Marine environments are highly heterogeneous, varying across scales of a few meters to entire ocean basins. Understanding the relationship between environmental variability and species distribution is essential for area-based management and conservation. However, this requires a precise alignment of seabed mapping with environmental and biological sampling, which is often difficult to achieve in the deep sea. There is thus an urgent need to tackle this challenge to effectively manage high-diversity habitats such as deep-sea coral and sponge aggregations. Relying on multiple subsea platforms, seafloor mapping, and imaging techniques, we mapped the distribution of megafaunal communities at Sur Ridge (780-1525-m depth; off central California) across multiple spatial scales. First, remotely operated vehicle video transects were conducted to characterize community distribution along the ridge in relation to substratum type, environmental conditions, and 1-m resolution bathymetry. Five distinct communities, located in specific areas of the ridge, were identified. These communities were primarily structured by depth, availability of hard substrata, and terrain complexity (slope and rugosity). Indicator taxa were identified for each community and their distributions were characterized at the centimeter scale from coregistered 5-mm resolution photomosaic and 5-cm lateral resolution bathymetry produced during low altitude remotely operated vehicle surveys. High-resolution mapping allowed the identification of associations between deep-sea coral and sponge and other benthic taxa and showed that, even at these small scales, different taxa associate with distinct microhabitats. These results highlight the importance of accounting for habitat heterogeneity, and its role in supporting biodiversity when designing management and conservation strategies.

Does warmth from hydrothermal springs play a vital role in the biology and ecology of abyssal animals? Deep off central California, thousands of octopus (Muusoctopus robustus) migrate through cold dark waters to hydrothermal springs near an extinct volcano to mate, nest, and die, forming the largest known aggregation of octopus on Earth. Warmth from the springs plays a key role by raising metabolic rates, speeding embryonic development, and presumably increasing reproductive success; we show that brood times for females are ~1.8 years, far faster than expected for abyssal octopods. Using a high-resolution subsea mapping system, we created landscape-scale maps and image mosaics that reveal 6000 octopus in a 2.5-ha area. Because octopuses die after reproducing, hydrothermal springs indirectly provide a food supplement to the local energy budget. Although localized deep-sea heat sources may be essential to octopuses and other warm-tolerant species, most of these unique and often cryptic habitats remain undiscovered and unexplored.

Deep-sea coral ecosystems represent oases of life in the deep ocean, often hosting abundant and diverse faunal communities. Although mounting evidence indicates that deep-sea benthic communities are highly dynamic and can change over scales of a few hours to seasons or years, such dynamics have never been characterized in deep-sea coral ecosystems. We used a time-lapse camera deployed for a year at a depth of 1230 m on Sur Ridge (Monterey Bay National Marine Sanctuary) to characterize hourly changes in megafaunal abundance and diversity in a deep-sea coral assemblage. The response of community dynamics to variation in environmental factors, including surface net primary production as well as current speed/direction, temperature and acoustic backscatter (a proxy for particle and zooplankton density) at depth, was also evaluated. Overall, 33 taxa from 6 phyla, including multiple commercially valuable species, were observed throughout the study period. The strong seasonal pattern and periodicities in the occurrence of the most abundant taxa likely drove the observed temporal trends in overall abundance and diversity. Fluctuations in food availability may have, at least partially, driven these trends, as indicated by the significant relationship between community dynamics, surface net primary production and acoustic backscatter at depth. However, the low explanatory power of environmental parameters tested here suggest that biotic factors such as individual behaviors and species interactions had a strong influence on community dynamics. This study emphasizes the role of deep-sea coral as habitat and the need for monitoring to better understand how environmental and biological processes interact to shape associated faunal communities.

Biological rhythms are widely known in terrestrial and marine systems, where the behaviour or function of organisms may be tuned to environmental variation over periods from minutes to seasons or longer. Although well characterized in coastal environments, phenology remains poorly understood in the deep sea. Here we characterized intra-annual dynamics of feeding activity for the deep-sea octocoral Paragorgia arborea. Hourly changes in polyp activity were quantified using a time-lapse camera deployed for a year on Sur Ridge (1230 m depth; Northeast Pacific). The relationship between feeding and environmental variables, including surface primary production, temperature, acoustic backscatter, current speed and direction, was evaluated. Feeding activity was highly seasonal, with a dormancy period identified between January and early April, reflecting seasonal changes in food availability as suggested by primary production and acoustic backscatter data. Moreover, feeding varied with tides, which likely affected food delivery through cyclic oscillation in current speed and direction. This study provides the first evidence of behavioural rhythms in a coral species at depth greater than 1 km. Information on the feeding biology of this cosmopolitan deep-sea octocoral will contribute to a better understanding of how future environmental change may affect deep-sea coral communities and the ecosystem services they provide.

Corals and sponges in rocky deep-sea environments are foundation species postulated to enhance local diversity by increasing biogenic habitat heterogeneity and enriching local carbon cycling. These key groups are highly vulnerable to disturbances (e.g., trawling, mining, and pollution) and are threatened by expansive changes in ocean conditions linked to climate change (acidification, warming, and deoxygenation). Once damaged by trawling or other disturbances, recolonization and regrowth may require centuries or longer, highlighting the need for stewardship of these deep-sea coral and sponge communities (DSCSCs). To this end, the sustainability of DSCSCs may be enhanced not only by protecting existing communities, but also repopulating disturbed areas using active restoration methods. Here, we report one of the first studies to explore methods to restore deep-sea coral populations by translocating coral fragments of multiple coral species. Branches of deep-sea corals were collected by ROV from 800 to 1300 m depth off central California and propagated into multiple fragments once at the surface. These fragments were then attached to "coral pots" using two different methods and placed in the same habitat to assess their survivorship (n = 113 total fragments, n = 7 taxa, n = 7 deployment groups). Mean survivorship for all translocated coral fragments observed within the first 365 days was similar to 52%, with the highest mortality occurring in the first 3 months. In addition to an initial temporal sensitivity, survival of coral fragments varied by attachment method and among species. All coral fragments attached to coral pots using zip ties died, while those attached by cement resulted in differential survivorship over time. The latter method resulted in 80-100% fragment survivorship after 1 year for Corallium sp., Lillipathes sp., and Swiftia kofoidi, 12-50% for the bamboo corals Keratoisis sp. and Isidella tentaculum, and 0-50% for the bubblegum corals Paragorgia arborea and Sibogagorgia cauliflora. These initial results indicate differences in sensitivities to transplanting methods among coral species, but also suggest that repopulation efforts may accelerate the recovery of disturbed DSCSCs.

In the California Current ecosystem, global climate change is predicted to trigger large-scale changes in ocean chemistry within this century. Ocean acidification—which occurs when increased levels of atmospheric CO2 dissolve into the ocean—is one of the biggest potential threats to marine life. In a coastal upwelling system, we compared the effects of chronic exposure to low pH (elevated pCO2) at four treatment levels (i.e., pCO2 = ambient [500], moderate [750], high [1900], and extreme [2800 μatm]) on behavior, physiology, and patterns of gene expression in white muscle tissue of juvenile rockfish (genus Sebastes), integrating responses from the transcriptome to the whole organism level. Experiments were conducted simultaneously on two closely related species that both inhabit kelp forests, yet differ in early life history traits, to compare high-CO2 tolerance among species. Our findings indicate that these congeners express different sensitivities to elevated CO2 levels. Copper rockfish (S. caurinus) exhibited changes in behavioral lateralization, reduced critical swimming speed, depressed aerobic scope, changes in metabolic enzyme activity, and increases in the expression of transcription factors and regulatory genes at high pCO2 exposure. Blue rockfish (S. mystinus), in contrast, showed no significant changes in behavior, swimming physiology, or aerobic capacity, but did exhibit significant changes in the expression of muscle structural genes as a function of pCO2, indicating acclimatization potential. The capacity of long-lived, late to mature, commercially important fish to acclimatize and adapt to changing ocean chemistry over the next 50–100 years is likely dependent on species-specific physiological tolerances.

Acidification, deoxygenation, and warming are escalating changes in coastal waters throughout the world ocean, with potentially severe consequences for marine life and ocean-based economies. To examine the influence of these oceanographic changes on a key biological process, we measured the effects of current and expected future conditions in the California Current Large Marine Ecosystem on the fertilization success of the red abalone (Haliotis rufescens). Laboratory experiments were used to assess abalone fertilization success during simultaneous exposure to various levels of seawater pH (gradient from 7.95 to 7.2), dissolved oxygen (DO) (∼60 and 180 µm.kg SW) and temperature (9, 13, and 18 °C). Fertilization success declined continuously with decreasing pH but dropped precipitously below a threshold near pH 7.55 in cool (9 °C—upwelling) to average (13 °C) seawater temperatures. Variation in DO had a negligible effect on fertilization. In contrast, warmer waters (18 °C) often associated with El Niño Southern Oscillation conditions in central California acted antagonistically with decreasing pH, largely reducing the strong negative influence below the pH threshold. Experimental approaches that examine the interactive effects of multiple environmental drivers and also strive to characterize the functional response of organisms along gradients in environmental change are becoming increasingly important in advancing our understanding of the real-world consequences of changing ocean conditions.

