ALBERT

Description: The interaction of clouds with solar and terrestrial radiation is one of the most important topics of climate research. In recent years it has been recognized that only a full three-dimensional (3D) treatment of this interaction can provide answers to many climate and remote sensing problems, leading to the worldwide development of numerous 3D radiative transfer (RT) codes. The international Intercomparison of 3D Radiation Codes (I3RC), described in this paper, sprung from the natural need to compare the performance of these 3D RT codes used in a variety of current scientific work in the atmospheric sciences. I3RC supports intercomparison and development of both exact and approximate 3D methods in its effort to 1) understand and document the errors/limits of 3D algorithms and their sources; 2) provide “baseline” cases for future code development for 3D radiation; 3) promote sharing and production of 3D radiative tools; 4) derive guidelines for 3D radiative tool selection; and 5) improve atmospheric science education in 3D RT. Results from the two completed phases of I3RC have been presented in two workshops and are expected to guide improvements in both remote sensing and radiative energy budget calculations in cloudy atmospheres.

Description: The Vasco—Cirene field experiment, in January—February 2007, targeted the Seychelles—Chagos thermocline ridge (SCTR) region, with the main purpose of investigating Madden—Julian Oscillation (MJO)-related SST events. The Validation of the Aeroclipper System under Convective Occurrences (Vasco) experiment (Duvel et al. 2009) and Cirene cruise were designed to provide complementary views of air—sea interaction in the SCTR region. While meteorological balloons were deployed from the Seychelles as a part of Vasco, the Research Vessel (R/V) Suroît was cruising the SCTR region as a part of Cirene. more: The Vasco—Cirene program explores how strong air—sea interactions promoted by the shallow thermocline and high sea surface temperature in the Seychelles—Chagos thermocline ridge results in marked variability at synoptic, intraseasonal, and interannual time scales. The Cirene oceanographic cruise collected oceanic, atmospheric, and air—sea flux observations in this region in January—February 2007. The contemporaneous Vasco field experiment complemented these measurements with balloon deployments from the Seychelles. Cirene also contributed to the development of the Indian Ocean observing system via deployment of a mooring and 12 Argo profilers. Unusual conditions prevailed in the Indian Ocean during January and February 2007, following the Indian Ocean dipole climate anomaly of late 2006. Cirene measurements show that the Seychelles—Chagos thermocline ridge had higher-than-usual heat content with subsurface anomalies up to 7°C. The ocean surface was warmer and fresher than average, and unusual eastward currents prevailed down to 800 m. These anomalous conditions had a major impact on tuna fishing in early 2007. Our dataset also sampled the genesis and maturation of Tropical Cyclone Dora, including high surface temperatures and a strong diurnal cycle before the cyclone, followed by a 1.5°C cooling over 10 days. Balloonborne instruments sampled the surface and boundary layer dynamics of Dora. We observed small-scale structures like dry-air layers in the atmosphere and diurnal warm layers in the near-surface ocean. The Cirene data will quantify the impact of these finescale features on the upper-ocean heat budget and atmospheric deep convection.

Description: The tropical oceans have long been recognized as the most important region for large-scale ocean–atmosphere interactions, giving rise to coupled climate variations on several time scales. During the Tropical Ocean Global Atmosphere (TOGA) decade, the focus of much tropical ocean research was on understanding El Niño–related processes and on development of tropical ocean models capable of simulating and predicting El Niño. These studies led to an appreciation of the vital role the ocean plays in providing the memory for predicting El Niño and thus making seasonal climate prediction feasible. With the end of TOGA and the beginning of Climate Variability and Prediction (CLIVAR), the scope of climate variability and predictability studies has expanded from the tropical Pacific and ENSO-centric basis to the global domain. In this paper the progress that has been made in tropical ocean climate studies during the early years of CLIVAR is discussed. The discussion is divided geographically into three tropical ocean basins with an emphasis on the dynamical processes that are most relevant to the coupling between the atmosphere and oceans. For the tropical Pacific, the continuing effort to improve understanding of large- and small-scale dynamics for the purpose of extending the skill of ENSO prediction is assessed. This paper then goes beyond the time and space scales of El Niño and discusses recent research activities on the fundamental issue of the processes maintaining the tropical thermocline. This includes the study of subtropical cells (STCs) and ventilated thermocline processes, which are potentially important to the understanding of the low-frequency modulation of El Niño. For the tropical Atlantic, the dominant oceanic processes that interact with regional atmospheric feedbacks are examined as well as the remote influence from both the Pacific El Niño and extratropical climate fluctuations giving rise to multiple patterns of variability distinguished by season and location. The potential impact of Atlantic thermohaline circulation on tropical Atlantic variability (TAV) is also discussed. For the tropical Indian Ocean, local and remote mechanisms governing low-frequency sea surface temperature variations are examined. After reviewing the recent rapid progress in the understanding of coupled dynamics in the region, this study focuses on the active role of ocean dynamics in a seasonally locked east–west internal mode of variability, known as the Indian Ocean dipole (IOD). Influences of the IOD on climatic conditions in Asia, Australia, East Africa, and Europe are discussed. While the attempt throughout is to give a comprehensive overview of what is known about the role of the tropical oceans in climate, the fact of the matter is that much remains to be understood and explained. The complex nature of the tropical coupled phenomena and the interaction among them argue strongly for coordinated and sustained observations, as well as additional careful modeling investigations in order to further advance the current understanding of the role of tropical oceans in climate.

