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Carneiro IM, Sá JA, Chiroque-Solano PM, Cardoso FC, Castro GM, Salomon PS, Bastos AC, Moura RL. Precision and accuracy of common coral reef sampling protocols revisited with photogrammetry. Mar Environ Res 2024; 194:106304. [PMID: 38142582 DOI: 10.1016/j.marenvres.2023.106304] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023]
Abstract
The rapid decline of coral reefs calls for cost-effective benthic cover data to improve reef health forecasts, policy building, management responses and evaluation. Reef monitoring has been largely based on divers' observations along transects, and secondarily on quadrat-based protocols, video and photographic records. However, the accuracy and precision of the most common sampling approaches are not yet fully understood. Here, we compared benthic cover estimates from three common sampling protocols: Reef Check (RC), Atlantic and Gulf Rapid Reef Assessment (AGRRA) and photoquadrats (PQ). The reef cover of two contrasting sites was reconstructed with ∼450 m2 orthomosaics built with high resolution Structure-from-Motion (SfM) photogrammetry, which were used as references for comparisons among protocols. In addition, we explored sample size requirements for each protocol and provided cost-effectiveness comparisons. Our results evidenced between-reef differences in the accuracy and precision of estimates with the different protocols. The three protocols performed similarly in the reef with low macroalgal cover (<0.5%), but PQ were more accurate and precise in the reef with relatively high (∼20%) macroalgal cover. The sample size for estimating coral cover with a 20% error margin and a 0.05 significance level was lower for PQ, followed by AGRRA and RC. Considering performance, cost surrogates and equipment needs, cost-effectiveness was higher for PQ. We also discuss costs, limitations and advantages/disadvantages of SfM photogrammetry as a sampling approach for coral reef monitoring.
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Affiliation(s)
- Ivan M Carneiro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - João A Sá
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Pamela M Chiroque-Solano
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernando C Cardoso
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Guilherme M Castro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Paulo S Salomon
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alex C Bastos
- Departamento de Oceanografia, Universidade Federal do Espirito Santo, Vitória, ES, Brazil
| | - Rodrigo L Moura
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Castro GM, Vargens RP, Carlos-Júnior LA, Cardoso FC, Salomon PS, Tenório MMB, Bastos AC, Oliveira N, Ghisolfi RD, Cordeiro RTS, Moura RL. Incised valleys drive distinctive oceanographic processes and biological assemblages within rhodolith beds. PLoS One 2023; 18:e0293259. [PMID: 37956173 PMCID: PMC10642839 DOI: 10.1371/journal.pone.0293259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/09/2023] [Indexed: 11/15/2023] Open
Abstract
Continental shelves encompass gently sloped seascapes that are highly productive and intensively exploited for natural resources. Islands, reefs and other emergent or quasi-emergent features punctuate these shallow (<100 m) seascapes and are well known drivers of increased biomass and biodiversity, as well as predictors of fishing and other human uses. On the other hand, relict mesoscale geomorphological features that do not represent navigation hazards, such as incised valleys (IVs), remain poorly charted. Consequently, their role in biophysical processes remains poorly assessed and sampled. Incised valleys are common within rhodolith beds (RBs), the most extensive benthic habitat along the tropical and subtropical portions of the mid and outer Brazilian shelf. Here, we report on a multi-proxy assessment carried out in a tropical-subtropical transition region (~20°S) off Eastern Brazil, contrasting physicochemical and biological variables in IVs and adjacent RBs. Valleys interfere in near bottom circulation and function as conduits for water and propagules from the slope up to the mid shelf. In addition, they provide a stable and structurally complex habitat for black corals and gorgonians that usually occur in deeper water, contrasting sharply with the algae-dominated RB. Fish richness, abundance and biomass were also higher in the IVs, with small planktivores and large-bodied, commercially important species (e.g. groupers, snappers and grunts) presenting smaller abundances or being absent from RBs. Overall, IVs are unique and vulnerable habitats that sustain diverse assemblages and important ecosystem processes. As new IVs are detected by remote sensing or bathymetric surveys, they can be incorporated into regional marine management plans as conservation targets and priority sites for detailed in situ surveys.
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Affiliation(s)
- Guilherme M. Castro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rafaela P. Vargens
- Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lélis A. Carlos-Júnior
- Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernando C. Cardoso
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Paulo S. Salomon
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Márcio M. B. Tenório
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alex C. Bastos
- Departamento de Oceanografia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Natacha Oliveira
- Departamento de Oceanografia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Renato D. Ghisolfi
- Departamento de Oceanografia, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Ralf T. S. Cordeiro
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, PE, Brazil
| | - Rodrigo L. Moura
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Moura RL, Abieri ML, Castro GM, Carlos-Júnior LA, Chiroque-Solano PM, Fernandes NC, Teixeira CD, Ribeiro FV, Salomon PS, Freitas MO, Gonçalves JT, Neves LM, Hackradt CW, Felix-Hackradt F, Rolim FA, Motta FS, Gadig OBF, Pereira-Filho GH, Bastos AC. Tropical rhodolith beds are a major and belittled reef fish habitat. Sci Rep 2021; 11:794. [PMID: 33436906 PMCID: PMC7804296 DOI: 10.1038/s41598-020-80574-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding habitat-level variation in community structure provides an informed basis for natural resources’ management. Reef fishes are a major component of tropical marine biodiversity, but their abundance and distribution are poorly assessed beyond conventional SCUBA diving depths. Based on a baited-video survey of fish assemblages in Southwestern Atlantic’s most biodiverse region we show that species composition responded mainly to the two major hard-bottom megahabitats (reefs and rhodolith beds) and to the amount of light reaching the bottom. Both megahabitats encompassed typical reef fish assemblages but, unexpectedly, richness in rhodolith beds and reefs was equivalent. The dissimilar fish biomass and trophic structure in reefs and rhodolith beds indicates that these systems function based on contrasting energy pathways, such as the much lower herbivory recorded in the latter. Rhodolith beds, the dominant benthic megahabitat in the tropical Southwestern Atlantic shelf, play an underrated role as fish habitats, and it is critical that they are considered in conservation planning.