Understanding the potential consequences of rising ocean carbon levels and related ocean changes for marine life and ecosystems is a high priority for the ocean research community and marine resource management.In the mid-1990s, two geoengineering proposals to mitigate global warming by carbon sequestration in the deep sea led to research measuring the effects of increased deep ocean carbon dioxide levels on marine animals.A few years later, ocean acidification and its effects on marine life became an international research priority.Here we provide an overview of several technical developments by scientists and engineers at the Monterey Bay Aquarium Research Institute (MBARI) that have enabled and enhanced deep-sea exploration and experiments to assess the effects of changing ocean conditions on benthic marine animals.Improvements in remotely operated vehicles (ROVs) have increased the efficiency of dive operations and enabled more complex measurements and experiments at great ocean depths.In situ respirometers and Free Ocean CO 2 Enrichment (FOCE) mesocosms have allowed measurement of physiological and behavioral responses of deep-sea animals to environmental change.A laboratory-based, gas-controlled aquarium system that regulates oxygen and pH in chilled waters was engineered to measure the physiological responses of deep-sea animals and biological communities to expected future environmental conditions.Recently, MBARI engineers and scientists developed an Upwelling Simulator, a lab-based aquarium control system that mimics ocean conditions during coastal upwelling.This system is programmable, allowing independent control of pH, oxygen, and temperature to enable experiments that examine the effects of present-day upwelling conditions, expected future conditions, or other changes in these environmental conditions.In sum, collaboration between the marine operations group, engineers, and scientists at MBARI has advanced methods to explore the ocean and understand the consequences of ocean change for marine organisms and ecosystems.

Deep-sea species are generally thought to be less tolerant of environmental variation than shallow-living species due to the relatively stable conditions in deepwaters for most parameters (e.g. temperature, salinity, oxygen, and pH). To explore the potential for deep-sea hermit crabs (Pagurus tanneri) to acclimate to future ocean acidification, we compared their olfactory and metabolic performance under ambient (pH similar to 7.6) and expected future (pH similar to 7.1) conditions. After exposure to reduced pH waters, metabolic rates of hermit crabs increased transiently and olfactory behaviour was impaired, including antennular flicking and prey detection. Crabs exposed to low pH treatments exhibited higher individual variation for both the speed of antennular flicking and speed of prey detection, than observed in the control pH treatment, suggesting that phenotypic diversity could promote adaptation to future ocean acidification.

Anthropogenic CO2 is now reaching depths over 1000 m in the Eastern Pacific, overlapping the Oxygen Minimum Zone (OMZ). Deep-sea animals are suspected to be especially sensitive to environmental acidification associated with global climate change. We have investigated the effects of elevated pCO2 and variable O2 on the deep-sea urchin Strongylocentrotus fragilis, a species whose range of 200–1200 m depth includes the OMZ and spans a pCO2 range of approx. 600–1200 μatm (approx. pH 7.6 to 7.8). Individuals were evaluated during two exposure experiments (1-month and 4 month) at control and three levels of elevated pCO2 at in situ O2 levels of approx. 10% air saturation. A treatment of control pCO2 at 100% air saturation was also included in experiment two. During the first experiment, perivisceral coelomic fluid (PCF) acid-base balance was investigated during a one-month exposure; results show S. fragilis has limited ability to compensate for the respiratory acidosis brought on by elevated pCO2, due in part to low non-bicarbonate PCF buffering capacity. During the second experiment, individuals were separated into fed and fasted experimental groups, and longer-term effects of elevated pCO2 and variable O2 on righting time, feeding, growth, and gonadosomatic index (GSI) were investigated for both groups. Results suggest that the acidosis found during experiment one does not directly correlate with adverse effects during exposure to realistic future pCO2 levels.

