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Kempher, Megan L; Tao, Xuanyu; Song, Rong; Wu, Bo; Stahl, David A; Wall, Judy D; Arkin, Adam P; Zhou, Aifen; Zhou, Jizhong
Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature. Journal Article
In: mBio, vol. 11, no. 4, 2020, ISSN: 2150-7511.
Abstract | Links | BibTeX | Tags: enigma
@article{kempher_2020,
title = {Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature.},
author = {Megan L Kempher and Xuanyu Tao and Rong Song and Bo Wu and David A Stahl and Judy D Wall and Adam P Arkin and Aifen Zhou and Jizhong Zhou},
url = {https://mbio.asm.org/content/11/4/e00569-20},
doi = {10.1128/mBio.00569-20},
issn = {2150-7511},
year = {2020},
date = {2020-08-18},
urldate = {2021-05-25},
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. Copyright copyright 2020 Kempher et al.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Simon Rouxb Ankita Kotharia, Hanqiao Zhanga
Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article
In: 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}
}
Kothari, Ankita; Roux, Simon; Zhang, Hanqiao; Prieto, Anatori; Soneja, Drishti; Chandonia, John-Marc; Spencer, Sarah J; Wu, Xiaoqin; Altenburg, Sarah; Fields, Matthew W; Deutschbauer, Adam M; Arkin, Adam P; Alm, Eric J; Chakraborty, Romy; Mukhopadhyay, Aindrila
Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance Journal Article
In: BioRxiv, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{kothari_2020,
title = {Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance},
author = {Ankita Kothari and Simon Roux and Hanqiao Zhang and Anatori Prieto and Drishti Soneja and John-Marc Chandonia and Sarah J Spencer and Xiaoqin Wu and Sarah Altenburg and Matthew W Fields and Adam M Deutschbauer and Adam P Arkin and Eric J Alm and Romy Chakraborty and Aindrila Mukhopadhyay},
url = {http://biorxiv.org/lookup/doi/10.1101/2020.07.14.203604},
doi = {10.1101/2020.07.14.203604},
year = {2020},
date = {2020-07-15},
urldate = {2021-05-25},
journal = {BioRxiv},
abstract = {Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes, however little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes and identified 200 viral sequences, which clustered into 41 ~ genus-level viral clusters (equivalent to viral genera) including 9 known and 32 putative new genera. We use publicly available bacterial whole genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. The publicly available microbial genome sequences enabled mapping bacterial hosts to a breadth of viral sequences. The WGS of groundwater isolates increased depth of host prediction by allowing identification of hosts at the strain level. The latter included 4 viruses that were almost entirely (textgreater99% query coverage, textgreater99% identity) identified as integrated in the genomes of specific Pseudomonas, Acidovorax and Castellaniella strains, resulting in very high-confidence host assignments. Lastly, 21 of these viruses encoded putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they act as key players in microbial adaption to environmental stress.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Price, Morgan N; Deutschbauer, Adam M; Arkin, Adam P
Gapmind: automated annotation of amino acid biosynthesis. Journal Article
In: mSystems, vol. 5, no. 3, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{price_2020,
title = {Gapmind: automated annotation of amino acid biosynthesis.},
author = {Morgan N Price and Adam M Deutschbauer and Adam P Arkin},
url = {http://dx.doi.org/10.1128/mSystems.00291-20},
doi = {10.1128/mSystems.00291-20},
year = {2020},
date = {2020-06-23},
urldate = {2021-05-25},
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. Copyright copyright 2020 Price et al.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Carlson, Hans K; Lui, Lauren M; Price, Morgan N; Kazakov, Alexey E; Carr, Alex V; Kuehl, Jennifer V; Owens, Trenton K; Nielsen, Torben; Arkin, Adam P; Deutschbauer, Adam M
Selective carbon sources influence the end products of microbial nitrate respiration. Journal Article
In: The ISME Journal, vol. 14, no. 8, pp. 2034-2045, 2020, ISSN: 1751-7362.
