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Arid subtropical climates often oscillate between drought and wet conditions, leading to a “flood or famine” paradigm for estuarine freshwater inflow, in which sporadic storm events drive dynamic changes in salinity and nutrient availability. Transitioning from prolonged drought to wet conditions can impact phytoplankton communities. The Mission‐Aransas Estuary, located on the south Texas coast, transitioned from a 5‐yr drought (2010–2015) to wet conditions (2015–2020), punctuated by several large flood events and the direct impact of category 4 Hurricane Harvey. Using an 8‐yr bimonthly sample set (2012–2019), we evaluated particulate organic carbon, chlorophylla, nutrient concentrations, and accessory pigments to characterize the response of the phytoplankton community to these climate events. We found that phytoplankton biomass was diminished during severe drought and increased during prolonged wet conditions. The phytoplankton community switched from being diatom‐dominated during drought to cyanobacteria‐dominated following estuarine freshening, driven by lower salinity and increased nutrient availability. Seasonal fluctuations between taxa persisted regardless of climate condition. The drought‐to‐wet transition prompted a regime shift of the estuarine phytoplankton community to a new quasi‐steady state in the studied estuary. Globally, changing climate regimes may cause longer periods of extreme drought or wet conditions for estuarine systems. Detailed, long‐term ecosystem monitoring is necessary to fully evaluate ecological responses to extreme weather events, especially links between biogeochemical cycling and ecosystem function. These results suggest that oscillations between distinct wet and dry periods have lasting effects on primary productivity, phytoplankton community composition, and organic matter cycling in subtropical estuaries with long residence times.

Dissolved organic nitrogen (DON) is actively involved in N cycling and transformation processes in the ocean, yet how this large N pool is formed remains elusive. Here we incubated¹⁵N‐labeled individual amino acids (Ala, Val, and Phe) in seawater and monitored their fates over 21 days. About 25%–45% of Phe‐N and Val‐N were transformed to “uncharacterizable DON,” as compared to only about 6% for Ala‐N, indicating the formation of refractory DON is related to specific amino acids. Through a stable isotope probing approach, 5 Phe‐derived DON molecules from the incubations were found to be present in natural waters, and their possible structures were proposed. These results shed new lights on the formation mechanisms of refractory DON, including the roles of specific amino acids and particular chemical structures that may resist decomposition in millennial time scales.

Proteins and peptides account for 20–75% of marine biota biomass, of which a major fraction is metabolized by bacteria, thus deciphering interactions between bacteria and peptides is important in understanding marine carbon and nitrogen cycling. To better understand capabilities of different bacterial strains on peptide decomposition, four Gammaproteobacteria (Pseudoalteromonas atlantica,Alteromonas sp.,Marinobacterium jannaschii,Amphritea japonica) were incubated in autoclaved seawater amended with tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO. While AVFA was decomposed greatly byPseudoalteromonas atlantica andAlteromonas sp, it remained nearly intact in theMarinobacterium jannaschiiandAmphritea japonicaincubations.PseudoalteromonasandAlteromonasdecomposed AVFA mainly through extracellular hydrolysis pathway, releasing 71–85% of the AVFA as hydrolysis products to the surrounding seawater. Overall, this study showed that Gammaproteobacterial strains differ greatly in their capabilities of metabolizing peptides physiologically, providing insights into interactions of bacteria and labile organic matter in marine environments.

Decomposition of particulate organic matter (POM) plays a key role in the formation of hypoxia in subsurface waters of coastal ocean, yet little is known about the lability and transformation of POM in the hypoxic zone. Suspended particles were collected from surface waters to overlying waters (~30 cm above the sediment‐water interface) along the shelf of northern Gulf of Mexico (nGOM) in late spring/early summer of 2010–2013. Total hydrolyzable amino acids (THAA) and pigments were measured in these particulate samples to trace organic matter lability. The degradation indices, derived from the THAA and chloropigments, were positively correlated with dissolved oxygen (DO) concentrations in the shelf region, suggesting that decomposition of POM contributed greatly to DO utilization. Bacterial degradation appears to be the major pathway for POM decomposition on both inner and mid shelves, while zooplankton grazing played a minor role. POM samples in the overlying water on the inner shelf were the most degraded from the THAA and pigment results, and they also had high C/N ratios (9–14) and depleted δ¹³C values (−29‰ to −24‰), pointing to a source of terrestrial C3 plant material. This distinct terrestrial signal of POM in the overlying water suggests strong selective degradation of marine‐sourced organic matter, but how the terrestrial organic matter is settled to this layer and its ultimate fate remain unclear. Taken together, these data offer new angles looking into the lability and degradation pathways of POM, and mechanisms of hypoxia formation in coastal waters.

Quantifying the fate of organic nitrogen in aquatic systems is important to improve understanding of its recycling efficiency and long‐term preservation. The fate of organic nitrogen can be investigated with¹⁵N labeling techniques, but relative amounts of¹⁵N in different chemical forms are difficult to quantify. We present a “streamlined” method by combining Ammonium Retention Time Shift‐High Performance Liquid Chromatography with zinc reduction, and UV oxidation. This method does not require a pre‐isolation step of different forms of nitrogen from the sample. At a sample volume of 50 mL, and a total N concentration in the range of 0.5–40 μmol N L⁻¹, and an¹⁵N atom% of 20–80%,¹⁵N concentrations for all N forms can be measured with this streamlined method, with a precision of within ±7%, and an accuracy of over 97%. We applied the method to investigating the short‐term fates of¹⁵N during the degradation of¹⁵N‐labeled amino acid and peptide. Recovery rates ranged from 93% to 110%, with an average of 102 ± 1.94%. As spiked¹⁵N labeled alanine and/or peptide (Ala‐Val‐Phe‐Val) disappeared during sample incubations, a large fraction (ca. 13–66%) of the¹⁵N was progressively transformed to non‐amino acid or non‐peptide dissolved organic nitrogen. This streamlined method offers quantitative estimates of potential fates of labile organic N compounds added to water samples containing in situ microbial consortia, and helps fulfill knowledge gaps in building the budget of N transformations of labile amino acids and peptides in aquatic systems.