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To confirm the Habitat Compression Hypothesis, a cruise to the Eastern Tropical North Pacific (ETNP) took place at the entrance of the Gulf of California, in an area rarely studied at the southern limit of the California Current, where it mixes with waters of the West Mexican Current and the Gulf of California. No significant day-night differences in the vertical distribution (0-500 m depth) of zooplankton were found based on 22 MOCNESS tows and, for the first time, a 48-h cycle of stratified zooplankton sampling. Most zooplankton groups were observed within the upper 100 m, above the oxycline, with oxygen concentrations as low as 45 µmol kg-1. Some California Current-influenced samples showed a slightly different vertical distribution. A ∼50% reduction in the number and abundance of 24 zooplankton groups was recorded within the Oxygen Minimum Zone, from 100 to 500 m depth. Vertical migrator's exceptions include some euphausiid species that migrate into the OMZ during the day. Principal Component Analyses showed that the vertical distribution of zooplankton is limited by oxygen, with a low zooplankton carbon density below ∼100 m depth within the OMZ. The difference between day and night for the upper 0-100 m layer was non-significant (U221 = 57; p = 0.947); however, the data showed great variability. Thus, zooplankton Carbon remains relatively constant, in the upper 100 m, and is available during day and night, in the studied area.

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Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.

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Four specimens of the sea cucumber Ypsilocucumis californiae Massin Hendrickx, 2011 were obtained during sampling operations off western Mexico. These specimens permit identification of this species as a member of the deep-water holothuroid community off the west coast of the Baja California Peninsula. Previous records correspond to four locations (including the type locality) in the Gulf of California, where eight specimens were collected. SEM ossicles images are provided for the first time and new ecological data associated with the presence of this species are available: temperature, 5.34‒8.38 °C; dissolved oxygen, 0.15‒0.28 ml O2/l and salinity, 34.42‒34.51 ups. The specimens were present in a wide variety of sediments with an organic carbon content of 3.18‒5.20 mg C/g (5.47‒8.95 % organic matter). Density values indicated low abundance of this species in the area (2.63‒3.94 orgs/ha). Records presented here were in a depth range from 540 to 776 m, which corresponds to the lower limit of the Oxygen Minimum Zone of the eastern Pacific. Additional records are provided for the West Atlantic Ypsilocucumis asperrima (Théel, 1886) and a key to the species of Ypsilocucumis is provided.

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Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2µM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.

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Microbial communities play a central role in the N cycle of oceanic oxygen minimum zones (OMZs), such as in the Eastern Tropical North Pacific (ETNP). We explored the spatial distribution of the genetic potential for ammonia oxidation (amoA gene for bacteria and archaea), denitrification (nirS and nirK), anaerobic ammonium oxidation (anammox) (hzo) and dissimilarity nitrate reduction to ammonia (DNRA) (nrfA) and their relationships with the hydrological variables and isotopic composition of nitrate in the ETNP off Mexico. Oxygen concentration, the availability of N chemical forms and the upwelling shaped the distribution of N cycling genes along the water column. The high abundance of N genes and the isotopic composition of nitrate suggest the N cycling is very dynamic in the OMZ core. The accumulation of nitrite, the high abundance of archaeal amoA genes, and the deviation of the N and O isotopes of nitrate from the expected 1:1 ratio for nitrate reduction in the upper portion of this OMZ indicate that nitrification is a relevant process that fuels the denitrifier community. Conversely, the high abundances of nitrate, ammonium and nrfA genes in the deeper layer indicate that DNRA is a crucial process enhancing anammox there. These results show the need for more detailed studies of the N processes in OMZs.

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There is a big imbalance between the input and output of oceanic nitrogen in global ocean nitrogen cycles, because a part of the fixed nitrogen is reduced to N2 or N2O and then lost from the ocean. Oxygen minimum zone (OMZ) is the most important area for nitrogen loss, which could lose fixed nitrogen up to 40 to 450 Tg·a-1 through the denitrification and anammox. A summary of the two main roles of nitrogen loss in the different OMZ sea areas reveals that heterotrophic denitrification dominates in eastern tropical Pacific, Arabian Sea, and marine sediments. The autotrophic denitrification has been found in Chile, Peru's coastal waters, and Arabian waters. In the Black Sea, the Benguela upwelling in southwestern Africa, and the northern coast of Chile, anaerobic ammonia oxidation is strong, with greater effects on the continental shelf than that in the ocean. In addition to the loss of nitrogen, nitrogen fixation, nitrification, and dissimilatory nitrate reduction to ammonium may affect the imbalance of nitrogen budget in the OMZ. The effects of nitrogen fixation can't be ignored. The total amount of nitrogen fixed in the global OMZ can reach 15-40 Tg·a-1, which is an important supplement to the loss of nitrogen in OMZ. Disentangling the relative contribution of denitrification and anammox to the loss of nitrogen, ascertaining the formation mechanism and quantitative evaluation method of N2O (another product of nitrogen loss) are the most important challenges in the current study of OMZ. Focusing on the existing problems, we put forward corresponding research ideas with references for related studies of the OMZs in the ocean.

