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1. Benthic oxygen fluxes in a coastal upwelling system (Ria de Vigo, NW Iberia) measured by aquatic eddy covariance

   https://doi.org/10.3354/meps13770  

   Amo-Seco, M; Castro, CG; Villacieros-Robineau, N; Alonso-Pérez, F; Graña, R; Rosón, G; Berg, P (July 2021, Marine Ecology Progress Series)

   Organic carbon mineralization and nutrient cycling in benthic environments are critically important for their biogeochemical functioning, but are poorly understood in coastal upwelling systems. The main objective of this study was to determine benthic oxygen fluxes in a muddy sediment in the Ria de Vigo (NW Iberian coastal upwelling), by applying the aquatic eddy covariance (AEC) technique during 2 campaigns in different seasons (June and October 2017). The main drivers of benthic fluxes were studied and compared among days in each season and between seasons. The 2 campaigns were characterized by an upwelling-relaxation period followed by a downwelling event, the last of which was due to the extratropical cyclone Ophelia in October. The mean (±SD) seasonal benthic oxygen fluxes were not significantly different for the 2 campaigns despite differences in hydrodynamic and biogeochemical conditions (June: -20.9 ± 7.1 mmol m -2 d -1 vs. October: -26.5 ± 3.1 mmol m -2 d -1 ). Benthic fluxes were controlled by different drivers depending on the season. June was characterized by sinking labile organic material, which enhanced benthic fluxes in the downwelling event, whereas October had a significantly higher bottom velocity that stimulated the benthic fluxes. Finally, a comparison with a large benthic chamber (0.50 m 2 ) was made during October. Despite methodological differences between AEC and chamber measurements, concurrent fluxes agreed within an acceptable margin (AEC:benthic chamber ratio = 0.78 ± 0.13; mean ± SD). Bottle incubations of water sampled from the chamber interior indicated that mineralization could explain this difference. These results show the importance of using non-invasive techniques such as AEC to resolve benthic flux dynamics. 

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2. Biological modification of coastal pH depends on community composition and time

   https://doi.org/10.1002/ecy.4113  

   Sorte, Cascade_J B; Kroeker, Kristy J; Miller, Luke P; Bracken, Matthew_E S (August 2023, Ecology)

   Abstract Biological processes play important roles in determining how global changes manifest at local scales. Primary producers can absorb increased CO₂via daytime photosynthesis, modifying pH in aquatic ecosystems. Yet producers and consumers also increase CO₂via respiration. It is unclear whether biological modification of pH differs across the year, and, if so, what biotic and abiotic drivers underlie temporal differences. We addressed these questions using the intensive study of tide pool ecosystems in Alaska, USA, including quarterly surveys of 34 pools over 1 year and monthly surveys of five pools from spring to fall in a second year. We measured physical conditions, community composition, and changes in pH and dissolved oxygen during the day and night. We detected strong temporal patterns in pH dynamics. Our measurements indicate that pH modification varies spatially (between tide pools) and temporally (across months). This variation in pH dynamics mirrored changes in dissolved oxygen and was associated with community composition, including both relative abundance and diversity of benthic producers and consumers, whose role differed across the year, particularly at night. These results highlight the importance of the time of year when considering the ways that community composition influences pH conditions in aquatic ecosystems. 

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3. Declines in an abundant aquatic insect, the burrowing mayfly, across major North American waterways

   https://doi.org/10.1073/pnas.1913598117  

   Stepanian, Phillip M.; Entrekin, Sally A.; Wainwright, Charlotte E.; Mirkovic, Djordje; Tank, Jennifer L.; Kelly, Jeffrey F. (February 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Seasonal animal movement among disparate habitats is a fundamental mechanism by which energy, nutrients, and biomass are transported across ecotones. A dramatic example of such exchange is the annual emergence of mayfly swarms from freshwater benthic habitats, but their characterization at macroscales has remained impossible. We analyzed radar observations of mayfly emergence flights to quantify long-term changes in annual biomass transport along the Upper Mississippi River and Western Lake Erie Basin. A single emergence event can produce 87.9 billion mayflies, releasing 3,078.6 tons of biomass into the airspace over several hours, but in recent years, production across both waterways has declined by over 50%. As a primary prey source in aquatic and terrestrial ecosystems, these declines will impact higher trophic levels and environmental nutrient cycling. 

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4. Technical note: Novel triple O₂ sensor aquatic eddy covariance instrument with improved time shift correction reveals central role of microphytobenthos for carbon cycling in coral reef sands

   https://doi.org/10.5194/bg-18-5381-2021  

   Merikhi, Alireza; Berg, Peter; Huettel, Markus (January 2021, Biogeosciences)

   Abstract. The aquatic eddy covariance technique stands out as a powerful method for benthic O2 flux measurements in shelf environments because itintegrates effects of naturally varying drivers of the flux such as current flow and light. In conventional eddy covariance instruments, the timeshift caused by spatial separation of the measuring locations of flow and O2 concentration can produce substantial flux errors that aredifficult to correct. We here introduce a triple O2 sensor eddy covariance instrument (3OEC) that by instrument design eliminates theseerrors. This is achieved by positioning three O2 sensors around the flow measuring volume, which allows the O2concentration to be calculated at the point of the current flow measurements. The new instrument was tested in an energetic coastal environment with highly permeablecoral reef sands colonised by microphytobenthos. Parallel deployments of the 3OEC and a conventional eddy covariance system (2OEC) demonstrate thatthe new instrument produces more consistent fluxes with lower error margin. 3OEC fluxes in general were lower than 2OEC fluxes, and the nighttimefluxes recorded by the two instruments were statistically different. We attribute this to the elimination of uncertainties associated with the timeshift correction. The deployments at ∼ 10 m water depth revealed high day- and nighttime O2 fluxes despite the relatively loworganic content of the coarse sediment and overlying water. High light utilisation efficiency of the microphytobenthos and bottom currents increasingpore water exchange facilitated the high benthic production and coupled respiration. 3OEC measurements after sunset documented a gradual transfer ofnegative flux signals from the small turbulence generated at the sediment–water interface to the larger wave-dominated eddies of the overlying watercolumn that still carried a positive flux signal, suggesting concurrent fluxes in opposite directions depending on eddy size and a memory effect oflarge eddies. The results demonstrate that the 3OEC can improve the precision of benthic flux measurements, including measurements in environmentsconsidered challenging for the eddy covariance technique, and thereby produce novel insights into the mechanisms that control flux. We consider thefluxes produced by this instrument for the permeable reef sands the most realistic achievable with present-day technology. 

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5. Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

   https://doi.org/10.1128/mSystems.00565-21  

   McNichol, Jesse; Berube, Paul M.; Biller, Steven J.; Fuhrman, Jed A. (June 2021, mSystems)

   Gilbert, Jack A. (Ed.)

   ABSTRACT Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly used primers with >300 million rRNA gene sequences retrieved from globally distributed marine metagenomes. The best-performing primers compared to 16S rRNA of bacteria and archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering cyanobacterial and chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA specific; 82%)—demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R 2 = 0.98, n  = 272), indicating amplicons can produce equally accurate community composition data compared with shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly completely universal primer set that could accurately quantify biogeochemically important taxa in ecosystems ranging from the deep sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data. IMPORTANCE PCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes. Our results demonstrate that primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is theoretically possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides, and present a software pipeline that can guide rational design of primers for any environment with available meta’omic data. 

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