191 results on '"Cadillo-Quiroz, Hinsby"'
Search Results
2. Vegetation and Peat Soil Characteristics of a Fire-Impacted Tropical Peatland in Costa Rica
- Author
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Pérez-Castillo, Ana Gabriela, Monge-Muñoz, Mayela, Durán-Quesada, Ana María, Giraldo-Sanclemente, Weynner, Méndez-Esquivel, Ana Cristina, Briceño-Soto, Néstor, and Cadillo-Quiroz, Hinsby
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- 2024
- Full Text
- View/download PDF
3. Expansion of the global RNA virome reveals diverse clades of bacteriophages
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Neri, Uri, Wolf, Yuri I, Roux, Simon, Camargo, Antonio Pedro, Lee, Benjamin, Kazlauskas, Darius, Chen, I Min, Ivanova, Natalia, Allen, Lisa Zeigler, Paez-Espino, David, Bryant, Donald A, Bhaya, Devaki, Consortium, RNA Virus Discovery, Narrowe, Adrienne B, Probst, Alexander J, Sczyrba, Alexander, Kohler, Annegret, Séguin, Armand, Shade, Ashley, Campbell, Barbara J, Lindahl, Björn D, Reese, Brandi Kiel, Roque, Breanna M, DeRito, Chris, Averill, Colin, Cullen, Daniel, Beck, David AC, Walsh, David A, Ward, David M, Wu, Dongying, Eloe-Fadrosh, Emiley, Brodie, Eoin L, Young, Erica B, Lilleskov, Erik A, Castillo, Federico J, Martin, Francis M, LeCleir, Gary R, Attwood, Graeme T, Cadillo-Quiroz, Hinsby, Simon, Holly M, Hewson, Ian, Grigoriev, Igor V, Tiedje, James M, Jansson, Janet K, Lee, Janey, VanderGheynst, Jean S, Dangl, Jeff, Bowman, Jeff S, Blanchard, Jeffrey L, Bowen, Jennifer L, Xu, Jiangbing, Banfield, Jillian F, Deming, Jody W, Kostka, Joel E, Gladden, John M, Rapp, Josephine Z, Sharpe, Joshua, McMahon, Katherine D, Treseder, Kathleen K, Bidle, Kay D, Wrighton, Kelly C, Thamatrakoln, Kimberlee, Nusslein, Klaus, Meredith, Laura K, Ramirez, Lucia, Buee, Marc, Huntemann, Marcel, Kalyuzhnaya, Marina G, Waldrop, Mark P, Sullivan, Matthew B, Schrenk, Matthew O, Hess, Matthias, Vega, Michael A, O’Malley, Michelle A, Medina, Monica, Gilbert, Naomi E, Delherbe, Nathalie, Mason, Olivia U, Dijkstra, Paul, Chuckran, Peter F, Baldrian, Petr, Constant, Philippe, Stepanauskas, Ramunas, Daly, Rebecca A, Lamendella, Regina, Gruninger, Robert J, McKay, Robert M, Hylander, Samuel, Lebeis, Sarah L, Esser, Sarah P, Acinas, Silvia G, Wilhelm, Steven S, Singer, Steven W, Tringe, Susannah S, Woyke, Tanja, Reddy, TBK, Bell, Terrence H, Mock, Thomas, McAllister, Tim, and Thiel, Vera
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Infectious Diseases ,Biotechnology ,Microbiome ,Infection ,Bacteriophages ,DNA-Directed RNA Polymerases ,Genome ,Viral ,Phylogeny ,RNA ,RNA Viruses ,RNA-Dependent RNA Polymerase ,Virome ,RNA Virus Discovery Consortium ,Bactriophage ,Functional protein annotation ,Metatranscriptomics ,RNA Virus ,RNA dependent RNA polymerase ,Viral Ecology ,Virus ,Virus - Host prediction ,viral phylogeny ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.
