Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador

Reznicek, Ondrej; Luesken, Francisca A.; Facey, Sandra J.; Hauer, Bernhard

doi:10.1128/genomea.00420-15

Cited by 8 publications

(10 citation statements)

References 7 publications

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“…In this study, order Rhizobiales in the class Alphaproteobacteria increased with the PW biochar addition. More recently, order Rhizobiales was found to degrade polycyclic aromatic hydrocarbons (PAHs; Reznicek, Luesken, Facey, & Hauer, ). During the pyrolytic production of biochar, PAHs can form on the surface of biochar.…”

Section: Resultsmentioning

confidence: 99%

Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions

et al. 2019

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Biochar and manure application can modify soil microbial community structure and enhance biochemical activities. However, the studies about the influence of biochar and manure on the microbial communities on different geomorphological landforms (depositional and eroded landscapes) are scarce. In this study, we investigated the responses of soil biochemical activities and microbial communities to the addition of pinewood biochar, dairy manure (DM), and the dairy manure and pinewood biochar mixture (DMP) at a rate of 10 Mg ha−1, respectively, in comparison with control (CNT) at eroded and depositional landscape positions over 5 years. Data showed that the DMP treatment significantly increased cold‐water‐soluble organic carbon and hot‐water‐soluble organic carbon at the depositional landscape than CNT soils. Application of DMP increased total phospholipid fatty acid (PLFA) and bacterial PLFA by 31% and 20% compared with the CNT at the depositional landscape, respectively. At eroded landscape, total PLFAs and total bacterial PLFAs biomass concentrations were found 39% and 90% higher with DM than CNT soils. The addition of DM and DMP increased the activities of enzymes that are involved in the major nutrient cycling at depositional and eroded landscapes. At the phylum level, the proportion of Bacteroidetes was found lower in DMP, but the proportion of phylum Proteobacteria and Acidobacteria were increased. In conclusion, our study revealed that DMP influenced the labile nutrient pool, altered the microbial community structure, and increased bacterial composition and enzymatic activities at both the landscape positions.

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Section: Resultsmentioning

confidence: 99%

Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions

et al. 2019

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“…increased in relative abundance more rapidly in soils exposed to the heat–heat treatment than in the control-heat treatment. Phenylobacterium strains are able to degrade phenolic compounds ( Reznicek et al, 2015 ; Jacquiod et al, 2017 ), which were likely released following the heat shock, and were probably more abundant after the second shock. Furthermore, Firmicutes OTUs which increased only transiently in both treatments (i.e., Planococcaceae incertae sedis and Paenisporosarcina ) exhibited a higher relative abundance during this “peak” in soils from the heat–heat treatment.…”

Section: Discussionmentioning

confidence: 99%

Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation

et al. 2017

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The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community’s response during succession. By altering dominance patterns, disturbance legacy affects the microbiome’s ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil’s disturbance history in the development of soil management practices in order to maintain the system’s resilience.

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“…Phenylobacterium , a taxon with high number of connections in our network, is not a well-studied genus at present, however sequences related to this bacterium have been detected in soils contaminated with crude oil35, PAHs41, polychlorinated biphenyl (PCB)44. The sequencing of the genome of Phenylobacterium immobile strain E (DSM 1986) has recently revealed the presence of a high number of Rieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs), a large family of multi-component enzymes involved in the initial step of degradation of aromatic compounds, which makes them enzymatically accessible for further degradation by other organisms45. This may well explain the high connectivity of Phenylobacterium with other hydrocarbon-degraders that we observed in our network analysis.…”

Section: Discussionmentioning

confidence: 99%

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

Yang

Shi

et al. 2016

Sci Rep

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Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

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Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador

Cited by 8 publications

References 7 publications

Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions

Biochar and manure addition influenced soil microbial community structure and enzymatic activities at eroded and depositional landscape positions

Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

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