches, etc., are duly connected and influencing each other. In recent years, the shifted river mouth has threatened these wetlands, causing severe hydrodynamic changes in the lagoon, especially in the core mangrove zone. The present study tested microplastics (MPs) contamination in the mangroves through brachyuran crabs as indicators. Three sampling sites, namely Pulau Layat, Kampung Pengkalan Gelap, and Pulau Sutung were chosen. The four abundant crab species Parasesarma eumolpe, Metaplax elegans, Austruca annulipes, and Scylla olivacea, which display different feeding behaviours were collected from all sites covering the dry (Feb-Mar 2021) and the wet (Dec 2021-Jan 2022) seasonal periods. There were significant differences in the seasonal abundance of MPs among crab species. The highest accumulation of MPs in the crab stomachs in the dry season could be linked to subdued water circulation and poor material dispersion. Besides the lower MPs in the wet period due to improved water exchange conditions, its significant presence in the stomachs of S. olivacea indicates the role of its feeding behaviour as a carnivore. In addition, the micro-Fourier transform infrared spectroscopy (micro-FTIR) revealed the widespread occurrence of polymers such as rayon and polyester in all species across the sites. Given the fact that crabs like S. olivacea are commercially important and the ones contaminated with MPs can cause detrimental effects on the local community's health, further managerial actions are needed to assure sustainable management of the Setiu Wetlands.
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Affiliation(s)
- Nur Hannah Abd Rahim
- Mangrove Research Unit (MARU), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia.
| | - Stefano Cannicci
- Department of Biology, University of Florence, 50019 Florence, Italy; Swire Institute for Marine Science, The University of Hong Kong, Hong Kong; Mangrove Specialist Group (MSG), Species Survival Commission (SSC), International Union for the Conservation of Nature (IUCN), c/o Zoological Society of London, London, United Kingdom
| | - Yusof Shuaib Ibrahim
- Mangrove Research Unit (MARU), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia; Microplastic Research Interest Group (MRIG), Faculty of Science and Marine Environment, Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia
| | - Christelle Not
- Environmental Geochemistry & Oceanography Research Group, Department of Earth Sciences, The University of Hong Kong, Hong Kong
| | - Izwandy Idris
- Mangrove Research Unit (MARU), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia; South China Sea Repository and Reference Centre, Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia
| | - Jarina Mohd Jani
- Mangrove Research Unit (MARU), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia; Biodiversity Conservation and Management Program, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia
| | - Farid Dahdouh-Guebas
- Mangrove Specialist Group (MSG), Species Survival Commission (SSC), International Union for the Conservation of Nature (IUCN), c/o Zoological Society of London, London, United Kingdom; Systems Ecology and Resource Management Research Unit (SERM), Université Libre de Bruxelles-ULB, 1050 Brussels, Belgium; Ecology & Biodiversity Research Unit, Department of Biology, Vrije Universiteit Brussel-VUB, 1050 Brussels, Belgium
| | - Behara Satyanarayana
- Mangrove Research Unit (MARU), Institute of Oceanography and Environment (INOS), Universiti Malaysia Terengganu (UMT), Kuala Nerus 21300, Malaysia; Mangrove Specialist Group (MSG), Species Survival Commission (SSC), International Union for the Conservation of Nature (IUCN), c/o Zoological Society of London, London, United Kingdom; Systems Ecology and Resource Management Research Unit (SERM), Université Libre de Bruxelles-ULB, 1050 Brussels, Belgium.
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5
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Fusi M, Ngugi DK, Marasco R, Booth JM, Cardinale M, Sacchi L, Clementi E, Yang X, Garuglieri E, Fodelianakis S, Michoud G, Daffonchio D. Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation. MICROBIOME 2023; 11:189. [PMID: 37612775 PMCID: PMC10463870 DOI: 10.1186/s40168-023-01629-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND The transition from water to air is a key event in the evolution of many marine organisms to access new food sources, escape water hypoxia, and exploit the higher and temperature-independent oxygen concentration of air. Despite the importance of microorganisms in host adaptation, their contribution to overcoming the challenges posed by the lifestyle changes from water to land is not well understood. To address this, we examined how microbial association with a key multifunctional organ, the gill, is involved in the intertidal adaptation of fiddler crabs, a dual-breathing organism. RESULTS Electron microscopy revealed a rod-shaped bacterial layer tightly connected to the gill lamellae of the five crab species sampled across a latitudinal gradient from the central Red Sea to the southern Indian Ocean. The gill bacterial community diversity assessed with 16S rRNA gene amplicon sequencing was consistently low across crab species, and the same actinobacterial group, namely Ilumatobacter, was dominant regardless of the geographic location of the host. Using metagenomics and metatranscriptomics, we detected that these members of actinobacteria are potentially able to convert ammonia to amino acids and may help eliminate toxic sulphur compounds and carbon monoxide to which crabs are constantly exposed. CONCLUSIONS These results indicate that bacteria selected on gills can play a role in the adaptation of animals in dynamic intertidal ecosystems. Hence, this relationship is likely to be important in the ecological and evolutionary processes of the transition from water to air and deserves further attention, including the ontogenetic onset of this association. Video Abstract.