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- 2022
4. Microbial DNA sample preservation and possible artifacts for field-based research in remote tropical peatlands
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Reynolds, Mark C. and Cadillo-Quiroz, Hinsby
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- 2024
- Full Text
- View/download PDF
5. BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
- Author
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Pavia, Michael J., Chede, Abhinav, Wu, Zijun, Cadillo-Quiroz, Hinsby, and Zhu, Qiyun
- Published
- 2023
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- View/download PDF
6. Detecting vulnerability of humid tropical forests to multiple stressors
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Saatchi, Sassan, Longo, Marcos, Xu, Liang, Yang, Yan, Abe, Hitofumi, André, Michel, Aukema, Juliann E, Carvalhais, Nuno, Cadillo-Quiroz, Hinsby, Cerbu, Gillian Ann, Chernela, Janet M, Covey, Kristofer, Sánchez-Clavijo, Lina María, Cubillos, Isai V, Davies, Stuart J, De Sy, Veronique, De Vleeschouwer, Francois, Duque, Alvaro, Durieux, Alice Marie Sybille, De Avila Fernandes, Kátia, Fernandez, Luis E, Gammino, Victoria, Garrity, Dennis P, Gibbs, David A, Gibbon, Lucy, Gowae, Gae Yansom, Hansen, Matthew, Harris, Nancy Lee, Healey, Sean P, Hilton, Robert G, Johnson, Christine May, Kankeu, Richard Sufo, Laporte-Goetz, Nadine Therese, Lee, Hyongki, Lovejoy, Thomas, Lowman, Margaret, Lumbuenamo, Raymond, Malhi, Yadvinder, Martinez, Jean-Michel M Albert, Nobre, Carlos, Pellegrini, Adam, Radachowsky, Jeremy, Román, Francisco, Russell, Diane, Sheil, Douglas, Smith, Thomas B, Spencer, Robert GM, Stolle, Fred, Tata, Hesti Lestari, del Castillo Torres, Dennis, Tshimanga, Raphael Muamba, Vargas, Rodrigo, Venter, Michelle, West, Joshua, Widayati, Atiek, Wilson, Sylvia N, Brumby, Steven, and Elmore, Aurora C
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Life on Land ,Climate Action - Abstract
Humid tropical forests play a dominant role in the functioning of Earth but are under increasing threat from changes in land use and climate. How forest vulnerability varies across space and time and what level of stress forests can tolerate before facing a tipping point are poorly understood. Here, we develop a tropical forest vulnerability index (TFVI) to detect and evaluate the vulnerability of global tropical forests to threats across space and time. We show that climate change together with land-use change have slowed the recovery rate of forest carbon cycling. Temporal autocorrelation, as an indicator of this slow recovery, increases substantially for above-ground biomass, gross primary production, and evapotranspiration when climate stress reaches a critical level. Forests in the Americas exhibit extensive vulnerability to these stressors, while in Africa, forests show relative resilience to climate, and in Asia reveal more vulnerability to land use and fragmentation. TFVI can systematically track the response of tropical forests to multiple stressors and provide early-warning signals for regions undergoing critical transitions.
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- 2021
7. Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands
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Buessecker, Steffen, Sarno, Analissa F., Reynolds, Mark C., Chavan, Ramani, Park, Jin, Fontánez Ortiz, Marc, Pérez-Castillo, Ana G., Panduro Pisco, Grober, Urquiza-Muñoz, José David, Reis, Leonardo P., Ferreira-Ferreira, Jefferson, Furtunato Maia, Jair M., Holbert, Keith E., Penton, C. Ryan, Hall, Sharon J., Gandhi, Hasand, Boëchat, Iola G., Gücker, Björn, Ostrom, Nathaniel E., and Cadillo-Quiroz, Hinsby
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- 2022
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8. Mineral-catalysed formation of marine NO and N2O on the anoxic early Earth
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Buessecker, Steffen, Imanaka, Hiroshi, Ely, Tucker, Hu, Renyu, Romaniello, Stephen J., and Cadillo-Quiroz, Hinsby
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- 2022
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9. Evaluation and improvement of the E3SM land model for simulating energy and carbon fluxes in an Amazonian peatland
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Yuan, Fenghui, Ricciuto, Daniel M., Xu, Xiaofeng, Roman, Daniel T., Lilleskov, Erik, Wood, Jeffrey D., Cadillo-Quiroz, Hinsby, Lafuente, Angela, Rengifo, Jhon, Kolka, Randall, Fachin, Lizardo, Wayson, Craig, Hergoualc'h, Kristell, Chimner, Rodney A., Frie, Alexander, and Griffis, Timothy J.
