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ABSTRACT Photoautotrophic diazotrophs, specifically the generaTrichodesmiumand UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution ofTrichodesmiumand UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera.Trichodesmiumexhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution.Trichodesmiumclades were primarily influenced by temperature and nutrient availability. They were particularly frequent in regions of phosphorus stress. In contrast, UCYN-A was most frequently observed in regions experiencing iron stress. UCYN-A clades demonstrated more homogeneous distributions, with a single sequence variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations ofTrichodesmiumand UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. These findings underscore the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing photoautotrophs.IMPORTANCEThis study provides insights into the global diversity and distribution of nitrogen-fixing photoautotrophs, specificallyTrichodesmiumand UCYN-A. We sequenced 954 oceanic samples of thenifHnitrogenase gene and uncovered significant differences in microdiversity and environmental associations between these genera.Trichodesmiumshowed high levels of sequence diversity and region-specific clades influenced by temperature and nutrient availability. In contrast, UCYN-A exhibited a more uniform distribution, thriving in iron-stressed regions. Quantifying these fine-scale genetic variations enhances our knowledge of their ecological roles and adaptations, emphasizing the need to characterize the genetic diversity of marine nitrogen-fixing prokaryotes. 

Climate warming is increasing ocean stratification, which in turn should decrease the nutrient flux to the upper ocean. This may slow marine primary productivity, causing cascading effects throughout food webs. However, observing changes in upper ocean nutrients is challenging because surface concentrations are often below detection limits. We show that the nutricline depth, where nutrient concentrations reach well-detected levels, is tied to productivity and upper ocean nutrient availability. Next, we quantify nutricline depths from a global database of observed vertical nitrate and phosphate profiles to assess contemporary trends in global nutrient availability (1972–2022). We find strong evidence that the P-nutricline (phosphacline) is mostly deepening, especially throughout the southern hemisphere, but the N-nutricline (nitracline) remains mostly stable. Earth System Model (ESM) simulations support the hypothesis that reduced iron stress and increased nitrogen fixation buffer the nitracline, but not phosphacline, against increasing stratification. These contemporary trends are expected to continue in the coming decades, leading to increasing phosphorus but not nitrogen stress for marine phytoplankton, with important ramifications for ocean biogeochemistry and food web dynamics. 

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. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are primarily Aurora Total Organic Carbon combustion analyses of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. A few samples from the final campaign in the dataset were analyzed with a Shimadzu instrument using a similar method. Data are from the 2022 water year (1 Oct 2021 to 30 Sep 2022) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA. 

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are total organic carbon combustion analyses (Shimadzu Scientific Instruments) of the concentration of organic carbon dissolved in filtered samples of well-mixed river thalweg water. Data are from the 2023 water year (1 Oct 2022 to 30 Sep 2023) from samples collected on the Upper Clark Fork River (USGS HUC 17010201) at project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA.