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4. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Author

Plominsky, Alvaro M, Henríquez-Castillo, Carlos, Delherbe, Nathalie, Podell, Sheila, Ramirez-Flandes, Salvador, Ugalde, Juan A, Santibañez, Juan F, van den Engh, Ger, Hanselmann, Kurt, Ulloa, Osvaldo, De la Iglesia, Rodrigo, Allen, Eric E, and Trefault, Nicole

Subjects
Microbiology, Biological Sciences, Genetics, Life Below Water, hypersaline environments, solar salterns, metagenomics, microbial ecology, environmental adaptation, functional metagenomics, artisanal crystallizer pond, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.

Published
2018

7. Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms?

Author

Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Agencia Estatal de Investigación (España), Arboleda-Baena, Clara, Freilich, Mara, Pareja, Claudia Belén, Logares, Ramiro, De la Iglesia, Rodrigo, Navarrete, Sergio A., Comisión Nacional de Investigación Científica y Tecnológica (Chile), Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), Agencia Estatal de Investigación (España), Arboleda-Baena, Clara, Freilich, Mara, Pareja, Claudia Belén, Logares, Ramiro, De la Iglesia, Rodrigo, and Navarrete, Sergio A.

Abstract

The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the “species” and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore

Published
2024

10. Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cáhuil Lagoon, Chile

Author

Plominsky, Alvaro M, Delherbe, Nathalie, Ugalde, Juan A, Allen, Eric E, Blanchet, Marine, Ikeda, Priscila, Santibañez, Francisco, Hanselmann, Kurt, Ulloa, Osvaldo, De la Iglesia, Rodrigo, von Dassow, Peter, Astorga, Marcia, Gálvez, María Jesús, González, María Lorena, Henríquez-Castillo, Carlos, Vaulot, Daniel, do Santos, Adriana Lopes, van den Engh, Gerrit, Gimpel, Carla, Bertoglio, Florencia, Delgado, Yolaine, Docmac, Felipe, Elizondo-Patrone, Claudia, Narváez, Silvia, Sorroche, Fernando, Rojas-Herrera, Marcelo, and Trefault, Nicole

Subjects
Microbiology, Biological Sciences, Biochemistry and Cell Biology, Genetics
Abstract

Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.

Published
2014

13. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author

Edwards, Robert A., Vega, Alejandro A., Norman, Holly M., Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A., Cinek, Ondrej, Aziz, Ramy K., McNair, Katelyn, Barr, Jeremy J., Bibby, Kyle, Brouns, Stan J. J., Cazares, Adrian, de Jonge, Patrick A., Desnues, Christelle, Díaz Muñoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V., Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M., Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K., Cantu, Vito Adrian, Carlton, Jane M., Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A. Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyöty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Khan Mirzaei, Mohammadali, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R., Lipson, David, Lisitsyna, Eugenia S., Llagostera, Montserrat, Maritz, Julia M., Marr, Linsey C., McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-phuong, Nigro, Olivia D., Nilsson, Anders S., O’Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A. O., Rossi, Alessandro, Santos, Ricardo, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, and Dutilh, Bas E.

Published
2019
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18. Isolation and characterization of an Antarctic Flavobacterium strain with agarase and alginate lyase activities

Author

Lavín Paris, Atala Cristian, Gallardo-Cerda Jorge, Gonzalez-Aravena Marcelo, De La Iglesia Rodrigo, Oses Rómulo, Torres-Díaz Cristian, Trefault Nicole, Molina-Montenegro Marco A., and Laughinghouse IV H. Dail

Subjects
Antarctic, King George Island, Flavobacterium, agarase, alginate-lyase, Geology, QE1-996.5
Abstract

Several bacteria that are associated with macroalgae can use phycocolloids as a carbon source. Strain INACH002, isolated from decomposing Porphyra (Rhodophyta), in King George Island, Antarctica, was screened and characterized for the ability to produce agarase and alginate-lyase enzymatic activities. Our strain INACH002 was identified as a member of the genus Flavobacterium, closely related to Flavobacterium faecale, using 16S rRNA gene analysis. The INACH002 strain was characterized as psychrotrophic due to its optimal temperature (17ºC) and maximum temperature (20°C) of growth. Agarase and alginate-lyase displayed enzymatic activities within a range of 10°C to 50°C, with differences in the optimal temperature to hydrolyze agar (50°C), agarose (50°C) and alginate (30°C) during the first 30 min of activity. Strain Flavobacterium INACH002 is a promising Antarctic biotechnological resource; however, further research is required to illustrate the structural and functional bases of the enzymatic performance observed during the degradation of different substrates at different temperatures.

