Ocean Sampling Research Articles

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

Geographic and depth distributions, ontogeny, and reproductive seasonality of decapod shrimps (Caridea: Oplophoridae) from the northeastern Gulf of Mexico

Presented here is the first description of the geographic and depth distributions of pelagic decapod shrimps in the area located around the Deepwater Horizon oil spill, based on the National Oceanic and Atmospheric Administration (NOAA) National Resource Damage Assessment (NRDA) samples collected from April to June 2011. This information is important in ecosystem models investigating trophic effects of the spill because pelagic decapod shrimps are consumed by organisms occupying higher trophic levels. One of the most abundant and diverse groups is the family Oplophoridae; however, past research on their distribution and reproductive biology has been limited. In the northeastern Gulf of Mexico (GOM), all previous studies have been conducted at Standard Station (27°N, 86°W). The present study: (1) provides data from a larger area of the northeastern GOM, where oplophorids have never been studied; (2) allows for comparisons of distributions and abundances of oplophorid species in both the mesopelagic and bathypelagic zones by using a continuous data set; and (3) compares assemblages from two distinct bathymetric environments, slope (200- to 1000-m bottom depth) and offshore (>1000 m). Our post-spill data set can be compared with data obtained during future Deep Pelagic Nekton Dynamics (DEEPEND Consortium of the GOM) cruises to monitor changes, or lack thereof, in the assemblage after exposure to Deepwater Horizon oil and dispersants in the water column.

Analysis of phytoplankton assemblage structure in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences

Studying taxonomic and ecological diversity of phytoplankton assemblages is often difficult because morphological analysis cannot provide a complete description of their composition. Therefore, more robust and feasible approaches have to be chosen to elucidate the interactions between environmental and human pressures and phytoplankton assemblages. The Ocean Sampling Day (OSD) allowed collecting seawater samples from a wide range of oceanic regions including the Mediterranean Sea. In this study, a total of 754,167 V4-18S ribosomal DNA (rDNA) metabarcodes derived from 20 plankton samples collected at 19 sampling sites across the coastal areas of the Mediterranean Sea were analyzed to explore the relationships between phytoplankton assemblages' composition, sub-regional environmental features and human pressures. We reduced the whole set of autotroph plankton (1398 OTUs) to a smaller number of ecologically relevant entities (205 taxa) and used the latter for analysing the structure of phytoplankton assemblages. Chaetoceros was the only genus occurring in all the samples, while the number of taxa was maximum in the W Mediterranean. Based on the assigned OTUs, the structure of E Mediterranean phytoplankton was the most homogeneous. Further, phytoplankton assemblages from the three Mediterranean sub-regions (Western, Adriatic and Eastern) were significantly different (R=0.25, p=0.0136) based on Jaccard similarity. We also observed that phytoplankton diversity and human impact on marine ecosystems were not significantly related to each other based on Mantel's test.

Volume 30 Issue 02 View Issue TOC Volume 30, No. 2 Satellites to Seafloor: Toward Fully Autonomous Ocean Sampling

Future ocean observing systems will rely heavily on autonomous vehicles to achieve the persistent and heterogeneous measurements needed to understand the ocean’s impact on the climate system. The day-to-day maintenance of these arrays will become increasingly challenging if significant human resources, such as manual piloting, are required. For this reason, techniques need to be developed that permit autonomous determination of sampling directives based on science goals and responses to in situ, remote-sensing, and model-derived information. Techniques that can accommodate large arrays of assets and permit sustained observations of rapidly evolving ocean properties are especially needed for capturing interactions between physical circulation and biogeochemical cycling. Here we document the first field program of the Satellites to Seafloor project, designed to enable a closed loop of numerical model prediction, vehicle path-planning, in situ path implementation, data collection, and data assimilation for future model predictions. We present results from the first of two field programs carried out in Monterey Bay, California, over a period of three months in 2016. While relatively modest in scope, this approach provides a step toward an observing array that makes use of multiple information streams to update and improve sampling strategies without human intervention.