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Affiliation(s)
- Marco Fusi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK.
| | - David K Ngugi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Ramona Marasco
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jenny Marie Booth
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Massimiliano Cardinale
- Institute of Applied Microbiology Research Center for BioSystems, Land Use, and Nutrition (IFZ) Justus-Liebig-University Giessen, D-35392, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Lecce-Monteroni, I-73100, Lecce, Italy
| | - Luciano Sacchi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Emanuela Clementi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Xinyuan Yang
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Stilianos Fodelianakis
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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6
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Booth JM, Fusi M, Marasco R, Daffonchio D. The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves. Microb Biotechnol 2023. [PMID: 37209285 PMCID: PMC10364319 DOI: 10.1111/1751-7915.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023] Open
Abstract
Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.
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Affiliation(s)
- Jenny M Booth
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
- Joint Nature Conservation Committee, Peterborough, UK
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Xi M, Zhang Q, Nie L, Xiong T, Yu Z. Quantitative comparison of clamworm (Perinereis aibuhitensis) and crab (Macrophthalmus japonicus) burrowing effects on nitrogen and phosphorus dynamics at the sediment-water interface. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159559. [PMID: 36270351 DOI: 10.1016/j.scitotenv.2022.159559] [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: 09/14/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Exploring nitrogen and phosphorus dynamics in estuarine ecosystems is of great significance for understanding the nutrient cycle in terrestrial and marine ecosystems. However, the ecological functions of common species remain unclear because there is a dearth of observational data. To quantitatively compare the bioturbation effects of the clamworm Perinereis aibuhitensis and crab Macrophthalmus japonicus on the migration of nitrogen and phosphorus in the sediment-pore water-overlying water interfaces, an indoor experiment was carried out using microcosms containing substrate, water, and living specimens collected from the Dagu Estuary, China. The physical structure of the sediments was greatly altered by both clamworms and crabs, and the amount of suspended particulate matter in the overlying water was in the order: crab > clamworm > control groups. Sediments, especially the 0-2 cm layer, were continuously mineralized under bioturbation, releasing NH3-N, NO2--N, NO3--N, and dissolved total phosphorus. During the experiment, the release rate of NH3-N (2.45 mg L-1 to 10.23 mg L-1), NO2--N (0.25 mg L-1 to 7.34 mg L-1), NO3--N (0.02 mg L-1 to 6.03 mg L-1), and dissolved total phosphorus (0.07 mg L-1 to 0.16 mg L-1) in the crab group was higher than that in the clamworm group (NH3-N, 0.93 mg L-1 to 6.11 mg L-1; NO2--N, 0.51 mg L-1 to 6.18 mg L-1; NO3--N, 0.01 mg L-1 to 5.24 mg L-1, and dissolved total P, 0.04 mg L-1 to 0.08 mg L-1). Our findings indicate that crabs might play a more important role in promoting nitrogen and phosphorus migration than clamworms because of their stronger bioturbation strategies in sediments. Bioturbation by both clamworms and crabs reduced nitrogen and phosphorus accumulation in surface sediments and accelerated organic matter mineralization in the sediments, which may promote nutrient recycling in estuarine ecosystems.
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Affiliation(s)
- Min Xi
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Qian Zhang
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Likai Nie
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China; Shandong Huankeyuan Environmental Engineering Co., Ltd., Jinan 250013, China
| | - Tianqi Xiong
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Zhengda Yu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
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8
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Marasco R, Michoud G, Sefrji FO, Fusi M, Antony CP, Seferji KA, Barozzi A, Merlino G, Daffonchio D. The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea. Front Microbiol 2023; 14:1155381. [PMID: 37200916 PMCID: PMC10185800 DOI: 10.3389/fmicb.2023.1155381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described. Methods To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria. Results and discussion This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.
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Rolli E, Marasco R, Fusi M, Scaglia B, Schubotz F, Mapelli F, Ciccazzo S, Brusetti L, Trombino L, Tambone F, Adani F, Borin S, Daffonchio D. Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield. Environ Microbiol 2022; 24:5998-6016. [PMID: 36325730 PMCID: PMC10099744 DOI: 10.1111/1462-2920.16268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m2 area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co-occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high-throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche-specific role of the micro-environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico-chemical and micro-climatic variations at the site-spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.