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- 2023
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10. A versatile gas flux chamber reveals high tree stem CH4 emissions in Amazonian peatland
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van Haren, Joost, Brewer, Paul E., Kurtzberg, Laura, Wehr, Rachel N., Springer, Vanessa L., Espinoza, Rodil Tello, Ruiz, Jorge Solignac, and Cadillo-Quiroz, Hinsby
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- 2021
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11. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments
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Browne, Patrick, Tamaki, Hideyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Imachi, Hiroyuki, Bräuer, Suzanna, Yavitt, Joseph B, Liu, Wen-Tso, Zinder, Stephen, and Cadillo-Quiroz, Hinsby
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Microbiology ,Biological Sciences ,Environmental Sciences ,Human Genome ,Genetics ,Climate Action ,Acclimatization ,Adaptation ,Physiological ,Ecosystem ,Genome ,Archaeal ,Genomics ,Methane ,Methanomicrobiales ,Phylogeny ,Soil ,Soil Microbiology ,Technology ,Biological sciences ,Environmental sciences - Abstract
Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.
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- 2017
12. Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland
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Cadillo-Quiroz, Hinsby, Browne, Patrick, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Detter, Chris, Yavitt, Joseph B, and Zinder, Stephen H
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology - Abstract
Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T), a methanogen isolated from a minerotrophic fen. This is the first genome report of the Methanosphaerula genus, within the Methanoregulaceae family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide range of ecological and geographical settings.
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- 2015
13. Potential shift from a carbon sink to a source in Amazonian peatlands under a changing climate
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Wang, Sirui, Zhuang, Qianlai, Lähteenoja, Outi, Draper, Frederick C., and Cadillo-Quiroz, Hinsby
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- 2018
14. Exometabolite niche partitioning among sympatric soil bacteria.
- Author
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Baran, Richard, Brodie, Eoin L, Mayberry-Lewis, Jazmine, Hummel, Eric, Da Rocha, Ulisses Nunes, Chakraborty, Romy, Bowen, Benjamin P, Karaoz, Ulas, Cadillo-Quiroz, Hinsby, Garcia-Pichel, Ferran, and Northen, Trent R
- Subjects
Bacteria ,Cyanobacteria ,Soil Microbiology ,Ecosystem ,Desert Climate ,Utah - Abstract
Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.
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- 2015
15. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
- Author
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da Rocha, Ulisses Nunes, Cadillo-Quiroz, Hinsby, Karaoz, Ulas, Rajeev, Lara, Klitgord, Niels, Dunn, Sean, Truong, Viet, Buenrostro, Mayra, Bowen, Benjamin P, Garcia-Pichel, Ferran, Mukhopadhyay, Aindrila, Northen, Trent R, and Brodie, Eoin L
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Microbiology ,Biological Sciences ,Ecology ,biological soil crusts ,culturability ,isolation ,dryland microbiology ,microbial diversity ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.
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- 2015
16. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.
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Nunes da Rocha, Ulisses, Cadillo-Quiroz, Hinsby, Karaoz, Ulas, Rajeev, Lara, Klitgord, Niels, Dunn, Sean, Truong, Viet, Buenrostro, Mayra, Bowen, Benjamin P, Garcia-Pichel, Ferran, Mukhopadhyay, Aindrila, Northen, Trent R, and Brodie, Eoin L
- Subjects
biological soil crusts ,culturability ,dryland microbiology ,isolation ,microbial diversity ,Microbiology ,Environmental Science and Management ,Soil Sciences - Abstract
Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.
- Published
- 2015
17. Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor
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Yamamoto, Kyosuke, Tamaki, Hideyuki, Cadillo-Quiroz, Hinsby, Imachi, Hiroyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Zinder, Stephen H, Kamagata, Yoichi, and Liu, Wen-Tso
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Biochemistry and Cell Biology - Abstract
Methanoregula formicica SMSP(T) is a mesophilic H2/formate-utilizing methanogenic archaeon and a representative of the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales. Here, we report a 2.8-Mb complete genome sequence of this methanogenic archaeon.
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- 2014
18. Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge
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Yamamoto, Kyosuke, Tamaki, Hideyuki, Cadillo-Quiroz, Hinsby, Imachi, Hiroyuki, Kyrpides, Nikos, Woyke, Tanja, Goodwin, Lynne, Zinder, Stephen H, Kamagata, Yoichi, and Liu, Wen-Tso
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Biochemistry and Cell Biology - Abstract
Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1(T), a methanogenic archaeon isolated from an anaerobic digested sludge. This is the first genome report of the genus Methanolinea isolate belonging to the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales.
