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| 284. | Berliner, Aaron; Makrygiorgos, George; Hill, Avery Extension of Equivalent System Mass for Human Exploration Missions on Mars (Journal Article) preprints.org, 2021. (Links | BibTeX | Tags: cubes) @article{Berliner2021, title = {Extension of Equivalent System Mass for Human Exploration Missions on Mars}, author = {Aaron Berliner and George Makrygiorgos and Avery Hill}, doi = {doi: 10.20944/preprints202101.0363.v1}, year = {2021}, date = {2021-01-01}, journal = {preprints.org}, publisher = {Preprints}, keywords = {cubes}, pubstate = {published}, tppubtype = {article} } |
| 283. | Xiaoxuan Ge Michael P. Thorgersen, Farris Poole II Adam Deutschbauer John-Marc Chandonia Pavel Novichkov Sara Gushgari-Doyle Lauren Lui Torben Nielsen Romy Chakraborty Paul Adams Adam Arkin Terry Hazen L M S M D P C; Adams, Michael W W Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation (Journal Article) 2020. (Links | BibTeX | Tags: enigma) @article{10.3389/fmicb.2020.587127, title = {Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation}, author = {Xiaoxuan Ge, Michael P. Thorgersen, Farris L. Poole II, Adam M. Deutschbauer, John-Marc Chandonia, Pavel S. Novichkov, Sara Gushgari-Doyle, Lauren M. Lui, Torben Nielsen, Romy Chakraborty, Paul D. Adams, Adam P. Arkin, Terry C. Hazen and Michael W. W. Adams}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.587127/full}, doi = {https://doi.org/10.3389/fmicb.2020.587127}, year = {2020}, date = {2020-10-19}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
| 282. | Matthew J. McNulty Yongao Xiong, Kevin Yates Kalimuthu Karuppanan Jacob Hilzinger Aaron Berliner Jesse Delzio Adam Arkin Nancy Lane Somen Nandi Karen McDonald M J P E A Molecular Pharming to Support Human Life on the Moon, Mars, and Beyond (Journal Article) Preprints, 2020. (Links | BibTeX | Tags: cubes) @article{McNulty2020, title = {Molecular Pharming to Support Human Life on the Moon, Mars, and Beyond}, author = {Matthew J. McNulty , Yongao Xiong , Kevin Yates , Kalimuthu Karuppanan , Jacob M. Hilzinger , Aaron J. Berliner , Jesse Delzio , Adam P. Arkin , Nancy E. Lane , Somen Nandi , Karen A. McDonald }, doi = {10.20944/preprints202009.0086.v1}, year = {2020}, date = {2020-09-03}, journal = {Preprints}, keywords = {cubes}, pubstate = {published}, tppubtype = {article} } |
| 281. | Moon, J W; Paradis, C J; Joyner, D C; von Netzer, F; Majumder, E L; Dixon, E R; Podar, M; Ge, X; Walian, P J; Smith, H J; Wu, X; Zane, G M; Walker, K F; Thorgersen, M P; Ii, Poole F L; Lui, L M; Adams, B G; Leon, De K B; Brewer, S S; Williams, D E; Lowe, K A; Rodriguez, M; Mehlhorn, T L; Pfiffner, S M; Chakraborty, R; Arkin, A P; Wall, J D; Fields, M W; Adams, M W W; Stahl, D A; Elias, D A; Hazen, T C Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer (Journal Article) Chemosphere, 255 , pp. 126951, 2020. (Abstract | BibTeX | Tags: enigma) @article{pmid32417512, title = {Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer}, author = {J W Moon and C J Paradis and D C Joyner and F von Netzer and E L Majumder and E R Dixon and M Podar and X Ge and P J Walian and H J Smith and X Wu and G M Zane and K F Walker and M P Thorgersen and F L Poole Ii and L M Lui and B G Adams and K B De Leon and S S Brewer and D E Williams and K A Lowe and M Rodriguez and T L Mehlhorn and S M Pfiffner and R Chakraborty and A P Arkin and J D Wall and M W Fields and M W W Adams and D A Stahl and D A Elias and T C Hazen}, year = {2020}, date = {2020-09-01}, journal = {Chemosphere}, volume = {255}, pages = {126951}, abstract = {The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments. |
| 280. | Megan L. Kempher Xuanyu Tao, Rong Song Bo Wu David Stahl Judy Wall Adam Arkin Aifen Zhou Jizhong Zhou A D P Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature (Journal Article) Mbio, 11 (4), pp. 2020, 2020. @article{kempher2020effects, title = {Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature}, author = {Megan L. Kempher, Xuanyu Tao, Rong Song, Bo Wu, David A. Stahl, Judy D. Wall, Adam P. Arkin, Aifen Zhou, Jizhong Zhou}, year = {2020}, date = {2020-08-18}, journal = {Mbio}, volume = {11}, number = {4}, pages = {2020}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
| 279. | Ankita Kotharia Simon Rouxb, Hanqiao Zhanga Anatori Prietoa Drishti Sonejaa John-MarcChandoniaa Sarah Spencer Xiaoqin Wud Sara Altenburgl Matthew Fields Adam M.Deutschbauer Adam Arkinc Eric Almh Romy Chakrabortyd Aindrila Mukhopadhyay W P J Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance (Journal Article) 2020. @article{kothari2020ecogenomics, title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance}, author = {Ankita Kotharia, Simon Rouxb, Hanqiao Zhanga, Anatori Prietoa, Drishti Sonejaa, John-MarcChandoniaa, Sarah Spencer, Xiaoqin Wud, Sara Altenburgl, Matthew W. Fields, Adam M.Deutschbauer, Adam P. Arkinc, Eric J. Almh, Romy Chakrabortyd, Aindrila Mukhopadhyay}, year = {2020}, date = {2020-07-15}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
| 278. | Meja-Almonte, C; Busby, S J W; Wade, J T; van Helden, J; Arkin, A P; Stormo, G D; Eilbeck, K; Palsson, B O; Galagan, J E; Collado-Vides, J Redefining fundamental concepts of transcription initiation in bacteria (Journal Article) Nat. Rev. Genet., 2020. @article{pmid32665585, title = {Redefining fundamental concepts of transcription initiation in bacteria}, author = {C Meja-Almonte and S J W Busby and J T Wade and J van Helden and A P Arkin and G D Stormo and K Eilbeck and B O Palsson and J E Galagan and J Collado-Vides}, year = {2020}, date = {2020-07-01}, journal = {Nat. Rev. Genet.}, abstract = {Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics. |
| 277. | Price, M N; Deutschbauer, A M; Arkin, A P GapMind: Automated Annotation of Amino Acid Biosynthesis (Journal Article) mSystems, 5 (3), 2020. (Abstract | BibTeX | Tags: arkin lab) @article{pmid32576650, title = {GapMind: Automated Annotation of Amino Acid Biosynthesis}, author = {M N Price and A M Deutschbauer and A P Arkin}, year = {2020}, date = {2020-06-01}, journal = {mSystems}, volume = {5}, number = {3}, abstract = {GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.}, keywords = {arkin lab}, pubstate = {published}, tppubtype = {article} } GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids. |
| 276. | Sean Carim Ashley L. Azadeh, Alexey Kazakov Morgan Price Peter Walian Romy Chakraborty Adam Deutschbauer Vivek Mutalik Adam Arkin E N J M K P Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins (Journal Article) 2020. (BibTeX | Tags: arkin lab, biodesign) @article{sean, title = {Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins}, author = {Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik, Adam P. Arkin}, year = {2020}, date = {2020-05-27}, keywords = {arkin lab, biodesign}, pubstate = {published}, tppubtype = {article} } |
