Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Rojas L, Cambronero JC, Chavarría M. Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes. Extremophiles. 2017;21(2):235–43.
Article
Google Scholar
Alvarado, G. E. Costa Rica y sus Volcanes; Editorial UCR, San José, 2021. ISBN 978-9968-46-776-6.
Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Martínez-Cruz M, de Moor JM, Pieper DH, Chavarría M. Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park. Costa Rica Extremophiles. 2019;23(2):177–87.
Article
Google Scholar
Jovanelly TJ, Rodríguez-Montero L, Sánchez-Gutiérrez R, Mena-Rivera L, Thomas D. Evaluating watershed health in Costa Rican national parks and protected areas. Sustain Water Resour Manag. 2020;6(5):1–14.
Article
Google Scholar
SINAC (Sistema Nacional de Áreas de Conservación). Informe Anual Estadísticas SEMEC 2018: SINAC en Números. Comp. B Pavlotzky. San José, CR, 2019. p 82.
Castellón E, Martínez M, Madrigal-Carballo S, Arias ML, Vargas WE, Chavarría M. Scattering of light by colloidal aluminosilicate particles produces the unusual sky-blue color of Río Celeste (Tenorio Volcano Complex, Costa Rica). PLoS ONE. 2013;8(9): e75165.
Article
Google Scholar
Ohsawa S, Kawamura T, Takamatsu N, Yusa Y. Rayleigh scattering by aqueous colloidal silica as a cause for the blue color of hydrothermal water. J Volcanol Geoth Res. 2002;113(1–2):49–60.
Article
CAS
Google Scholar
Oyama Y, Shibahara A. Simulation of water colors in a shallow acidified lake, Lake Onneto, Japan, using colorimetric analysis and bio-optical modeling. Limnology. 2009;10(1):47–56.
Article
CAS
Google Scholar
Takagai Y, Abe R, Endo A, Yokoyama A, Konno M. Unique aluminosilicate-based natural nanoparticles in the volcanogenic Goshiki-numa pond. Environ Chem Lett. 2016;14(4):565–9.
Article
CAS
Google Scholar
Parkhurst DL, Appelo CAJ. Description of input and examples for PHREEQC version 3—a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. US Geol Survey Tech Methods. 2013;6(A43):497.
Google Scholar
Bohorquez LC, Delgado-Serrano L, López G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM. In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb Ecol. 2012;63(1):103–15.
Article
Google Scholar
Camarinha-Silva A, Jáuregui R, Chaves-Moreno D, Oxley AP, Schaumburg F, Becker K, Wos-Oxley ML, Pieper DH. Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing. Environ Microbiol. 2014;16(9):2939–52.
Article
CAS
Google Scholar
Burbach K, Seifert J, Pieper DH, Camarinha-Silva A. Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions. Microbiology open. 2016;5(1):70–82.
Article
CAS
Google Scholar
Puente-Sánchez F, Aguirre J, Parro V. A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies. Nucleic Acids Res. 2016;44(4):e40–e40.
Article
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3.
Article
CAS
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research. 2012;41(D1):D590–6.
Article
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Weber CF. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.
Article
CAS
Google Scholar
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2011;27(4):592–3.
Article
CAS
Google Scholar
Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007;73(5):1576–85.
Article
CAS
Google Scholar
Chen J, Chen MJ (2018) Package ‘GUniFrac’. The Comprehensive R Archive Network (CRAN).
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10(4): e1003531.
Article
Google Scholar
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’hara RB, Simpson GL, Solymos P, Stevens MH, Wagner H, Oksanen MJ. Package ‘vegan.’ Commun Ecol Package Vers. 2013;2(9):1–295.
Google Scholar
Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012;28(16):2106–13.
Article
CAS
Google Scholar
Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28(14):1823–9.
Article
CAS
Google Scholar
Puente-Sánchez F, García-García N, Tamames J. SQMtools: automated processing and visual analysis of’omics data with R and anvi’o. BMC Bioinformatics. 2020;21(1):1–11.
Article
Google Scholar
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12(9):635–45.
Article
CAS
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(D1):D633–42.
Article
CAS
Google Scholar
Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Zaretskaya I. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41(W1):W29–33.
Article
Google Scholar
Decelle J, Romac S, Stern RF, Bendif EM, Zingone A, Audic S, Guiry MD, Guillou L, Tessier D, Le Gall F, Christen R. Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour. 2015;15(6):1435–45.
Article
CAS
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–100.