- Published
- 2014
19. Assessment of vegetation and peat soil characteristics of a fire-impacted tropical peatland in Costa Rica
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Pérez-Castillo, Ana Gabriela, primary, Monge-Muñoz, Mayela, additional, Durán-Quesada, Ana María, additional, Giraldo-Sanclemente, Weynner, additional, Méndez-Esqu, Ana Cristina, additional, Briceño, Néstor, additional, and Cadillo-Quiroz, Hinsby, additional
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- 2023
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20. Genes and genome‐resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients.
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Pavia, Michael J., Finn, Damien, Macedo‐Tafur, Franco, Tello‐Espinoza, Rodil, Penaccio, Christa, Bouskill, Nicholas, and Cadillo‐Quiroz, Hinsby
- Subjects
PEATLANDS ,METAGENOMICS ,MICROORGANISM populations ,MICROBIAL communities ,CRISPRS ,MICROBIAL diversity - Abstract
The Pastaza‐Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene‐ and genome‐centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin–antitoxin and CRISPR‐Cas systems were enriched in oligotrophic soils, suggesting that non‐metabolic interactions may exert additional controls in low‐nutrient environments. Additionally, we reconstructed 519 metagenome‐assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands. [ABSTRACT FROM AUTHOR]
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- 2023
- Full Text
- View/download PDF
21. Unraveling the functional dark matter through global metagenomics
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Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, Kyrpides, Nikos C., Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Acinas, Silvia G., Ahlgren, Nathan, Attwood, Graeme, Baldrian, Petr, Berry, Timothy, Bhatnagar, Jennifer M., Bhaya, Devaki, Bidle, Kay D., Blanchard, Jeffrey L., Boyd, Eric S., Bowen, Jennifer L., Bowman, Jeff, Brawley, Susan H., Brodie, Eoin L., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Cadillo-Quiroz, Hinsby, Campbell, Barbara J., Cavicchioli, Ricardo, Chuckran, Peter F., Coleman, Maureen, Crowe, Sean, Colman, Daniel R., Currie, Cameron R., Dangl, Jeff, Delherbe, Nathalie, Denef, Vincent J., Dijkstra, Paul, Distel, Daniel D., Eloe-Fadrosh, Emiley, Fisher, Kirsten, Francis, Christopher, Garoutte, Aaron, Gaudin, Amelie, Gerwick, Lena, Godoy-Vitorino, Filipa, Guerra, Peter, Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hentschel, Ute, Hess, Matthias, Hirsch, Ann M., Hug, Laura A., Hultman, Jenni, Hunt, Dana E., Huntemann, Marcel, Inskeep, William P., James, Timothy Y., Jansson, Janet, Johnston, Eric R., Kalyuzhnaya, Marina, Kelly, Charlene N., Kelly, Robert M., Klassen, Jonathan L., Nüsslein, Klaus, Kostka, Joel E., Lindow, Steven, Lilleskov, Erik, Lynes, Mackenzie, Mackelprang, Rachel, Martin, Francis M., Mason, Olivia U., McKay, R. Michael, McMahon, Katherine, Mead, David A., Medina, Monica, Meredith, Laura K., Mock, Thomas, Mohn, William W., Moran, Mary Ann, Murray, Alison, Neufeld, Josh D., Neumann, Rebecca, Norton, Jeanette M., Partida-Martinez, Laila P., Pietrasiak, Nicole, Pelletier, Dale, Reddy, T. B. K., Reese, Brandi Kiel, Reichart, Nicholas J., Reiss, Rebecca, Saito, Mak A., Schachtman, Daniel P., Seshadri, Rekha, Shade, Ashley, Sherman, David, Simister, Rachel, Simon, Holly, Stegen, James, Stepanauskas, Ramunas, Sullivan, Matthew, Sumner, Dawn Y., Teeling, Hanno, Thamatrakoln, Kimberlee, Treseder, Kathleen, Tringe, Susannah, Vaishampayan, Parag, Valentine, David L., Waldo, Nicholas B., Waldrop, Mark P., Walsh, David A., Ward, David M., Wilkins, Michael, Whitman, Thea, Woolet, Jamie, Woyke, Tanja, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, and Kyrpides, Nikos C.