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Affiliation(s)
- Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - Barbara Scaglia
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy-Gruppo Ricicla Lab, University of Milan, Milan, Italy
| | - Florence Schubotz
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sonia Ciccazzo
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Luca Trombino
- Department of Earth Sciences 'Ardito Desio', University of Milan, Milan, Italy
| | - Fulvia Tambone
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy-Gruppo Ricicla Lab, University of Milan, Milan, Italy
| | - Fabrizio Adani
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy-Gruppo Ricicla Lab, University of Milan, Milan, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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10
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Blanco-Sacristán J, Johansen K, Duarte CM, Daffonchio D, Hoteit I, McCabe MF. Mangrove distribution and afforestation potential in the Red Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157098. [PMID: 35779736 DOI: 10.1016/j.scitotenv.2022.157098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Mangrove ecosystems represent one of the most effective natural environments for fixing and storing carbon (C). Mangroves also offer significant co-benefits, serving as nurseries for marine species, providing nutrients and food to support marine ecosystems, and stabilizing coastlines from erosion and extreme events. Given these considerations, mangrove afforestation and associated C sequestration has gained considerable attention as a nature-based solution to climate adaptation (e.g., protect against more frequent storm surges) and mitigation (e.g. offsetting other C-producing activities). To advance our understanding and description of these important ecosystems, we leverage Landsat-8 and Sentinel-2 satellite data to provide a current assessment of mangrove extent within the Red Sea region and also explore the effect of spatial resolution on mapping accuracy. We establish that Sentinel-2 provides a more precise spatial record of extent and subsequently use these data together with a maximum entropy (MaxEnt) modeling approach to: i) map the distribution of Red Sea mangrove systems, and ii) identify potential areas for future afforestation. From these current and potential mangrove distribution maps, we then estimate the carbon sequestration rate for the Red Sea (as well as for each bordering country) using a meta-analysis of sequestration values surveyed from the available literature. For the mangrove classification, we obtained mapping accuracies of 98 %, with a total Red Sea mangrove extent estimated at approximately 175 km2. Based on the MaxEnt approach, which used soil physical and environmental variables to identify the key factors limiting mangrove growth and distribution, an area of nearly 410 km2 was identified for potential mangrove afforestation expansion. The factors constraining the potential distribution of mangroves were related to soil physical properties, likely reflecting the low sediment load and limited nutrient input of the Red Sea. The current rate of carbon sequestration was calculated as 1034.09 ± 180.53 Mg C yr-1, and the potential sequestration rate as 2424.49 ± 423.26 Mg C yr-1. While our results confirm the maintenance of a positive trend in mangrove growth over the last few decades, they also provide the upper bounds on above ground carbon sequestration potential for the Red Sea mangroves.
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Affiliation(s)
- Javier Blanco-Sacristán
- Climate and Livability Initiative, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Kasper Johansen
- Climate and Livability Initiative, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ibrahim Hoteit
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Matthew F McCabe
- Climate and Livability Initiative, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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11
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Capparelli MV, Martínez-Colón M, Lucas-Solis O, Valencia-Castañeda G, Celis-Hernández O, Ávila E, Moulatlet GM. Can the bioturbation activity of the fiddler crab Minuca rapax modify the distribution of microplastics in sediments? MARINE POLLUTION BULLETIN 2022; 180:113798. [PMID: 35665620 DOI: 10.1016/j.marpolbul.2022.113798] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Fiddler crabs are known as "eco-engineers" who maintain habitat health through sediment bioturbation. They regularly interact with microplastics (MPs) due to their contact with the sediment. In this study we compared MPs concentration between burrows and pellets resulting from bioturbation, and MPs bioaccumulation in the soft tissues of Minuca rapax (Smith, 1870), along a gradient of urbanization in Isla del Carmen, southern Gulf of Mexico. Overall, MPs shape and color in the pellets and in the tissues reflected those of the burrow's sediments. MPs were more abundant and diverse in burrows (9 ± 12 MPs.g-1) than in pellets (5 ± 5 MPs.g-1) or in the soft tissues (1.3 ± 1.2 MPs.g-1). Bioturbation can concentrate MPs in pellets and tissues, depending on the MPs contamination and urbanization level. M. rapax is an important structuring agent of sedimentary MPs, showing a strong top-down translocation of MPs in subtropical tidal flats.