Description: Microbial degradation of substrates to terminal products is commonly understood as a unidirectional process. In individual enzymatic reactions, however, reversibility (reverse reaction and product back flux) is common. Hence, it is possible that entire pathways of microbial degradation are associated with back flux from the accumulating product pool through intracellular intermediates into the substrate pool. We investigated carbon and sulfur back flux during the anaerobic oxidation of methane (AOM) with sulfate, one of the least exergonic microbial catabolic processes known. The involved enzymes must operate not far from the thermodynamic equilibrium. Such an energetic situation is likely to favor product back flux. Indeed, cultures of highly enriched archaeal–bacterial consortia, performing net AOM with unlabeled methane and sulfate, converted label from 14C-bicarbonate and 35S-sulfide to 14C-methane and 35S-sulfate, respectively. Back fluxes reached 5% and 13%, respectively, of the net AOM rate. The existence of catabolic back fluxes in the reverse direction of net reactions has implications for biogeochemical isotope studies. In environments where biochemical processes are close to thermodynamic equilibrium, measured fluxes of labeled substrates to products are not equal to microbial net rates. Detection of a reaction in situ by labeling may not even indicate a net reaction occurring in the direction of label conversion but may reflect the reverse component of a so far unrecognized net reaction. Furthermore, the natural isotopic composition of the substrate and product pool will be determined by both the forward and back flux. This finding may have to be considered in the interpretation of stable isotope records.

Description: Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed fromonly the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed picoprymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, pico-prymnesiophytes formed 25 of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.

Description: Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of & SIM;1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.

Description: Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15–46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Description: The anaerobic oxidation of methane (AOM) is one of the major sinks of this substantial greenhouse gas in marine environments. Recent investigations have shown that diverse communities of anaerobic archaea and sulfate-reducing bacteria are involved in AOM. Most of the relevant archaea are assigned to two distinct phylogenetic clusters, ANME-1 and ANME-2. A suite of specific 13C-depleted lipids demonstrating the presence of consortia mediating AOM in fossil and recent environments has been established. Here we report on substantial differences in the lipid composition of microbial consortia sampled from distinct compartments of AOM-driven carbonate reefs growing in the northwestern Black Sea. Communities in which the dominant archaea are from the ANME-1 cluster yield internally cyclized tetraether lipids typical of thermophiles. Those in which ANME-2 archaea are dominant yield sn-2-hydroxyarchaeol accompanied by crocetane and crocetenes. The bacterial lipids from these communities are also distinct even though the sulfate-reducing bacteria all belong to the Desulfosarcina/Desulfococcus group. Nonisoprenoidal glycerol diethers are predominantly associated with ANME-1-dominated communities. Communities with ANME-2 yield mainly conventional, ester-linked diglycerides. ANME-1 archaea and associated sulfate-reducing bacteria seem to be enabled to use low concentrations of methane and to grow within a broad range of temperatures. Our results offer a tool for the study of recent and especially of fossil methane environments.

Description: The western Pacific subtropical high (WPSH) is closely related to Asian climate. Previous examination of changes in the WPSH found a westward extension since the late 1970s, which has contributed to the inter-decadal transition of East Asian climate. The reason for the westward extension is unknown, however. The present study suggests that this significant change of WPSH is partly due to the atmosphere's response to the observed Indian Ocean-western Pacific (IWP) warming. Coordinated by a European Union's Sixth Framework Programme, Understanding the Dynamics of the Coupled Climate System (DYNAMITE), five AGCMs were forced by identical idealized sea surface temperature patterns representative of the IWP warming and cooling. The results of these numerical experiments suggest that the negative heating in the central and eastern tropical Pacific and increased convective heating in the equatorial Indian Ocean/ Maritime Continent associated with IWP warming are in favor of the westward extension of WPSH. The SST changes in IWP influences the Walker circulation, with a subsequent reduction of convections in the tropical central and eastern Pacific, which then forces an ENSO/Gill-type response that modulates the WPSH. The monsoon diabatic heating mechanism proposed by Rodwell and Hoskins plays a secondary reinforcing role in the westward extension of WPSH. The low-level equatorial flank of WPSH is interpreted as a Kelvin response to monsoon condensational heating, while the intensified poleward flow along the western flank of WPSH is in accord with Sverdrup vorticity balance. The IWP warming has led to an expansion of the South Asian high in the upper troposphere, as seen in the reanalysis.

Description: Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.