We assessed nutrient limitation in the Mississippi River plume and Louisiana continental shelf during the summer of 2002 (04-08 July). We measured nutrient concentrations, alkaline phosphatase (AP) activities, chlorophyll a (Chl a) concentrations, and four fast repetition rate fluorescence (FRRF) parameters: the maximum quantum yield of photochemistry in photosystem II (PSII), F v : F m ; the functional absorption cross section for PSII, s PSII ; the time for photosynthetic electron transport on the acceptor side of PSII, t Qa ; and the connectivity factor, p, in 24-h-long nutrient addition bioassays near the Mississippi River delta. Low phosphorus (P) concentrations, elevated inorganic nitrogen-to-phosphorus ratios, high AP activities, and Chl a increases in response to P additions in the bioassays all indicated phosphorus limitation that was confirmed by the response of FRRF parameters. This is the first study to use FRRF to confirm results from basic oceanographic methods to demonstrate phosphorus limitation in a marine setting. F v : F m and p responded positively to phosphorus addition, while s PSII and t Qa decreased in the same treatments. When nitrate alone was added, none of the measured parameters differed significantly from the control. We therefore suggest that FRRF can be used to rapidly detect phosphorus limitation in marine ecosystems.Nutrient limitation of net primary production can be an important control on phytoplankton growth in aquatic environments, and understanding it can help to limit eutrophication (Howarth and Marino 2006). Determining the extent of nutrient limitation has been a fundamentally important question of aquatic scientists for decades. Many methods, both direct and indirect, are available for addressing this problem, including nutrient concentrations and ratios, enzyme assays, fluorescence parameters, and nutrient addition bioassays (Beardall et al. 2001b). Fast repetition rate fluorescence (FRRF) allows quick, noninvasive assessment of phytoplankton in vivo fluorescence signatures that provides the user with photosynthetic parameters including F v : F m , s PSII , t Qa , and p (Kolber et al. 1998). F v : F m is an indicator of the photosynthetic efficiency of a cell or community when measured in a darkacclimated state. Healthy algae can have an F v : F m as high as 0.65 (Kolber et al. 1998). The absorption cross section of PSII (s PSII ) changes in response to cellular pigment concentrations and the efficiency of energy transfer from pigments to PSII reaction centers, thus making it subject to both nutrient and light availability (Kolber et al. 1988;Moore et al. 2006). s PSII is typically lower in nutrientreplete cells relative to unhealthy cells (Kolber et al. 1988). The time constant for photosynthetic electron transfer on the acceptor side of PSII (t Qa ) reflects the minimum turnover time for electron transport (Kolber et al. 1988). p is the probability of energy transfer between PSII reaction centers (Kolber et al. 1998). Higher p values indicate higher probabil...

The production of extracellular polymeric substances (EPS) by planktonic microbes can influence the fate of oil and chemical dispersants in the ocean through emulsification, degradation, dispersion, aggregation, and/or sedimentation. In turn, microbial community structure and function, including the production and character of EPS, is influenced by the concentration and chemical composition of oil and chemical dispersants. For example, the production of marine oil snow and its sedimentation and flocculent accumulation to the seafloor were observed on an expansive scale after the Deepwater Horizon oil spill in the Northern Gulf of Mexico in 2010, but little is known about the underlying control of these processes. Here, we review what we do know about microbially produced EPS, how oil and chemical dispersant can influence the production rate and chemical and physical properties of EPS, and ultimately the fate of oil in the water column. To improve our response to future oil spills, we need a better understanding of the biological and physiochemical controls of EPS production by microbes under a range of environmental conditions, and in this paper, we provide the key knowledge gaps that need to be filled to do so. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Scientific Significance StatementExtracellular polymeric substances (EPS) are a group of chemically heterogeneous polymers released into the environment by microbes (bacteria, archaea, and phytoplankton), often in response to environmental stresses. EPS serve an important role in determining the fate and transport of oil after a spill, but relatively little is known about EPS production in relation to oil and dispersants, especially at molecular and chemical levels. Here, we summarize the scope of our current knowledge and identify major knowledge gaps. 3Limnology and Oceanography Letters 1, 2016, 3-26

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27 Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making 28 them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic 29 Fe-oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a 30 homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is 31 not well verified in neutrophilic Fe-oxidizers, particularly in Fe-oxidizing environments. Toward 32 this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-33 quality metagenome assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, 34 Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis 35 demonstrated conservation of Cyc2 sequences among most neutrophilic Fe-oxidizers, suggesting 36 a common function. We confirmed the widespread distribution of cyc2 and other model Fe 37 oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of 38

SummaryTerrestrial runoff can negatively impact marine ecosystems through stressors including excess nutrients, freshwater, and contaminants. Severe storms, which are increasing with global climate change, generate massive inputs of runoff over short timescales (hours to days); such runoff impacted offshore reefs in the northwest Gulf of Mexico (NW GoM) following severe storms in 2016 and 2017. Several weeks after coastal flooding from these events, NW GoM reefs experienced mortality (2016 only) and/or sub-lethal stress (both years). To assess the impact of storm-derived runoff on reef filter feeders, we characterized the microbiomes of two sponges, Agelas clathrodes and Xestospongia muta, during periods of lethal stress, sub-lethal stress, and no stress over a three-year period (2016-2018). Increased anaerobes during lethal stress indicate hypoxic conditions were associated with the 2016 mortality event. Additionally, we found evidence of wastewater contamination (based on 16S libraries and quantitative PCR) in sponges 185 km offshore following storms (2016 and 2017), but not during the non-flooding year (2018). We show that water quality changes following severe storms can impact offshore benthic organisms, highlighting the need for molecular and microbial time series from near- and offshore reef ecosystems, and for the continued mitigation of stormwater runoff and climate change impacts.Originality-Significance StatementStressors associated with terrestrial runoff have contributed to substantial population declines in nearshore marine ecosystems worldwide over the last three decades. It has been assumed that offshore marine ecosystems (>100 km from land) are largely unaffected by terrestrial runoff. Our findings, however, suggest that flooding events can significantly impact offshore marine organisms, based on the detection of shifted microbiomes and human pathogens in offshore sponges after extreme storm events across two separate years, and lack of detection in a non-flooding year.