Coordinated Navigation of Surface and Underwater Marine Robotic Vehicles for Ocean Sampling and Environmental Monitoring

Water pollution generated by accidental spill of hazardous materials is a growing problem worldwide. There is an urgent need for a tool that would help environmental response teams perform rapid understanding of the location and the extent of the spill to effectively establish an appropriate response. This paper presents a cooperative robotic system for environmental monitoring consisting of an autonomous underwater vehicle (AUV) and an autonomous unmanned surface vehicle (USV). The main contributions of the paper are a systematic description of the design and implementation of the proposed cooperative robotic system, a novel human-on-the-loop (HOTL) approach applied on the system for environmental monitoring, and demonstration of the results of the open-sea experiments on pollution deliberately caused by harmless Rhodamine water tracing (WT), carried out in Cartagena, Spain, in June 2015. The proposed HOTL system provides near real-time pollution measurement data, while not consuming a significant amount of human time and effort. It supports decision-making and allows the operator to initiate the most adequate mission in a current situation, i.e., ensures mission change on-the-fly. While the AUV samples the ocean, the USV maintains the localization and communication data transfer to the control center and corrects the AUV's dead reckoning error.

In silico approach to designing rational metagenomic libraries for functional studies

BackgroundWith the development of Next Generation Sequencing technologies, the number of predicted proteins from entire (meta-) genomes has risen exponentially. While for some of these sequences protein functions can be inferred from homology, an experimental characterization is still a requirement for the determination of protein function. However, functional characterization of proteins cannot keep pace with our capabilities to generate more and more sequence data.ResultsHere, we present an approach to reduce the number of proteins from entire (meta-) genomes to a reasonably small number for further experimental characterization without loss of important information. About 6.1 million predicted proteins from the Global Ocean Sampling Expedition Metagenome project were distributed into classes based either on homology to existing hidden markov models (HMMs) of known families, or de novo by assessment of pairwise similarity. 5.1 million of these proteins could be classified in this way, yielding 18,437 families. For 4,129 protein families, which did not match existing HMMs from databases, we could create novel HMMs. For each family, we then selected a representative protein, which showed the closest homology to all other proteins in this family. We then selected representatives of four families based on their homology to known and well-characterized lipases. From these four synthesized genes, we could obtain the novel esterase/lipase GOS54, validating our approach.ConclusionsUsing an in silico approach, we were able improve the success rate of functional screening and make entire (meta-) genomes amenable for biochemical characterization.

Thermally altered marine dissolved organic matter in hydrothermal fluids

Hydrothermal vent fluids contain thermally modified dissolved organic matter (DOM) originally entrained from sediments and seawater. We hypothesized that in hydrothermal systems DOM molecular composition is modulated by (i) fluid contribution, (ii) thermal decomposition and pH, and (iii) aspects particular to the vent system. Hence, solid phase extracted (SPE) DOM samples collected along the Mid-Atlantic Ridge (MAR) were molecularly characterized via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The molecular character of an oceanic DOM sample was also determined before and after thermal (300°C) decomposition at acidic and neutral pH. Multivariate statistical analysis indicated that DOM composition was strongly influenced by fluid contribution (Mg2+ concentration between 12 and 54mM), which correlated positively with measured temperature (between 8 and 375°C). In comparison, pH of the fluids (between 2.5 and 6.9) had a minor influence. Seafloor pressure, used as a theoretical maximum fluid temperature at the seafloor, separated the fluids collected at Menez Gwen from deeper locations, due to the higher abundance of peptide, carboxyl-rich alicyclic (CRAM) and aromatic molecular formulae at Menez Gwen. Compared with seawater DOM, thermally decomposed DOM had on average lower molecular mass, lower O/C ratios, fewer double bond equivalents, and fewer CRAM formulae but higher aromaticity - the same molecular features displayed by MAR hydrothermal fluids. The study provides evidence that thermal reworking plays a major role in shaping DOM mixtures from hydrothermal fluids along the MAR, which partly represent thermally reworked marine DOM that survived hydrothermal circulation.

Targeted ocean sampling guidance for tropical cyclones

AbstractA 3‐D variational ocean data assimilation adjoint approach is used to examine the impact of ocean observations on coupled tropical cyclone (TC) model forecast error for three recent hurricanes: Isaac (2012), Hilda (2015), and Matthew (2016). In addition, this methodology is applied to develop an innovative ocean observation targeting tool validated using TC model simulations that assimilate ocean temperature observed by Airborne eXpendable Bathy Thermographs and Air‐Launched Autonomous Micro‐Observer floats. Comparison between the simulated targeted and real observation data assimilation impacts reveals a positive maximum mean linear correlation of 0.53 at 400–500 m, which implies some skill in the targeting application. Targeted ocean observation regions from these three hurricanes, however, show that the largest positive impacts in reducing the TC model forecast errors are sensitive to the initial prestorm ocean conditions such as the location and magnitude of preexisting ocean eddies, storm‐induced ocean cold wake, and model track errors.

Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs.

ABSTRACTCoral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial.IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater.

The link between Hawaiian mantle plume composition, magmatic flux, and deep mantle geodynamics

Oceanic island basalts sample mantle reservoirs that are isotopically and compositionally heterogeneous. The Hawaiian–Emperor chain represents ∼85 Myr of volcanism supplied by a deep mantle plume. Two geographically and geochemically delineated trends, Kea and Loa, are well documented within the Hawaiian Islands. Enriched Loa compositions originate from subduction recycled or primordial material stored in deep mantle reservoirs such as the large low shear velocity province (LLSVP) below Hawai‘i. Loa compositions have not been observed along the Emperor Seamounts (>50 Ma), whereas lavas on the Hawaiian Islands (<6.5 Ma) sample both Kea and Loa sources. Lead isotopes in shield lavas along the Northwest Hawaiian Ridge (NWHR) spanning ∼42 Myr between the bend in the chain and the Hawaiian Islands record the geochemical evolution of the Hawaiian mantle plume over a time period when many geophysical parameters (volcanic propagation rate, magmatic flux, mantle potential temperature) increased significantly. Along the NWHR, the Loa geochemical component appears ephemerally, which we link to the sampling of different lower mantle compositional domains by the Hawaiian mantle plume. The plume initially sampled only the deep Pacific mantle (Kea component) from outside the LLSVP during the formation of the Emperor Seamounts. Southward migration and anchoring of the plume on the LLSVP led to entrainment of increasing amounts of LLSVP material (Loa component) along the NWHR as documented by an increase in 208Pb*/206Pb* with decreasing age. The correlation between 208Pb*/206Pb* and magmatic flux suggests source composition affects the magmatic flux, and explains why the Hawaiian mantle plume has dramatically strengthened through time.

Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry.

Flow cytometry provides a tool to physically sort single algal cells in order to obtain clonal cultures. During sorting, cells are submitted to physical stress factors such as high fluidic pressure, exposure to the laser beam, electrostatic charges, deflection through high voltage fields, and collisions with container surfaces. All of these can damage the cells of interest and success rates for initiation of cultures from flow-sorted cells are generally very low. We found that the addition of bovine serum albumin in the culture medium into which cells were sorted drastically improved the success of initiation of pico- and nano-eukaryotic phytoplankton strains. Adding a mixture of antibiotics (Penicillin, Neomycin, Streptomycin) to the medium in order to slow down bacterial growth further improved culture development. This approach was successfully used to isolate taxonomically diverse strains, including novel taxa, from a fresh sample obtained in the English Channel and from enrichment cultures established during an Atlantic meridional transect cruise. We anticipate that these improvements will be useful to clone or purify existing cultures and to isolate novel cultures from oceanic samples.

Magnesium isotopic variation of oceanic island basalts generated by partial melting and crustal recycling

Ocean island basalts (OIBs) are geochemically diverse in radiogenic isotopes, a feature that is commonly ascribed to record the chemical heterogeneity of their deep-mantle source, where significant compositional variation relates to variable amounts of ancient recycled crustal material. Although Mg is a major constituent of the mantle, it is still unclear whether Mg isotopes of OIBs predominantly correspond to deep-mantle source heterogeneity or processes such as partial melting. Here, we present Mg isotopic and trace-element compositional data for OIBs from the Hawaii islands, the Louisville seamounts, and for altered oceanic crust samples from the South Pacific. The δ26Mg value range of these OIBs is −0.29±0.07‰ (2SD, n=17), which is a variation approximately twice as large as the known compositional variation of the peridotitic mantle (−0.23±0.04‰, 2SD). Moreover, alkaline basalt (−0.31±0.04‰, 2SD, n=12) is relatively enriched in light Mg isotopes compared to tholeiitic basalt (−0.24±0.02‰, 2SD, n=5). In contrast, altered oceanic crust analyzed in this study has heavier Mg isotopic composition (−0.18±0.08‰, 2SD, n=13) relative to the basalts and to the peridotitic mantle. An evaluation of our and published data shows that the δ26Mg values of most OIBs negatively correlate with melting-sensitive trace-element ratios, but that they are uncorrelated with source-sensitive elemental ratios. This implies that Mg isotopic variation in most OIBs is largely controlled by variable degrees of partial melting and not by source heterogeneity. Negative correlation between Nb/Zr (or La/Sm) versus δ26Mg suggests that altered oceanic crust with heavier Mg isotopic composition is a more suitable source candidate for common OIBs. However, for a given melting degree, Louisville basalts have lower δ26Mg values than other OIBs, suggesting a different source, e.g. a peridotitic mantle. Modeling calculations suggest that melting of both garnet pyroxenite (recycled altered oceanic crust) and garnet peridotite can generate melts with low-δ26Mg signature for low-degree partial melting. Therefore, if the degree of partial melting can be independently constrained for the generation of parental OIB magma, the Mg isotopic compositions of their source can be estimated to investigate the chemical heterogeneity of the deep mantle.

