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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.

Determining the stability and consistency of grain yield performance requires accurate evaluation of genotypes in different environments. In Mexico, annual national spring wheat irrigated trials (ENTRI) are conducted to assess elite bread (Triticum aestivumL.) and durum (Triticum durumL.) wheat performance in different testing environments (TEs) in the main wheat‐growing areas. These trials provide data supporting release of new cultivars and aim to also address Mexican wheat value chain grain needs. This study analyzed grain yield performance of 30 bread and durum wheat cultivars grown in trials in the 2012–2013 and 2013–2014 growing cycles conducted across TEs in northwest, north, and central Mexico. Environmental variability (location, sowing timing, and irrigation schemes) across the ENTRI enabled genotype by environment interaction to be effectively evaluated. Bread and durum wheat genotypes with high and stable grain yield were also identified and compared across TEs of the wheat‐growing areas of Mexico. The bread wheat cultivars Bacorehuis F2015 and Borlaug100 F2014, and the durum cultivars Barobampo C2015, CONASIST C2015, and Anatoly C2011 were high yielding and gave stable performance in most of the TEs. This analysis demonstrates the utility of multi‐year, multi‐environment testing and analysis to identify improved wheat cultivars to meet wheat production demand in Mexico. It also provides useful testing and analysis methods for selection of suitable broadly as well as locally adapted varieties in other wheat producing regions of the world. We identified cultivars with high and stable grain yield in Mexico.Environmental variability enabled G × E interaction to be effectively evaluated.Multi‐year, multi‐environment testing and analysis is useful to identify improved wheat cultivars.

Lodging affects grain quality and grain yield in wheat (Triticum aestivumL.) and is difficult to breed for because its sporadic incidence and laborious protocols to measure lodging traits. Thus, developing molecular markers for these traits can increase selection efficiency in breeding programs. The aim of this article is to identify quantitative trait loci (QTL) associated with stem/anchorage strength and leverage traits (lodging traits) in a doubled‐haploid population of UK bread wheat Avalon × Cadenza. Field experiments were conducted in the UK during 2012–2013 near High Mowthorpe and during 2013–2014 at Sutton Bonington. Phenotypic and genetic analysis indicated significant genetic variation for all traits. Stem strength (diameter, wall width, and material strength) and leverage (plant height) traits were highly heritable (0.64–0.95), whereas anchorage strength traits (root plate spread and structural rooting depth) and ear number per plant (leverage trait) were less heritable (0.21–0.33). This study identified 18 QTL for lodging traits and grain yield in chromosomes 1D, 2B, 2D, 3A, 3B, 4A, 4D, 5B, and 6B. Two QTL for stem strength on chromosome 1D and 3B explaining 49.6% of the total phenotypic variation (PVE) are estimated to reduce stem lodging risk and shortening the plant height by 12 cm. One QTL for root plate spread on chromosome 5B explaining 22.4% of the PVE could increase root lodging resistance. Sixteen quantitative trait loci identified for lodging resistance traits.Specific region in chromosome 3B related to overall stem strength.Specific region in chromosome 5B related to root plate spread.

Small pelagic fisheries management is difficult because they exhibit large natural abundance fluctuations and are considered forage fish. We discuss the challenges faced by these fisheries within the Marine Stewardship Council (MSC) sustainability certification framework, which evaluates the sustainability of fish stocks, the environmental impact, and effective fisheries management. Certification suspension is frequently linked to the sustainability of stocks. For MSC certification, scientific research will need to play a major role in filling key knowledge gaps, particularly on the nature and causes of ecosystem productivity changes (including climate change), and the role of small pelagics in the ecosystem. Different from other cases where MSC certification creates a direct market incentive through price premiums, in these fisheries, the incentive is related to fisher's public image and improves the bases for negotiation with authorities and the conservation sector. In this context, strategic cooperation between fisheries under the certification process may provide them more benefits than competition.

