Monterey Bay Aquarium Research Institute

Marine protected areas (MPAs) are widely implemented tools for long‐term ocean conservation and resource management. Assessments of MPA performance have largely focused on specific ecosystems individually and have rarely evaluated performance across multiple ecosystems either in an individual MPA or across an MPA network. We evaluated the conservation performance of 59 MPAs in California's large MPA network, which encompasses 4 primary ecosystems (surf zone, kelp forest, shallow reef, deep reef) and 4 bioregions, and identified MPA attributes that best explain performance. Using a meta‐analytic framework, we evaluated the ability of MPAs to conserve fish biomass, richness, and diversity. At the scale of the network and for 3 of 4 regions, the biomass of species targeted by fishing was positively associated with the level of regulatory protection and was greater inside no‐take MPAs, whereas species not targeted by fishing had similar biomass in MPAs and areas open to fishing. In contrast, species richness and diversity were not as strongly enhanced by MPA protection. The key features of conservation effectiveness included MPA age, preimplementation fisheries pressure, and habitat diversity. Important drivers of MPA effectiveness for single MPAs were consistent across MPAs in the network, spanning regions and ecosystems. With international targets aimed at protecting 30% of the world's oceans by 2030, MPA design and assessment frameworks should consider conservation performance at multiple ecologically relevant scales, from individual MPAs to MPA networks.

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible (FAIR) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

The gravitational settling of organic particles in the ocean drives long‐term sequestration of carbon from surface waters to the deep ocean. Quantifying the magnitude of carbon sequestration flux at high spatiotemporal resolution is critical for monitoring the ocean's ability to sequester carbon as ecological conditions change. Here, we propose a computer vision‐based method for classifying images of sinking marine particles and using allometric relationships to estimate the amount of carbon that the particles transport to the deep ocean. We show that our method reduces the amount of time required by a human image annotator by at least 90% while producing ecologically informed estimates of carbon flux that are comparable to estimates based on purely manual review and chemical bulk carbon measurements. This method utilizes a human‐in‐the‐loop domain adaptation approach to leverage images collected from previous sampling campaigns in classifying images from novel campaigns in the future. If used in conjunction with autonomous imaging platforms deployed throughout the world's oceans, this method has the potential to provide estimates of carbon sequestration fluxes at high spatiotemporal resolution while facilitating an understanding of the ecological pathways that are most important in driving these fluxes.

One debated scenario for the termination of the Messinian salinity crisis 5.33 million years ago is cataclysmic refilling of the Mediterranean Sea through the Zanclean megaflood. Here we present a clear line of onshore-to-offshore evidence for this megaflood spilling over a shallow-water marine corridor in south-east Sicily into the nearby subaqueous Noto Canyon: (i) >300 asymmetric and streamlined erosional ridges aligned with the megaflood direction, (ii) poorly-sorted breccia deposited between the Messinian and Lower Zanclean Trubi Formations, (iii) soft-sediment deformation structures and clastic injections in the breccia and underlying units, and (iv) a 20 kilometre wide erosional shelf channel connecting the ridges with Noto Canyon. Numerical modelling results support the modulation of flow velocity and direction by the excavation of the channel and Noto Canyon. Our findings demonstrate that the Messinian salinity crisis was terminated through a cataclysmic flood, which implies pronounced Mediterranean sea-level drawdown prior to the flooding.

Marine oxygen deficient zones (ODZs) play a major role in the Earth's biogeochemical cycles and are responsible for nitrogen and sulfur removal from the oceans. Microbial-reducing reaction processes generate nitrite (NO2-) and sulfur compounds as intermediaries that may accumulate in these zones. Current assessments on microbial transformations inside ODZs are based on shipboard measurements, and there are no well-resolved seasonal to annual observations or high-resolution vertical sampling that would characterize variability. Here, we propose an alternative statistical approach to analyze the raw output of the nitrate sensor from BGC-Argo floats, with the ability to detect NO2-and thiosulfate (S2O32-) concentrations in addition to nitrate. The new approach provides data with great vertical and spatiotemporal resolution. The method can be applied to UV-spectrometer output data from SUNAs and ISUS nitrate sensors, commonly deployed on various observing platforms. We validated the technique in the field by matching shipboard NO2-bottle data with float data from the eastern tropical North Pacific (ETNP) and eastern tropical South Pacific (ETSP) ODZs. We then show a complete time series of three floats as study cases. The ability to detect NO2-and S2O32-concomitantly with other key chemical variables (i.e., oxygen, pH, and bio-optics) at such fine scale allows for novel insights into the nitrogen and sulfur cycling of ODZs and processes driving these cycles. This new approach will enable fine-scale remote quantification of NO2-and S2O32-to support a better understanding of the biogeochemical transformations happening inside these already-expanding deoxygenated regions. Hosted file nit_method_paper_VF.docx available at https://authorea.com/users/873272/articles/1253636-bgc-argo-floats-reveal-nitrite-and-thiosulfate-dynamics-in-the-oceans-with-high-spatiotemporal-resolution Hosted file supporting information.docx available at https://authorea.com/users/873272/articles/1253636-bgc-argo-floats-reveal-nitrite-and-thiosulfate-dynamics-in-the-oceans-with-high-spatiotemporal-resolution 1

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.

Marine eastern boundary current ecosystems, such as the California Current System (CCS), involve productive, mesotrophic transition zones. The CCS exhibits highly variable primary production (PP), yet factors driving the variability and underlying phytoplankton communities remain poorly understood. We integrated physicochemical and biological data from surface waters sampled during 10 CCS expeditions, spanning 13 yr, and resolved regimes with distinct phytoplankton communities. Additional to an oligotrophic regime (OR), mesotrophic waters beyond the coastal area partitioned into Meso‐High and Meso‐Low regimes, differing in nitrate concentrations and PP. The OR was dominated by Prochlorococcus High‐Light I (HLI), and eukaryotic phytoplankton were largely predatory mixotrophs. Eukaryotes dominated Meso‐Low and Meso‐High phytoplankton biomass. Within the Meso‐Low, Pelagomonas calceolata was important, and Prochlorococcus Low‐Light I (LLI) rose in prominence. In the Meso‐High, the picoprasinophyte Ostreococcus lucimarinus was abundant, and Synechococcus Clade IV was notable. The Meso‐High exhibited the highest PP (38 ± 16 mg C m⁻³ d⁻¹; p < 0.01) and higher growth rates for photosynthetic eukaryotes (0.84 ± 0.02 d⁻¹) than for Prochlorococcus (0.61 ± 0.01 d⁻¹) and Synechococcus (0.31 ± 0.05 d⁻¹). An experiment simulating seasonal oligotrophic seawater intrusion into the Meso‐High resulted in growth rates reaching 1.18 ± 0.10 d⁻¹ (O. lucimarinus), 0.75 ± 0.21 d⁻¹ (Prochlorococcus LLI), and 0.50 ± 0.04 d⁻¹ (Synechococcus EPC2). Thus, variable PP is underpinned by distinct phytoplankton communities across CCS mesotrophic regimes, and their dynamic nature is influenced by the rapidity with which specific taxa respond to changing environmental conditions or possibly transient nutrient release from viral encounters. Future work should assess whether these dynamics are consistent across eastern boundary current ecosystems and over temporal variations.

The Southern Ocean is rich in highly dynamic mesoscale eddies and substantially modulates global biogeochemical cycles. However, the overall surface and subsurface effects of eddies on the Southern Ocean biogeochemistry have not been quantified observationally at a large scale. Here, we co‐locate eddies, identified in the Meta3.2DT satellite altimeter‐based product, with biogeochemical Argo floats to determine the effects of eddies on the dissolved inorganic carbon (DIC), nitrate, and dissolved oxygen concentrations in the upper 1,500 m of the ice‐free Southern Ocean, as well as the eddy effects on the carbon fluxes in this region. DIC and nitrate concentrations are lower in anticyclonic eddies (AEs) and increased in cyclonic eddies (CEs), while dissolved oxygen anomalies switch signs above (CEs: positive, AEs: negative) and below the mixed layer (CEs: negative, AEs: positive). We attribute these anomalies primarily to eddy pumping (isopycnal heave), as well as eddy trapping for oxygen. Maximum anomalies in all tracers occur at greater depths in the subduction zone north of the Antarctic Circumpolar Current (ACC) compared to the upwelling region in the ACC, reflecting differences in background vertical structures. Eddy effects on air–sea CO2 ${\text{CO}}_{2}$ exchange have significant seasonal variability, with additional outgassing in CEs in fall (physical process) and additional oceanic uptake in AEs and CEs in spring (biological and physical process). Integrated over the Southern Ocean, AEs contribute ∼0.03± ${\sim} 0.03\pm$ 0.01 Pg C yr−1 ${\text{yr}}^{-1}$ (7 ±2% $\pm 2\%$) to the Southern Ocean carbon uptake, and CEs offset this by ∼0.01± ${\sim} 0.01\pm$0.01 Pg C yr−1 ${\text{yr}}^{-1}$ (2 ±2% $\pm 2\%$). These findings underscore the importance of considering eddy impacts in observing networks and climate models.

To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified and proposed as Paraescarpia formosa sp. nov. through morphological and phylogenetic analyses. The endosymbionts in the trunk of P. formosa analyzed by a 16S rRNA gene clone library represented only one phylotype, which belonged to the family Sedimenticolaceae in Gammaproteobacteria. In addition, the archaeal and bacterial communities in the habitat of tubeworm P. formosa were investigated by using high-phylogenetic-resolution full-length 16S rRNA gene amplicon sequencing. The results showed that anerobic methane-oxidizing archaea (ANME)-1b was most abundant and ANME-2ab was minor in a consortia of the anerobic oxidation of methane (AOM). The known sulfate-reducing bacteria (SRB) partners in AOM consortia, such as SEEP-SRB1, -SRB2, and -SRB4, Desulfococcus and Desulfobulbus, occurred in a small population (0–5.7%) at the SYER cold seep, and it was suggested that ANME-1b and ANME-2ab might be coupled with multiple SRB in AOM consortia. Besides AOM consortia, various methanogenic archaea, including Bathyarchaeota (Subgroup-8), Methanocellales, Methanomicrobiales, Methanosarcinales, Methanofastidiosales and Methanomassiliicoccales, were identified, and sulfur-oxidizing bacteria Sulfurovum and Sulfurimonas in phylum Epsilonbacteraeota were dominant. This study revealed the first investigation of microbiota in and around tubeworm P. formosa discovered at the SYER cold seep offshore southwestern Taiwan. We could gain insights into the chemosynthetic communities in the deep sea, especially regarding the cold seep ecosystems at the SCS.

Ontogenetic changes in area use, habitat use, and trophic interactions play an important role in the ecology, demography, and ultimately population dynamics of many species. Assumed to be driven by shifting life‐history requirements, trophic niche shifts in white sharks (Carcharodon carcharias) are well documented, but the timing of the spatial niche shift that is hypothesized to occur with the trophic niche shift remains poorly understood. To document how fine‐scale area use varies as sharks age and the timing of the ontogenetic spatial shift of this top predator, we tracked individual white sharks tagged as young‐of‐the‐year or young juveniles over multiple years. Using data from juvenile white sharks detected over multiple years in a nursery habitat with a high‐density receiver array, we found no difference in area use with age. However, using a coast‐wide receiver array including nursery and adult habitat, we found the probability of detecting a juvenile white shark in nursery habitat decreased with age, with a concurrent increasing probability of detection in adult habitat. As the conservation and management of this species relies on understanding nursery habitat use and age‐related movements, data presented here address an important knowledge gap for the understudied juvenile to subadult life stages and the ontogenetic habitat shift of this species.

Marine phytoplankton biomass and chlorophyll-a concentration are often estimated from pigment fluorescence measurements, which have become routine despite known variability in the fluorescent response for a given amount of chlorophyll-a. Here, we present a near-global, monthly climatology of chlorophyll-a fluorescence measurements from profiling floats combined with ocean color satellite estimates of chlorophyll-a concentration to illuminate seasonal biases in the fluorescent response and expand upon previously observed regional patterns in this bias. Global biases span over an order of magnitude, and can vary seasonally by a factor of 10. An independent estimate of chlorophyll-a from light attenuation shows similar global patterns in the chlorophyll-fluorescence bias when compared to biases derived from satellite estimates. Without accounting for these biases, studies or models using fluorescence-estimated chlorophyll-a will inherit the seasonal and regional biases described here.