Plutonium Isotopes (239-241Pu) Dissolved in Pacific Ocean Waters Detected by Accelerator Mass Spectrometry: No Effects of the Fukushima Accident Observed.

The concentration of plutonium (Pu) and the isotopic ratios of 240Pu to 239Pu and 241Pu to 239Pu were determined by accelerator mass spectrometry (AMS) in Pacific Ocean water samples (20 L each) collected in late 2012. The isotopic Pu ratios are important indicators of different contamination sources and were used to identify a possible release of Pu into the ocean by the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident. In particular, 241Pu is a well-suited indicator for a recent entry of Pu because 241Pu from fallout of nuclear weapon testings has already significantly decayed. A total of 10 ocean water samples were prepared at the Radiochemie München of the TUM and analyzed at the Vienna Environmental Research Laboratory (VERA). Several samples showed a slightly elevated 240Pu/239Pu ratio of up to 0.22 ± 0.02 compared to global fallout (240Pu/239Pu = 0.180 ± 0.007), whereas all measured 241Pu-to-239Pu ratios were consistent with nuclear weapon fallout (241Pu/239Pu < 2.4 × 10-3), which means that no impact from the Fukushima accident was detected. From the average 241Pu-to-239Pu ratio of 8-2+3 ×10-4 at a sampling station located at a distance of 39.6 km to FDNPP, the 1-σ upper limit for the FDNPP contribution to the 239Pu inventory in the water column was estimated to be 0.2%. Pu, with the signature of weapon-grade Pu was found in a single sample collected around 770 km off the west coast of the United States.

Design of a controllable variable buoyancy module and its performance analysis as a cascaded system for selective underwater deployment

Variable buoyancy systems (VBSs) are commonly used in underwater vehicles to achieve efficient heave motion. Most of the time, these systems are used as a part of conventional underwater vehicles with diverse methods to achieve the necessary buoyancy variation. The potential of VBSs as standalone systems for heave motion underwater has not been given due attention and is still an unexplored area. In this paper, the design of a VBS as a standalone module for heave control and the possibility of using multiple such modules in a cascaded structure for selective underwater deployment is presented. Such cascaded systems have a variety of applications ranging from coastal surveillance to selective deployment for ocean sampling, and so on. A metallic-bellows-based variable buoyancy module (VBM), actuated using linear actuators, is proposed here. The mathematical modelling of the VBM and its open-loop performance are analysed for suitability with regards to the system to be cascaded. Two prototypes have been developed based on the optimal design requirements and tested. The developed modules are simple and efficient for shallow water applications, and can be used as add-ons for existing underwater vehicles or can just be used as standalone systems. These two modules are then cascaded and the performance of the cascaded system is analysed with simulations and experiments. The analysis shows the suitability of the system for selective deployment at various depths.

Identification and bioactive potential of marine microorganisms from selected Florida coastal areas.

The ocean, with its rich untapped chemical biodiversity, continues to serve as a source of potentially new therapeutic agents. The evaluation of the diversity of cultivable microorganisms from the marine sponge Halichondria panicea and ocean sediment samples were examined and their potential as sources of antimicrobial and antiproliferative agents were investigated. The marine sponge and sediments were collected at different depths (0.9–6 meters) and locations in Florida, including Florida Keys, Port St. Joe in Pensacola, Pensacola Bay, Pensacola Beach, and Fort Pickens. Twenty‐one cultivatable isolates were grouped according to their morphology and identified using 16S rRNA molecular taxonomy. The bacterial community identified consisted of members belonging to the Actinobacteria, Bacteroidetes, Proteobacteria (Alpha‐ and Gamma‐classes) and Firmicutes phylogeny. Seven of the microbes exhibited mild to significant cytotoxic activities against five microbial indicators but no significant cytotoxic activities were observed against the pancreatic (PANC‐1) nor the multidrug‐resistant ovarian cancer cell lines (NCI/ADR). This work reaffirms the phyla Actinobacteria and Proteobacteria as sources of potential bioactive natural product candidates for drug discovery and development.