Published
2016
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21. Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities

Author

Comisión Nacional de Investigación Científica y Tecnológica (Chile), Agencia Nacional de Investigación y Desarrollo (Chile), Pontificia Universidad Católica de Chile, Agencia Estatal de Investigación (España), Arboleda-Baena, Clara, Pareja, Claudia Belén, Pla, Isidora, Logares, Ramiro, De la Iglesia, Rodrigo, Navarrete, Sergio A., Comisión Nacional de Investigación Científica y Tecnológica (Chile), Agencia Nacional de Investigación y Desarrollo (Chile), Pontificia Universidad Católica de Chile, Agencia Estatal de Investigación (España), Arboleda-Baena, Clara, Pareja, Claudia Belén, Pla, Isidora, Logares, Ramiro, De la Iglesia, Rodrigo, and Navarrete, Sergio A.

Abstract

In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on

Published
2022

25. Testing the Test: A Comparative Study of Marine Microbial Corrosion under Laboratory and Field Conditions

Author

Canales, Camila, primary, Galarce, Carlos, additional, Rubio, Francisca, additional, Pineda, Fabiola, additional, Anguita, Javiera, additional, Barros, Ramón, additional, Parragué, Mirtala, additional, Daille, Leslie K., additional, Aguirre, Javiera, additional, Armijo, Francisco, additional, Pizarro, Gonzalo E., additional, Walczak, Magdalena, additional, De la Iglesia, Rodrigo, additional, Navarrete, Sergio A., additional, and Vargas, Ignacio T., additional

Published
2021
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26. Summer phyto- and bacterioplankton communities during low and high productivity scenarios in the Western Antarctic Peninsula

Author

Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Fuentes, Sebastián, Arroyo, José I, Rodríguez-Marconi, Susana, Masotti, Italo, Alarcón-Schumacher, Tomás, Polz, Martin F, Trefault, Nicole, De la Iglesia, Rodrigo, Díez, Beatriz, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Fuentes, Sebastián, Arroyo, José I, Rodríguez-Marconi, Susana, Masotti, Italo, Alarcón-Schumacher, Tomás, Polz, Martin F, Trefault, Nicole, De la Iglesia, Rodrigo, and Díez, Beatriz

Abstract

Phytoplankton blooms taking place during the warm season drive high productivity in Antarctic coastal seawaters. Important temporal and spatial variations exist in productivity patterns, indicating local constraints influencing the phototrophic community. Surface water in Chile Bay (Greenwich Island, South Shetlands) is influenced by freshwater from the melting of sea ice and surrounding glaciers; however, it is not a widely studied system. The phyto- and bacterioplankton communities in Chile Bay were studied over two consecutive summers; during a low productivity period (chlorophyll a < 0.05 mg m−3) and an ascendant phototrophic bloom (chlorophyll a up to 2.38 mg m−3). Microbial communities were analyzed by 16S rRNA—including plastidial—gene sequencing. Diatoms (mainly Thalassiosirales) were the most abundant phytoplankton, particularly during the ascendant bloom. Bacterioplankton in the low productivity period was less diverse and dominated by a few operational taxonomic units (OTUs), related to Colwellia and Pseudoalteromonas. Alpha diversity was higher during the bloom, where several Bacteroidetes taxa absent in the low productivity period were present. Network analysis indicated that phytoplankton relative abundance was correlated with bacterioplankton phylogenetic diversity and the abundance of several bacterial taxa. Hubs—the most connected OTUs in the network—were not the most abundant OTUs and included some poorly described taxa in Antarctica, such as Neptunomonas and Ekhidna. In summary, the results of this study indicate that in Antarctic Peninsula coastal waters, such as Chile Bay, higher bacterioplankton community diversity occurs during a phototrophic bloom. This is likely a result of primary production, providing a source of fresh organic matter to bacterioplankton.