Article
CAS
Google Scholar
Comba ME, Kaiser KL. Suspended particulate concentrations in the St. Lawrence River (1985–1987) determined by centrifugation and filtration. Sci Total Environ. 1990;97:191–206.
Article
Google Scholar
Nordstrom DK. The effect of sulfate on aluminum concentrations in natural waters: some stability relations in the system Al2O3-SO3-H2O at 298 K. Geochim Cosmochim Acta. 1982;46(4):681–92.
Article
CAS
Google Scholar
Bigham JM, Nordstrom DK. Iron and aluminum hydroxysulfates from acid sulfate waters. Rev Mineral Geochem. 2000;40(1):351–403.
Article
CAS
Google Scholar
Wanner C, Pöthig R, Carrero S, Fernandez-Martinez A, Jäger C, Furrer G. Natural occurrence of nanocrystalline Al-hydroxysulfates: Insights on formation, Al solubility control and As retention. Geochim Cosmochim Acta. 2018;238:252–69.
Article
CAS
Google Scholar
Sánchez-España J, Yusta I, Diez-Ercilla M. Schwertmannite and hydrobasaluminite: A re-evaluation of their solubility and control on the iron and aluminium concentration in acidic pit lakes. Appl Geochem. 2011;26(9–10):1752–74.
Article
Google Scholar
Takagai Y, Abe R. Concerning the chemical similarities and differences between the blue-coloured waters of Goshikinuma and blue pond in Biei Town, Hokkaido. Fukushima Univ Sci Eng Group Symbiotic Syst. 2014;14:80–7.
Google Scholar
Du P, Yuan P, Thill A, Annabi-Bergaya F, Liu D, Wang S. Insights into the formation mechanism of imogolite from a full-range observation of its sol-gel growth. Appl Clay Sci. 2017;150:115–24.
Article
CAS
Google Scholar
Doucet FJ, Schneider C, Bones SJ, Kretchmer A, Moss I, Tekely P, Exley C. The formation of hydroxyaluminosilicates of geochemical and biological significance. Geochim Cosmochim Acta. 2001;65(15):2461–7.
Article
CAS
Google Scholar
Strekopytov S, Jarry E, Exley C. Further insight into the mechanism of formation of hydroxyaluminosilicates. Polyhedron. 2006;25(17):3399–404.
Article
CAS
Google Scholar
Beardmore J, Lopez X, Mujika JI, Exley C. What is the mechanism of formation of hydroxyaluminosilicates? Sci Rep. 2016;6(1):1–8.
Article
Google Scholar
Dobrzyński D. Silica solubility in groundwater from Permian volcanogenic rocks (the Sudetes Mts., SW Poland)–the role of reversible aluminosilicate solids. Geol Quarterly. 2006;50(4):407–17.
Google Scholar
Dobrzyński D. Chemistry of neutral and alkaline waters with low Al3+ activity against hydroxyaluminosilicate HASB solubility. The evidence from ground and surface waters of the Sudetes Mts. (SW Poland). Aquatic Geochem. 2007;13(3):197–210.
Article
Google Scholar
Parfitt RL. Allophane in New Zealand-a review. Soil Res. 1990;28(3):343–60.
Article
CAS
Google Scholar
Montarges-Pelletier E, Bogenez S, Pelletier M, Razafitianamaharavo A, Ghanbaja J, Lartiges B, Michot L. Synthetic allophane-like particles: textural properties. Colloids Surf A. 2005;255(1–3):1–10.
Article
CAS
Google Scholar
Lenhardt KR, Breitzke H, Buntkowsky G, Reimhult E, Willinger M, Rennert T. Synthesis of short-range ordered aluminosilicates at ambient conditions. Sci Rep. 2021;11(1):1–13.
Article
Google Scholar
Caraballo MA, Wanty RB, Verplanck PL, Navarro-Valdivia L, Ayora C, Hochella MF Jr. Aluminum mobility in mildly acidic mine drainage: Interactions between hydrobasaluminite, silica and trace metals from the nano to the meso-scale. Chem Geol. 2019;519:1–10.
Article
CAS
Google Scholar
Sánchez-España J, Yusta I, Burgos WD. Geochemistry of dissolved aluminum at low pH: Hydrobasaluminite formation and interaction with trace metals, silica and microbial cells under anoxic conditions. Chem Geol. 2016;441:124–37.
Article
Google Scholar
Du X, Wang Y, Su X, Li J. Influences of pH value on the microstructure and phase transformation of aluminum hydroxide. Powder Technol. 2009;192(1):40–6.
