Basset, A., Elliott, M., West, R. J. & Wilson, J. G. Estuarine and lagoon biodiversity and their natural goods and services. Estuar. Coast. Shelf Sci. 132, 1–4 (2013).
Google Scholar
Newton, A. et al. Assessing, quantifying and valuing the ecosystem services of coastal lagoons. J. Nat. Conserv. 44, 50–65 (2018).
Heck, K. L., Able, K. W., Roman, C. T. & Fahay, M. P. Composition, abundance, biomass, and production of macrofauna in a New England estuary: Comparisons among eelgrass meadows and other nursery habitats. Estuaries 18, 379–389 (1995).
Franco, A. et al. Use of shallow water habitats by fish assemblages in a Mediterranean coastal lagoon. Estuar. Coast. Shelf Sci. 66, 67–83 (2006).
Barbosa, F. A. R., Scarano, F. R., Sabará, M. & Esteves, F. A. Brazilian LTER: Ecosystem and biodiversity information in support of decision-making. Environ. Monit. Assess. 90, 121–133 (2004).
Google Scholar
Esteves, F. et al. Neotropical coastal lagoons: An appraisal of their biodiversity, functioning, threats and conservation management. Braz. J. Biol. 68, 967–981 (2008).
Google Scholar
Kjerfve, B. Coastal lagoons. Elsevier Oceanogr. Ser. 60, 1–8 (1994).
Whitfield, A. K. Coastal lagoons—Critical habitats of environmental change. Mar. Biol. Res. 7, 416–417 (2011).
Obolewski, K. et al. Patterns of salinity regime in coastal lakes based on structure of benthic invertebrates. PLoS ONE 13, 1–19 (2018).
Schallenberg, M., Hall, C. J. & Burns, C. W. Consequences of climate-induced salinity increases on zooplankton abundance and diversity in coastal lakes. Mar. Ecol. Prog. Ser. 251, 181–189 (2003).
Broman, E. et al. Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem. Mol. Ecol. 28, 3813–3829 (2019).
Google Scholar
Bird, E. C. F. Physical setting and geomorphology of coastal lagoons. Elsevier Oceanogr. Ser. 60, 9–39 (1994).
Barnes, N., Bamber, R. N., Moncrieff, C. B., Sheader, M. & Ferrero, T. J. Estuarine, Coastal and Shelf Science Meiofauna in closed coastal saline lagoons in the United Kingdom: Structure and biodiversity of the nematode assemblage. Estuar. Coast. Shelf Sci. 79, 328–340 (2008).
Frühe, L. et al. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Mol. Ecol. 00, 1–19 (2020).
Cordier, T. et al. Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy). Mar. Environ. Res. 146, 24–34 (2019).
Google Scholar
Balzano, S., Abs, E. & Leterme, S. C. Protist diversity along a salinity gradient in a coastal lagoon. Aquat. Microb. Ecol. 74, 263–277 (2015).
Polinski, J. M., Bucci, J. P., Gasser, M. & Bodnar, A. G. Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary. Sci. Rep. 9, 14820 (2019).
Google Scholar
López-Escardó, D. et al. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Sci. Rep. 8, 1–14 (2018).
Günther, B., Knebelsberger, T., Neumann, H., Silke, L. & Arbizu, P. M. Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Sci. Rep. 8, 1–13 (2018).
Park, D. S. & Razafindratsima, O. H. Anthropogenic threats can have cascading homogenizing effects on the phylogenetic and functional diversity of tropical ecosystems. Ecography (Cop.) 42, 148–161 (2019).
Pan, Y., Yang, J., McManus, G. B., Lin, S. & Zhang, W. Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales. Limnol. Oceanogr. 65, 1103–1115 (2020).
Wangensteen, O. S., Palacín, C., Guardiola, M. & Turon, X. DNA metabarcoding of littoral hard-bottom communities: High diversity and database gaps revealed by two molecular markers. PeerJ 6, e4705 (2018).
Google Scholar
Polanco Fernández, A. et al. Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environ. DNA 3, 1–15 (2020).
Armeli Minicante, S. et al. Habitat heterogeneity and connectivity: Effects on the planktonic protist community structure at two adjacent coastal sites (the lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) revealed by metabarcoding. Front. Microbiol. 10, 1–16 (2019).
Alves-De-Souza, C. et al. Does environmental heterogeneity explain temporal β diversity of small eukaryotic phytoplankton? Example from a tropical eutrophic coastal lagoon. J. Plankton Res. 39, 698–714 (2017).
Grzebyk, D. et al. Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene. Harmful Algae 68, 1–16 (2017).
Google Scholar
Lallias, D. et al. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. ISME J. 9, 1208–1221 (2015).