Published
2021

27. Molecular and population analyses of a recombination event in the catabolic plasmid pJP4

Author

Larrain-Linton, Juanita, De la Iglesia, Rodrigo, Melo, Francisco, and Gonzalez, Bernardo

Subjects
Recombinant molecules -- Research, Plasmids -- Research, Bacterial genetics -- Research, Biological sciences
Abstract

Cupriavidus necator JMP134(pJP4) harbors a catabolic plasmid, pJP4, which confers the ability to grow on chloroaromatic compounds. Repeated growth on 3-chlorobenzoate (3-CB) results in selection of a recombinant strain, which degrades 3-CB better but no longer grows on 2,4-dichlorophenoxyacetate (2,4-D). We have previously proposed that this phenotype is due to a double homologous recombination event between inverted repeats of the multicopies of this plasmid within the cell. One recombinant form of this plasmid (pJp4-F3) explains this phenotype, since it harbors two copies of the chlorocatechol degradation tfd gene clusters, which are essential to grow on 3-CB, but has lost the tfdA gene, encoding the first step in degradation of 2,4-D. The other recombinant plasmid (pJP4-FM) should harbor two copies of the tfdA gene but no copies of the tfd gene clusters. A molecular analysis using a multiplex PCR approach to distinguish the wild-type plasmid pJP4 from its two recombinant forms, was carried out. Expected PCR products confirming this recombination model were found and sequenced. Few recombinant plasmid forms in cultures grown in several carbon sources were detected. Kinetic studies indicated that cells containing the recombinant plasmid pJP4-FM were not selectable by sole carbon source growth pressure, whereas those cells harboring recombinant plasmid pJP4-F3 were selected upon growth on 3-CB. After 12 days of repeated growth on 3-CB, the complete plasmid population in C. necator JMP134 apparently corresponds to this form. However, wild-type plasmid forms could be recovered after growing this culture on 2,4-D, indicating that different plasmid forms can be found in C. necator JMP134 at the population level.

Published
2006

32. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Edwards, Robert A., Vega, Alejandro A., Norman, Holly M., Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A., Cinek, Ondrej, Aziz, Ramy K., McNair, Katelyn, Barr, Jeremy J., Bibby, Kyle, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, Desnues, Christelle, Díaz Muñoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V., Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M., Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K., Cantu, Vito Adrian, Carlton, Jane M., Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A. Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyöty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Mirzaei, Mohammadali Khan, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R., Lipson, David, Lisitsyna, Eugenia S., Llagostera, Montserrat, Maritz, Julia M., Marr, Linsey C., McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-phuong, Nigro, Olivia D., Nilsson, Anders S., O’Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, Santos, Ricardo, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Edwards, Robert A., Vega, Alejandro A., Norman, Holly M., Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A., Cinek, Ondrej, Aziz, Ramy K., McNair, Katelyn, Barr, Jeremy J., Bibby, Kyle, Shimashita, John, Stachler, Elyse N., Stene, Lars C., Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J., Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, Brouns, Stan J.J., White, Bryan, Whiteley, Andy, Whiteson, Katrine L., Wijmenga, Cisca, Zambrano, Maria M., Zschach, Henrike, Dutilh, Bas E., Cazares, Adrian, Jonge, Patrick A. de, Desnues, Christelle, Díaz Muñoz, Samuel L., Fineran, Peter C., Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T., Nobrega, Franklin L., Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V., Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M., Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K., Cantu, Vito Adrian, Carlton, Jane M., Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A., De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P., Dominy, Nathaniel J., Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A. Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M., Haggerty, John M., Head, Steven R., Hendriksen, Rene S., Hill, Colin, Hyöty, Heikki, Ilina, Elena N., Irwin, Mitchell T., Jeffries, Thomas C., Jofre, Juan, Junge, Randall E., Kelley, Scott T., Mirzaei, Mohammadali Khan, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R., Lipson, David, Lisitsyna, Eugenia S., Llagostera, Montserrat, Maritz, Julia M., Marr, Linsey C., McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-phuong, Nigro, Olivia D., Nilsson, Anders S., O’Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin II, Aaron J., Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A.O., Rossi, Alessandro, and Santos, Ricardo

Abstract

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Published
2019

33. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Edwards, Robert A, Vega, Alejandro A, Norman, Holly M, Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A, Cinek, Ondrej, Aziz, Ramy K, McNair, Katelyn, Barr, Jeremy J, Bibby, Kyle, Brouns, Stan J J, Cazares, Adrian, de Jonge, Patrick A, Desnues, Christelle, Díaz Muñoz, Samuel L, Fineran, Peter C, Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T, Nobrega, Franklin L, Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V, Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M, Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K, Cantu, Vito Adrian, Carlton, Jane M, Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A, De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P, Dominy, Nathaniel J, Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M, Haggerty, John M, Head, Steven R, Hendriksen, Rene S, Hill, Colin, Hyöty, Heikki, Ilina, Elena N, Irwin, Mitchell T, Jeffries, Thomas C, Jofre, Juan, Junge, Randall E, Kelley, Scott T, Khan Mirzaei, Mohammadali, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R, Lipson, David, Lisitsyna, Eugenia S, Llagostera, Montserrat, Maritz, Julia M, Marr, Linsey C, McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-Phuong, Nigro, Olivia D, Nilsson, Anders S, O'Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin Ii, Aaron J, Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A O, Rossi, Alessandro, Santos, Ricardo, Shimashita, John, Stachler, Elyse N, Stene, Lars C, Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J, Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Edwards, Robert A, Vega, Alejandro A, Norman, Holly M, Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A, Cinek, Ondrej, Aziz, Ramy K, McNair, Katelyn, Barr, Jeremy J, Bibby, Kyle, Brouns, Stan J J, Cazares, Adrian, de Jonge, Patrick A, Desnues, Christelle, Díaz Muñoz, Samuel L, Fineran, Peter C, Kurilshikov, Alexander, Lavigne, Rob, Mazankova, Karla, McCarthy, David T, Nobrega, Franklin L, Reyes Muñoz, Alejandro, Tapia, German, Trefault, Nicole, Tyakht, Alexander V, Vinuesa, Pablo, Wagemans, Jeroen, Zhernakova, Alexandra, Aarestrup, Frank M, Ahmadov, Gunduz, Alassaf, Abeer, Anton, Josefa, Asangba, Abigail, Billings, Emma K, Cantu, Vito Adrian, Carlton, Jane M, Cazares, Daniel, Cho, Gyu-Sung, Condeff, Tess, Cortés, Pilar, Cranfield, Mike, Cuevas, Daniel A, De la Iglesia, Rodrigo, Decewicz, Przemyslaw, Doane, Michael P, Dominy, Nathaniel J, Dziewit, Lukasz, Elwasila, Bashir Mukhtar, Eren, A Murat, Franz, Charles, Fu, Jingyuan, Garcia-Aljaro, Cristina, Ghedin, Elodie, Gulino, Kristen M, Haggerty, John M, Head, Steven R, Hendriksen, Rene S, Hill, Colin, Hyöty, Heikki, Ilina, Elena N, Irwin, Mitchell T, Jeffries, Thomas C, Jofre, Juan, Junge, Randall E, Kelley, Scott T, Khan Mirzaei, Mohammadali, Kowalewski, Martin, Kumaresan, Deepak, Leigh, Steven R, Lipson, David, Lisitsyna, Eugenia S, Llagostera, Montserrat, Maritz, Julia M, Marr, Linsey C, McCann, Angela, Molshanski-Mor, Shahar, Monteiro, Silvia, Moreira-Grez, Benjamin, Morris, Megan, Mugisha, Lawrence, Muniesa, Maite, Neve, Horst, Nguyen, Nam-Phuong, Nigro, Olivia D, Nilsson, Anders S, O'Connell, Taylor, Odeh, Rasha, Oliver, Andrew, Piuri, Mariana, Prussin Ii, Aaron J, Qimron, Udi, Quan, Zhe-Xue, Rainetova, Petra, Ramírez-Rojas, Adán, Raya, Raul, Reasor, Kim, Rice, Gillian A O, Rossi, Alessandro, Santos, Ricardo, Shimashita, John, Stachler, Elyse N, Stene, Lars C, Strain, Ronan, Stumpf, Rebecca, Torres, Pedro J, Twaddle, Alan, Ugochi Ibekwe, MaryAnn, Villagra, Nicolás, Wandro, Stephen, White, Bryan, Whiteley, Andy, Whiteson, Katrine L, Wijmenga, Cisca, Zambrano, Maria M, Zschach, Henrike, and Dutilh, Bas E