Nitrification plays a key role in marine ecosystems where Thaumarchaeotaare thought to be responsible for most of the ammonia oxidation in the water column. Over a 2‐yr, near‐monthly time series at two sites in Monterey Bay we observed repeatable seasonal and depth‐based patterns of Thaumarchaeotaecotype abundance that highlighted a clear delineation between populations in shallow euphotic (< 50 m) vs. deeper mesopelagic (60–500 m) depths. Euphotic depths show greater seasonality and influence from light, while mesopelagic waters have trends based on water mass and other covarying features with depth. Three major ecotypes were recovered: a Nitrosopumilus‐like (NP) group, a Nitrosopelagicus‐like ecotype containing “shallow” water column A (WCA) members, and an ecotype affiliated with the “deep” water column B (WCB) Thaumarchaeota. These ecotypes show a strong depth distribution, with WCB dominant at ≥ 200 m depth and WCA most abundant in surface (5–100 m) waters. The NP ecotype was found throughout the water column with the highest abundance in summer, and was the only ecotype showing a correlation with measured nitrification rates. We also found three abundant taxa related to Nitrospina—the major nitrite‐oxidizing bacteria in the ocean; these showed clear connections to each of the three Thaumarchaeotaecotypes, suggesting a specific relationship between both steps of nitrification. Our results support the importance of ecotype‐based analysis of Thaumarchaeotaand show that their abundance and distribution are controlled based on their water column position, with a distinct shift at 50 m between euphotic and mesopelagic depths.

Ecological factors contributing to depth-related diversification of marine Thaumarchaeotapopulations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity—water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters—were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeotaand heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobiaand Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and NitrospinaOTUs. Even at depths where WCB-like Thaumarchaeotadominated, NitrospinaOTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.

Ecological factors contributing to depth-related diversification of marine Thaumarchaeotapopulations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity—water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters—were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeotaand heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobiaand Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and NitrospinaOTUs. Even at depths where WCB-like Thaumarchaeotadominated, NitrospinaOTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.

Photosynthesis in the surface ocean converts atmospheric CO2into organic particles, with the fraction sinking to depth representing a major part of the ocean's biological pump. Although sinking particles are known to be altered by attached‐bacteria during transit, most prior organic geochemical data indicated only minor replacement of plankton‐derived particles by bacterial material. We exploit bacteria‐specific biomarkers (d‐amino acids) in a multi‐year sediment trap in the Pacific Ocean (1,200 m) and suggest a different view. Major d‐amino acids were consistently measured at abundance demonstrating widespread accumulation of bacterial material in sinking particles. Bacterial detritus was estimated to account for up to 19% of particulate organic carbon and up to 36% of particulate nitrogen, much higher than cell count‐based values. The bacterial relative contribution increased with decreasing export production. Our results indicate that bacterial material constitutes an underappreciated component of the biological pump, a role expected to rise as the ocean warms. Phytoplankton photosynthesis in the surface ocean plays a critical role in stabilizing atmospheric CO2. It converts CO2into organic particles that sink and are reworked by colonizing bacteria. Bacteria respire most particles back to CO2while also transforming some into their cell components. Although the involvement of bacteria can replace the plankton‐derived particles to bacterial material, most past organic geochemical data have suggested that the deep‐sea particles are still comprised mainly of plankton remnants. This renders the contribution of bacterial material to total particle export an unresolved and yet important question, because the source and composition of particles are important to their fate in the ocean. Here, we analyzed bacteria‐specific molecules in deep‐sea sinking particles and found that bacterial organic matter actually made up a large fraction of the particles. In addition, the relative contribution of bacterial material to the sinking particles increased as the total carbon export decreased. This has important implications for the future ocean carbon cycle, because modeling work predicts a scenario of lower carbon export to the deep sea as the ocean warms. In this context, our findings imply a greater importance of bacteria in marine organic matter export and sequestration in a warming ocean. We exploit d‐amino acid biomarkers in multi‐year deep‐sea sediment trap time series to evaluate bacterial contribution to total exportBacterial detritus accounts for up to 19 ± 8% of sinking POC and up to 36 ± 14% of PN, making up a large unrecognized part of biological pumpThe relative contribution of bacterial detritus to sinking particles increases with decreased export production We exploit d‐amino acid biomarkers in multi‐year deep‐sea sediment trap time series to evaluate bacterial contribution to total export Bacterial detritus accounts for up to 19 ± 8% of sinking POC and up to 36 ± 14% of PN, making up a large unrecognized part of biological pump The relative contribution of bacterial detritus to sinking particles increases with decreased export production