Carrying assorted cargo and covered with paints of varying toxicity, lost intermodal containers may take centuries to degrade on the deep seafloor. In June 2004, scientists from Monterey Bay Aquarium Research Institute (MBARI) discovered a recently lost container during a Remotely Operated Vehicle (ROV) dive on a sediment-covered seabed at 1281 m depth in Monterey Bay National Marine Sanctuary (MBNMS). The site was revisited by ROV in March 2011. Analyses of sediment samples and high-definition video indicate that faunal assemblages on the container's exterior and the seabed within 10 m of the container differed significantly from those up to 500 m. The container surface provides hard substratum for colonization by taxa typically found in rocky habitats. However, some key taxa that dominate rocky areas were absent or rare on the container, perhaps related to its potential toxicity or limited time for colonization and growth. Ecological effects appear to be restricted to the container surface and the benthos within ∼10 m.

The influence of ocean acidification in deep-sea ecosystems is poorly understood but is expected to be large because of the presumed low tolerance of deep-sea taxa to environmental change. We used a newly developed deep-sea free ocean CO2 enrichment (dp-FOCE) system to evaluate the potential consequences of future ocean acidification on the feeding behavior of a deep-sea echinoid, the sea urchin, Strongylocentrotus fragilis. The dp-FOCE system simulated future ocean acidification inside an experimental enclosure where observations of feeding behavior were performed. We measured the average movement (speed) of urchins as well as the time required (foraging time) for S. fragilis to approach its preferred food (giant kelp) in the dp-FOCE chamber (-0.46 pH units) and a control chamber (ambient pH). Measurements were performed during each of 4 trials (days -2, 2, 24, 27 after CO2 injection) during the month-long period when groups of urchins were continuously exposed to low pH or control conditions. Although urchin speed did not vary significantly in relation to pH or time exposed, foraging time was significantly longer for urchins in the low-pH treatment. This first deep-sea FOCE experiment demonstrated the utility of the FOCE system approach and suggests that the chemosensory behavior of a deep-sea urchin may be impaired by ocean acidification.

The open source Free Ocean CO2 Enrichment (xFOCE) technology is a resource to enable the oceanographic community to study the long-term impacts of rising levels of CO2 in the world's ocean environment.The issue of worldwide ocean acidification (OA) is a well-established fact. The impact of this change on the organisms and ecosystem of the ocean is not well understood, and has become a focal point for scientific inquiry. Meanwhile OA research is transitioning from laboratory experiments to in situ experiments. The Monterey Bay Aquarium Research Institute (MBARI) has been at the forefront of in-situ OA research through the use of the Free Ocean CO2 Enrichment (FOCE) concept.FOCE uses fundamental concepts in OA research to conduct in-situ research in a stabilized, long term, user-defined pH environment. Stemming from its experience, MBARI has taken the initiative to develop xFOCE. The "x" in xFOCE denotes the multi-disciplinary nature of OA research, and refers to the many and varied environments for experimentation.xFOCE is intended to provide the OA community with resources to help address their specific needs. Economic realities have resulted in stiff competition for funding to conduct ocean acidification research and xFOCE helps by providing a free reference design, community advice and cost saving information. The expectation is that xFOCE will be a long-term repository of FOCE information for OA research.The xFOCE website is a community-driven repository for information such as suitable materials, experiment chamber fabrication techniques, chamber stabilization, sensor recommendations, software and applications, and numerous other tools to assist researchers with their OA work. Although MBARI is providing the initial framework for xFOCE, the intention is that the OA community will use the open source concept and contribute resources to enrich the OA community.

The Monterey Bay Aquarium Research Institute (MBARI) has a long history of developing state of the art underwater instruments to support its scientific research. Often these devices are one of a kind, highly engineered pieces of equipment. While MBARI has successfully transferred technology to outside organizations, this generally required extensive training and end users with a specialized skill set. Often times, these instruments require precise machining and come with a high financial price tag. This paper outlines an approach to developing lower cost, easy to use scientific modules that have wide applicability to the greater oceanographic community. With this approach, MBARI is seeking increase access to ocean technology for science. The devices covered in this paper grew out of the development of the exportable Free Ocean CO2 Enrichment (xFOCE) system. The core of this system is a series of modular building blocks which add design flexibility and ease of fabrication and maintenance. Two of the base building blocks are the Gateway Node and Sensor Node. The Gateway Node acts as a central computer which is able to control any underwater experiment. The Sensor Node acts as multi-port interface to a wide range of scientific instruments. Both nodes were designed to be open source, and thus modifiable by the end user.