- Abstract
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
- Published
- 2023
- Full Text
- View/download PDF
22. Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients
- Author
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Pavia, Michael J., primary, Finn, Damien, additional, Macedo-Tafur, Franco, additional, Tello-Espinoza, Rodil, additional, Penaccio, Christa, additional, Bouskill, Nicholas, additional, and Cadillo-Quiroz, Hinsby, additional
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- 2022
- Full Text
- View/download PDF
23. Water Vapor Adsorption Provides Daily, Sustainable Water to Soils of the Hyperarid Atacama Desert
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Glaser, Donald M., primary, Hartnett, Hilairy E., additional, Finn, Damien R., additional, Perez-Montaño, Saul, additional, Cadillo-Quiroz, Hinsby, additional, and Desch, Steven, additional
- Published
- 2022
- Full Text
- View/download PDF
24. BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
- Author
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Pavia, Michael J, primary, Chede, Abhinav, additional, Wu, Zijun, additional, Cadillo-Quiroz, Hinsby, additional, and Zhu, Qiyun, additional
- Published
- 2022
- Full Text
- View/download PDF
25. A map of global peatland extent created using machine learning (Peat-ML)
- Author
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Melton, Joe R., primary, Chan, Ed, additional, Millard, Koreen, additional, Fortier, Matthew, additional, Winton, R. Scott, additional, Martín-López, Javier M., additional, Cadillo-Quiroz, Hinsby, additional, Kidd, Darren, additional, and Verchot, Louis V., additional
- Published
- 2022
- Full Text
- View/download PDF
26. Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill
- Author
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Reynolds, Mark C., primary, Finn, Damien, additional, Sarno, Analissa F., additional, Allen, Richard, additional, Deathrage, J. David, additional, Krajmalnik-Brown, Rosa, additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2022
- Full Text
- View/download PDF
27. Methanogen diversity and community composition in peatlands of the central to northern Appalachian Mountain region, North America
- Author
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Yavitt, Joseph B., Yashiro, Erika, Cadillo-Quiroz, Hinsby, and Zinder, Stephen H.
- Published
- 2012
- Full Text
- View/download PDF
28. Peatland core domain sets: building consensus on what should be measured in research and monitoring
- Author
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Reed, Mark S., Young, Dylan M., Taylor, Nigel G., Andersen, Roxane, Bell, Nicholle G.A., Cadillo-Quiroz, Hinsby, Grainger, Matthew, Heinemeyer, Andreas, Hergoualc’h, Kristell, Gerrand, Adam M., Kieft, Johannes, Krisnawati, Haruni, Lilleskov, Erik A., Lopez-Gonzalez, Gabriela, Melling, Lulie, Rudman, Hannah, Sjogersten, Sophie, Walker, Jonathan S., and Stewart, Gavin
- Subjects
evidence-based policy and practice ,Basic biosciences: 470 [VDP] ,evidence synthesis ,standardisation ,Basale biofag: 470 [VDP] ,outcomes - Abstract
It is often difficult to compile and synthesise evidence across multiple studies to inform policy and practice because different outcomes have been measured in different ways or datasets and models have not been fully or consistently reported. In the case of peatlands, a critical terrestrial carbon store, this lack of consistency hampers the evidence-based decisions in policy and practice that are needed to support effective restoration and conservation. This study adapted methods pioneered in the medical community to reach consensus over peatland outcomes that could be consistently measured and reported to improve the synthesis of data and reduce research waste. Here we report on a methodological framework for identifying, evaluating and prioritising the outcomes that should be measured. We discuss the subsequent steps to standardise methods for measuring and reporting outcomes in peatland research and monitoring. The framework was used to identify and prioritise sets of key variables (known as core domain sets) for UK blanket and raised bogs, and for tropical peat swamps. Peatland experts took part in a structured elicitation and prioritisation process, comprising two workshops and questionnaires, that focused on climate (32 and 18 unique outcomes for UK and tropical peats, respectively), hydrology (26 UK and 16 tropical outcomes), biodiversity (8 UK and 22 tropical outcomes) and fire-related outcomes (13, for tropical peatlands only). Future research is needed to tackle the challenges of standardising methods for data collection, management, analysis, reporting and re-use, and to extend the approach to other types of peatland. The process reported here is a first step towards creating datasets that can be synthesised to inform evidence-based policy and practice, and contribute towards the conservation, restoration and sustainable management of this globally significant carbon store. evidence-based policy and practice, evidence synthesis, outcomes, standardisation
- Published
- 2022
29. Diversity and Community Structure of Archaea Inhabiting the Rhizoplane of Two Contrasting Plants from an Acidic Bog
- Author
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Cadillo-Quiroz, Hinsby, Yavitt, Joseph B., Zinder, Stephen H., and Thies, Janice E.