Abstract | Links | BibTeX | Tags: enigma
@article{carlson_2020,
title = {Selective carbon sources influence the end products of microbial nitrate respiration.},
author = {Hans K Carlson and Lauren M Lui and Morgan N Price and Alexey E Kazakov and Alex V Carr and Jennifer V Kuehl and Trenton K Owens and Torben Nielsen and Adam P Arkin and Adam M Deutschbauer},
url = {http://www.nature.com/articles/s41396-020-0666-7},
doi = {10.1038/s41396-020-0666-7},
issn = {1751-7362},
year = {2020},
date = {2020-05-05},
urldate = {2021-05-25},
journal = {The ISME Journal},
volume = {14},
number = {8},
pages = {2034-2045},
abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Caitlin M. Gionfriddo Regina L. Wilpiszeski, Ann M. Wymore
In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations Journal Article
In: 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}
}
Tian, Renmao; Ning, Daliang; He, Zhili; Zhang, Ping; Spencer, Sarah J; Gao, Shuhong; Shi, Weiling; Wu, Linwei; Zhang, Ya; Yang, Yunfeng; Adams, Benjamin G; Rocha, Andrea M; Detienne, Brittny L; Lowe, Kenneth A; Joyner, Dominique C; Klingeman, Dawn M; Arkin, Adam P; Fields, Matthew W; Hazen, Terry C; Stahl, David A; Alm, Eric J; Zhou, Jizhong
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Journal Article
In: Microbiome, vol. 8, no. 1, pp. 51, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{tian_2020,
title = {Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.},
author = {Renmao Tian and Daliang Ning and Zhili He and Ping Zhang and Sarah J Spencer and Shuhong Gao and Weiling Shi and Linwei Wu and Ya Zhang and Yunfeng Yang and Benjamin G Adams and Andrea M Rocha and Brittny L Detienne and Kenneth A Lowe and Dominique C Joyner and Dawn M Klingeman and Adam P Arkin and Matthew W Fields and Terry C Hazen and David A Stahl and Eric J Alm and Jizhong Zhou},
url = {http://dx.doi.org/10.1186/s40168-020-00825-w},
doi = {10.1186/s40168-020-00825-w},
year = {2020},
date = {2020-04-06},
urldate = {2021-05-25},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {51},
abstract = {BACKGROUND: 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 textgreater 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. RESULTS: Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of textgreater 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. CONCLUSIONS: 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}
}
Torben N. Nielsen Lauren M. Lui, Adam P. Arkin
A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article
In: 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}
}
Lui, Lauren M; Nielsen, Torben N; Arkin, Adam P
A method for achieving complete microbial genomes and better quality bins from metagenomics data Journal Article
In: BioRxiv, 2020.
Abstract | Links | BibTeX | Tags: enigma
@article{lui_2020,
title = {A method for achieving complete microbial genomes and better quality bins from metagenomics data},
author = {Lauren M Lui and Torben N Nielsen and Adam P Arkin},
url = {http://biorxiv.org/lookup/doi/10.1101/2020.03.05.979740},
doi = {10.1101/2020.03.05.979740},
year = {2020},
date = {2020-03-06},
urldate = {2021-05-25},
journal = {BioRxiv},
abstract = {Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Only 63 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one copy of ribosomal RNA genes. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Mengting Yuan Daliang Ning, Linwei Wu
A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming Journal Article
In: 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}
}
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
In: mBio, vol. 11, no. 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}
}
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
In: Microbiome, vol. 8, no. 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}
}
Carlson, H K; Lui, L M; Price, M N; Kazakov, A E; Carr, A V; Kuehl, J V; Owens, T K; Nielsen, T; Arkin, A P; Deutschbauer, A M
Selective carbon sources influence the end products of microbial nitrate respiration Journal Article
In: ISME J, vol. 14, no. 8, pp. 2034–2045, 2020.
Abstract | BibTeX | Tags: arkin lab, enigma
@article{pmid32372050,
title = {Selective carbon sources influence the end products of microbial nitrate respiration},
author = {H K Carlson and L M Lui and M N Price and A E Kazakov and A V Carr and J V Kuehl and T K Owens and T Nielsen and A P Arkin and A M Deutschbauer},
year = {2020},
date = {2020-00-01},
journal = {ISME J},
volume = {14},
number = {8},
pages = {2034--2045},
abstract = {Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.},
keywords = {arkin lab, enigma},
pubstate = {published},
tppubtype = {article}
}
Zelaya, A J; Parker, A E; Bailey, K L; Zhang, P; Nostrand, J Van; Ning, D; Elias, D A; Zhou, J; Hazen, T C; Arkin, A P; Fields, M W
Ħigh spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer Journal Article
In: Water Res., vol. 164, pp. 114917, 2019.
Abstract | BibTeX | Tags: enigma
@article{pmid31387058,
title = {Ħigh spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer},
author = {A J Zelaya and A E Parker and K L Bailey and P Zhang and J Van Nostrand and D Ning and D A Elias and J Zhou and T C Hazen and A P Arkin and M W Fields},
year = {2019},
date = {2019-11-01},
journal = {Water Res.},
volume = {164},
pages = {114917},
abstract = {Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average > 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Zelaya, Anna J; Parker, Albert E; Bailey, Kathryn L; Zhang, Ping; Nostrand, Joy Van; Ning, Daliang; Elias, Dwayne A; Zhou, Jizhong; Hazen, Terry C; Arkin, Adam P; Fields, Matthew W
High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Journal Article
In: Water Research, vol. 164, pp. 114917, 2019.