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Affiliation(s)
- Mariana V Capparelli
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico.
| | - Michael Martínez-Colón
- School of the Environment, Florida A&M University, 1515 S MLK Boulevard, Tallahassee, FL 32307, United States of America
| | - Oscar Lucas-Solis
- Facultad de Ciencias de la Tierra y Agua, Universidad Regional Amazónica Ikiam, 150150 Tena, Napo, Ecuador
| | - Gladys Valencia-Castañeda
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de Mexico, Unidad Académica Mazatlán, Mexico
| | - Omar Celis-Hernández
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico; Dirección de Cátedras CONACYT, Av. Insurgentes Sur 1582, Alcaldía Benito Juárez 03940, Ciudad de México, Mexico
| | - Enrique Ávila
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico
| | - Gabriel M Moulatlet
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
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12
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Fusi M, Booth JM, Marasco R, Merlino G, Garcias-Bonet N, Barozzi A, Garuglieri E, Mbobo T, Diele K, Duarte CM, Daffonchio D. Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System. Microbiol Spectr 2022; 10:e0111722. [PMID: 35647697 PMCID: PMC9241789 DOI: 10.1128/spectrum.01117-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023] Open
Abstract
In intertidal systems, the type and role of interactions among sediment microorganisms, animals, plants and abiotic factors are complex and not well understood. Such interactions are known to promote nutrient provision and cycling, and their dynamics and relationships may be of particular importance in arid microtidal systems characterized by minimal nutrient input. Focusing on an arid mangrove ecosystem on the central Red Sea coast, we investigated the effect of crab bioturbation intensity (comparing natural and manipulated high levels of bioturbation intensity) on biogeochemistry and bacterial communities of mangrove sediments, and on growth performance of Avicennia marina, over a period of 16 months. Along with pronounced seasonal patterns with harsh summer conditions, in which high sediment salinity, sulfate and temperature, and absence of tidal flooding occur, sediment bacterial diversity and composition, sediment physicochemical conditions, and plant performance were significantly affected by crab bioturbation intensity. For instance, bioturbation intensity influenced components of nitrogen, carbon, and phosphate cycling, bacterial relative abundance (i.e., Bacteroidia, Proteobacteria and Rhodothermi) and their predicted functionality (i.e., chemoheterotrophy), likely resulting from enhanced metabolic activity of aerobic bacteria. The complex interactions among bacteria, animals, and sediment chemistry in this arid mangrove positively impact plant growth. We show that a comprehensive approach targeting multiple biological levels provides useful information on the ecological status of mangrove forests. IMPORTANCE Bioturbation is one of the most important processes that governs sediment biocenosis in intertidal systems. By facilitating oxygen penetration into anoxic layers, bioturbation alters the overall sediment biogeochemistry. Here, we investigate how high crab bioturbation intensity modifies the mangrove sediment bacterial community, which is the second largest component of mangrove sediment biomass and plays a significant role in major biogeochemical processes. We show that the increase in crab bioturbation intensity, by ameliorating the anoxic condition of mangrove sediment and promoting sediment bacterial diversity in favor of a beneficial bacterial microbiome, improves mangrove tree growth in arid environments. These findings have significant implications because they show how crabs, by farming the mangrove sediment, can enhance the overall capacity of the system to sustain mangrove growth, fighting climate change.
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Affiliation(s)
- Marco Fusi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Jenny Marie Booth
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Ramona Marasco
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alan Barozzi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tumeka Mbobo
- National Research Foundation-South African Institute for Aquatic Biodiversity Institute, Makhanda, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Karen Diele
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Carlos M. Duarte
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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13
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Li L, Peng C, Yang Z, He Y, Liang M, Cao H, Qiu Q, Song J, Su Y, Gong B. Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37582-37597. [PMID: 35066825 DOI: 10.1007/s11356-021-18134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO42--S) and Fe but lower concentrations of total phosphorus (TP) and NO3--N were detected in ZZW and Qin. Nutrient elements (NO3--N, NH4+-N, organic matter (OM), SO42--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO3--N was the most important factor. NO3--N, SO42--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.
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Affiliation(s)
- Lu Li
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Chunyan Peng
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Zicong Yang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Yu He
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Meng Liang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Hongmin Cao
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Qinghua Qiu
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Jingjing Song
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China.
| | - Youlu Su
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Bin Gong
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China.
