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1. High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism

Author

Hedlund, Brian P, Murugapiran, Senthil K, Huntemann, Marcel, Clum, Alicia, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Stamatis, Dimitrios, Reddy, TBK, Ngan, Chew Yee, Daum, Chris, Duffy, Kecia, Shapiro, Nicole, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, Williams, Amanda J, Cole, Jessica K, Dodsworth, Jeremy A, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome
Abstract

The draft genome of Kallotenue papyrolyticum JKG1(T), a member of the order Kallotenuales, class Chloroflexia, consists of 4,475,263 bp in 4 contigs and encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The genome is consistent with a heterotrophic lifestyle including catabolism of polysaccharides and amino acids.

Published
2015

5. Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm

Author

Anderton, Christopher R., primary, Mobberley, Jennifer M., additional, Cole, Jessica K., additional, Nunez, Jamie R., additional, Starke, Robert, additional, Boaro, Amy A., additional, Yesiltepe, Yasemin, additional, Morton, Beau R., additional, Cory, Alexandra B., additional, Cardamone, Hayley C., additional, Hofmockel, Kirsten S., additional, Lipton, Mary S., additional, Moran, James J., additional, Renslow, Ryan S., additional, Fredrickson, James K., additional, and Lindemann, Stephen R., additional

Published
2020
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6. Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae

Author

Cole, Jessica K., primary, Morton, Beau R., additional, Cardamone, Hayley C., additional, Lake, Hannah R. R., additional, Dohnalkova, Alice C., additional, Kim, Young-Mo, additional, Kyle, Jennifer E., additional, Maezato, Yukari, additional, Dana, Karl L., additional, Metz, Thomas O., additional, Romine, Margaret F., additional, Nelson, William C., additional, and Lindemann, Stephen R., additional

Published
2018
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7. Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae

Author

Cole, Jessica K., primary, Morton, Beau R., additional, Cardamone, Hayley C., additional, Lake, Hannah R. R., additional, Dohnalkova, Alice C., additional, Kim, Young-Mo, additional, Kyle, Jennifer E., additional, Maezato, Yukari, additional, Dana, Karl L., additional, Metz, Thomas O., additional, Romine, Margaret F., additional, Nelson, William C., additional, and Lindemann, Stephen R., additional

Published
2018
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8. Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

Author

Lindemann, Stephen R., primary, Mobberley, Jennifer M., additional, Cole, Jessica K., additional, Markillie, L. M., additional, Taylor, Ronald C., additional, Huang, Eric, additional, Chrisler, William B., additional, Wiley, H. S., additional, Lipton, Mary S., additional, Nelson, William C., additional, Fredrickson, James K., additional, and Romine, Margaret F., additional

Published
2017
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10. High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1 T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism

Author

Hedlund, Brian P., primary, Murugapiran, Senthil K., additional, Huntemann, Marcel, additional, Clum, Alicia, additional, Pillay, Manoj, additional, Palaniappan, Krishnaveni, additional, Varghese, Neha, additional, Mikhailova, Natalia, additional, Stamatis, Dimitrios, additional, Reddy, T. B. K., additional, Ngan, Chew Yee, additional, Daum, Chris, additional, Duffy, Kecia, additional, Shapiro, Nicole, additional, Markowitz, Victor, additional, Ivanova, Natalia, additional, Kyrpides, Nikos, additional, Williams, Amanda J., additional, Cole, Jessica K., additional, Dodsworth, Jeremy A., additional, and Woyke, Tanja, additional

Published
2015
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11. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

Author

Dodsworth, Jeremy A., primary, Gevorkian, Jonathan, additional, Despujos, Fairuz, additional, Cole, Jessica K., additional, Murugapiran, Senthil K., additional, Ming, Hong, additional, Li, Wen-Jun, additional, Zhang, Gengxin, additional, Dohnalkova, Alice, additional, and Hedlund, Brian P., additional

Published
2014
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12. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

Author

Cole, Jessica K., primary, Hutchison, Janine R., additional, Renslow, Ryan S., additional, Kim, Young-Mo, additional, Chrisler, William B., additional, Engelmann, Heather E., additional, Dohnalkova, Alice C., additional, Hu, Dehong, additional, Metz, Thomas O., additional, Fredrickson, Jim K., additional, and Lindemann, Stephen R., additional