- Published
- 2010
30. Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands
- Author
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Buessecker, Steffen, primary, Sarno, Analissa F, additional, Reynolds, Mark C, additional, Chavan, Ramani, additional, Park, Jin, additional, Fontanez Ortiz, Marc, additional, Perez-Castillo, Ana G, additional, Panduro Pisco, Grober, additional, Urquiza-Munoz, Jose David, additional, Reis, Leonardo P, additional, Ferreira-Ferreira, Jefferson, additional, Furtunato Maia, Jair M, additional, Holbert, Keith E, additional, Penton, Christopher Ryan, additional, Hall, Sharon J, additional, Ghandi, Hasand, additional, Boechat, Iola G, additional, Guecker, Bjoern, additional, Ostrom, Nathaniel E, additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2022
- Full Text
- View/download PDF
31. Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin
- Author
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Buessecker, Steffen, primary, Zamora, Zacary, additional, Sarno, Analissa F., additional, Finn, Damien Robert, additional, Hoyt, Alison M., additional, van Haren, Joost, additional, Urquiza Muñoz, Jose D., additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2021
- Full Text
- View/download PDF
32. A genomic catalog of Earth’s microbiomes
- Author
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Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium
- Abstract
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
- Published
- 2021
33. Detecting vulnerability of humid tropical forests to multiple stressors
- Author
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Centre Tecnològic de Vilanova i la Geltrú, Universitat Politècnica de Catalunya. LAB - Laboratori d'Aplicacions Bioacústiques, Longo, Marcos, Saatchi, Sassan, Xu, Liang, Yang, Yan, André, Michel, Carvalhais, Nuno, Cadillo-Quiroz, Hinsby, Chernela, Janet M., Duque, Alvaro, Hansen, Matthew, Centre Tecnològic de Vilanova i la Geltrú, Universitat Politècnica de Catalunya. LAB - Laboratori d'Aplicacions Bioacústiques, Longo, Marcos, Saatchi, Sassan, Xu, Liang, Yang, Yan, André, Michel, Carvalhais, Nuno, Cadillo-Quiroz, Hinsby, Chernela, Janet M., Duque, Alvaro, and Hansen, Matthew
- Abstract
Humid tropical forests play a dominant role in the functioning of Earth but are under increasing threat from changes in land use and climate. How forest vulnerability varies across space and time and what level of stress forests can tolerate before facing a tipping point are poorly understood. Here, we develop a tropical forest vulnerability index (TFVI) to detect and evaluate the vulnerability of global tropical forests to threats across space and time. We show that climate change together with land-use change have slowed the recovery rate of forest carbon cycling. Temporal autocorrelation, as an indicator of this slow recovery, increases substantially for above-ground biomass, gross primary production, and evapotranspiration when climate stress reaches a critical level. Forests in the Americas exhibit extensive vulnerability to these stressors, while in Africa, forests show relative resilience to climate, and in Asia reveal more vulnerability to land use and fragmentation. TFVI can systematically track the response of tropical forests to multiple stressors and provide early-warning signals for regions undergoing critical transitions., Peer Reviewed, Postprint (published version)
- Published
- 2021
34. Marine mineral-catalyzed NO and N2O formation on the anoxic early Earth
- Author
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Buessecker, Steffen, Ely, Tucker, Hu, Renyu, Cadillo-Quiroz, Hinsby, Imanaka, Hiroshi, and Romaniello, Stephen
- Subjects
bepress|Physical Sciences and Mathematics ,bepress|Physical Sciences and Mathematics|Earth Sciences ,bepress|Physical Sciences and Mathematics|Earth Sciences|Geochemistry ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Geochemistry ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences ,equipment and supplies ,EarthArXiv|Physical Sciences and Mathematics - Abstract
Microbial metabolisms were limited by available terminal electron acceptors in the anoxic environment of the early Archean. However, iron mineral phases in Fe2+-rich (ferruginous) oceans could have catalyzed reactions with abiotically fixed nitrogen leading to the formation of nitrous oxide (N2O), a potentially favorable terminal electron acceptor. We experimentally simulated anoxic surface-catalyzed reduction of nitrite and nitrate via green rust and magnetite. Besides N2O, we detected and quantified the formation of substantial amounts of nitric oxide (NO). While N2O escaped into the gas phase (63% of nitrite-nitrogen, with green rust as catalyst), NO remained associated with precipitates (7% of nitrite-nitrogen). Using diffusion and photochemical modeling, we show that marine N2O emissions could have sustained atmospheric N2O pools of 1-7 ppb. Although this concentration was insufficient to cause significant warming, the seawater enriched in N2O and NO could have critically affected early benthic life by providing the opportunity to conserve energy.
