Metabarcoding supports regional ocean acidification monitoring and identifies novel bioindicators in the Southern California Bight

2026-05-16

The impacts of ocean acidification (OA) on marine communities are a growing concern for coastal upwelling ecosystems, such as the Southern California Bight (Bight). Successful management of coastal resources in the face of OA requires accurate assessment tools to understand the status and trends of OA impacts on biological communities. Current methods often rely on the condition of individual organisms (e.g., shell dissolution) and are resource- and labor-intensive. As a result, they are difficult to scale to population-level effects or to impacts on the community as a whole, which limits impact assessments and hinders implementation by coastal resource managers. DNA-based monitoring methods can address these gaps, and represent a scalable and cost-effective complement to traditional OA biomonitoring efforts. We applied a DNA metabarcoding approach to analyze mesozooplankton (>200 µm) samples in the Bight to investigate novel OA biomonitoring approaches and target organisms. We sequenced the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and analyzed mesozooplankton community composition across 20 locations and four seasons. We found communities largely structured by seasonal gradients and dominated by copepods and krill. A subset of taxa corresponded strongly to carbonate chemistry variability; taxa in the Order Cheilostomatida (encrusting bryozoans), along with the copepod species Clausocalanus furcatus and Oncaea scottodicarloi corresponded to high aragonite saturation state values. In contrast, other species like Calanus pacificus (calanoid copepod) and Euphausia pacifica (krill) corresponded with low aragonite saturation state. We also investigated the ubiquity and relative abundance of routine target organisms (pteropods and larval crabs) versus alternative targets. Pteropods were rare and only found in the wintertime, while other larval stages of benthic calcifiers were more relatively abundant and ubiquitous. Our findings highlight the utility of DNA-based methods to guide OA biomonitoring and lay the groundwork for future research on OA indicators in this region.

Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations

Microbiology Spectrum · 2025-03-14 · 8 citations

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 clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus . 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. IMPORTANCE Oil 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 the in situ bacterial response is quantified for the first time.

Effect of Rising Temperature and Carbon Dioxide on the Growth, Photophysiology, and Elemental Ratios of Marine Synechococcus: A Multistressor Approach

Sustainability · 2022 · 8 citations

• Environmental chemistry
• Chemistry
• Environmental science

Marine picocyanobacteria belonging to the genus Synechococcus are one of the most abundant photosynthetic organisms on Earth. They are often exposed to large fluctuations in temperature and CO2 concentrations in the ocean, which are expected to further change in the coming decades due to ocean acidification and warming resulting from rising atmospheric CO2 levels. To decipher the effect of changing temperature and CO2 levels on Synechococcus, six Synechococcus strains previously isolated from various coastal and open ocean sites were exposed to a matrix of three different temperatures (22 °C, 24 °C and 26 °C) and CO2 levels (400 ppm, 600 ppm and 800 ppm). Thereafter, the specific growth rates, photophysiological parameters (σPSII and Fv/Fm), C/N (mol/mol) ratios and the nitrogen stable isotopic composition (δ15N (‰)) of the strains were measured. Temperature was found to be a stronger driver of the changes in specific growth rates and photophysiology in the Synechococcus strains. Carbon-concentrating mechanisms (CCM) operational in these strains that shield the photosynthetic machinery from directly sensing ambient changes in CO2 possibly played a major role in causing minimal changes in the specific growth rates under the varying CO2 levels.