The effects of low-pH, high-pCO2 conditions on deep-sea organisms were examined during four deep-sea CO2 release experiments simulating deep-ocean C sequestration by the direct injection of CO2 into the deep sea. We examined the survival of common deep-sea, benthic organisms (microbes; macrofauna, dominated by Polychaeta, Nematoda, Crustacea, Mollusca; megafauna, Echinodermata, Mollusca, Pisces) exposed to low-pH waters emanating as a dissolution plume from pools of liquid carbon dioxide released on the seabed during four abyssal CO2-release experiments. Microbial abundance in deep-sea sediments was unchanged in one experiment, but increased under environmental hypercapnia during another, where the microbial assemblage may have benefited indirectly from the negative impact of low-pH conditions on other taxa. Lower abyssal metazoans exhibited low survival rates near CO2 pools. No urchins or holothurians survived during 30–42 days of exposure to episodic, but severe environmental hypercapnia during one experiment (E1; pH reduced by as much as ca. 1.4 units). These large pH reductions also caused 75% mortality for the deep-sea amphipod, Haploops lodo, near CO2 pools. Survival under smaller pH reductions (ΔpH<0.4 units) in other experiments (E2, E3, E5) was higher for all taxa, including echinoderms. Gastropods, cephalopods, and fish were more tolerant than most other taxa. The gastropod Retimohnia sp. and octopus Benthoctopus sp. survived exposure to pH reductions that episodically reached −0.3 pH units. Ninety percent of abyssal zoarcids (Pachycara bulbiceps) survived exposure to pH changes reaching ca. −0.3 pH units during 30–42 day-long experiments.

Chemical fluxes into and out of permeable seafloor sediments, such as those found on much of the continental shelf, are difficult to measure using conventional techniques. To overcome this difficulty, the eddy correlation method was adapted by oceanographers to determine oxygen flux across the sediment‐water interface. In this article, we demonstrate that the eddy correlation method can also be used to measure nitrate flux across the sediment‐water interface. A modified ISUS (In Situ Ultraviolet Spectrophotometer) optical nitrate sensor was used to measure dissolved nitrate at a frequency of 1.8 Hz. These observations were combined with vertical velocity measurements to calculate nitrate fluxes. Oxygen fluxes were also determined using a fast oxygen electrode system. The results for nitrate and oxygen flux compare well with simultaneous benthic flux chamber measurements made at a muddy sediment site at 95 m depth in Monterey Bay on the central California coast. The nitrate fluxes determined by the eddy correlation technique were considerably higher than benthic flux chamber values at sandy sediment sites at similar depths to the north and south of Monterey Bay. This difference is expected in permeable sediments where lateral flow through sediments will ventilate chamber water.

Ocean carbon sequestration by direct carbon dioxide injection to the deep-sea or by the fertilization of the upper ocean with iron to accelerate the biological pump are methods under consideration to mitigate rapidly rising atmospheric carbon dioxide levels and avoid, in part, excessive greenhouse gas warming. Both sequestration efforts will elevate carbon dioxide levels in the deep ocean, which after reaction with the seawater carbonate system, will decrease the pH of the ocean. In addition, ocean acidification is occurring through the passive influx of carbon dioxide through the ocean surface. Efforts to understand the effects of accelerating ocean acidification from carbon sequestration efforts or passive CO2 absorbance will require study of marine ecosystems from the surface to the deep-sea. In many deep-sea environments, hypoxia can also be stressful for marine organisms. Therefore, studies to assess the impacts of ocean acidification in deep-sea habitats should also include examination of the effects of hypoxia, due to the potentially synergistic interaction between these stressors. In this report, we describe the development of a gas-controlled aquarium (GCA) system used for laboratory studies of the effects of hypoxia or ocean acidification or both on marine animals. The GCA system is capable of regulating the temperature, oxygen, and carbon dioxide content of waters in three aquarium tanks for use in assays of growth and metabolic rate studies or various marine animals. The GCA design uses a main reservoir and 3 aquarium tanks in which different set-points for oxygen and carbon dioxide levels are possible. Membrane contactors connected to recirculation pumps and gas sources are used to control gas concentrations in each tank. A LabVIEW software system integrated with mass flow controllers for oxygen, carbon dioxide, and nitrogen sources allows real-time, automated regulation of gas concentrations in each tank.