Google Scholar
Avó, A. P. et al. DNA barcoding and morphological identification of benthic nematodes assemblages of estuarine intertidal sediments: Advances in molecular tools for biodiversity assessment. Front. Mar. Sci. 4, 1–16 (2017).
Behera, P. et al. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon. Sci. Total Environ. 595, 472–485 (2017).
Google Scholar
Alsaffar, Z. et al. The role of seagrass vegetation and local environmental conditions in shaping benthic bacterial and macroinvertebrate communities in a tropical coastal lagoon. Sci. Rep. 10, 1–17 (2020).
Spalding, M. D. et al. Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. Bioscience 57, 573–583 (2007).
Lara-Lara, J. Los ecosistemas marinos. Cap. Nat. Méx. 1, 135–159 (2008).
García-Grajales, J. & Buenrostro-Silva, A. E. Parque Nacional Lagunas de Chacahua, Oaxaca: Perspectivas a sus 75 años. Cienc. Ergo Sum. 21, 149–153 (2014).
Zamorano, P., Barrientos-Luján, N. A. & Ahumada-Sempoal, M. Á. Moluscos bentónicos de dos sistemas lagunares de la costa chica de Oaxaca, México y su relación con parámetros fisicoquímicos. Cienc. y Mar. 14, 13–28 (2012).
Sanay-González, R., MonrealGómez, M. A. & de León, D. A. S. Simulación de la circulación en el sistema lagunar Chacahua-Pastoría, Oaxaca, México. Cienc. y Mar. 10, 3–16 (2006).
Comisión Nacional de Acuacultura y Pesca. Obras de dragado y escolleras en Boca de Oro, laguna de Corralero, Oaxaca (2010).
Sánchez-Meraz, B. & Martínez-Vega, J. A. Inmigración de Postlarvas de Camarón Litopenaeus sp. y Farfantepenaeus sp. a través la Boca El Oro del Sistema Lagunar Corralero-Alotengo, Oaxaca. Cienc. y Mar. 4, 29–46 (2000).
Angel-Pérez, C., Serrano-Guzmán, S. J. & Ahumada-Sempoal, M. A. Ciclo reproductivo del molusco Atrina maura (Pterioidea: Pinnidae) en un sistema lagunar costero, al sur del Pacífico tropical mexicano. Rev. Biol. Trop. 55, 839–852 (2007).
Google Scholar
Sánchez Méndez, E., Urbano Alonso, B., Sierra Hernández, S. & Garcés Salazar, J. L. Características malacológicas y sociales de la pesquería artesanal de moluscos en la Laguna de Chacahua, Oaxaca, México. Cienc. y Mar. 19, 3–11 (2015).
Cowart, D. A. et al. Metabarcoding is powerful yet still blind: A comparative analysis of morphological and molecular surveys of seagrass communities. PLoS ONE 10, 1–26 (2015).
Holman, L. E. et al. Detection of novel and resident marine species using environmental DNA metabarcoding of sediment and water. Sci. Rep. https://doi.org/10.1038/s41598-019-47899-7 (2019).
Google Scholar
Bojorges-Baños, J. C. Riqueza y diversidad de especies de aves asociadas a manglar en tres sistemas lagunares en la región costera de Oaxaca, México. Rev. Mex. Biodivers. 82, 205–215 (2011).
Ahumada-Sempoal, M. Á. & Ruiz-García, N. Características fisicoquímicas de la Laguna Pastoría, Oaxaca, México. Cienc. y Mar. 12, 3–17 (2008).
Aylagas, E., Mendibil, I., Borja, Á. & Rodríguez-ezpeleta, N. Marine sediment sample pre-processing for macroinvertebrates metabarcoding: Mechanical enrichment and homogenization. Front. Mar. Sci. 3, 1–8 (2016).
Hestetun, J. T., Lanzén, A., Skaar, K. S. & Dahlgren, T. G. The impact of DNA extract homogenization and replication on marine sediment metabarcoding diversity and heterogeneity. Environ. DNA 3, 997–1006 (2021).
Comeau, M., Li, W. K. W., Carmack, E. C. & Lovejoy, C. Arctic ocean microbial community structure before and after the 2007 record sea ice minimum. PLoS ONE 6, 1–12 (2011).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Google Scholar
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Google Scholar
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
Google Scholar
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).
Ratnasingham, S. & Hebert, P. D. N. BOLD: The barcode of life data system. Mol. Ecol. Notes 7, 355–364 (2007).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing (2018).
Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). Wiley StatsRef Stat. Ref. Online. https://doi.org/10.1002/9781118445112.stat07841 (2017).
Google Scholar
Ter Braak, C. J. F. Canonical correspondence analysis: A new eigenvector technique for multivariate direct gradient analysis. Ecology 67, 1167–1179 (1986).
Ter Braak, C. J. F. The analysis of vegetation-environment relationships by canonical correspondence analysis*. Vegetatio 69, 69–77 (1987).
