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ABSTRACT An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing cladeCandidatusThioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteriaSynechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill’s impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of thein situbacterial response is quantified for the first time. 

ABSTRACT Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response ofSphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplantedSphingomonasclade and functional composition would correspond with site conditions and reflect theSphingomonascomposition of native communities. We extractedSphingomonassequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 majorSphingomonasclades were found at varying relative abundances along the climate gradient, and transplantedSphingomonasclade composition shifted after 18 months. Site had a significant effect (PERMANOVA;P< 0.001) on the distribution of bothSphingomonasfunctional (R²= 0.465) and clade composition (R²= 0.400), suggesting thatSphingomonascomposition depends on climate parameters. Additionally, for bothSphingomonasclade and functional composition, ordinations revealed that the transplanted communities shifted closer to the nativeSphingomonascomposition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determineSphingomonasclade and functional composition.IMPORTANCESphingomonasis the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whetherSphingomonasresponds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. WithinSphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change. 

ABSTRACT Polycyclic aromatic hydrocarbons (PAHs) are common toxic and carcinogenic pollutants in marine ecosystems. Despite their prevalence in these habitats, relatively little is known about the natural microflora and biochemical pathways that contribute to their degradation. Approaches to investigate marine microbial PAH degraders often heavily rely on genetic biomarkers, which requires prior knowledge of specific degradative enzymes and genes encoding them. As such, these biomarker-reliant approaches cannot efficiently identify novel degradation pathways or degraders. Here, we screen 18 marine bacterial strains representing the Pseudomonadota, Bacillota, and Bacteroidota phyla for degradation of two model PAHs, pyrene (high molecular weight) and phenanthrene (low molecular weight). Using a qualitative PAH plate screening assay, we determined that 16 of 18 strains show some ability to degrade either or both compounds. Degradative ability was subsequently confirmed with a quantitative high-performance liquid chromatography approach, where an additional strain showed some degradation in liquid culture. Several members of the prominent marineRoseobacteraceaefamily degraded pyrene and phenanthrene with varying efficiency (1.2%–29.6% and 5.2%–52.2%, respectively) over 26 days. Described PAH genetic biomarkers were absent in all PAH degrading strains for which genome sequences are available, suggesting that these strains harbor novel transformation pathways. These results demonstrate the utility of culture-based approaches in expanding the knowledge landscape concerning PAH degradation in marine systems. IMPORTANCEPolycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.