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Abstract Pseudomonas aeruginosa is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aerobic and anaerobic conditions provides adaptability to environmental changes and in confronting immune responses. We applied native 2-dimensional metalloproteomics to P. aeruginosa to examine how use of iron within the metallome responds to oxic and anoxic conditions. Analyses revealed four iron peaks comprised of metalloproteins with synergistic functions, including (1) respiratory and metabolic enzymes, (2) oxidative stress response enzymes, (3) DNA synthesis and nitrogen assimilation enzymes, and (4) denitrification enzymes and related copper enzymes. Fe Peaks were larger under anoxic conditions, consistent with increased iron demand due to anaerobic metabolism and with the denitrification peak absent under oxic conditions. Three ferritins co-eluted with the first and third iron peaks, localizing iron storage with these functions. Several enzymes were more abundant at low oxygen, including alkylhydroperoxide reductase C that deactivates organic radicals produced by denitrification, all three classes of ribonucleotide reductases (including monomer and oligomer forms), ferritin (increasing in ratio relative to bacterioferritin), and denitrification enzymes. Superoxide dismutase and homogentisate 1,2-dioxygenase were more abundant at high oxygen. Several Fe Peaks contained iron metalloproteins that co-eluted earlier than their predicted size, implying additional protein–protein interactions and suggestive of cellular organization that contributes to iron prioritization in Pseudomonas with its large genome and flexible metabolism. This study characterized the iron metalloproteome of one of the more complex prokaryotic microorganisms, attributing enhanced iron use under anaerobic denitrifying metabolism to its specific metalloprotein constituents. 

Abstract Scarce dissolved surface ocean concentrations of the essential algal micronutrient zinc suggest that Zn may influence the growth of phytoplankton such as diatoms, which are major contributors to marine primary productivity. However, the specific mechanisms by which diatoms acclimate to Zn deficiency are poorly understood. Using global proteomic analysis, we identified two proteins (ZCRP-A/B, Zn/Co Responsive Protein A/B) among four diatom species that became abundant under Zn/Co limitation. Characterization using reverse genetic techniques and homology data suggests putative Zn/Co chaperone and membrane-bound transport complex component roles for ZCRP-A (a COG0523 domain protein) and ZCRP-B, respectively. Metaproteomic detection of ZCRPs along a Pacific Ocean transect revealed increased abundances at the surface (<200 m) where dZn and dCo were scarcest, implying Zn nutritional stress in marine algae is more prevalent than previously recognized. These results demonstrate multiple adaptive responses to Zn scarcity in marine diatoms that are deployed in low Zn regions of the Pacific Ocean. 

Abstract. Zinc (Zn) is an essential micronutrient for most eukaryotic phytoplankton. Zn uptake by phytoplankton within the euphotic zone results in nutrient-like dissolved Zn (dZn) profiles with a large dynamic range. The combination of key biochemical uses for Zn and large vertical gradients in dZn implies the potential for rapid rates of Zn removal from the surface ocean. However, due to the ease of contamination at sea, direct measurements of dZn uptake within natural environments have not been previously made. To investigate the demand for dZn and for dissolved cadmium (dCd; a closely related nutrient-like element) within Southern Ocean phytoplankton communities, we conducted 67Zn and 110Cd tracer uptake experiments within the Amundsen Sea, Ross Sea, and Terra Nova Bay of the Southern Ocean. We observed a high magnitude of Zn uptake (ρZn > 100 pmol dZn L−1 d−1) into the particulate phase that was consistent with ambient depleted dZn surface concentrations. High biomass and low partial pressure of carbon dioxide in seawater (seawater pCO2) appeared to contribute to ρZn, which also led to increases in ρCd likely through the upregulation of shared transport systems. These high ρZn measurements further imply that only short timescales are needed to deplete the large winter dZn inventory down to the observed surface levels in this important carbon-capturing region. Overall, the high magnitude of Zn uptake into the particulate fraction suggests that even in the Zn-rich waters of the Southern Ocean, high Zn uptake rates can lead to Zn depletion and potential Zn scarcity. 

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change. 