A simple combination of wind‐driven nutrient upwelling, surface currents, and plankton growth/grazing equations generates zooplankton patchiness and hotspots in coastal upwelling regions. Starting with an initial input of nitrate from coastal upwelling, growth and grazing equations evolve phytoplankton and zooplankton over time and space following surface currents. The model simulates the transition from coastal (large phytoplankton, e.g., diatoms) to offshore (picophytoplankton and microzooplankton) communities, and in between generates a large zooplankton maximum. The method was applied to four major upwelling systems (California, Peru, Northwest Africa, and Benguela) using latitudinal estimates of wind‐driven nitrate supply and satellite‐based surface currents. The resulting zooplankton simulations are patchy in nature; areas of high concentrations coincide with previously documented copepod and krill hotspots. The exercise highlights the importance of the upwelling process and surface currents in shaping plankton communities. Plankton growth and grazing equations initialized by coastal nitrate supply represent offshore plankton succession in upwelling systemsWhen coupled with surface currents, the model simulates a patchy zooplankton distribution and known zooplankton hotspotsSurface currents are a key driver of zooplankton hotspots Copepods and krill are important prey species for a diverse array of predators and a key link in oceanic food webs. These zooplankton concentrate in “hotspots” that draw fish, marine mammals, and other predators. Here we present results from a simple ecosystem model that is coupled to winds and surface currents estimated from satellite. When applied to coastal upwelling systems (California, Peru, Northwest Africa, and Benguela), the model predicts locations of zooplankton hotspots that are very similar to those identified from ship‐based surveys. The results indicate that surface currents are a key driver of zooplankton spatial distribution.

During 2014 exceptionally warm water temperatures developed across a wide area off the California coast and within San Francisco Bay (SFB) and persisted into 2016. Observations and numerical model output are used to document this warming and determine its origins. The coastal warming was mostly confined to the upper 100 m of the ocean and was manifested strongly in the two leading modes of upper ocean (0–100 m) temperature variability in the extratropical eastern Pacific. Observations suggest that the coastal warming in 2014 propagated into nearshore regions from the west while later indicating a warming influence that propagated from south to north into the region associated with the 2015–2016 El Niño event. An analysis of the upper ocean (0–100 m) heat budget in a Regional Ocean Modeling System (ROMS) simulation confirmed this scenario. The results from a set of sensitivity runs with the model in which the lateral boundary conditions varied supported the conclusions drawn from the heat budget analysis. Concerning the warming in the SFB, an examination of the observations and the heat budget in an unstructured‐grid numerical model simulation suggested that the warming during the second half of 2014 and early 2016 originated in the adjacent California coastal ocean and propagated through the Golden Gate into the Bay. The finding that the coastal and Bay warming are due to the relatively slow propagation of signals from remote sources raises the possibility that such warming events may be predictable many months or even several seasons in advance. The origins of the exceptionally warm water temperatures that developed off the California coast and in San Francisco Bay were studied using observations and computer model experiments. The coastal warming was mostly confined to the upper ocean. The coastal warming in 2014 was found to have moved into coastal waters from further offshore in the northeastern Pacific. Warming persisted into 2015‐2016 as a warming influence from the south associated with the 2015‐16 El Niño event in the tropical Pacific Ocean. The model experiments suggested confirmed that propagation of the warming signals from the west and north into the California coastal ocean and suggested that the warming in San Francisco Bay was found to have originated primarily in the adjacent California coastal ocean. The finding that the coastal and Bay warming are due to the relatively slow propagation of signals from remote sources raises the possibility that such warming events may be predictable many months or even several seasons in advance. Observations and model heat budget analyses show warming to be a result of propagation of signals from the west (Blob) and south (El Niño)Results from model sensitivity experiments support the conclusions drawn from the heat budget analysesThe relatively slow propagation of the remote signals means that such warming events may be predictable months in advance

