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Capó-Bauçà S, Iñiguez C, Galmés J. The diversity and coevolution of Rubisco and CO 2 concentrating mechanisms in marine macrophytes. New Phytol 2024; 241:2353-2365. [PMID: 38197185 DOI: 10.1111/nph.19528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
The kinetic properties of Rubisco, the most important carbon-fixing enzyme, have been assessed in a small fraction of the estimated existing biodiversity of photosynthetic organisms. Until recently, one of the most significant gaps of knowledge in Rubisco kinetics was marine macrophytes, an ecologically relevant group including brown (Ochrophyta), red (Rhodophyta) and green (Chlorophyta) macroalgae and seagrasses (Streptophyta). These organisms express various Rubisco types and predominantly possess CO2 -concentrating mechanisms (CCMs), which facilitate the use of bicarbonate for photosynthesis. Since bicarbonate is the most abundant form of dissolved inorganic carbon in seawater, CCMs allow marine macrophytes to overcome the slow gas diffusion and low CO2 availability in this environment. The present review aims to compile and integrate recent findings on the biochemical diversity of Rubisco and CCMs in the main groups of marine macrophytes. The Rubisco kinetic data provided demonstrate a more relaxed relationship among catalytic parameters than previously reported, uncovering a variability in Rubisco catalysis that has been hidden by a bias in the literature towards terrestrial vascular plants. The compiled data indicate the existence of convergent evolution between Rubisco and biophysical CCMs across the polyphyletic groups of marine macrophytes and suggest a potential role for oxygen in shaping such relationship.
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Affiliation(s)
- Sebastià Capó-Bauçà
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
| | - Concepción Iñiguez
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
- Department of Ecology, Faculty of Sciences, University of Malaga, Boulevard Louis Pasteur s/n, 29010, Málaga, Spain
| | - Jeroni Galmés
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, 07122, Palma, Balearic Islands, Spain
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Korlević M, Markovski M, Zhao Z, Herndl GJ, Najdek M. Selective DNA and Protein Isolation From Marine Macrophyte Surfaces. Front Microbiol 2021; 12:665999. [PMID: 34108951 PMCID: PMC8180852 DOI: 10.3389/fmicb.2021.665999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 12/04/2022] Open
Abstract
Studies of unculturable microbes often combine methods, such as 16S rRNA sequencing, metagenomics, and metaproteomics. To apply these techniques to the microbial community inhabiting the surfaces of marine macrophytes, it is advisable to perform a selective DNA and protein isolation prior to the analysis to avoid biases due to the host material being present in high quantities. Two protocols for DNA and protein isolation were adapted for selective extractions of DNA and proteins from epiphytic communities inhabiting the surfaces of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea. Protocols showed an almost complete removal of the epiphytic community regardless of the sampling season, station, settlement, or host species. The obtained DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low presence of host DNA and proteins in the samples indicated a high specificity of the protocols. The procedures are based on universally available laboratory chemicals making the protocols widely applicable. Taken together, the adapted protocols ensure an almost complete removal of the macrophyte epiphytic community. The procedures are selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins applicable in 16S rRNA sequencing, metagenomics, and metaproteomics.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands.,Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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Ortega A, Geraldi NR, Díaz-Rúa R, Ørberg SB, Wesselmann M, Krause-Jensen D, Duarte CM. A DNA mini-barcode for marine macrophytes. Mol Ecol Resour 2020; 20:920-935. [PMID: 32279439 DOI: 10.1111/1755-0998.13164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/13/2020] [Accepted: 03/27/2020] [Indexed: 11/26/2022]
Abstract
Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%-100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny-based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini-barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.
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Affiliation(s)
- Alejandra Ortega
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nathan R Geraldi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rubén Díaz-Rúa
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sarah B Ørberg
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Marlene Wesselmann
- Global Change Research Group, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Spain
| | - Dorte Krause-Jensen
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Carlos M Duarte
- 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
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Galloway AWE, Britton-Simmons KH, Duggins DO, Gabrielson PW, Brett MT. FATTY ACID SIGNATURES DIFFERENTIATE MARINE MACROPHYTES AT ORDINAL AND FAMILY RANKS(1). J Phycol 2012; 48:956-65. [PMID: 27009005 DOI: 10.1111/j.1529-8817.2012.01173.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Primary productivity by plants and algae is the fundamental source of energy in virtually all food webs. Furthermore, photosynthetic organisms are the sole source for ω-3 and ω-6 essential fatty acids (EFA) to upper trophic levels. Because animals cannot synthesize EFA, these molecules may be useful as trophic markers for tracking sources of primary production through food webs if different primary producer groups have different EFA signatures. We tested the hypothesis that different marine macrophyte groups have distinct fatty acid (FA) signatures by conducting a phylogenetic survey of 40 marine macrophytes (seaweeds and seagrasses) representing 36 families, 21 orders, and four phyla in the San Juan Archipelago, WA, USA. We used multivariate statistics to show that FA composition differed significantly (P < 0.001) among phyla, orders, and families using 44 FA and a subset of seven EFA (P < 0.001). A second analysis of published EFA data of 123 additional macrophytes confirmed that this pattern was robust on a global scale (P < 0.001). This phylogenetic differentiation of macrophyte taxa shows a clear relationship between macrophyte phylogeny and FA content and strongly suggests that FA signature analyses can offer a viable approach to clarifying fundamental questions about the contribution of different basal resources to food webs. Moreover, these results imply that taxa with commercially valuable EFA signatures will likely share such characteristics with other closely related taxa that have not yet been evaluated for FA content.
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Affiliation(s)
- Aaron W E Galloway
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAFriday Harbor Laboratories, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAUniversity of North Carolina Herbarium, CB# 3280, Coker Hall, Chapel Hill, NC, 27599-3280, USACivil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98195-2700, USA
| | - Kevin H Britton-Simmons
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAFriday Harbor Laboratories, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAUniversity of North Carolina Herbarium, CB# 3280, Coker Hall, Chapel Hill, NC, 27599-3280, USACivil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98195-2700, USA
| | - David O Duggins
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAFriday Harbor Laboratories, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAUniversity of North Carolina Herbarium, CB# 3280, Coker Hall, Chapel Hill, NC, 27599-3280, USACivil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98195-2700, USA
| | - Paul W Gabrielson
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAFriday Harbor Laboratories, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAUniversity of North Carolina Herbarium, CB# 3280, Coker Hall, Chapel Hill, NC, 27599-3280, USACivil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98195-2700, USA
| | - Michael T Brett
- Friday Harbor Laboratories, School of Aquatic and Fishery Sciences, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAFriday Harbor Laboratories, University of Washington, 620 University Rd., Friday Harbor, WA, 98250, USAUniversity of North Carolina Herbarium, CB# 3280, Coker Hall, Chapel Hill, NC, 27599-3280, USACivil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98195-2700, USA
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