Published
2019

34. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author

Edwards, Robert, primary, Vega, Alejandro, additional, Norman, Holly, additional, Ohaeri, Maria Cynthia, additional, Levi, Kyle, additional, Dinsdale, Elizabeth, additional, Cinek, Ondrej, additional, Aziz, Ramy, additional, McNair, Katelyn, additional, Barr, Jeremy, additional, Bibby, Kyle, additional, Brouns, Stan, additional, Cazares, Adrian, additional, de Jonge, Patrick A., additional, Desnues, Christelle, additional, Diaz-Munoz, Samuel, additional, Fineran, Peter, additional, Kurilshikov, Alexander, additional, Lavigne, Rob, additional, Mazankova, Karla, additional, McCarthy, David, additional, Nobrega, Franklin, additional, Reyes, Alejandro, additional, Tapia, German, additional, Trefault, Nicole, additional, Tyakht, Alexander, additional, Vinuesa, Pablo, additional, Wagemans, Jeroen, additional, Zhernakova, Alexandra, additional, Aarestrup, Frank, additional, Ahmadov, Gunduz, additional, Alassaf, Abeer, additional, Anton, Josefa, additional, Asangba, Abigail, additional, Billings, Emma, additional, Cantu, Adrian, additional, Carlton, Jane, additional, Cazares Lopez, Daniel, additional, Cho, Gyu-Sung, additional, Condeff, Tess, additional, Cortes, Pilar, additional, Cranfield, Micheal, additional, Cuevas, Daniel, additional, De la Iglesia, Rodrigo, additional, Decewicz, Przemyslaw, additional, Doane, Michael, additional, Dominy, Nathaniel, additional, Dziewit, Lukasz, additional, Elmahi, Bashir, additional, Eren, Murat, additional, Franz, Charles, additional, Fu, Jingyuan, additional, Garcia-Aljaro, Cristina, additional, Ghedin, Elodie, additional, Gulino, Kristen, additional, Haggerty, John, additional, Head, Steven, additional, Hendriksen, Rene S., additional, Hill, Colin, additional, Hyoty, Heikki, additional, Ilina, Elena, additional, Irwin, Mitchell, additional, Jeffries, Thomas, additional, Jofre, Juan, additional, Junge, Randall, additional, Kelley, Scott, additional, Kowalewski, Martin, additional, Kumaresan, Deepak, additional, Leigh, Steven, additional, Lisitsyna, Eugenia, additional, Llagostera, Montserrat, additional, Maritz, Julia M., additional, Marr, Linsey, additional, McCann, Angela, additional, Khan Mirzaei, Mohammadali, additional, Molshanski-Mor, Shahar, additional, Monteiro, Silvia, additional, Moreira-Grez, Benjamin, additional, Morris, Megan, additional, Mugisha, Lawrence, additional, Muniesa, Maite, additional, Neve, Horst, additional, Nguyen, Nam-phuong, additional, Nigro, Olivia, additional, Nilsson, Anders, additional, O'Connell, Taylor, additional, Odeh, Rasha, additional, Oliver, Andrew, additional, Piuri, Mariana, additional, Prussin, Aaron, additional, Qimron, Udi, additional, Quan, Zhe-Xue, additional, Rainetova, Petra, additional, Ramirez-Rojas, Adan, additional, Raya, Raul, additional, Rice, Gillian, additional, Rossi, Alessandro, additional, Santos, Ricardo, additional, Shimashita, John, additional, Stachler, Elyse, additional, Stene, Lars, additional, Strain, Ronan, additional, Stumpf, Rebecca, additional, Torres, Pedro, additional, Twaddle, Alan, additional, Ibekwe, Maryann Ugochi, additional, Villagra, Nicolas, additional, Wandro, Stephen, additional, White, Bryan, additional, Whiteley, Andrew, additional, Whiteson, Katrine, additional, Wijmenga, Cisca, additional, Zambrano, Maria Mercedes, additional, Zschach, Henrike, additional, and Dutilh, Bas E., additional