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Specimens of the sea cucumber Synallactes virgulasolida were obtained during sampling operations off western Mexico. Based on a total of 190 specimens and on additional records available in the Scripps Institution of Oceanography collections, new geographical (southern California to Chile) and bathymetric (712‒1300 m) distributions are provided. SEM photographs of ossicles are provided for the first time for this species. New ecological data associated with the presence of this species are also provided: 4.17‒5.81 °C, 0.15‒0.48 ml O2/l, and in 34.40‒34.48 ups. The species occurs in a wide variety of sediments with an organic carbon content of 17.93‒52.02 mg/g (1.79-5.20 % of organic matter) and is occasionally very dense (up to 170.32 orgs/ha). All Mexican records correspond to a bathymetric fringe located below the Oxygen Minimum Zone, thus indicating that S. virgulasolida is able to tolerate hypoxic conditions.

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Marine oxygen minimum zones (OMZs) are characterized by the presence of subsurface suboxic or anoxic waters where diverse microbial processes are responsible for the removal of fixed nitrogen. OMZs have expanded over past decades and are expected to continue expanding in response to the changing climate. The implications for marine biogeochemistry, particularly nitrogen cycling, are uncertain. Cell membrane lipids (biomarkers), such as bacterial bacteriohopanepolyols (BHPs) and their degradation products (hopanoids), have distinctive structural attributes that convey information about their biological sources. Since the discovery of fossil hopanoids in ancient sediments, the study of BHPs has been of great biogeochemical interest due to their potential to serve as proxies for bacteria in the geological record. A stereoisomer of bacteriohopanetetrol (BHT), BHT II, has been previously identified in OMZ waters and has as been unequivocally identified in culture enrichments of anammox bacteria, a key group contributing to nitrogen loss in marine OMZs. We tested BHT II as a proxy for suboxia/anoxia and anammox bacteria in suspended organic matter across OMZ waters of the Humboldt Current System off northern Chile, as well as in surface and deeply buried sediments (125-150 ky). The BHT II ratio (BHT II/total BHT) increases as oxygen content decreases through the water column, consistent with previous results from Perú, the Cariaco Basin and the Arabian Sea, and in line with microbiological evidence indicating intense anammox activity in the Chilean OMZ. Notably, BHT II is transported from the water column to surface sediments, and preserved in deeply buried sediments, where the BHT II ratio correlates with changes in δ15 N sediment values during glacial-interglacial transitions. This study suggests that BHT II offers a proxy for past changes in the relative importance of anammox, and fluctuations in nitrogen cycling in response to ocean redox changes through the geological record.

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Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

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A variety of ecological strategies for tolerance of low-oxygen conditions within the Costa Rica Dome (CRD) area of the Eastern Tropical Pacific are documented for the copepod family Eucalanidae. During the summer of 2010, we compared the ecological strategies used by the Eucalanidae inside and outside the central CRD region. We compared the vertical and horizontal distributions of five species, Eucalanus inermis, Subeucalanus subtenuis, Subeucalanus subcrassus, Subeucalanus pileatus and Pareucalanus attenuatus together with Rhincalanus species, in the epipelagic (upper 200 m) among four locations, which we grouped into a section roughly crossing the core CRD area (inside-outside core CRD). The coastal area outside the CRD supported the most diverse assemblage, whereas overall abundance of Eucalanidae in the central CRD was 2-fold greater than outside and dominated by E. inermis (>60%). Eucalanidae in the central CRD had a shallow depth distribution, closely associated with the shallow thermocline (10-20 m). There was no evidence of daily vertical migration in the central CRD, but E. inermis demonstrated vertical migration outside the CRD. The vertical abundance patterns of Eucalanidae in the CRD region reflect complex interactions between subtle physical-chemical differences and food resources.

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Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.

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The aerobic and anaerobic enzymatic activity of two important commercial bathypelagic species living in the Juan Fernández seamounts was analyzed: alfonsino (Beryx splendens) and orange roughy (Hoplostethus atlanticus). These seamounts are influenced by the presence of an oxygen minimum zone (OMZ) located between 160 and 250 m depth. Both species have vertical segregation; alfonsino is able to stay in the OMZ, while orange roughy remains at greater depths. In this study, we compare the aerobic and anaerobic capacity of these species, measuring the activity of key metabolic enzymes in different body tissues (muscle, heart, brain and liver). Alfonsino has higher anaerobic potential in its white muscle due to greater lactate dehydrogenase (LDH) activity (190.2 µmol NADH min(-1) g ww(-1)), which is related to its smaller body size, but it is also a feature shared with species that migrate through OMZs. This potential and the higher muscle citrate synthase and electron transport system activities indicate that alfonsino has greater swimming activity level than orange roughy. This species has also a high MDH/LDH ratio in its heart, brain and liver, revealing a potential capacity to conduct aerobic metabolism in these organs under prolonged periods of environmental low oxygen conditions, preventing lactic acid accumulation. With these metabolic characteristics, alfonsino may have increased swimming activity to migrate and also could stay for a period of time in the OMZ. The observed differences between alfonsino and orange roughy with respect to their aerobic and anaerobic enzymatic activity are consistent with their characteristic vertical distributions and feeding behaviors.

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