Article
CAS
Google Scholar
Hem JD, Roberson CE, Lind CJ, Polxer WL (1973) Chemical interactions of aluminum with aqueous silica at 25 degrees Celsius (No. 1827-E). US Govt. Print. Off.
Letterman RD, editor. Water quality and treatment: a handbook of community water supplies. 5th ed. New York: McGraw-Hill; 1999.
Google Scholar
Faust SD, Aly OM. Chemistry of water treatment. Boca Raton: CRC; 2018.
Google Scholar
Meier DV, Pjevac P, Bach W, Hourdez S, Girguis PR, Vidoudez C, Amann R, Meyerdierks A. Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. ISME J. 2017;11(7):1545–58.
Article
CAS
Google Scholar
Lopez Bedogni G, Massello FL, Giaveno A, Donati ER, Urbieta MS. A deeper look into the biodiversity of the extremely acidic copahue volcano-río agrio system in Neuquén. Argentina Microorg. 2020;8(1):58.
Article
Google Scholar
Li J, Zhou H, Peng X, Wu Z, Chen S, Fang J. Microbial diversity and biomineralization in low-temperature hydrothermal iron–silica-rich precipitates of the Lau Basin hydrothermal field. FEMS Microbiol Ecol. 2012;81(1):205–16.
Article
CAS
Google Scholar
Amils R, González-Toril E, Fernández-Remolar D, Gómez F, Aguilera Á, Rodríguez N, Malki M, García-Moyano A, Fairén AG, de la Fuente V, Sanz JL. Extreme environments as Mars terrestrial analogs: The Rio Tinto case. Planetary Space Sci. 2007;55(3):370–81.
Article
CAS
Google Scholar
Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Martínez M, Pieper DH, Chavarría M. Microbial community structure along a horizontal oxygen gradient in a Costa Rican volcanic influenced acid rock drainage system. Microbial Ecol. 2020;80(4):793–808.
Article
Google Scholar
Niemann H, Linke P, Knittel K, MacPherson E, Boetius A, Brückmann W, Larvik G, Wallmann K, Schacht U, Omoregie E, Rehder G. Methane-carbon flow into the benthic food web at cold seeps–a case study from the Costa Rica subduction zone. PLoS One. 2013;8(10):e74894.
Article
CAS
Google Scholar
Hubalek V, Wu X, Eiler A, Buck M, Heim C, Dopson M, Bertilsson S, Ionescu D. Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME J. 2016;10(10):2447–58.
Article
Google Scholar
Duan JL, Sun JW, Ji MM, Ma Y, Cui ZT, Tian RK, Xu PC, Sun WL, Yuan XZ. Indicatory bacteria and chemical composition related to sulfur distribution in the river-lake systems. Microbiol Res. 2020;236:126453.
Article
CAS
Google Scholar
Salonen IS, Chronopoulou PM, Bird C, Reichart GJ, Koho KA. Enrichment of intracellular sulphur cycle–associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis. Sci Rep. 2019;9(1):1–12.
Article
Google Scholar
Holmes P, Niccolls LM, Sartory DP. The ecology of mesophilic Aeromonas in the aquatic environment. The Genus Aeromonas. 1996; 127–150.
Janda JM, Abbott SL. The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev. 2010;23(1):35–73.
Article
CAS
Google Scholar
Rippey SR, Cabelli VJ. Use of the thermotolerant Aeromonas group for the trophic state classification of freshwaters. Water Res. 1989;23(9):1107–14.
Article
CAS
Google Scholar
Ali AD, Ezra AG, Abdul SD. Species composition and distribution of freshwater diatoms from Upper Dilimi River, Jos, Nigeria. 2015.
Molinero J, Barrado M, Guijarro M, Ortiz M, Carnicer O, Zuazagoitia D. The Teaone River: a snapshot of a tropical river from the coastal region of Ecuador. Limnetica. 2019;38(2):587–605.
Article
Google Scholar
Haque M, Jewel M, Sayed A, Akhi M, Atique U, Paul AK, et al. Seasonal dynamics of phytoplankton community and functional groups in a tropical river. Environ Monitor Assess. 2021;193(11):1–16.
Article
Google Scholar
Silva-Benavides AM. The epilithic diatom flora of a pristine and a polluted river in Costa Rica, Central America. Diatom Res. 1996;11(1):105–42.