Published
2019
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37. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Author

Plominsky, Alvaro M., primary, Henríquez-Castillo, Carlos, additional, Delherbe, Nathalie, additional, Podell, Sheila, additional, Ramirez-Flandes, Salvador, additional, Ugalde, Juan A., additional, Santibañez, Juan F., additional, van den Engh, Ger, additional, Hanselmann, Kurt, additional, Ulloa, Osvaldo, additional, De la Iglesia, Rodrigo, additional, Allen, Eric E., additional, and Trefault, Nicole, additional

Published
2018
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38. Ostreococcus tauri Luminescent Reporter Lines as Biosensors for Detecting Pollution From Copper-Mine Tailing Effluents in Coastal Environments

Author

Henríquez-Castillo, Carlos, primary, Botebol, Hugo, additional, Mouton, Adelaide, additional, Ramírez-Flandes, Salvador, additional, Lozano, Jean-Claude, additional, Lelandais, Gaelle, additional, Andrade, Santiago, additional, Trefault, Nicole, additional, De la Iglesia, Rodrigo, additional, and Bouget, François-Yves, additional

Published
2018
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43. Marine photosynthetic eukaryotes in polar systems: Unveiling phytoplankton diversity and composition in Antarctic waters

Author

DE LA IGLESIA,RODRIGO and TREFAULT,NICOLE

Subjects
fitoplancton, Antártica, fungi, phytoplankton, Antarctic, photosynthetic eukaryotes, eucariontes fotosintéticos, biodiversity, biodiversidad
Abstract

Antarctic waters are a particular marine environment mainly due to the strong seasonal variations that various parameters are subject to, like light availability and temperature. As in all oceanographic regions, food webs are sustained by photosynthetic microorganisms, which in the case of Antarctic environments seem to be strongly dominated by its eukaryote component. Assessing the ecological role of photosynthetic microbial eukaryotes requires a basic knowledge of their diversity and community composition. This review integrates the available information regarding this component of Antarctic phytoplankton as a way to unveil its diversity and how they respond to the strong changes that occur in this environment. Although several studies indicate the presence of a highly endemic biota in Antarctica, data sets on marine photosynthetic eukaryotes diversity suggests that endemism may be strongly influenced by the low coverage that Antarctic marine areas have been subjected. Moreover, most studies demonstrate that climate change is occurring faster than expected, especially in the Antarctic Peninsula and that this could result in a significant loss of global microbial biodiversity. The changes that eukaryote phytoplankton experience due to this phenomenon may have strong repercussion on the food webs in the Southern Ocean. The knowledge of both the diversity and variation of marine eukaryote phytoplankton in Antarctic waters is crucial for the proper understanding and predictability regarding how these environments can respond to a changing ocean.

Published
2012

44. Marine photosynthetic eukaryotes in polar systems: Unveiling phytoplankton diversity and composition in Antarctic waters

Author

DE LA IGLESIA, RODRIGO and TREFAULT, NICOLE

Subjects
fitoplancton, Antártica, phytoplankton, Antarctic, photosynthetic eukaryotes, eucariontes fotosintéticos, biodiversity, biodiversidad
Abstract

