Complete Genome Sequence of Pantoea agglomerans TH81, Isolated from a Permafrost Thaw Gradient

Humphrey, Jennie; Seitz, Taylor J.; Haan, Tracie J.; Ducluzeau, Anne-Lise; Drown, Devin M.

doi:10.1128/mra.01486-18

Cited by 9 publications

(4 citation statements)

References 5 publications

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“… van der Voort et al (2016) and Yang et al (2020) have also showed that soils stressed by drought and heat disturbance, respectively, were found to have overrepresented populations of known plant pathogens including members of Comamonadaceae and Erwiniaceae. Although few studies have looked at the effects of physical disturbances on microbiomes specifically in arctic or subarctic soils, in previous research we cultured and isolated bacterial strains belonging to Erwiniaceae from the FPES MD soil plot ( Humphrey et al, 2019 ). It is possible that the higher presence of bacterial groups including known plant-pathogenic bacteria found in the MD soil microbiomes is leading to the decrease in associated plant growth, caused by a disruption in nutrient cycling and direct alterations to the plant rhizospheres.…”

Section: Discussionmentioning

confidence: 99%

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

2021

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Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant productivity by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant productivity was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased productivity compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost differ in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant productivity can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant productivity in Boreal forests and more broadly, ecosystem health.

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Section: Discussionmentioning

confidence: 99%

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

2021

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“…The unicycler_polish tool of Unicycler version 0.4.8 [ 32 ] was used to polish the flye assemblies with the Illumina reads as input. For isolates TH26, TH81 and TH88, ONT long-read assemblies that were previously published in Haan et al 2019 and Humphrey et al 2019 respectively were used as inputs for unicycler_polish [ 33 , 34 ].…”

Section: Methodsmentioning

confidence: 99%

Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska

Haan

Drown

2021

Microorganisms

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Monitoring antibiotic resistance genes (ARGs) across ecological niches is critical for assessing the impacts distinct microbial communities have on the global spread of resistance. In permafrost-associated soils, climate and human driven disturbances augment near-surface thaw shifting the predominant bacteria that shape the resistome in overlying active layer soils. This thaw is of concern in Alaska, because 85% of land is underlain by permafrost, making soils especially vulnerable to disturbances. The goal of this study is to assess how soil disturbance, and the subsequent shift in community composition, will affect the types, abundance, and mobility of ARGs that compose the active layer resistome. We address this goal through the following aims: (1) assess resistance phenotypes through antibiotic susceptibility testing, and (2) analyze types, abundance, and mobility of ARGs through whole genome analyses of bacteria isolated from a disturbance-induced thaw gradient in Interior Alaska. We found a high proportion of isolates resistant to at least one of the antibiotics tested with the highest prevalence of resistance to ampicillin. The abundance of ARGs and proportion of resistant isolates increased with disturbance; however, the number of ARGs per isolate was explained more by phylogeny than isolation site. When compared to a global database of soil bacteria, RefSoil+, our isolates from the same genera had distinct ARGs with a higher proportion on plasmids. These results emphasize the hypothesis that both phylogeny and ecology shape the resistome and suggest that a shift in community composition as a result of disturbance-induced thaw will be reflected in the predominant ARGs comprising the active layer resistome.

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“…The unicycler_polish tool of Unicycler v0.4.8 (Wick et al 2017) was used for genome polishing with the Illumina reads and the Flye assembly as inputs. For isolates TH26 and TH81, ONT long-read assemblies previously published in Haan et al 2019 and Humphrey et al 2019 respectively were used as inputs for unicycler_polish. These assemblies were annotated with RAST tool kit (RASTtk) in PATRIC v3.6.3 using the Genome Annotation Service (Brettin et al 2015).…”

Section: Methodsmentioning

confidence: 99%

Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw

Haan

Drown

2020

Preprint

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Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance. In permafrost associated soils, climate and human driven forces augment near-surface thaw altering the overlying active layer. Physiochemical changes shift bacterial community composition and metabolic functioning, however, it is unknown if permafrost thaw will affect ARGs comprising the boreal soil resistome. To assess how thaw shifts the resistome, we performed susceptibility testing and whole genome sequencing on soil isolates from a disturbance-induced thaw gradient in Interior Alaska. We found resistance was widespread in the Alaskan isolates, with 87% of the 90 isolates resistant to at least one of the five antibiotics. We also observed positive trends in both the proportion of resistant isolates and the abundance of ARGs with permafrost thaw. However, the number of ARGs per genome and types of genes present were shown to cluster more strongly by bacterial taxa rather than thaw emphasizing the evolutionary origins of resistance and the role vertical gene transfer has in shaping the predominantly chromosomally encoded ARGs. The observed higher proportion of plasmid-borne and distinct ARGs in our isolates compared to RefSoil+ suggests local conditions affect the composition of the resistome along with selection for ARG mobility. Overall taxonomy and geography shape the resistome, suggesting that as microbial communities shift in response to permafrost thaw so will the ARGs in the boreal active layer.

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Complete Genome Sequence of Pantoea agglomerans TH81, Isolated from a Permafrost Thaw Gradient

Cited by 9 publications

References 5 publications

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska

Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw

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