Mitochondrial DNA variation reveals distinct lineages in Penaeus semisulcatus (Decapoda, Penaeidae) from the Indo‐West Pacific Ocean

AbstractPenaeus semisulcatus, the green tiger prawn, is an ecologically and economically important penaeid shrimp in the Indo‐West Pacific region, especially in rice‐shrimp farming and capture fisheries in Bangladesh and Sri Lanka, respectively. Genetic variation and phylogeography of samples of this species from Bangladesh and Sri Lanka were studied utilizing different mitochondrial DNA markers, i.e. cytochrome oxidase subunit 1 (CO1), control region (CR) and 16S rRNA genes. No evidence of population structure was observed in Bangladesh, but distinct variations were found among the Sri Lankan samples (ΦST = 0.04, p = .002; FST = 0.07, p = .001), with the western sample differing from the northwestern and southern samples. The Bangladesh population had lower genetic diversity than two of the three Sri Lanka populations. The phylogeography of P. semisulcatus revealed two distinct mitochondrial DNA (mtDNA) lineages, one in the Western Pacific Ocean and second in the Indian Ocean. The Bangladesh samples showed highest levels of similarity with samples from Sri Lanka, India and Malaysia, with the Bangladesh and Sri Lanka populations sharing the most common recent ancestry. Among the Indian Ocean samples, high levels of variation were observed in the samples from Iran, indicating admixture of two distinct mtDNA lineages, one shared by the populations from the Bay of Bengal and the other possibly originating from Eastern Africa. The genetic and phylogeographic information obtained in this study will be useful in appropriate planning for management and conservation of shrimp fisheries in Bangladesh and Sri Lanka, and in the Indo‐West Pacific region.

Service agent–transport agent task planning incorporating robust scheduling techniques

As the use of cooperative, heterogeneous teams of autonomous robots to perform tasks such as autonomous package delivery and long-duration ocean sampling becomes more prevalent, the is a quickly-emerging need to study the high-level interaction of specialized robotic agents that perform service tasks, and specialized transport agents that transport the service agents between service areas. If the service routes, docking, and deployment schedules are not carefully planned, the overall schedule is inefficient at best, and possibly even infeasible due to fuel limitations at worst. We introduce a new problem in the area of scheduling and route planning operations called the service agent transport problem (SATP). Within the SATP, autonomous service agents must perform tasks at a number of locations. The agents are free to move between locations, however, the agents may also be transported throughout the region by a limited number of faster-moving transport agents. The goal of the SATP is to plan a schedule of service agent and transport agent actions such that all locations are serviced in the shortest amount of time. We believe the SATP formulation is unique because there is strong coupling between vehicle constraints as well as between the task allocation component of the problem and the scheduling component of the problem. We present a solution to the problem using a mixed-integer linear programming optimization framework and compare several complexity reduction heuristics to full optimization. Additionally, we include methods to account for relative uncertainty in the duration of planned tasks in such a manner as to balance the risk of schedule slips (conflicts) to the risk of creating an overly conservative and sub-optimal schedule.

Survey of the green picoalga Bathycoccus genomes in the global ocean.

Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters.

Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1-A7 and B1-B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.

Incorporating prior knowledge in observability-based path planning for ocean sampling

Observability-based path planning of autonomous sampling platforms for flow estimation is a technique by which candidate trajectories are evaluated based on their ability to enhance the observability of underlying flow-field parameters. Until now, observability-based path planning has focused primarily on forward-in-time integration. We present a novel approach that makes use of the background error covariance at the current time to account properly for uncertainty of the underlying flow. The reduced Hessian of an optimal, linear data-assimilation strategy properly accounts for prior knowledge in the linear case and must be full rank to infer the initial state. The reduced Hessian represents an observability Gramian augmented with an inverse prior covariance. We extend this concept to the nonlinear case to yield a new criterion for scoring candidate trajectories: the empirical augmented unobservability index. Solving the differential covariance Riccati equation of the Kalman Filter for deterministic dynamics also properly accounts for prior knowledge in the linear case, but at a later time. The solution to this equation reveals the important distinctions between observability-based, augmented observability-based, and anticipated covariance-based path planning. Path planning based on this unobservability index in the presence of prior information yields the desired behavior in numerical experiments of a guided Lagrangian sensor in a two-vortex flow pertinent to ocean sampling.