Hammer, Ø., Harper, D. A. T. & Ryan, P. D. PAST: Paleontological statisticssofware package for education and data analysis. Palaeontol. Electron. 4, 1–9 (2001).
Coan, E. V. & Valentich-Scott, P. Bivalve Seashells of Tropical West America. Marine Bivalve Mollusks from Baja California to Northern Peru (Santa Barbara Museum of Natural History, 2012).
MolluscaBase. MolluscaBase. Mytella strigata (Hanley, 1843) (2022).
Aylagas, E., Borja, Á., Muxika, I. & Rodríguez-ezpeleta, N. Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecol. Indic. 95, 194–202 (2018).
Cronin-O’Reilly, S. et al. Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment. Sci. Rep. 8, 1–10 (2018).
Forster, D. et al. Benthic protists: The under-charted majority. FEMS Microbiol. Ecol. 92, 1–11 (2016).
Kim, H., Kim, H., Hwang, H. S. & Kim, W. Metagenomic analysis of the marine coastal invertebrates of South Korea as assessed by Ilumina MiSeq. Anim. Cells Syst. (Seoul) 21, 37–44 (2017).
Brannock, P. M., Wang, L., Ortmann, A. C., Waits, D. S. & Halanych, K. M. Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico. Mar. Environ. Res. 119, 166–175 (2016).
Google Scholar
Guardiola, M. et al. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 4, e2807 (2016).
Google Scholar
Barnes, M. A. & Turner, C. R. The ecology of environmental DNA and implications for conservation genetics. Conserv. Genet. 17, 1–17 (2016).
Google Scholar
Bastida-Zavala, J. R. et al. Marine and coastal biodiversity of Oaxaca, Mexico. Check List 9, 329–390 (2013).
Nascimento, F. J. A., Lallias, D., Bik, H. M. & Creer, S. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci. Rep. https://doi.org/10.1038/s41598-018-30179-1 (2018).
Google Scholar
In the Wrong Place: Alien Marine Crustaceans: Distribution, Biology and Impacts, Vol. 6 (2011).
Rodríguez-Almaraz, G. A. & García-Madrigal, M. D. S. Crustáceos exóticos invasores. Especies Acuáticas Invasoras en México 347–371 (2014).
Gómez, S., Fleeger, J. W., Rocha, A. & Foltz, D. Four new species of Cletocamptus Schmankewitsch, 1875, closely related to Cletocamptus deitersi (Richard) (Copepoda: Harpacticoida). J. Nat. Hist. 38, 2669. https://doi.org/10.1080/0022293031000156240 (2004).
Google Scholar
Ciros Pérez, J., Silva Briano, M. & Elías Gutierrez, M. A new species of Macrothrix (Anomopoda: Macrothricidae) from Central Mexico. Hydrobiologia 319, 159–166 (1996).
Fuentes-Reines, J. M., De Roa, E. Z., Morón, E., Gámez, D. & López, C. Conocimiento de la fauna de cladocera (Crustacea: Branchiopoda) de la ciénaga grande de Santa Marta, Colombia. Bol. Investig. Mar. y Costeras 41, 121–164 (2012).
Thakur, R. K., Jindal, R., Singh, U. B. & Ahluwalia, A. S. Plankton diversity and water quality assessment of three freshwater lakes of Mandi (Himachal Pradesh, India) with special reference to planktonic indicators. Environ. Monit. Assess. 185, 8355–8373 (2013).
Google Scholar
Band-Schmidt, C. J., Bustillos-Guzmán, J. J., López-Cortés, D. J., Núñez-Vázquez, E. & Hernández-Sandoval, F. E. The actual state of the study of harmful algal blooms in Mexico. Hidrobiológica 21, 381–413 (2011).
Maciel-Baltazar, E. Dinoflagelados (Dinoflagellata) tóxicos de la costa de Chiapas, México, Pacífico centro oriental. UNED Res. J. 7, 39–48 (2015).
Okolodkov, Y. B. & Gárete-Izárraga, I. An annotated checklist od dinoflagellates (Dinophyceae) from the Mexican Pacific. Acta Bot. Mex. 74, 1–154 (2006).
Murray, S. A. et al. A fish kill associated with a bloom of Amphidinium carterae in a coastal lagoon in Sydney, Australia. Harmful Algae 49, 19–28 (2015).
Google Scholar
Gárate-Lizárraga, I. et al. Seasonality of the dinoflagellate Amphidinium cf. carterae (Dinophyceae: Amphidiniales) in Bahía de la Paz, Gulf of California. Mar. Pollut. Bull. 146, 532–541 (2019).
Google Scholar
Varona-Cordero, F. & Gutiérrez, J. Seasonal phytoplankton composition of two coastal lagoons of the tropical Pacific. Hidrobiológica 16, 159–174 (2006).