Integrated use of molecular and morphological methods reveals unexpected diversity in the cosmopolitan siphonophore genus Nanomia. Species delimitation analyses based on COI and 16S sequences suggest up to three distinct lineages in addition to the previously accepted Nanomia bijuga (Delle Chiaje, 1844) and N. cara A. Agassiz, 1865. Here, we describe the North Pacific Nanomia septata sp. n., previously confused with both N. cara and N. bijuga, and provide improved morphological characters for the identification of these three Nanomia species. Phylogenetic analyses suggest two additional, hitherto undescribed clades from Japanese and Chinese waters, respectively, but the lack of morphological material prevents describing these putative species. The geographic distribution of molecularly and/or morphologically verified observations confirm a warm circumglobal distribution for N. bijuga and a boreal North Atlantic distribution for N. cara. Interestingly, four distinct lineages occur in the North Pacific, sometimes in close proximity. These contrasting patterns of distribution raise questions about pelagic speciation processes. Nanomia septata sp. n.: urn:lsid:zoobank.org:act:DAF15EA3-AFEA-4AE8-984F-BDFBCFE7E514 urn:lsid:zoobank.org:pub:478049FC-F672-4D34-ABAE-CF4345EC64D7

Circulation and water masses in the greater Prydz Bay region were surveyed in the austral summer 2021 (January-March) during the ‘Trends in Euphausiids off Mawson, Predators and Oceanography’ (TEMPO) experiment, and are described in this paper. The Southern Antarctic Circumpolar Current Front is found in the northern part of the survey area, generally near 63-64°S, whereas the Southern Boundary Front is located between 64 and 65.5°S. The westward flowing Antarctic Slope Front (ASF) is found in the southern part of the survey area near the continental slope on most transects. Highest concentrations of oxygen (> 300 µmol kg⁻¹) are found in shelf waters at stations in Prydz Bay, south of 67°S along 75°E, whereas the lowest oxygen values are found in the Circumpolar Deep Water layer, with an average of roughly 215 µmol kg⁻¹. North of the northern extension of the ASF, surface mixed layers are between 20 and 60 m deep. Mixed layers tend to deepen slightly in the northern part of the survey, generally increasing north of 64°S where the ocean has been ice-free the longest. We find evidence of upwelling of waters into the surface layers, based on temperature anomaly, particularly strong along 80°E. Enhanced variability of biogeochemical properties - nutrients, DIC, DO - in the AASW layer is driven by a combination of sea-ice and biological processes. Antarctic Bottom Water, defined as water with neutral density > 28.3 kg m⁻³, was sampled at all the offshore full-depth stations, with a colder/fresher variety along western transects and a warmer/saltier variety in the east. Newly formed Antarctic Bottom Water – the coldest, freshest, and most recently ventilated – is mostly found in the deep ocean along 65°E, in the base of the Daly Canyon.

Multiple autonomous underwater vehicles (AUVs) working in collaboration can achieve scientific goals more effectively than independently operated vehicles. In this article, we present a case of using two long-range AUVs (LRAUVs) for persistent environmental DNA (eDNA) sampling of a targeted feature. Each LRAUV was equipped with a third-generation environmental sample processor (3G-ESP), a robotic instrument for acquiring and processing water samples for molecular analysis. Each 3G-ESP can collect and process 60 samples. For continuous and persistent eDNA sampling of vertically migrating organisms at a targeted depth layer, we deployed two LRAUVs which alternately triggered the ESP, extending the total time of collecting samples. We developed a method of coordinated sampling by time shift and a collaborative sampling method that uses acoustic handshakes. In the time-shift method, each vehicle switched between two behaviors: sample collection at the targeted depth and spiraling over a large depth range to make contextual measurement. The second vehicle's mission started later than the first vehicle's by a time shift equal to the duration of one sampling event, such that at a given time one vehicle sampled at the targeted depth while the other vehicle spiraled up and down. In the acoustic-handshake method, the two LRAUVs exchanged sample-start and sample-end messages. On receiving vehicle #1’s sample-end message, vehicle #2 triggered a sampling event and transmitted a sample-start message to vehicle #1. Then, vehicle #1 waited for vehicle #2’s sample-end message before triggering the next sampling event, and so forth. The time-shift method is simple, whereas the acoustic-handshake method is accurate and adaptive. Both methods were demonstrated in experiments in Monterey Bay.