Antarctic waters are a particular marine environment mainly due to the strong seasonal variations that various parameters are subject to, like light availability and temperature. As in all oceanographic regions, food webs are sustained by photosynthetic microorganisms, which in the case of Antarctic environments seem to be strongly dominated by its eukaryote component. Assessing the ecological role of photosynthetic microbial eukaryotes requires a basic knowledge of their diversity and community composition. This review integrates the available information regarding this component of Antarctic phytoplankton as a way to unveil its diversity and how they respond to the strong changes that occur in this environment. Although several studies indicate the presence of a highly endemic biota in Antarctica, data sets on marine photosynthetic eukaryotes diversity suggests that endemism may be strongly influenced by the low coverage that Antarctic marine areas have been subjected. Moreover, most studies demonstrate that climate change is occurring faster than expected, especially in the Antarctic Peninsula and that this could result in a significant loss of global microbial biodiversity. The changes that eukaryote phytoplankton experience due to this phenomenon may have strong repercussion on the food webs in the Southern Ocean. The knowledge of both the diversity and variation of marine eukaryote phytoplankton in Antarctic waters is crucial for the proper understanding and predictability regarding how these environments can respond to a changing ocean. Las aguas antárticas son un ambiente marino peculiar debido principalmente a las fuertes variaciones estacionales a las que están sujetos varios parámetros, como disponibilidad de luz y temperatura. Al igual que en todas las regiones oceanográficas, las tramas tróficas se encuentran sustentadas por microorganismos fotosintéticos, que en el caso de ambientes antárticos parecen estar fuertemente dominados por su componente eucarionte. Este trabajo integra la información disponible respecto a este componente del fitoplancton antártico como una forma de descubrir su diversidad y cómo estos organismos responden a las variaciones a las que se ven sujetos en estos ambientes. Aunque varios estudios indican la presencia de una biota altamente endémica en la Antártica, el conjunto de datos sobre la diversidad de eucariontes marinos fotosintéticos sugiere que este endemismo puede estar fuertemente influenciado por la baja cobertura a la que las áreas marinas antárticas han sido sometidas. Por otro lado, la mayoría de los estudios demuestran que el cambio climático está ocurriendo más rápido de lo esperado, especialmente en la Península Antártica y que esto podría resultar en una pérdida significativa de biodiversidad microbiana global. Además, los cambios que el fitoplancton eucarionte experimente debido a este fenómeno pueden tener fuertes repercusiones en las cadenas tróficas en el océano Austral. El conocimiento tanto de la diversidad como la variación de los microorganismos marinos eucariontes en aguas antárticas es información crucial para la correcta comprensión y capacidad de predicción respecto a cómo estos ambientes pueden responder a los cambios a los que está sujeto.

Published
2012

48. Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond at Cáhuil Lagoon, Chile

Author

Plominsky, Alvaro M., primary, Delherbe, Nathalie, additional, Ugalde, Juan A., additional, Allen, Eric E., additional, Blanchet, Marine, additional, Ikeda, Priscila, additional, Santibañez, Francisco, additional, Hanselmann, Kurt, additional, Ulloa, Osvaldo, additional, De la Iglesia, Rodrigo, additional, von Dassow, Peter, additional, Astorga, Marcia, additional, Gálvez, María Jesús, additional, González, María Lorena, additional, Henríquez-Castillo, Carlos, additional, Vaulot, Daniel, additional, Lopes do Santos, Adriana, additional, van den Engh, Gerrit, additional, Gimpel, Carla, additional, Bertoglio, Florencia, additional, Delgado, Yolaine, additional, Docmac, Felipe, additional, Elizondo-Patrone, Claudia, additional, Narváez, Silvia, additional, Sorroche, Fernando, additional, Rojas-Herrera, Marcelo, additional, and Trefault, Nicole, additional

Published
2014
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49. Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

Author

Vaulot, Daniel, Lepere, Cecile, Toulza, Eve, De La Iglesia, Rodrigo, Poulain, Julie, Gaboyer, Frederic, Moreau, Herve, Vandepoele, Klaas, Ulloa, Osvaldo, Gavory, Frederick, Piganeau, Gwenael, Vaulot, Daniel, Lepere, Cecile, Toulza, Eve, De La Iglesia, Rodrigo, Poulain, Julie, Gaboyer, Frederic, Moreau, Herve, Vandepoele, Klaas, Ulloa, Osvaldo, Gavory, Frederick, and Piganeau, Gwenael

Abstract

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.

Published
2012
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