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

Abstract

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.

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

“…2). 2, Supporting Information Table S3 for complete list), which are well-known hydrocarbon degraders in cold environments, and known to increase the efficiency of bioremediation processes (Jiao et al, 2016;Yang et al, 2016;Vergeynst et al, 2018). In Antarctica, at the final time point, they accounted for 0.2% (AE 0.16%) of the total community, suggesting a slower or weaker response to ADOC than the one observed in Arctic waters (Supporting Information Fig.…”

Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation

“…This includes a [NiFe] hydrogenase in candidate Desulfatiglans TRIP_1 (Supporting Information Table S1) and four genes encoding [FeFe] hydrogenases, as well as genes required for fermentation of carbohydrates in candidate Spirochaetaceae TRIP_4 (Table 6). Paludibacter species related to candidate Paludibacter TRIP_3 have also been reported in PAHs-contaminated sites (Yang et al, 2016). Also these microorganisms are able to grow with dead biomass, which could explain their persistance in the TRIP culture (Yang et al, 2016).…”

“…Paludibacter species related to candidate Paludibacter TRIP_3 have also been reported in PAHs-contaminated sites (Yang et al, 2016). Also these microorganisms are able to grow with dead biomass, which could explain their persistance in the TRIP culture (Yang et al, 2016).…”

“…A potential role in phenanthrene degradation of the four microorganisms other than candidate Desulfatiglans TRIP_1 could thus only be indirect. Paludibacter species related to candidate Paludibacter TRIP_3 have also been reported in PAHs-contaminated sites (Yang et al, 2016). The rodshape Spirochaete R. cohabitans was isolated from the naphthalene-degrading enrichment culture N47 where it is involved in necromass recycling providing hydrogen and possibly nutrients to the naphthalene-degrading Deltaproteobacterium N47 (Dong et al, 2018).…”

“…The genome of candidate Spirochaetaceae TRIP_4 suggests metabolic capacities similar to Rectinema cohabitans. Also these microorganisms are able to grow with dead biomass, which could explain their persistance in the TRIP culture (Yang et al, 2016). Although the genetic elements for hydrogen transfer between the candidate Spirochaetaceae TRIP_4 and the candidate Desulfatiglans TRIP_1 are present, the corresponding gene products were not detected durig growth of the TRIP culture with phenanthrene.…”