- Published
- 2020
35. Effects of sterilization techniques on chemodenitrification and N2O production in tropical peat soil microcosms
- Author
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Buessecker, Steffen, Tylor, Kaitlyn, Nye, Joshua, Holbert, Keith E., Urquiza-Muñoz, Jose D., Glass, Jennifer B., Hartnett, Hilairy E., and Cadillo-Quiroz, Hinsby
- Abstract
Chemodenitrification – the non-enzymatic process of nitrite reduction – may be an important sink for fixed nitrogen in tropical peatlands. Rates and products of chemodenitrification are dependent on O2, pH, Fe2+ concentration, and organic matter composition, which are variable across peat soils. Assessing abiotic reaction pathways is difficult because sterilization and inhibition agents can alter the availability of reactants by changing iron speciation and organic matter composition. We compared six commonly used soil sterilization techniques – γ irradiation, chloroform, autoclaving, and the use of three different chemical inhibitors (mercury, zinc, and azide) – for their compatibility with chemodenitrification assays for tropical peatland soils (organic-rich, low-pH soil from the eastern Amazon). Out of the six techniques, γ irradiation resulted in soil treatments with the lowest cell viability and denitrification activity and the least effect on pH, iron speciation, and organic matter composition. Nitrite depletion rates in γ-irradiated soils were highly similar to untreated (live) soils, whereas other sterilization techniques showed deviations. Chemodenitrification was a dominant process of nitrite consumption in tropical peatland soils assayed in this study. Nitrous oxide (N2O) is one possible product of chemodenitrification reactions. Abiotic N2O production was low to moderate (3 %–16 % of converted nitrite), and different sterilization techniques lead to significant variations on production rates due to inherent processes or potential artifacts. Our work represents the first methodological basis for testing the abiotic denitrification and N2O production potential in tropical peatland soil.
- Published
- 2019
36. Marine mineral-catalyzed NO and N2O formation on the anoxic early Earth
- Author
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Buessecker, Steffen, primary, Imanaka, Hiroshi, additional, Ely, Tucker, additional, Hu, Renyu, additional, Romaniello, Stephen, additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2020
- Full Text
- View/download PDF
37. Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia
- Author
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Finn, Damien Robert, primary, Ziv-El, Michal, additional, van Haren, Joost, additional, Park, Jin Gyoon, additional, del Aguila-Pasquel, Jhon, additional, Urquiza–Muñoz, Jose David, additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2020
- Full Text
- View/download PDF
38. Isotopic Insights into Methane Production and Emission in Diverse Amazonian Peatlands
- Author
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Hoyt, Alison, primary, Cadillo-Quiroz, Hinsby, additional, Xu, Xiaomei, additional, Torn, Margaret, additional, Bazán Pacaya, Arturo, additional, Jacobs, Marie, additional, Shapiama Peña, Rony, additional, Ramirez Navarro, Diego, additional, Urquiza-Muñoz, David, additional, and Trumbore, Susan, additional
- Published
- 2020
- Full Text
- View/download PDF
39. Effects of sterilization techniques on chemodenitrification and N<sub>2</sub>O production in tropical peat soil microcosms
- Author
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Buessecker, Steffen, primary, Tylor, Kaitlyn, additional, Nye, Joshua, additional, Holbert, Keith E., additional, Urquiza Muñoz, Jose D., additional, Glass, Jennifer B., additional, Hartnett, Hilairy E., additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2019
- Full Text
- View/download PDF
40. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA
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Cadillo-Quiroz, Hinsby, Bräuer, Suzanna, Yashiro, Erika, Sun, Christine, Yavitt, Joseph, and Zinder, Stephen
- Published
- 2006
41. Isolation of a novel acidiphilic methanogen from an acidic peat bog
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Bräuer, Suzanna L., Cadillo-Quiroz, Hinsby, Yashiro, Erika, Yavitt, Joseph B., and Zinder, Stephen H.
