@article{wilpiszeski_2020,

title = {In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.},

author = {Regina L Wilpiszeski and Caitlin M Gionfriddo and Ann M Wymore and Ji-Won Moon and Kenneth A Lowe and Mircea Podar and Sa'ad Rafie and Matthew W Fields and Terry C Hazen and Xiaoxuan Ge and Farris Poole and Michael W W Adams and Romy Chakraborty and Yupeng Fan and Joy D Van Nostrand and Jizhong Zhou and Adam P Arkin and Dwayne A Elias},

url = {http://dx.doi.org/10.1371/journal.pone.0232437},

doi = {10.1371/journal.pone.0232437},

year  = {2020},

date = {2020-09-28},

urldate = {2021-05-26},

journal = {Plos One},

volume = {15},

number = {9},

pages = {e0232437},

abstract = {Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@article{ning_2020,

title = {A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming.},

author = {Daliang Ning and Mengting Yuan and Linwei Wu and Ya Zhang and Xue Guo and Xishu Zhou and Yunfeng Yang and Adam P Arkin and Mary K Firestone and Jizhong Zhou},

url = {http://dx.doi.org/10.1038/s41467-020-18560-z},

doi = {10.1038/s41467-020-18560-z},

year  = {2020},

date = {2020-09-18},

urldate = {2021-05-25},

journal = {Nature Communications},

volume = {11},

number = {1},

pages = {4717},

abstract = {Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and specificity (0.95-0.98) on simulated communities, which are 10-160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%). Interestingly, warming decreases 'drift' over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology.},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{moon_2020,

title = {Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer},

author = {Ji-Won Moon and Charles J Paradis and Dominique C Joyner and Frederick von Netzer and Erica L Majumder and Emma R Dixon and Mircea Podar and Xiaoxuan Ge and Peter J Walian and Heidi J Smith and Xiaoqin Wu and Grant M Zane and Kathleen F Walker and Michael P Thorgersen and Farris L Poole {II} and Lauren M Lui and Benjamin G Adams and Kara B De León and Sheridan S Brewer and Daniel E Williams and Kenneth A Lowe and Miguel Rodriguez and Tonia L Mehlhorn and Susan M Pfiffner and Romy Chakraborty and Adam P Arkin and Judy D Wall and Matthew W Fields and Michael W W Adams and David A Stahl and Dwayne A Elias and Terry C Hazen},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653520311449},

doi = {10.1016/j.chemosphere.2020.126951},

issn = {00456535},

year  = {2020},

date = {2020-09-01},

urldate = {2021-05-25},

journal = {Chemosphere},

volume = {255},

pages = {126951},

keywords = {enigma},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}