Published
2014
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13. Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

Author

Cole, Jessica K., primary, Gieler, Brandon A., additional, Heisler, Devon L., additional, Palisoc, Maryknoll M., additional, Williams, Amanda J., additional, Dohnalkova, Alice C., additional, Ming, Hong, additional, Yu, Tian Tian, additional, Dodsworth, Jeremy A., additional, Li, Wen-Jun, additional, and Hedlund, Brian P., additional

Published
2013
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15. The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

Author

Lindemann, Stephen R., primary, Moran, James J., additional, Stegen, James C., additional, Renslow, Ryan S., additional, Hutchison, Janine R., additional, Cole, Jessica K., additional, Dohnalkova, Alice C., additional, Tremblay, Julien, additional, Singh, Kanwar, additional, Malfatti, Stephanie A., additional, Chen, Feng, additional, Tringe, Susannah G., additional, Beyenal, Haluk, additional, and Fredrickson, James K., additional

Published
2013
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17. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities.

Author

Cole, Jessica K, Peacock, Joseph P, Dodsworth, Jeremy A, Williams, Amanda J, Thompson, Daniel B, Dong, Hailiang, Wu, Geng, and Hedlund, Brian P

Subjects
*SEDIMENT microbiology, *HOT springs, *TEMPERATURE effect, *BIOGEOCHEMICAL cycles, *THERMOPHILIC bacteria, *NUCLEOTIDE sequence
Abstract

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87-80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (\[pmacr]=36.1%), Aeropyrum (\[pmacr]=16.6%), the archaeal lineage pSL4 (\[pmacr]=15.9%), the archaeal lineage NAG1 (\[pmacr]=10.6%) and Thermocrinis (\[pmacr]=7.6%). The ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (\[pmacr]=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles. [ABSTRACT FROM AUTHOR]

Published
2013
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18. Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment.

Author

Peacock, Joseph P., Cole, Jessica K., Murugapiran, Senthil K., Dodsworth, Jeremy A., Fisher, Jenny C., Moser, Duane P., and Hedlund, Brian P.

Subjects
*CELLULOLYTIC bacteria, *LIGNOCELLULOSE, *HOT springs, *TEMPERATURE measurements, *AQUATIC microbiology, *FERMENTATION, *COMPUTATIONAL biology, *INDUSTRIAL microbiology
Abstract

To characterize high-temperature cellulolytic microbial communities, two lignocellulosic substrates, ammonia fiber-explosion-treated corn stover and aspen shavings, were incubated at average temperatures of 77 and 85°C in the sediment and water column of Great Boiling Spring, Nevada. Comparison of 109,941 quality-filtered 16S rRNA gene pyrosequences (pyrotags) from eight enrichments to 37,057 quality-filtered pyrotags from corresponding natural samples revealed distinct enriched communities dominated by phylotypes related to cellulolytic and hemicellulolytic Thermotoga and Dictyoglomus, cellulolytic and sugar-fermenting Desulfurococcales, and sugar-fermenting and hydrogenotrophic Archaeoglobales. Minor enriched populations included close relatives of hydrogenotrophic Thermodesulfobacteria, the candidate bacterial phylum OP9, and candidate archaeal groups C2 and DHVE3. Enrichment temperature was the major factor influencing community composition, with a negative correlation between temperature and richness, followed by lignocellulosic substrate composition. This study establishes the importance of these groups in the natural degradation of lignocellulose at high temperatures and suggests that a substantial portion of the diversity of thermophiles contributing to consortial cellulolysis may be contained within lineages that have representatives in pure culture. [ABSTRACT FROM AUTHOR]

Published
2013
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19. High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.

Author

Hedlund BP, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Cole JK, Dodsworth JA, and Woyke T

Abstract

The draft genome of Kallotenue papyrolyticum JKG1(T), a member of the order Kallotenuales, class Chloroflexia, consists of 4,475,263 bp in 4 contigs and encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The genome is consistent with a heterotrophic lifestyle including catabolism of polysaccharides and amino acids., (Copyright © 2015 Hedlund et al.)

Published
2015
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