| 275. | Samuel M. D. Seaver Filipe Liu, Qizhi Zhang James Jeffryes José Faria Janaka Edirisinghe Michael Mundy Nicholas Chia Elad Noor Moritz Beber Aaron Best Matthew DeJongh Jeffrey Kimbrel Patrik D'haeseleer Erik Pearson Shane Canon Elisha Wood-Charlson Robert Cottingham Adam Arkin P N E A A M W P; Henry, Christopher S The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes (Journal Article) 2020. @article{seaver2020modelseed, title = {The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes}, author = {Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael Mundy, Nicholas Chia, Elad Noor, Moritz E. Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin and Christopher S. Henry}, year = {2020}, date = {2020-05-12}, keywords = {kbase}, pubstate = {published}, tppubtype = {article} } |
| 274. | Benjamin A. Adler Crystal Zhong, Hualan Liu Elizabeth Kutter Adam Deutschbauer Vivek Mutalik Adam Arkin M K P Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens (Journal Article) bioRxiv, 2020. (BibTeX | Tags: arkin lab, biodesign) @article{adler2020systematic, title = {Systematic Discovery of Salmonella Phage-Host Interactions via High-Throughput Genome-Wide Screens}, author = {Benjamin A. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M. Deutschbauer, Vivek K. Mutalik, Adam P. Arkin}, year = {2020}, date = {2020-04-28}, journal = {bioRxiv}, keywords = {arkin lab, biodesign}, pubstate = {published}, tppubtype = {article} } |
| 273. | Price, Morgan N; Arkin, Adam P Short Methionine Synthases (Journal Article) 2020. @article{morgan, title = {Short Methionine Synthases}, author = {Morgan N. Price and Adam P. Arkin}, year = {2020}, date = {2020-04-23}, keywords = {arkin lab}, pubstate = {published}, tppubtype = {article} } |
| 272. | Regina L. Wilpiszeski Caitlin M. Gionfriddo, Ann Wymore Ji-Won Moon Kenneth Lowe Mircea Podar Sa’ad Rafie Matthew Fields Terry Hazen Xiaoxuan Ge Farris Poole Michael Adams Romy Chakraborty Yupeng Fan Joy Van Nostrand Jizhong Zhou Adam Arkin Dwayne Elias M A W C W W D P A In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations (Journal Article) bioRxiv, 2020. @article{uwu, title = {In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations}, author = {Regina L. Wilpiszeski, Caitlin M. Gionfriddo, Ann M. Wymore, Ji-Won Moon, Kenneth A. Lowe, Mircea Podar, Sa’ad Rafie, Matthew W. Fields, Terry C. Hazen, Xiaoxuan Ge, Farris Poole, Michael W.W. Adams, Romy Chakraborty, Yupeng Fan, Joy D. Van Nostrand, Jizhong Zhou, Adam P. Arkin, Dwayne A. Elias}, year = {2020}, date = {2020-04-19}, journal = {bioRxiv}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
| 271. | Lauren M. Lui Torben N. Nielsen, Adam Arkin P A method for achieving complete microbial genomes and better quality bins from metagenomics data (Journal Article) BioRxiv, 2020. (BibTeX | Tags: arkin lab, enigma) @article{lui2020method, title = {A method for achieving complete microbial genomes and better quality bins from metagenomics data}, author = {Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin}, year = {2020}, date = {2020-03-06}, journal = {BioRxiv}, keywords = {arkin lab, enigma}, pubstate = {published}, tppubtype = {article} } |
| 270. | Daliang Ning Mengting Yuan, Linwei Wu Ya Zhan Xue Guo Xishu Zhou Yunfeng Yang Adam Arkin Mary Firestone Jizhong Zhou P K A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming (Journal Article) 2020. @article{ning2020quantitativeb, title = {A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming}, author = {Daliang Ning, Mengting Yuan, Linwei Wu, Ya Zhan, Xue Guo, Xishu Zhou , Yunfeng Yang, Adam P. Arkin, Mary K. Firestone, Jizhong Zhou}, year = {2020}, date = {2020-02-25}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