Abstract. Over the past decade, the GEOTRACES and wider trace metalgeochemical community has made substantial contributions towardsconstraining the marine cobalt (Co) cycle and its major biogeochemicalprocesses. However, few Co speciation studies have been conducted in theNorth and equatorial Pacific Ocean, a vast portion of the world's oceans byvolume and an important end-member of deep thermohaline circulation.Dissolved Co (dCo) samples, including total dissolved and labile Co, weremeasured at-sea during the GEOTRACES Pacific Meridional Transect (GP15) expedition along the 152∘ W longitudinal from 56∘ N to20∘ S. Along this transect, upper-ocean dCo (σ0<26) was linearly correlated with dissolved phosphate (slope = 82±3, µmol : mol) due to phytoplankton uptake and remineralization.As depth increased, dCo concentrations became increasingly decoupled fromphosphate concentrations due to co-scavenging with manganese oxide particlesin the mesopelagic. The transect revealed an organically bound coastalsource of dCo to the Alaskan Stream associated with low-salinity waters. Anintermediate-depth hydrothermal flux of dCo was observed off the Hawaiiancoast at the Loihi Seamount, and the elevated dCo was correlated withpotential xs3He at and above the vent site; however, the Loihi Seamountlikely did not represent a major source of Co to the Pacific basin. Elevatedconcentrations of dCo within oxygen minimum zones (OMZs) in the equatorialNorth and South Pacific were consistent with the suppression of oxidativescavenging, and we estimate that future deoxygenation could increase the OMZdCo inventory by 18 % to 36 % over the next century. In Pacific Deep Water(PDW), a fraction of elevated ligand-bound dCo appeared protected fromscavenging by the high biogenic particle flux in the North Pacific basin.This finding is counter to previous expectations of low dCo concentrationsin the deep Pacific due to scavenging over thermohaline circulation.Compared to a Co global biogeochemical model, the observed transectdisplayed more extreme inventories and fluxes of dCo than predicted by themodel, suggesting a highly dynamic Pacific Co cycle. 

Abstract Pseudoalteromonas (BB2-AT2) is a ubiquitous marine heterotroph, often associated with labile organic carbon sources in the ocean (e.g. phytoplankton blooms and sinking particles). Heterotrophs hydrolyze exported photosynthetic materials, components of the biological carbon pump, with the use of diverse metalloenzymes containing zinc (Zn), manganese (Mn), cobalt (Co), and nickel (Ni). Studies on the metal requirements and cytosolic utilization of metals for marine heterotrophs are scarce, despite their relevance to global carbon cycling. Here, we characterized the Zn, Mn, Co, and Ni metallome of BB2-AT2. We found that the Zn metallome is complex and cytosolic Zn is associated with numerous proteins for transcription (47.2% of the metallome, obtained from singular value decomposition of the metalloproteomic data), translation (33.5%), proteolysis (12.8%), and alkaline phosphatase activity (6.4%). Numerous proteolytic enzymes also appear to be putatively associated with Mn, and to a lesser extent, Co. Putative identification of the Ni-associated proteins, phosphoglucomutase and a protein in the cupin superfamily, provides new insights for Ni utilization in marine heterotrophs. BB2-AT2 relies on numerous transition metals for proteolytic and phosphatase activities, inferring an adaptative potential to metal limitation. Our field observations of increased alkaline phosphatase activity upon addition of Zn in field incubations suggest that such metal limitation operates in sinking particulate material collected from sediment traps. Taken together, this study improves our understanding of the Zn, Mn, Co, and Ni metallome of marine heterotrophic bacteria and provides novel and mechanistic frameworks for understanding the influence of nutrient limitation on biogeochemical cycling. 

Abstract. Bioactive trace metals are critical micronutrients for marinemicroorganisms due to their role in mediating biological redox reactions,and complex biogeochemical processes control their distributions.Hydrothermal vents may represent an important source of metals tomicroorganisms, especially those inhabiting low-iron waters, such as in thesouthwest Pacific Ocean. Previous measurements of primordial 3Heindicate a significant hydrothermal source originating in the northeastern (NE)Lau Basin, with the plume advecting into the southwest Pacific Ocean at1500–2000 m depth (Lupton etal., 2004). Studies investigating the long-range transport of trace metalsassociated with such dispersing plumes are rare, and the biogeochemicalimpacts on local microbial physiology have not yet been described. Here wequantified dissolved metals and assessed microbial metaproteomes across atransect spanning the tropical and equatorial Pacific with a focus on thehydrothermally active NE Lau Basin and report elevated iron and manganeseconcentrations across 441 km of the southwest Pacific. The most intensesignal was detected near the Mangatolo Triple Junction (MTJ) and NortheastLau Spreading Center (NELSC), in close proximity to the previously reported3He signature. Protein content in distal-plume-influenced seawater,which was high in metals, was overall similar to background locations,though key prokaryotic proteins involved in metal and organic uptake,protein degradation, and chemoautotrophy were abundant compared to deepwaters outside of the distal plume. Our results demonstrate that tracemetals derived from the NE Lau Basin are transported over appreciabledistances into the southwest Pacific Ocean and that bioactive chemicalresources released from submarine vent systems are utilized by surroundingdeep-sea microbes, influencing both their physiology and their contributionsto ocean biogeochemical cycling.