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Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.

Background With 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. Results Here, 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. Conclusions Using an in silico approach, we were able improve the success rate of functional screening and make entire (meta-) genomes amenable for biochemical characterization.

Background Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals. Results Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu. Conclusions We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed \"fragment recruitment,\" addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed \"extreme assembly,\" made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Observations of sea surface and land–near-surface merged temperature anomalies are used to monitor climate variations and to evaluate climate simulations; therefore, it is important to make analyses of these data as accurate as possible. Analysis uncertainty occurs because of data errors and incomplete sampling over the historical period. This manuscript documents recent improvements in NOAA’s merged global surface temperature anomaly analysis, monthly, in spatial 5° grid boxes. These improvements allow better analysis of temperatures throughout the record, with the greatest improvements in the late nineteenth century and since 1985. Improvements in the late nineteenth century are due to improved tuning of the analysis methods. Beginning in 1985, improvements are due to the inclusion of bias-adjusted satellite data. The old analysis (version 2) was documented in 2005, and this improved analysis is called version 3.

This paper explores the use of the linear response function (LRF) to relate the mean sea surface temperature (SST) response to prescribed ocean heat convergence (q flux) forcings. Two methods for constructing the LRF based on the fluctuation–dissipation theorem (FDT) and Green’s function (GRF) are examined. A 900-yr preindustrial simulation by the Community Earth System Model coupled with a slab ocean model (CESM–SOM) is used to estimate the LRF using FDT. For GRF, 106 pairs of CESM–SOM simulations with warm and cold q-flux patches are performed. FDT is found to have some skill in estimating the SST response to a q-flux forcing when the local SST response is strong, but it fails in inverse estimation of the q-flux forcing for a given SST pattern. In contrast, GRF is shown to be reasonably accurate in estimating both SST response and q-flux forcing. Possible degradation in FDT may be attributed to insufficient data sampling, significant departure of the SST distribution from Gaussianity, and the nonnormality of the constructed operator. The GRF-based LRF is then used to (i) generate a global surface temperature sensitivity map that shows the q-flux forcing in higher latitudes to be 3–4 times more effective than low latitudes in producing global surface warming, and (ii) identify the most excitable SST mode (neutral vector) that shows marked resemblance to the interdecadal Pacific oscillation (IPO). The latter discovery suggests that the IPO-like fluctuation exists in the absence of the coupling to the ocean dynamics. Coupling to the ocean dynamics in CESM, on the other hand, only enhances the spectral power of the IPO at interannual time scales.

This paper describes a state-of-the-art research catamaran to investigate processes such as air–sea gas exchange, heat exchange, surface blooms, and photochemistry at the sea surface microlayer (SML) with high-resolution measurements of 0.1-Hz frequency. As the boundary layer between the ocean and the atmosphere, the SML covers 70% of Earth. The remote-controlled Sea Surface Scanner is based on a glass disk sampler to automate the sampling of the thin SML, overcoming the disadvantages of techniques such as low volume sampling and ex situ measurement of the SML. A suite of in situ sensors for seven biogeochemical parameters (temperature, pH, dissolved oxygen, salinity, chromophoric dissolved organic matter, chlorophyll- a , and photosynthetic efficiency) was implemented to characterize the SML in reference to the mixed bulk water. The Sea Surface Scanner has the capability to collect 24 discrete water samples with a volume of 1 L each for further laboratory analysis. Meteorological parameters such as wind speed influence SML properties and are continuously monitored. This paper reports the use of the Sea Surface Scanner to identify and study (i) upwelling regions and associated fronts, (ii) rain events, and (iii) the occurrence of surface blooms. The high patchiness of the SML was detected during the observed sea surface phenomena, and high-resolution mapping of the biogeochemical parameters of the oceanic boundary layer to the atmosphere are presented for the first time. The Sea Surface Scanner is a new technology to map and understand sea surface processes and, ultimately, to fill the gaps in knowledge about ocean–atmosphere interactions relevant to ocean and climate science.

The Arctic is nutrient limited, particularly by nitrogen, and is impacted by anthropogenic global warming which occurs approximately twice as fast compared to the global average. Arctic warming intensifies thawing of permafrost-affected soils releasing their large organic nitrogen reservoir. This organic nitrogen reaches hydrological systems, is remineralized to reactive inorganic nitrogen, and is transported to the Arctic Ocean via large rivers. We estimate the load of nitrogen supplied from terrestrial sources into the Arctic Ocean by sampling in the Lena River and its Delta. We took water samples along one of the major deltaic channels in winter and summer in 2019 and sampling station in the central delta over a one-year cycle. Additionally, we investigate the potential release of reactive nitrogen, including nitrous oxide from soils in the Delta. We found that the Lena transported nitrogen as dissolved organic nitrogen to the coastal Arctic Ocean and that eroded soils are sources of reactive inorganic nitrogen such as ammonium and nitrate. The Lena and the Deltaic region apparently are considerable sources of nitrogen to nearshore coastal zone. The potential higher availability of inorganic nitrogen might be a source to enhance nitrous oxide emissions from terrestrial and aquatic sources to the atmosphere.

A novel sub‐sampling method has been used to isolate the dynamic effects of the response of the North Atlantic Oscillation (NAO) and the Siberian High (SH) from the total response to projected Arctic sea‐ice loss under 2°C global warming above preindustrial levels in very large initial‐condition ensemble climate simulations. Thermodynamic effects of Arctic warming are more prominent in Europe while dynamic effects are more prominent in Asia/East Asia. This explains less‐severe cold extremes in Europe but more‐severe cold extremes in Asia/East Asia. For Northern Eurasia, dynamic effects overwhelm the effect of increased moisture from a warming Arctic, leading to an overall decrease in precipitation. We show that the response scales linearly with the dynamic response. However, caution is needed when interpreting inter‐model differences in the response because of internal variability, which can largely explain the inter‐model spread in the NAO and SH response in the Polar Amplification Model Intercomparison Project. Plain Language Summary The projected loss of Arctic sea‐ice under 2°C global warming will cause large warming in the Arctic region and climate and weather anomalies outside the Arctic. The warming in the Arctic will mean warmer airmasses coming from the Arctic and also more moisture from the open Arctic Ocean. Furthermore, it will also change atmospheric circulation. These effects together will determine the impacts of Arctic warming. In this study, we introduce a novel sub‐sampling method to isolate atmospheric circulation change in response to the Arctic warming. The method involves selecting members of simulations from the experiment with future Arctic sea‐ice conditions, the average of which is equal to the average of the members of simulations in the experiment with present‐day Arctic sea‐ice conditions. We found that atmospheric circulation change in European regions is relatively weak so that warming effects will dominate the climate and weather response there. On the other hand, atmospheric circulation change will dominate the climate and weather response in East Eurasia. We also found that stronger atmospheric circulation changes will generally increase the response to the Arctic warming. We suggest caution when assessing whether different responses in different models can be interpreted as true differences in model physics. Key Points A novel sub‐sampling method is introduced to isolate the role of dynamics in the response to projected Arctic sea‐ice loss A dynamical Siberian High response dominates the temperature response over East Eurasia while that of the North Atlantic Oscillation is weak Inter‐model differences in Polar Amplification Model Intercomparison Project likely contain a large fraction of internal variability due to the unconstrained dynamic effects