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| 17. | 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} } |
| 16. | 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. |
| 15. | 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} } |
| 14. | 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} } |
| 13. | 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} } |
| 12. | 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} } |
| 11. | 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} } |
| 10. | 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. |
| 9. | 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. |
| 8. | 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) ISME J, 14 (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} } 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. |
| 7. | Zelaya, A J; Parker, A E; Bailey, K L; Zhang, P; Nostrand, Van J; 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) Water Res., 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} } 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. |
| 6. | Paradis, C J; Dixon, E R; Lui, L M; Arkin, A P; Parker, J C; Istok, J D; Perfect, E; McKay, L D; Hazen, T C Improved Method for Estimating Reaction Rates Đuring Push-Pull Ŧests (Journal Article) Ground Water, 57 (2), pp. 292–302, 2019. (Abstract | BibTeX | Tags: enigma) @article{pmid29656383, title = {Improved Method for Estimating Reaction Rates Đuring Push-Pull Ŧests}, author = {C J Paradis and E R Dixon and L M Lui and A P Arkin and J C Parker and J D Istok and E Perfect and L D McKay and T C Hazen}, year = {2019}, date = {2019-01-01}, journal = {Ground Water}, volume = {57}, number = {2}, pages = {292--302}, abstract = {The breakthrough curve obtained from a single-well push-pull test can be adjusted to account for dilution of the injection fluid in the aquifer fluid. The dilution-adjusted breakthrough curve can be analyzed to estimate the reaction rate of a solute. The conventional dilution-adjusted method assumes that the ratios of the concentrations of the nonreactive and reactive solutes in the injection fluid vs. the aquifer fluid are equal. If this assumption is invalid, the conventional method will generate inaccurate breakthrough curves and may lead to erroneous conclusions regarding the reactivity of a solute. In this study, a new method that generates a dilution-adjusted breakthrough curve was theoretically developed to account for any possible combination of nonreactive and reactive solute concentrations in the injection and aquifer fluids. The newly developed method was applied to a field-based data set and was shown to generate more accurate dilution-adjusted breakthrough curves. The improved dilution-adjusted method presented here is simple, makes no assumptions regarding the concentrations of the nonreactive and reactive solutes in the injection and aquifer fluids, and easily allows for estimating reaction rates during push-pull tests.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } The breakthrough curve obtained from a single-well push-pull test can be adjusted to account for dilution of the injection fluid in the aquifer fluid. The dilution-adjusted breakthrough curve can be analyzed to estimate the reaction rate of a solute. The conventional dilution-adjusted method assumes that the ratios of the concentrations of the nonreactive and reactive solutes in the injection fluid vs. the aquifer fluid are equal. If this assumption is invalid, the conventional method will generate inaccurate breakthrough curves and may lead to erroneous conclusions regarding the reactivity of a solute. In this study, a new method that generates a dilution-adjusted breakthrough curve was theoretically developed to account for any possible combination of nonreactive and reactive solute concentrations in the injection and aquifer fluids. The newly developed method was applied to a field-based data set and was shown to generate more accurate dilution-adjusted breakthrough curves. The improved dilution-adjusted method presented here is simple, makes no assumptions regarding the concentrations of the nonreactive and reactive solutes in the injection and aquifer fluids, and easily allows for estimating reaction rates during push-pull tests. |
| 5. | Ge, X; Vaccaro, B J; Thorgersen, M P; Poole, F L; Majumder, E L; Zane, G M; Le?n, De K B; Lancaster, W A; Moon, J W; Paradis, C J; von Netzer, F; Stahl, D A; Adams, P D; Arkin, A P; Wall, J D; Hazen, T C; Adams, M W W Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle (Journal Article) Environ. Microbiol., 21 (1), pp. 152–163, 2019. (Abstract | BibTeX | Tags: enigma) @article{pmid30289197, title = {Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle}, author = {X Ge and B J Vaccaro and M P Thorgersen and F L Poole and E L Majumder and G M Zane and K B De Le?n and W A Lancaster and J W Moon and C J Paradis and F von Netzer and D A Stahl and P D Adams and A P Arkin and J D Wall and T C Hazen and M W W Adams}, year = {2019}, date = {2019-01-01}, journal = {Environ. Microbiol.}, volume = {21}, number = {1}, pages = {152--163}, abstract = {Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO42- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO42- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment. |
| 4. | Thorgersen, M P; Ge, X; Poole, F L; Price, M N; Arkin, A P; Adams, M W W Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Ħeavily Contaminated Oak Ridge Reservation (Journal Article) 85 (17), 2019. (Abstract | BibTeX | Tags: arkin lab, enigma) @article{pmid31253673, title = {Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Ħeavily Contaminated Oak Ridge Reservation}, author = {M P Thorgersen and X Ge and F L Poole and M N Price and A P Arkin and M W W Adams}, year = {2019}, date = {2019-01-01}, 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.}, keywords = {arkin lab, enigma}, pubstate = {published}, tppubtype = {article} } 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. |
| 3. | Carlson, H K; Price, M N; Callaghan, M; Aaring, A; Chakraborty, R; Liu, H; Kuehl, J V; Arkin, A P; Deutschbauer, A M Ŧhe selective pressures on the microbial community in a metal-contaminated aquifer (Journal Article) ISME J, 13 (4), pp. 937–949, 2019. (Abstract | BibTeX | Tags: enigma) @article{pmid30523276, title = {Ŧhe selective pressures on the microbial community in a metal-contaminated aquifer}, author = {H K Carlson and M N Price and M Callaghan and A Aaring and R Chakraborty and H Liu and J V Kuehl and A P Arkin and A M Deutschbauer}, year = {2019}, date = {2019-01-01}, journal = {ISME J}, volume = {13}, number = {4}, pages = {937--949}, abstract = {In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities. |
| 2. | Smith, H J; Zelaya, A J; Le?n, De K B; Chakraborty, R; Elias, D A; Hazen, T C; Arkin, A P; Cunningham, A B; Fields, M W Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments (Journal Article) FEMS Microbiol. Ecol., 94 (12), 2018. (Abstract | BibTeX | Tags: enigma) @article{pmid30265315, title = {Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments}, author = {H J Smith and A J Zelaya and K B De Le?n and R Chakraborty and D A Elias and T C Hazen and A P Arkin and A B Cunningham and M W Fields}, year = {2018}, date = {2018-01-01}, journal = {FEMS Microbiol. Ecol.}, volume = {94}, number = {12}, abstract = {Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance. |
| 1. | Daliang Ning Mengting Yuan, Linwei Wu Ya Zhang Xue Guo Xishu Zhou Yunfeng Yang Adam Arkin Mary Firestone P K; Zhou, Jizhong A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming (Journal Article) 0000. @article{ning2020quantitative, 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 Zhang , Xue Guo, , Xishu Zhou , Yunfeng Yang , Adam P. Arkin , Mary K. Firestone , and Jizhong Zhou}, keywords = {enigma}, pubstate = {published}, tppubtype = {article} } |