Article
Google Scholar
Khan IN. Assessment of water pollution using diatom community structure and species distribution—a case study in a tropical river basin. Internationale Revue der gesamten Hydrobiologie und Hydrographie. 1990;75(3):317–38.
Article
CAS
Google Scholar
De Master DJ, Knapp GB, Nittrouer CA. Biological uptake and accumulation of silica on the Amazon continental shelf. Geochim Cosmochim Acta. 1983;47(10):1713–23.
Article
Google Scholar
Conley DJ. Riverine contribution of biogenic silica to the oceanic silica budget. Limnol Oceanogr. 1997;42(4):774–7.
Article
CAS
Google Scholar
Ran X, Liu S, Liu J, Zang J, Che H, Ma Y, Wang Y. Composition and variability in the export of biogenic silica in the Changjiang River and the effect of Three Gorges Reservoir. Sci Total Environ. 2016;571:1191–9.
Article
CAS
Google Scholar
Admiraal W, Breugem P, Jacobs DMLHA, Van Steveninck EDR. Fixation of dissolved silicate and sedimentation of biogenic silicate in the lower river Rhine during diatom blooms. Biogeochemistry. 1990;9(2):175–85.
Article
CAS
Google Scholar
Krause JW, Brzezinski MA, Landry MR, Baines SB, Nelson DM, Selph KE, Taylor AG, Twiningf BS. The effects of biogenic silica detritus, zooplankton grazing, and diatom size structure on silicon cycling in the euphotic zone of the eastern equatorial Pacific. Limnol Oceanogr. 2010;55(6):2608–22.
Article
CAS
Google Scholar
Carbonnel V, Vanderborght JP, Lionard M, Chou L. Diatoms, silicic acid and biogenic silica dynamics along the salinity gradient of the Scheldt estuary (Belgium/The Netherlands). Biogeochemistry. 2013;113(1):657–82.
Article
CAS
Google Scholar
Losic D, Mitchell JG, Voelcker NH. Diatom culture media contain extracellular silica nanoparticles which form opalescent films. In: Smart Materials V (Vol. 7267, p. 726712). International Society for Optics and Photonics. 2008.
Huang Y, Mi W, Hu Z, Bi Y. Effects of the three Gorges Dam on spatiotemporal distribution of silicon in the tributary: evidence from the Xiangxi River. Environ Sci Pollut Res. 2019;26(5):4645–53.
Article
CAS
Google Scholar
Le Meur M, Montargès-Pelletier E, Bauer A, Gley R, Migot S, Barres O, Delus C, Villiéras F. Characterization of suspended particulate matter in the Moselle River (Lorraine, France): evolution along the course of the river and in different hydrologic regimes. J Soils Sediments. 2016;16(5):1625–42.
Article
Google Scholar
Kravchishina MD, Lisitzyn AP. Grain-size composition of the suspended particulate matter in the marginal filter of the Severnaya Dvina River. Oceanology. 2011;51(1):89–104.
Article
Google Scholar
Passow U, Alldredge AL. Aggregation of a diatom bloom in a mesocosm: The role of transparent exopolymer particles (TEP). Deep Sea Res Part II. 1995;42(1):99–109.
Article
CAS
Google Scholar
Hamm CE. Interactive aggregation and sedimentation of diatoms and clay-sized lithogenic material. Limnol Oceanogr. 2002;47(6):1790–5.
Article
Google Scholar
Gehlen M, Beck L, Calas G, Flank AM, Van Bennekom AJ, Van Beusekom JEE. Unraveling the atomic structure of biogenic silica: evidence of the structural association of Al and Si in diatom frustules. Geochim Cosmochim Acta. 2002;66(9):1601–9.
Article
CAS
Google Scholar
Dixit S, Van Cappellen P. Surface chemistry and reactivity of biogenic silica. Geochim Cosmochim Acta. 2002;66(14):2559–68.
Article
CAS
Google Scholar
Wu B, Liu SM, Ren JL. Dissolution kinetics of biogenic silica and tentative silicon balance in the Yellow Sea. Limnol Oceanogr. 2017;62(4):1512–25.
Article
CAS
Google Scholar
Presti M, Michalopoulos P. Estimating the contribution of the authigenic mineral component to the long-term reactive silica accumulation on the western shelf of the Mississippi River Delta. Cont Shelf Res. 2008;28(6):823–38.
Article
Google Scholar
Stanton C, Cosmidis J, Kump L. A re-examination of the mechanism of whiting events: A new role for diatoms in Fayetteville Green Lake. New York, USA; 2021.