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14
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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15
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Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
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Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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16
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Guo L, Zhao L, Ye J, Ji Z, Tang JJ, Bai K, Zheng S, Hu L, Chen X. Using aquatic animals as partners to increase yield and maintain soil nitrogen in the paddy ecosystems. eLife 2022; 11:73869. [PMID: 35190027 PMCID: PMC8863371 DOI: 10.7554/elife.73869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/13/2022] [Indexed: 12/31/2022] Open
Abstract
Whether species coculture can overcome the shortcomings of crop monoculture requires additional study. Here, we show how aquatic animals (i.e. carp, crabs, and softshell turtles) benefit paddy ecosystems when cocultured with rice. Three separate field experiments and three separate mesocosm experiments were conducted. Each experiment included a rice monoculture (RM) treatment and a rice-aquatic animal (RA) coculture treatment; RA included feed addition for aquatic animals. In the field experiments, rice yield was higher with RA than with RM, and RA also produced aquatic animal yields that averaged 0.52–2.57 t ha-1. Compared to their corresponding RMs, the three RAs had significantly higher apparent nitrogen (N)-use efficiency and lower weed infestation, while soil N contents were stable over time. Dietary reconstruction analysis based on 13C and 15N showed that 16.0–50.2% of aquatic animal foods were from naturally occurring organisms in the rice fields. Stable-isotope-labeling (13C) in the field experiments indicated that the organic matter decomposition rate was greater with RA than with RM. Isotope 15N labeling in the mesocosm experiments indicated that rice used 13.0–35.1% of the aquatic animal feed-N. All these results suggest that rice-aquatic animal coculture increases food production, increases N-use efficiency, and maintains soil N content by reducing weeds and promoting decomposition and complementary N use. Our study supports the view that adding species to monocultures may enhance agroecosystem functions. Monoculture, where only one type of crop is grown to the exclusion of any other organism, is a pillar of modern agriculture. Yet this narrow focus disregards how complex inter-species interactions can increase crop yield and biodiversity while decreasing the need for fertilizers or pesticides. For example, many farmers across Asia introduce carps, crabs, turtles or other freshwater grazers into their rice paddies. This coculture approach yields promising results but remains poorly understood. In particular, it is unclear how these animals’ behaviours and biological processes benefit the ecosystem. To examine these questions, Guo, Zhao et al. conducted three separate four-year field experiments; they compared rice plots inhabited by either carp, mitten crabs or Chinese softshell turtles with fields where these organisms were not present. With animals, the rice paddies had less weeds, better crop yields and steady levels of nitrogen (a natural fertiliser) in their soil. These ecosystems could breakdown organic matter faster, use it better and had a reduced need for added fertilizer. While animal feed was provided in the areas that were studied, carp, crabs and turtles obtained up to half their food from the field itself, eating weeds, algae and pests and therefore reducing competition for the crops. This work helps to understand the importance of species interactions, showing that diversifying monocultures may boost yields and make agriculture more sustainable.
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Affiliation(s)
- Liang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lufeng Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junlong Ye
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zijun Ji
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Jun Tang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Keyu Bai
- Bioversity International, Maccarese, Italy
| | - Sijun Zheng
- Bioversity International, Maccarese, Italy.,Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Liangliang Hu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
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17
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Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Insights Into the Cultivable Bacterial Fraction of Sediments From the Red Sea Mangroves and Physiological, Chemotaxonomic, and Genomic Characterization of Mangrovibacillus cuniculi gen. nov., sp. nov., a Novel Member of the Bacillaceae Family. Front Microbiol 2022; 13:777986. [PMID: 35250919 PMCID: PMC8894767 DOI: 10.3389/fmicb.2022.777986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022] Open
Abstract
Mangrove forests are dynamic and productive ecosystems rich in microbial diversity; it has been estimated that microbial cells in the mangrove sediments constitute up to 91% of the total living biomass of these ecosystems. Despite in this ecosystem many of the ecological functions and services are supported and/or carried out by microorganisms (e.g., nutrient cycling and eukaryotic-host adaptation), their diversity and function are overlooked and poorly explored, especially for the oligotrophic mangrove of the Red Sea coast. Here, we investigated the cultivable fraction of bacteria associated with the sediments of Saudi Arabian Red Sea mangrove forest by applying the diffusion-chamber-based approach in combination with oligotrophic medium and long incubation time to allow the growth of bacteria in their natural environment. Cultivation resulted in the isolation of numerous representatives of Isoptericola (n = 51) and Marinobacter (n = 38), along with several less abundant and poorly study taxa (n = 25) distributed across ten genera. Within the latest group, we isolated R1DC41T, a novel member of the Bacillaceae family in the Firmicutes phylum. It showed 16S rRNA gene similarity of 94.59–97.36% with closest relatives of Rossellomorea (which was formerly in the Bacillus genus), Domibacillus, Bacillus, and Jeotgalibacillus genera. Based on the multilocus sequence analysis (MLSA), R1DC41T strain formed a separated branch from the listed genera, representing a novel species of a new genus for which the name Mangrovibacillus cuniculi gen. nov., sp. nov. is proposed. Genomic, morphological, and physiological characterizations revealed that R1DC41T is an aerobic, Gram-stain-variable, rod-shaped, non-motile, endospore-forming bacterium. A reduced genome and the presence of numerous transporters used to import the components necessary for its growth and resistance to the stresses imposed by the oligotrophic and salty mangrove sediments make R1DC41T extremely adapted to its environment of origin and to the competitive conditions present within.
