The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-s data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES-edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. Gonzalez.

Recent studies point to the importance of oxygen (O-2) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O-2 tension in oceanic oxygen minimum zones (OMZs), and O-2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low M O-2 concentrations, characteristic of suboxic regions of OMZs (<10 mu M O-2), and that atmospheric concentrations of O-2 may inhibit the growth of some environmental populations. We quantify the increasing N2O production by marine AOA with decreasing O-2 tensions, consistent with the plausibility of an AOA contribution to the accumulation of N2O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.

The 2013 US GEOTRACES Eastern Pacific Zonal Transect (GP16) extended from the Peruvian coast to Tahiti, along a line that fell between 10 and 15 degrees S. This transect sampled the Peruvian oxygen deficient zone (ODZ) and the hydrothermal plume extending from the East Pacific Rise (EPR) for a variety of trace elements and isotopes (TEIs). Here we report nutrient and hydrographic measurements collected on this cruise, as well as results from an Optimum Multiparameter Analysis (OMPA) to quantify the fractional contributions of endmember water masses in each sample. The primary goals of this study were to better understand the distribution of water masses in the eastern tropical Pacific, and to help interpret TEI measurements collected on this cruise, as well as related studies carried out in the region. In the thermocline, Equatorial Subsurface Water (ESSW) dominated the low oxygen waters of the eastern tropical South Pacific, blending into Eastern South Pacific Intermediate Water (ESPIW) and South Pacific Central Water (SPCW) further west. Below the thermocline, distributions of Antarctic Intermediate Water (AAIW) and Equatorial Pacific Intermediate Water (EqPIW) were relatively homogenous along the section between 800 and 1200 m depth. Deeper in the water column, distinct water mass signatures were found on opposite sides of the EPR: southward flowing Pacific Deep Water (PDW) dominated the basin east of the EPR, while the northward flowing Antarctic Bottom Water (AABW) and Lower Circumpolar Deep Water (LCDW) had the strongest contributions on the western side of the EPR. These findings support previous studies that indicate the Peruvian ODZ is largely contained within ESSW and that the EPR plays an important role in steering water mass distributions in the deep waters of the tropical Pacific. Overall, these results agree well with previous water mass analyses in this region and are consistent with the general circulation patterns in the eastern tropical Pacific.

Organisms within all domains of life require the cofactor cobalamin (vitamin B-12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalaminlikely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean.

Copper (Cu) is required by the enzyme nitrous oxide reductase (N2OR), which catalyzes the last step of the complete denitrification pathway in denitrifying bacteria. Some denitrifiers also require copper for nitrite reductase (NiRK), whereas others use the iron nitrite reductase (NiRS). We report the inhibition of the activity of these enzymes in three strains of denitrifiers (two containing NiRK, the other NiRS), by forming nonbioavailable complexes with 1,4,8,11-tetraazacyclotetradecane1,4,8,11-tetraacetic acid hydrochoride hydrate (TETA), a strong Cu(II) chelator, and tetrathiomolybdate (TTMo), a strong Cu(I) chelator. Both ligands complex Cu with stability constants comparable to naturally occurring ligands and much more strongly than other widely used chelators, such as ethylenediaminetetraacetic acid. Addition of TETA to growth media lowered free Cu2+ concentrations below 10(-16) mol L-1 and induced Cu limitation in all organisms. While Cu is strongly complexed in seawater, 10(-16) mol L-1 free Cu2+ is lower than most reported values, suggesting that the organisms have evolved high-affinity Cu transport systems. TTMo had different effects, and inhibited NiRK more effectively than N2OR. It is likely that TTMo inhibits NiRK through direct, noncompetitive inhibition, as reported for other reduced sulfur compounds, rather than by inducing Cu limitation. The activity of NiRK may be sensitive to trace levels of reduced sulfur, which could account for its scarcity in marine systems. While Cu limitation of denitrification is probably uncommon in aquatic systems, the presence of reduced sulfur compounds may induce Cu limitation or enzyme inhibition leading to the accumulation of nitrite and nitrous oxide.