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Affiliation(s)
- Rodrigo L Moura
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Maria L Abieri
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Guilherme M Castro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lélis A Carlos-Júnior
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Pamela M Chiroque-Solano
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Nicole C Fernandes
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carolina D Teixeira
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Felipe V Ribeiro
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Paulo S Salomon
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Matheus O Freitas
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Juliana T Gonçalves
- Instituto de Biologia and SAGE/COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Leonardo M Neves
- Laboratório de Ecologia Aquática e Educação Ambiental, Universidade Federal Rural do Rio de Janeiro, Três Rios, RJ, Brazil
| | - Carlos W Hackradt
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, BA, Brazil
| | - Fabiana Felix-Hackradt
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, BA, Brazil
| | - Fernanda A Rolim
- Instituto de Biociências, Laboratório de Pesquisa de Elasmobrânquios, Universidade Estadual Paulista, São Vicente, SP, Brazil
| | - Fábio S Motta
- Laboratório de Ecologia e Conservação Marinha, Instituto Do Mar, Universidade Federal de São Paulo, Santos, SP, Brazil
| | - Otto B F Gadig
- Instituto de Biociências, Laboratório de Pesquisa de Elasmobrânquios, Universidade Estadual Paulista, São Vicente, SP, Brazil
| | - Guilherme H Pereira-Filho
- Laboratório de Ecologia e Conservação Marinha, Instituto Do Mar, Universidade Federal de São Paulo, Santos, SP, Brazil
| | - Alex C Bastos
- Universidade Federal do Espírito Santo, Vitória, ES, Brazil
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Ventura-Oliveira D, Vilella CA, Zanin ME, Castro GM, Moreira Filho DC, Zollner RL. Kinetics of TNF-alpha and IFN-gamma mRNA expression in islets and spleen of NOD mice. Braz J Med Biol Res 2002; 35:1347-55. [PMID: 12426635 DOI: 10.1590/s0100-879x2002001100013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Insulin-dependent diabetes mellitus is caused by autoimmune destruction of pancreatic beta cells. Non-obese diabetic (NOD) mice spontaneously develop diabetes similar to the human disease. Cytokines produced by islet-infiltrating mononuclear cells may be directly cytotoxic and can be involved in islet destruction coordinated by CD4+ and CD8+ cells. We utilized a semiquantitative RT-PCR assay to analyze in vitro the mRNA expression of TNF-alpha and IFN-gamma cytokine genes in isolated islets (N = 100) and spleen cells (5 x 10(5) cells) from female NOD mice during the development of diabetes and from female CBA-j mice as a related control strain that does not develop diabetes. Cytokine mRNAs were measured at 2, 4, 8, 14 and 28 weeks of age from the onset of insulitis to the development of overt diabetes. An increase in IFN-gamma expression in islets was observed for females aged 28 weeks (149 +/- 29 arbitrary units (AU), P<0.05, Student t-test) with advanced destructive insulitis when compared with CBA-j mice, while TNF-alpha was expressed in both NOD and CBA-j female islets at the same level at all ages studied. In contrast, TNF-alpha in spleen was expressed at higher levels in NOD females at 14 weeks (99 +/- 8 AU, P<0.05) and 28 weeks (144 +/- 17 AU, P<0.05) of age when compared to CBA-j mice. The data suggest that IFN-gamma and TNF-alpha expression in pancreatic islets of female NOD mice is associated with beta cell destruction and overt diabetes.
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Affiliation(s)
- D Ventura-Oliveira
- Disciplina e Laboratório de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
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5
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Diaz-Bardales BM, Novaski SM, Goes AE, Castro GM, Mengel J, Santos LM. Modulation of the severity of experimental autoimmune encephalomyelitis by gammadelta T lymphocytes activated by mycobacterial antigens. Immunol Invest 2001; 30:245-58. [PMID: 11570644 DOI: 10.1081/imm-100105068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Immunity to mycobacterial antigens may contribute to the maintenance of self-tolerance. Exposure of the immune system to mycobacterial antigen might well stimulate the immune system to exert control over unwanted self-reactive clones. We demonstrated that in vivo administration of Mycobacterium tuberculosis, PPD, and PPD peptide (180-196) prior to immunization with Myelin Basic Protein (MBP) led to a moderate increase of gammadelta T cells, suppression of the immune response, and reduction in the severity of Experimental Autoimmune Encephalomyelitis. The immunosuppression observed is due, at least in part, to the production of Transforming growth factor-beta (TGFbeta) by the gammadelta T lymphocytes.
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MESH Headings
- Adoptive Transfer
- Animals
- Antigenic Modulation
- Antigens, Bacterial/immunology
- Antigens, Bacterial/pharmacology
- Cell Division/immunology
- Cells, Cultured
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Female
- Lymphocyte Activation/immunology
- Mycobacterium/immunology
- Myelin Basic Protein/immunology
- Myelin Basic Protein/pharmacology
- Rats
- Rats, Inbred Lew
- Receptors, Antigen, T-Cell, gamma-delta/drug effects
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
- Transforming Growth Factor beta/biosynthesis
- Tuberculin/pharmacology
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Affiliation(s)
- B M Diaz-Bardales
- Department of Microbiology and Immunology, University of Campinas, Sao Paulo, Brazil
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