Abstract | Links | BibTeX | Tags: enigma
@article{zelaya_2019,
title = {High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer.},
author = {Anna J Zelaya and Albert E Parker and Kathryn L Bailey and Ping Zhang and Joy Van Nostrand and Daliang Ning and Dwayne A Elias and Jizhong Zhou and Terry C Hazen and Adam P Arkin and Matthew W Fields},
url = {http://dx.doi.org/10.1016/j.watres.2019.114917},
doi = {10.1016/j.watres.2019.114917},
year = {2019},
date = {2019-11-01},
urldate = {2021-05-25},
journal = {Water Research},
volume = {164},
pages = {114917},
abstract = {Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average textgreater 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry. Copyright copyright 2019 Elsevier Ltd. All rights reserved.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Thorgersen, Michael P; Ge, Xiaoxuan; Poole, Farris L; Price, Morgan N; Arkin, Adam P; Adams, Michael W W
Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Journal Article
In: Applied and Environmental Microbiology, vol. 85, no. 17, 2019.
Abstract | Links | BibTeX | Tags: enigma
@article{thorgersen_2019,
title = {Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation.},
author = {Michael P Thorgersen and Xiaoxuan Ge and Farris L Poole and Morgan N Price and Adam P Arkin and Michael W W Adams},
url = {http://dx.doi.org/10.1128/AEM.00896-19},
doi = {10.1128/AEM.00896-19},
year = {2019},
date = {2019-09-01},
urldate = {2021-05-25},
journal = {Applied and Environmental Microbiology},
volume = {85},
number = {17},
abstract = {Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities. Copyright copyright 2019 American Society for Microbiology.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Price, Morgan N; Zane, Grant M; Kuehl, Jennifer V; Melnyk, Ryan A; Wall, Judy D; Deutschbauer, Adam M; Arkin, Adam P
Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. Journal Article
In: PLoS Genetics, vol. 15, no. 4, pp. e1008106, 2019.
Abstract | Links | BibTeX | Tags: enigma
@article{price_2019b,
title = {Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.},
author = {Morgan N Price and Grant M Zane and Jennifer V Kuehl and Ryan A Melnyk and Judy D Wall and Adam M Deutschbauer and Adam P Arkin},
url = {http://dx.doi.org/10.1371/journal.pgen.1008106},
doi = {10.1371/journal.pgen.1008106},
year = {2019},
date = {2019-04-03},
urldate = {2021-05-25},
journal = {PLoS Genetics},
volume = {15},
number = {4},
pages = {e1008106},
abstract = {[This corrects the article DOI: 10.1371/journal.pgen.1007147.].},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Price, Morgan N; Arkin, Adam P
Curated BLAST for genomes. Journal Article
In: mSystems, vol. 4, no. 2, 2019.
Abstract | Links | BibTeX | Tags: enigma
@article{price_2019a,
title = {Curated BLAST for genomes.},
author = {Morgan N Price and Adam P Arkin},
url = {http://dx.doi.org/10.1128/mSystems.00072-19},
doi = {10.1128/mSystems.00072-19},
year = {2019},
date = {2019-04-01},
urldate = {2021-05-25},
journal = {mSystems},
volume = {4},
number = {2},
abstract = {Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme's name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated. IMPORTANCE Given a microbe's genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Price, Morgan N; Ray, Jayashree; Iavarone, Anthony T; Carlson, Hans K; Ryan, Elizabeth M; Malmstrom, Rex R; Arkin, Adam P; Deutschbauer, Adam M
Oxidative pathways of deoxyribose and deoxyribonate catabolism. Journal Article
In: mSystems, vol. 4, no. 1, 2019.
Abstract | Links | BibTeX | Tags: enigma
@article{price_2019,
title = {Oxidative pathways of deoxyribose and deoxyribonate catabolism.},
author = {Morgan N Price and Jayashree Ray and Anthony T Iavarone and Hans K Carlson and Elizabeth M Ryan and Rex R Malmstrom and Adam P Arkin and Adam M Deutschbauer},
url = {http://dx.doi.org/10.1128/mSystems.00297-18},
doi = {10.1128/mSystems.00297-18},
year = {2019},
date = {2019-02-05},
urldate = {2021-05-25},
journal = {mSystems},
volume = {4},
number = {1},
abstract = {Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants' abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}
Mutalik, Vivek K; Novichkov, Pavel S; Price, Morgan N; Owens, Trenton K; Callaghan, Mark; Carim, Sean; Deutschbauer, Adam M; Arkin, Adam P
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Journal Article
In: Nature Communications, vol. 10, no. 1, pp. 308, 2019, ISSN: 2041-1723.
Abstract | Links | BibTeX | Tags: enigma
@article{mutalik_2019,
title = {Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria.},
author = {Vivek K Mutalik and Pavel S Novichkov and Morgan N Price and Trenton K Owens and Mark Callaghan and Sean Carim and Adam M Deutschbauer and Adam P Arkin},
url = {http://www.nature.com/articles/s41467-018-08177-8},
doi = {10.1038/s41467-018-08177-8},
issn = {2041-1723},
year = {2019},
date = {2019-01-18},
urldate = {2021-05-25},
journal = {Nature Communications},
volume = {10},
number = {1},
pages = {308},
abstract = {A major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.},
keywords = {enigma},
pubstate = {published},
tppubtype = {article}
}