Copper (Cu) is required by the enzyme nitrous oxide reductase (N2OR), which catalyzes the last step of the complete denitrification pathway in denitrifying bacteria. Some denitrifiers also require copper for nitrite reductase (NiRK), whereas others use the iron nitrite reductase (NiRS). We report the inhibition of the activity of these enzymes in three strains of denitrifiers (two containing NiRK, the other NiRS), by forming nonbioavailable complexes with 1,4,8,11-tetraazacyclotetradecane1,4,8,11-tetraacetic acid hydrochoride hydrate (TETA), a strong Cu(II) chelator, and tetrathiomolybdate (TTMo), a strong Cu(I) chelator. Both ligands complex Cu with stability constants comparable to naturally occurring ligands and much more strongly than other widely used chelators, such as ethylenediaminetetraacetic acid. Addition of TETA to growth media lowered free Cu2+ concentrations below 10(-16) mol L-1 and induced Cu limitation in all organisms. While Cu is strongly complexed in seawater, 10(-16) mol L-1 free Cu2+ is lower than most reported values, suggesting that the organisms have evolved high-affinity Cu transport systems. TTMo had different effects, and inhibited NiRK more effectively than N2OR. It is likely that TTMo inhibits NiRK through direct, noncompetitive inhibition, as reported for other reduced sulfur compounds, rather than by inducing Cu limitation. The activity of NiRK may be sensitive to trace levels of reduced sulfur, which could account for its scarcity in marine systems. While Cu limitation of denitrification is probably uncommon in aquatic systems, the presence of reduced sulfur compounds may induce Cu limitation or enzyme inhibition leading to the accumulation of nitrite and nitrous oxide.

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O-2 NO3-, NO2-, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe binding proteins was negatively correlated with 02, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with 02 content. A comparison of the taxonomy of genes encoding Fe- and Cu binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe proteins in the genome of a marine planctomycete vs higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes a-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured K-m of 98 +/- 14 nmol l(-1) was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 degrees C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a K-m for the natural community to better constrain ammonia oxidation rates determined with the commonly used (NH4+)-N-15 dilution technique.

Oxygen minimum zones (OMZs) have been proposed to be an important source of dissolved iron (Fe) into the interior ocean. However, previous studies in OMZs have shown a sharp decrease in total dissolved Fe (dFe) and/or dissolved Fe (II) (dFe(II)) concentrations at the shelf-break, despite constant temperature, salinity and continued lack of oxygen across the shelf-break. The loss of both total dFe and dFe(II) suggests a conversion of the dFe to particulate form, but studies that have coupled the reduction-oxidation (redox) speciation of both dissolved and particulate phases have not previously been done. Here we have measured the redox speciation and concentrations of both dissolved and particulate forms of Fe in samples collected during the U.S. GEOTRACES Eastern tropical Pacific Zonal Transect (EPZT) cruise in 2013 (GP16). This complete data set allows us to assess possible mechanisms for loss of dFe. We observed an offshore loss of dFe(II) within the oxygen deficient zone (ODZ), where dissolved oxygen is undetectable, accompanied by an increase in total particulate Fe (pFe). Total pFe concentrations were highest in the upper ODZ. X-ray absorption spectroscopy revealed that the pFe maximum was primarily in the Fe(III) form as Fe(III) oxyhydroxides. The remarkable similarity in the distributions of total particulate iron and nitrite suggests a role for nitrite in the oxidation of dFe(II) to pFe(III). We present a conceptual model for the rapid redox cycling of Fe that occurs in ODZs, despite the absence of oxygen. (C) 2017 Elsevier Ltd. All rights reserved.

Marine picocyanobacteria, comprised of the genera Synechococcus and Prochlorococcus, are the most abundant and widespread primary producers in the ocean. More than 20 genetically distinct clades of marine Synechococcus have been identified, but their physiology and biogeography are not as thoroughly characterized as those of Prochlorococcus. Using clade-specific qPCR primers, we measured the abundance of 10 Synechococcus clades at 92 locations in surface waters of the Atlantic and Pacific Oceans. We found that Synechococcus partition the ocean into four distinct regimes distinguished by temperature, macronutrients and iron availability. Clades I and IV were prevalent in colder, mesotrophic waters; clades II, III and X dominated in the warm, oligotrophic open ocean; clades CRD1 and CRD2 were restricted to sites with low iron availability; and clades XV and XVI were only found in transitional waters at the edges of the other biomes. Overall, clade II was the most ubiquitous clade investigated and was the dominant clade in the largest biome, the oligotrophic open ocean. Co-occurring clades that occupy the same regime belong to distinct evolutionary lineages within Synechococcus, indicating that multiple ecotypes have evolved independently to occupy similar niches and represent examples of parallel evolution. We speculate that parallel evolution of ecotypes may be a common feature of diverse marine microbial communities that contributes to functional redundancy and the potential for resiliency.

Abstract This article is in Free Access Publication and may be downloaded using the “Download Full Text PDF” link at right.

Cobalt and manganese uptake onto suspended particles was studied in waters collected from Waquoit Bay, Massachusetts and the upper water column of the Sargasso Sea using radiotracers, coupled with protocols used previously for Mn and Ce to distinguish biological and redox processes.