Genotype to ecotype in niche environments: adaptation of <i>Arthrobacter</i> to carbon availability and environmental conditions

Gushgari-Doyle, Sara; Lui, Lauren M.; Nielsen, Torben; Wu, Xiaoqin; Malana, Ria G.; Hendrickson, Andrew J.; Carion, Héloïse; Poole, Farris L.; Adams, Michael W. W.; Arkin, Adam P.; Chakraborty, Romy

doi:10.1038/s43705-022-00113-8

Cited by 13 publications

(9 citation statements)

References 89 publications

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“…are thermophilic bacteria capable of degrading a broad spectrum of carbon compounds (Anders et al., 2014; García‐López et al., 2019). The presence of nematodes also had a strong stimulatory effect on the bacterial genus Actinobacteria , a group of bacteria that are known to transform various organic carbon substrates (e.g., aromatic hydrocarbons and carbohydrates) (Crocker et al., 2000) and adapt to carbon availability and environmental conditions (Gushgari‐Doyle et al., 2022).…”

Section: Discussionmentioning

confidence: 99%

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Guden,

Haegeman,

Ruttink

et al. 2024

Molecular Ecology

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Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species‐rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial‐mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen‐fixing and methane‐oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

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Section: Discussionmentioning

confidence: 99%

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Guden,

Haegeman,

Ruttink

et al. 2024

Molecular Ecology

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“…[ 27 ], Gushgari-Doyle et al. [ 28 ], or from the publicly accessible US Department of Energy Office of Science Subsurface Biogeochemical Research web page ( https://www.esd.ornl.gov/orifrc/ ) [ 29 ]. For this study, we performed additional mercury analyses by ICP-MS ( Supplemental Methods ).…”

Section: Methodsmentioning

confidence: 99%

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Goff,

Lui,

Nielsen

et al. 2024

ISME Communications

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Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation (ORR) subsurface. This meta-mobilome was compared to one derived from samples collected from unimpacted regions of the ORR subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

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“…The majority of the sub-surface well geochemistry data were obtained from publicly available datasets, either from Smith, et al 26 , Wilpiszeski, et al 27 , Gushgari-Doyle et al 28 , or from the publicly accessible U.S. Department of Energy Office of Science Subsurface Biogeochemical Research web page (https://www.esd.ornl.gov/orifrc/) 29 . For this study, we performed additional mercury analyses by ICP-MS ( Supplemental Methods ).…”

Section: Methodsmentioning

confidence: 99%

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

Goff,

Lui,

Nielsen

et al. 2023

Preprint

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Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal contaminated regions of the Oak Ridge Reservation (ORR) subsurface. This meta-mobilome was compared to one derived from samples collected from unimpacted regions of the ORR subsurface. We assembled 1,615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

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Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Cited by 13 publications

References 89 publications

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

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