Hyeon, S. & Jin, H. Gyrodinium jinhaense n. sp., a new heterotrophic unarmored dinoflagellate from the coastal waters of Korea. J. Eukaryot. Microbiol. 66, 821–835 (2019).
Onuma, R., Watanabe, K. & Horiguchi, T. Pellucidodinium psammophilum gen. & sp. nov. and Nusuttodinium desymbiontum sp. nov. (Dinophyceae), two novel heterotrophs closely related to kleptochloroplastidic dinoflagellates. Phycologia 54, 192–209 (2015).
Elliott, M. & Whitfield, A. K. Challenging paradigms in estuarine ecology and management. Estuar. Coast. Shelf Sci. 94, 306–314 (2011).
Sreenivasulu, G., Jayaraju, N. & Sundara Raja, R. Physico-chemical parameters of coastal water from Tupilipalem coast, Southeast coast of India. J. Coast. Sci. 2, 34–39 (2015).
Landa-Jaime, V. Benthic mollusc assemblage of the Agua Dulce / El Ermitaño lagoon estuarine system, Jalisco, Mexico. Ciencias Mar. 29, 169–184 (2003).
Smyth, K. & Elliott, M. Effects of changing salinity on the ecology of the marine environment. In Stressors in the Marine Environment: Physiological and Ecological Responses (eds Solan, M. & Whiteley, N.) 384 (Societal Implications. Oxford University Press, 2016).
Rivera-Velázquez, G., Soto, L. A., Salgado-Ugarte, I. H. & Naranjo, E. J. Growth, mortality and migratory pattern of white shrimp (Litopenaeus vannamei, Crustacea, Penaeidae) in the Carretas-Pereyra coastal lagoon system, Mexico. Rev. Biol. Trop. 56, 523–533 (2008).
Google Scholar
Gainey, L. F. & Greenberg, M. J. Physiological basis of the species abundance-salinity relationship in molluscs: A speculation*. Mar. Biol. 40, 41–49 (1977).
Google Scholar
Baqueiro-Cárdenas, E. R., Borabe, L. & Goldaracena-Islas, C. G. Mollusks and pollution. A review. Rev. Mex. Biodivers. 78, 1–7 (2007).
Purcell, J. E., Uye, S. & Lo, W. Anthropogenic causes of jellyfish blooms and their direct consequences for humans: A review. Mar. Ecol. Prog. Ser. 350, 153–174 (2007).
Nemcová, Y., Pusztai, M., Skaloudová, M. & Neustupa, J. Silica-scaled chrysophytes (Stramenopiles, Ochrophyta) along a salinity gradient: A case study from the Gulf of Bothnia western shore (northern Europe). Hydrobiologia 764, 187–197 (2016).
Li, R., Jiao, N., Warren, A. & Xu, D. Changes in community structure of active protistan assemblages from the lower Pearl River to coastal Waters of the South China Sea. Eur. J. Protistol. 63, 72–82 (2018).
Google Scholar
Kataoka, T. & Kondo, R. Estuarine, coastal and shelf science protistan community composition in anoxic sediments from three salinity-disparate Japanese lakes ☆. Estuar. Coast. Shelf Sci. 224, 34–42 (2019).
Google Scholar
Sun, P. et al. Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the ‘abundant’ and ‘intermediate’ biospheres. Sci. Rep. https://doi.org/10.1038/s41598-017-10308-y (2017).
Google Scholar
Contreras, E. F. O., Castañeda, L. R., Torres, A. & Pérez, M. A. H. Problemática sobre las lagunas costeras mexicanas V, Pesquerías. ContactoSS 25, 36–46 (1998).
Reizopoulou, S. & Nicolaidou, A. Benthic diversity of coastal brackish-water lagoons in western Greece. Aquat. Conserv. Mar. Freshw. Ecosyst. 14, 93–102 (2004).
Zamorano, P., Barrientos-luján, N. A. & Ramírez-luna, S. Malacofauna del infralitoral rocoso de Agua Blanca, Santa Elena Cozoaltepec, Oaxaca. Cienc. y Mar. 12, 19–33 (2008).
Chávez-lópez, Y. & Cruz-gómez, C. New records of polychaetes (Annelida: Polychaeta) from three locations of Oaxaca. Mexico. 67, 157–168 (2019).
Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012).
Google Scholar
Thomsen, P. F. & Willerslev, E. Environmental DNA—An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183, 4–18 (2015).
Miller, S. E., Hausmann, A., Hallwachs, W. & Janzen, D. H. Advancing taxonomy and bioinventories with DNA barcodes. Philos. Trans. R. Soc. B Biol. Sci. 371, 20150339 (2016).
Source: Ecology - nature.com