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18
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Tongununui P, Kuriya Y, Murata M, Sawada H, Araki M, Nomura M, Morioka K, Ichie T, Ikejima K, Adachi K. Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling. PLoS One 2022; 16:e0261654. [PMID: 34972143 PMCID: PMC8719709 DOI: 10.1371/journal.pone.0261654] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/07/2021] [Indexed: 11/29/2022] Open
Abstract
Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.
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Affiliation(s)
- Prasert Tongununui
- Department of Marine Science and Environment, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Tambon Maifad, Amphur Sikao, Trang, Thailand
| | - Yuki Kuriya
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masahiro Murata
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Hideki Sawada
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Kyoto, Japan
| | - Michihiro Araki
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Mika Nomura
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Katsuji Morioka
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Tomoaki Ichie
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kou Ikejima
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Kohsuke Adachi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
- * E-mail:
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19
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Marasco R, Fusi M, Rolli E, Ettoumi B, Tambone F, Borin S, Ouzari H, Boudabous A, Sorlini C, Cherif A, Adani F, Daffonchio D. Aridity modulates belowground bacterial community dynamics in olive tree. Environ Microbiol 2021; 23:6275-6291. [PMID: 34490977 PMCID: PMC9290347 DOI: 10.1111/1462-2920.15764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Marco Fusi
- School of Applied SciencesEdinburgh Napier UniversityEdinburghUK
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Besma Ettoumi
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Fulvia Tambone
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Hadda‐Imene Ouzari
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Abdellatif Boudabous
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Claudia Sorlini
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Ameur Cherif
- Institut Supérieur de Biotechnologie Sidi Thabet (ISBST)BVBGR‐LR11ES31, Biotechpole Sidi Thabet, University ManoubaArianaTunisia
| | - Fabrizio Adani
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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20
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Béziat NS, Duperron S, Halary S, Azede C, Gros O. Bacterial ectosymbionts colonizing gills of two Caribbean mangrove crabs. Symbiosis 2021. [DOI: 10.1007/s13199-021-00801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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A functional analysis reveals extremely low redundancy in global mangrove invertebrate fauna. Proc Natl Acad Sci U S A 2021; 118:2016913118. [PMID: 34312251 PMCID: PMC8364210 DOI: 10.1073/pnas.2016913118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Global mangrove deforestation and degradation drive the loss of the associated invertebrate fauna vital to ecosystem services. The functional diversity and resilience of this fauna has not been assessed. We show that even small mangrove patches host functionally diverse faunal assemblages and can act as biodiversity reservoirs. However, globally, functional redundancy of mangrove invertebrates (i.e., the average number of species performing a similar functional role in an assemblage) is extremely low, except in Southeast Asia. Thus, even a modest local loss of invertebrate diversity will have significant negative consequences for mangrove functionality and resilience. Current approaches to assess threats to mangroves heavily rely on loss in areal extent, but our results suggest that loss of function may be more vulnerable. Deforestation results in habitat fragmentation, decreasing diversity, and functional degradation. For mangroves, no data are available on the impact of deforestation on the diversity and functionality of the specialized invertebrate fauna, critical for their functioning. We compiled a global dataset of mangrove invertebrate fauna comprising 364 species from 16 locations, classified into 64 functional entities (FEs). For each location, we calculated taxonomic distinctness (Δ+), functional richness (FRi), functional redundancy (FRe), and functional vulnerability (FVu) to assess functional integrity. Δ+ and FRi were significantly related to air temperature but not to geomorphic characteristics, mirroring the global biodiversity anomaly of mangrove trees. Neither of those two indices was linked to forest area, but both sharply decreased in human-impacted mangroves. About 60% of the locations showed an average FRe < 2, indicating that most of the FEs comprised one species only. Notable exceptions were the Eastern Indian Ocean and west Pacific Ocean locations, but also in this region, 57% of the FEs had no redundancy, placing mangroves among the most vulnerable ecosystems on the planet. Our study shows that despite low redundancy, even small mangrove patches host truly multifunctional faunal assemblages, ultimately underpinning their services. However, our analyses also suggest that even a modest local loss of invertebrate diversity could have significant negative consequences for many mangroves and cascading effects for adjacent ecosystems. This pattern of faunal-mediated ecosystem functionality is crucial for assessing the vulnerability of mangrove forests to anthropogenic impact and provides an approach to planning their effective conservation and restoration.