| 269. | Vivek K. Mutalik Benjamin A. Adler, Harneet Rishi Denish Piya Crystal Zhong Britt Koskella Richard Calendar Pavel Novichkov Morgan Price Adam Deutschbauer Adam Arkin S N M P High-throughput mapping of the phage resistance landscape in E. coli (Journal Article) 2020. (BibTeX | Tags: arkin lab, biodesign) @article{Mutalik2020, title = {High-throughput mapping of the phage resistance landscape in E. coli}, author = {Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong,Britt Koskella, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin}, year = {2020}, date = {2020-02-16}, keywords = {arkin lab, biodesign}, pubstate = {published}, tppubtype = {article} } |
| 268. | Abel, Anthony J; Hilzinger, Jacob M; Arkin, Adam P; Clark, Douglas S Systems-informed genome mining for electroautotrophic microbial production (Journal Article) bioRxiv, 2020. @article{Abel2020, title = {Systems-informed genome mining for electroautotrophic microbial production}, author = {Anthony J Abel and Jacob M Hilzinger and Adam P Arkin and Douglas S Clark}, year = {2020}, date = {2020-01-01}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, keywords = {cubes}, pubstate = {published}, tppubtype = {article} } |
| 267. | Berliner, Aaron; Hilzinger, Jacob M; Abel, Anthony J; McNulty, Matthew; Makrygiorgos, George; Averesch, Nils J H; Gupta, Soumyajit Sen; Benvenuti, Alexander; Caddell, Daniel; Cestellos-Blanco, Stefano Towards a Biomanufactory on Mars (Journal Article) preprints.org, 2020. (Links | BibTeX | Tags: cubes) @article{Berliner2020, title = {Towards a Biomanufactory on Mars}, author = {Aaron Berliner and Jacob M Hilzinger and Anthony J Abel and Matthew McNulty and George Makrygiorgos and Nils J H Averesch and Soumyajit Sen Gupta and Alexander Benvenuti and Daniel Caddell and Stefano Cestellos-Blanco}, doi = {doi: 10.20944/preprints202012.0714.v1}, year = {2020}, date = {2020-01-01}, journal = {preprints.org}, publisher = {Preprints}, keywords = {cubes}, pubstate = {published}, tppubtype = {article} } |
| 266. | Tian, R; Ning, D; He, Z; Zhang, P; Spencer, S J; Gao, S; Shi, W; Wu, L; Zhang, Y; Yang, Y; Adams, B G; Rocha, A M; Detienne, B L; Lowe, K A; Joyner, D C; Klingeman, D M; Arkin, A P; Fields, M W; Hazen, T C; Stahl, D A; Alm, E J; Zhou, J Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity (Journal Article) Microbiome, 8 (1), pp. 51, 2020. (Abstract | BibTeX | Tags: enigma) @article{pmid32252814, title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity}, author = {R Tian and D Ning and Z He and P Zhang and S J Spencer and S Gao and W Shi and L Wu and Y Zhang and Y Yang and B G Adams and A M Rocha and B L Detienne and K A Lowe and D C Joyner and D M Klingeman and A P Arkin and M W Fields and T C Hazen and D A Stahl and E J Alm and J Zhou}, year = {2020}, date = {2020-01-01}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {51}, abstract = {The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty. |
| 265. | Kempher, M L; Tao, X; Song, R; Wu, B; Stahl, D A; Wall, J D; Arkin, A P; Zhou, A; Zhou, J Effects of Genetic and Physiological Đivergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Ŧemperature (Journal Article) mBio, 11 (4), 2020. (Abstract | BibTeX | Tags: enigma) @article{pmid32817099, title = {Effects of Genetic and Physiological Đivergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Ŧemperature}, author = {M L Kempher and X Tao and R Song and B Wu and D A Stahl and J D Wall and A P Arkin and A Zhou and J Zhou}, year = {2020}, date = {2020-01-01}, journal = {mBio}, volume = {11}, number = {4}, abstract = {Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes.IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes.IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints. |