Costs and Limitations of Marine Synechococcus Blue-Green Chromatic Acclimation

Frontiers in Marine Science · 2021 · 9 citations

• Biology
• Botany
• Ecology

Benefits and trade-offs of blue/green chromatic acclimation (CA4) have received limited study. We investigated the energetic costs associated with executing chromatic acclimation using a fluorescence-based calculation of light use efficiency. Using laboratory cultures and artificial light environments, we show that the delayed response to acclimation known to occur in marine Synechococcus acclimating strains (generalists) in green light do not reduce light use efficiency in green light, but that only one generalist, RCC307, with a much smaller range of acclimation, had higher light use efficiency than blue and green light specialist strains. Generalists with a wider acclimation range either had the same or >30% lower light use efficiencies in blue and green light environments. From this work, we propose that advantages from CA4 may not be geared at direct competition with other Synechococcus specialists with fixed pigment types, but may serve to expand the ecological range of Synechococcus in spectral competition with other genera. As all eight Synechococcus strains tested had higher light use efficiency in green light, regardless of a fixed or flexible light harvesting strategy, we add evidence to the suitability of the Synechococcus genus to greener ocean niches, whether stable, or variable.

Seawater Trace Metal Concentrations from China incubation experiment conducted in April 2011

Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) · 2021-07-16

This dataset reports trace metal concentrations in seawater from an incubation experiment carried out in China in April 2011.

Major nutrient concentrations in seawater from an incubation experiment carried out in China in April 2011

Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) · 2021-07-16

This dataset reports major nutrient concentrations in seawater from an incubation experiment carried out in China in April 2011.

Upper Ocean Dynamics Select for Synechococcus Light Color Generalists

2021-04-14

The ocean has many underwater light niches, but the selection pressure for chromatic acclimaters (generalists) compared to blue or green-specialists is not well understood. Here, we tested the hypothesis that changes in ocean spectra brought about by mixing on the order of days preferentially selects for generalists within a Synechococcus population. We investigated ocean conditions that led to high proportions of Synechococcus generalists versus specialists in a model ocean column, and compared simulations with in situ metagenomic and physical oceanographic data from major Bio-GO-SHIP cruises, supplemented with GEOTRACES and TARA Oceans, as well as the GOOS Argo Program and sea surface height from AVISO. We found that greater mixed layer depths selected for generalists in simulated Synechococcus populations, but explained only 14% of the partitioning between strategies in situ. Rather, variability due to upwelling and ocean fronts had larger effects, explaining ~40% of the partitioning between Synechococcus generalists and specialists in the ocean. Physical oceanographic drivers therefore offer a significant selection pressure on marine Synechococcus light-harvesting strategies. Our results motivate further study of the in situ light environments of upwelling zones and ocean fronts, which are currently understudied as potential light-driven niche habitats.

Modeling Ocean Color Niche Selection by <i>Synechococcus</i> Blue‐Green Acclimaters

Journal of Geophysical Research Oceans · 2021-09-23 · 5 citations

Abstract Light penetration through the ocean creates underwater light color niches and photosynthetic organisms use specific strategies to capture light in these niches. The selection pressure for some cyanobacteria strains in the genus Synechococcus that change color to absorb either blue or green light (chromatic acclimaters, or generalists) is not well understood. Here, we tested the hypothesis that changes in ocean spectra brought about by mixing preferentially selects for generalists within a Synechococcus population. We investigated ocean conditions that led to high proportions of Synechococcus generalists versus specialists in a model ocean column, and compared simulations with in situ metagenomic and physical oceanographic data from major Bio‐GO‐SHIP cruises, supplemented with GEOTRACES and TARA Oceans, as well as the GOOS Argo Program and sea surface height from AVISO. We found that greater mixed layer depths selected for generalists in simulated Synechococcus populations, but did not account for much of the variance in the partitioning of light‐harvesting strategies in situ. Rather, oceanographic signatures for upwelling areas and ocean fronts explained more of the variation between Synechococcus generalists and specialists in the ocean. Our results motivate further study of the in situ light environments of upwelling zones and ocean fronts, which are currently understudied as potential light‐driven niche habitats.

Seasonal variation of aerosol composition in Orange County, Southern California

Atmospheric Environment · 2020 · 19 citations

• Environmental science
• Oceanography
• Atmospheric sciences

The impact of wildfire aerosols on near surface climate and gross primary production in the E3SM Earth System Model

AGU Fall Meeting Abstracts · 2019-12-01