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22
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Sefrji FO, Michoud G, Marasco R, Merlino G, Daffonchio D. Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34214025 PMCID: PMC8489838 DOI: 10.1099/ijsem.0.004866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium, designated strain R1DC9T, was isolated from sediments of a mangrove stand on the Red Sea coast of Saudi Arabia via diffusion chamber cultivation. Strain R1DC9T grew at 20-40 °C (optimum, 37 °C), pH 6-10 (optimum, pH 8) and 3-11 % NaCl (optimum, 7-9 %) in the cultivation medium. The genome of R1DC9T was 4 661 901 bp long and featured a G+C content of 63.1 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis using 120 concatenated single-copy genes revealed that R1DC9T represents a distinct lineage in the order Cytophagales and the phylum Bacteroidetes separated from the Roseivirgaceae and Marivirgaceae families. R1DC9T displayed 90 and 89 % 16S rRNA gene sequence identities with Marivirga sericea DSM 4125T and Roseivirga ehrenbergii KMM 6017T, respectively. The predominant quinone was MK7. The polar lipids were phosphatidylethanolamine, two unknown phospholipids and two unknown lipids. The predominant cellular fatty acids were the saturated branch chain fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 0, along with a low percentage of the monounsaturated fatty acid C16 : 1 ω5c. Based on differences in phenotypic, physiological and biochemical characteristics from known relatives, and the results of phylogenetic analyses, R1DC9T (=KCTC 72349T=JCM 33609T=NCCB 100698T) is proposed to represent a novel species in a new genus, and the name Mangrovivirga cuniculi gen. nov., sp. nov. is proposed. The distinct phylogenetic lineage among the families in the order Cytophagales indicates that R1DC9T represents a new family for which the name Mangrovivirgaceae fam. nov. is proposed.
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Affiliation(s)
- Fatmah O Sefrji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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23
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Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales. Int J Syst Evol Microbiol 2021; 71:004806. [PMID: 33999795 PMCID: PMC8289202 DOI: 10.1099/ijsem.0.004806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).
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Affiliation(s)
- Fatmah O. Sefrji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kholoud A. Seferji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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24
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Craig H, Kennedy JP, Devlin DJ, Bardgett RD, Rowntree JK. Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field-based experiment. Ecol Evol 2020; 10:13957-13967. [PMID: 33391694 PMCID: PMC7771162 DOI: 10.1002/ece3.6989] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/03/2020] [Accepted: 10/14/2020] [Indexed: 11/25/2022] Open
Abstract
Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.
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Affiliation(s)
- Hayley Craig
- Department of Earth and Environmental SciencesThe University of ManchesterManchesterUK
| | - John Paul Kennedy
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
- Smithsonian Marine StationFort PierceFLUSA
| | - Donna J. Devlin
- Department of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTXUSA
| | - Richard D. Bardgett
- Department of Earth and Environmental SciencesThe University of ManchesterManchesterUK
| | - Jennifer K. Rowntree
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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25
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Xiang H, Li K, Cao L, Zhang Z, Yang H. Impacts of pollution, sex, and tide on the time allocations to behaviours of Uca arcuata in mangroves. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140609. [PMID: 32721739 DOI: 10.1016/j.scitotenv.2020.140609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/13/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
Fiddler crabs (Uca) are ecosystem engineers in coastal ecosystems. Many anthropogenic and natural factors can affect the time allocated to various behaviours in Uca. However, the behaviour of U. arcuata, a widely distributed fiddler crab in Asia, has not been studied in mainland China. Here, we used binoculars to record the time budget of ten behaviours of U. arcuata to investigate the potential effects of sex, tides, and pollution on these behaviours. We found that the crabs spent 42.3%, 27.0%, and 10.6% of their time on feeding, feeding while walking, and stationary respectively. The crabs spent <1.5% of their time on copulation and grooming. The total foraging time (feeding + feeding while walking) did not differ among the three polluted sites. However, crabs spent more time on feeding but less time on feeding while walking. The feeding rate and probability of burrowing and grooming decreased while the possibility of locomotion and stay in burrow increased with increasing nutrient concentration. Females spent 13.9% more time on feeding and fed 54.9% faster than males. Males had a higher tendency to grooming and combat while they were less likely to walk than females. Regarding to the influence of tide, fiddler crabs fed 11.2% faster at ebb tides than at flood tides, and they were more likely to walk and stay in burrows at flood tides than at ebb tides. Our results indicated that nutrient pollution had stronger impacts on the behaviours of crabs than sex and tide. In polluted mangroves, increasing nutrient concentration reduced the quantity of sediment processed by fiddler crabs due to their smaller feeding area, slower feeding rate, and reduced frequency of burrowing activities. These results imply that mitigating nutrient pollution in mangroves may benefit the restoration and management of coastal ecosystems through the enhanced engineering functions of fiddler crabs.