- Published
- 2006
42. response to reviews
- Author
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Cadillo-Quiroz, Hinsby, primary
- Published
- 2019
- Full Text
- View/download PDF
43. T-REX: software for the processing and analysis of T-RFLP data
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Culman Steven W, Bukowski Robert, Gauch Hugh G, Cadillo-Quiroz Hinsby, and Buckley Daniel H
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Results Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model. Conclusion T-REX provides a free, platform-independent tool to the research community that allows for an integrated, rapid, and more robust analysis of T-RFLP data.
- Published
- 2009
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44. Examining methanogens in northern peatlands: Potential role of ecological and latitudinal trends
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Cadillo-Quiroz, Hinsby
- Published
- 2011
- Full Text
- View/download PDF
45. Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen
- Author
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Cadillo-Quiroz, Hinsby, Yashiro, Erica, Yavitt, Joseph B., and Zinder, Stephen H.
- Subjects
New York -- Natural resources ,Archaeabacteria -- Environmental aspects ,Archaeabacteria -- Identification and classification ,Archaeabacteria -- Genetic aspects ,Methanobacteriaceae -- Environmental aspects ,Methanobacteriaceae -- Genetic aspects ,Restriction fragment length polymorphism analysis -- Usage ,Mineralogical research ,Biological sciences - Abstract
A broad characterization of the archaeal community in a minerotrophic fen in central New York State was achieved by using several 16S rRNA-based primer sets.
- Published
- 2008
46. Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient
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Chapman, Eric J., primary, Cadillo-Quiroz, Hinsby, additional, Childers, Daniel L., additional, Turetsky, Merritt R., additional, and Waldrop, Mark P., additional
- Published
- 2017
- Full Text
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47. Endosymbiont diversity and evolution across weevil tree of life
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Zhang, Guanyang, primary, Browne, Patrick, additional, Zhen, Geng, additional, Johnston, Andrew, additional, Cadillo-Quiroz, Hinsby, additional, and Franz, Nico, additional
- Published
- 2017
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- View/download PDF
48. M ethanosphaerula
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Zinder, Stephen, primary and Cadillo‐Quiroz, Hinsby, additional
- Published
- 2016
- Full Text
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49. Effects of sterilization techniques on chemodenitrification and N2O production in tropical peat soil microcosms.
- Author
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Buessecker, Steffen, Tylor, Kaitlyn, Nye, Joshua, Holbert, Keith E., Urquiza-Muñoz, Jose D., Glass, Jennifer B., Hartnett, Hilairy E., and Cadillo-Quiroz, Hinsby
- Subjects
PEAT soils ,CHEMICAL inhibitors ,ORGANIC compounds ,SOIL acidity ,PH effect ,MERCURY - Abstract
Chemodenitrification - the non-enzymatic process of nitrite reduction - may be an important sink for fixed nitrogen in tropical peatlands with low oxygen, low pH, high organic matter, and variable ferrous iron concentrations. Assessing abiotic reaction pathways is difficult because sterilization/inhibition agents can alter the availability of reactants by changing iron speciation and organic matter composition. We compared six commonly used soil sterilization techniques - γ-irradiation, chloroform, autoclaving, and chemical inhibitors (mercury, zinc, and azide) - for their compatibility with chemodenitrification assays for tropical peatland soils (organic-rich low pH soil from the Eastern Amazon). Out of the six techniques, γ-irradiation resulted in soil treatments with lowest cell viability and denitrification activity, and least effect on pH, iron speciation, and organic matter composition. Nitrite depletion rates in γ-irradiated soils were highly similar to untreated/live soils, whereas other sterilization techniques showed deviations. Chemodenitrification was a dominant process in tropical peatland soils assayed in this study. Abiotic N
2 O production was low to moderate (3-16 % of converted nitrite), and different sterilization techniques lead to significant variations on production rates due to inherent processes or potential artifacts. Our work represents the first methodological basis for testing the abiotic denitrification and N2 O production potential in tropical peatland soil. [ABSTRACT FROM AUTHOR]- Published
- 2019
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50. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments
- Author
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Browne, Patrick, primary, Tamaki, Hideyuki, additional, Kyrpides, Nikos, additional, Woyke, Tanja, additional, Goodwin, Lynne, additional, Imachi, Hiroyuki, additional, Bräuer, Suzanna, additional, Yavitt, Joseph B, additional, Liu, Wen-Tso, additional, Zinder, Stephen, additional, and Cadillo-Quiroz, Hinsby, additional
- Published
- 2016
- Full Text
- View/download PDF
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