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Affiliation(s)
- Hongyong Xiang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, Jilin 130024, China; Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650500, China
| | - Kun Li
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, Heilongjiang University, Harbin 150080, China
| | - Lina Cao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun, Jilin 130024, China; Ecology and Environment Department of Jilin Province, Changchun, Jilin 130024, China
| | - Zhenxing Zhang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun, Jilin 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun, Jilin 130024, China.
| | - Haijun Yang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650500, China.
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26
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Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. mSystems 2020; 5:5/5/e00658-20. [PMID: 33082281 PMCID: PMC7577295 DOI: 10.1128/msystems.00658-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.
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27
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Zilius M, Bonaglia S, Broman E, Chiozzini VG, Samuiloviene A, Nascimento FJA, Cardini U, Bartoli M. N 2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont. Sci Rep 2020; 10:13966. [PMID: 32811860 PMCID: PMC7435186 DOI: 10.1038/s41598-020-70834-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.
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Affiliation(s)
- Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | | | | | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Ulisse Cardini
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Napoli, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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Crab Bioturbation and Seasonality Control Nitrous Oxide Emissions in Semiarid Mangrove Forests (Ceará, Brazil). APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonality and crab activity affects the nutrients and physicochemical parameters in mangrove soils, thus, affecting the emissions of greenhouse gases, such as nitrous oxide (N2O). Climate change may intensify rainfall and/or enhance droughts, affecting mangroves and associated biota. Crabs are natural soil bioturbators responsible for soil aeration and turnover. We evaluated the effect of Ucides cordatus crab on N2O emissions from mangrove soils under a semiarid climate in Northeastern Brazil. Soil and gas samples were collected over the rainy and dry seasons in crab-naturally-bioturbated and crab-exclusion mangrove plots. We measured the soil’s pH, redox potential, and the total contents of carbon, nitrogen, and sulfur. We found higher N2O emissions in the crab-exclusion sites compared to the bioturbated sites, as well as higher N2O emissions in the rainy season compared to the dry season. The fluxes of N2O (µg m−2 h−1) were 47.3 ± 9.7 and 8.9 ± 0.5 for the crab-exclusion sites, and 36.5 ± 7.8 and 4.5 ± 2.1 for the bioturbated sites (wet and dry seasons, respectively). The soil turning over by macrofauna led to lower N2O fluxes in natural crab-bioturbated areas, and seasonality was the environmental factor that contributed the most to the changes in N2O emissions. Broadly, anthropic activities and seasonality influence nitrogen fate, N2O emissions, and ecological services in coastal ecosystems.
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29
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A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509-1520. [PMID: 31636428 DOI: 10.1038/s41559-019-0999-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.
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Marie Booth J, Fusi M, Marasco R, Michoud G, Fodelianakis S, Merlino G, Daffonchio D. The role of fungi in heterogeneous sediment microbial networks. Sci Rep 2019; 9:7537. [PMID: 31101834 PMCID: PMC6525233 DOI: 10.1038/s41598-019-43980-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/28/2019] [Indexed: 12/20/2022] Open
Abstract
While prokaryote community diversity and function have been extensively studied in soils and sediments, the functional role of fungi, despite their huge diversity, is widely unexplored. Several studies have, nonetheless, revealed the importance of fungi in provisioning services to prokaryote communities. Here, we hypothesise that the fungal community plays a key role in coordinating entire microbial communities by controlling the structure of functional networks in sediment. We selected a sediment environment with high niche diversity due to prevalent macrofaunal bioturbation, namely intertidal mangrove sediment, and explored the assembly of bacteria, archaea and fungi in different sediment niches, which we characterised by biogeochemical analysis, around the burrow of a herbivorous crab. We detected a high level of heterogeneity in sediment biogeochemical conditions, and diverse niches harboured distinct communities of bacteria, fungi and archaea. Saprotrophic fungi were a pivotal component of microbial networks throughout and we invariably found fungi to act as keystone species in all the examined niches and possibly acting synergistically with other environmental variables to determine the overall microbial community structure. In consideration of the importance of microbial-based nutrient cycling on overall sediment ecosystem functioning, we underline that the fungal microbiome and its role in the functional interactome cannot be overlooked.
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Affiliation(s)
- Jenny Marie Booth
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Marco Fusi
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia.
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK.
| | - Ramona Marasco
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Stilianos Fodelianakis
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Giuseppe Merlino
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia.
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