We organized environmental observations (Sea Surface Temperature, chlorophyll concentration, and primary productivity) and biological diversity indices based on reconstructed fisheries landings obtained from the Sea Around Usproject to address two objectives: 1) to understand whether adjacent Large Marine Ecosystems (LMEs) of the Americas form megaregions for assemblages of commercially-valuable fish; and 2) to assess changes in the diversity of fisheries landings in LMEs of the Americas over time (1982 to 2010). To test for similarities between LMEs, we used the seascape approach of unsupervised clustering of annual mean environmental observations and fisheries-derived diversity indices. Beta-diversity estimates based on fisheries landings were used to evaluate the degree to which species spanned LMEs. Temporal trends were computed for each dataset by linear least-squares. Three megaregions emerged when considering similarities in species composition of fisheries landings, fisheries-derived diversity indices, and characteristic environmental conditions among LMEs. These include (A) the South Brazil Shelf, East Brazil Shelf, and North Brazil Shelf LMEs, (B) the Gulf of Mexico and Southeast U.S. Continental Shelf LMEs, and (C) the Northeast U.S. Continental Shelf, Scotian Shelf, and Newfoundland-Labrador Shelf LMEs. No megaregions emerged for the Pacific Ocean. While there were some shared species assemblages between the California Current and the Gulf of Alaska, the Gulf of California, and the Pacific Central-American Coastal LMEs, these showed different average environmental conditions and fishery-derived diversity indices, so they did not cluster as a megaregion. In the Pacific Ocean, the high dissimilarity in the fisheries is in part related to different top-down pressures and strong regional differences in oceanographic properties, including upwelling and impacts of El-Niño Southern Oscillation events. Overall, between 1982 and 2010, seven LMEs diversified their fisheries (Pacific Central-America Coastal, Patagonian Shelf, South Brazil Shelf, East Brazil Shelf, North Brazil Shelf, Southeast U.S. Continental Shelf, and Newfoundland-Labrador Shelf). This may be due to a number of reasons including decreasing fishing pressure but expansion of target stocks due to management quotas, changes in regional markets, competition, effort, or a decrease in particular target stocks. Three LMEs showed increasingly less diversified fisheries, namely the California Current, the Northeast U.S. Continental Shelf, and the Caribbean Sea LMEs. While in some cases this may be related to historical overfishing, such as in the Northeast U.S. Continental Shelf LME, the California Current LME has been subjected to strong and conservative management practices. The Caribbean Sea LME was likely subjected to heavy fishing at a time of rapid environmental change.

Photosynthetic conversion of CO2to organic carbon and the transport of this carbon from the surface to the deep ocean is an important regulator of atmospheric CO2. To understand the controls on carbon fluxes in a productive region impacted by upwelling, we measured biological productivity via multiple methods during a cruise in Monterey Bay, California. We quantified net community production and gross primary production from measurements of O2/Ar and O2triple isotopes ( 17Δ), respectively. We simultaneously conducted incubations measuring the uptake of 14C, 15NO3−, and 15NH4+, and nitrification, and deployed sediment traps. At the start of the cruise (Phase 1) the carbon cycle was at steady state and the estimated net community production was 35(10) and 35(8) mmol C m−2d−1from O2/Ar and 15N incubations, respectively, a remarkably good agreement. During Phase 1, net primary production was 96(27) mmol C m−2d−1from C uptake, and gross primary production was 209(17) mmol C m−2d−1from 17Δ. Later in the cruise (Phase 2), recently upwelled water with higher nutrient concentrations entered the study area, causing 14C and 15NO3−uptake to increase substantially. Continuous O2/Ar measurements revealed submesoscale variability in water mass structure and likely productivity in Phase 2 that was not evident from the incubations. These data demonstrate that O2/Ar and 15Nincubation‐based NCP estimates can give equivalent results in an N‐limited, coastal system, when the nonsteady state O2fluxes are negligible or can be quantified. We measured gross and net productivity using a combination of in situ gas tracer, incubation, and sediment trap methods in Monterey BayNet community production estimates from oxygen/argon ratios and nitrate incubations agreed very well when the system was at steady stateFollowing the arrival of recently upwelled water to the study area, incubation‐based carbon and nitrogen uptake increased

Synchrony in the second modes of an empirical orthogonal function (EOF) analysis of global physical and biological properties is described for the 1993–2010 time period. High correlations are found between the El Niño Modoki index and principal component time series of sea surface temperature, sea surface salinity, photosynthetically active radiation, precipitation, surface currents, surface chlorophyll concentration, and equatorial temperature profiles. Spatial patterns indicate that the second mode is also associated with the North Pacific Gyre Oscillation (NPGO). Biological changes during traditional El Niños (first EOF mode) have been explained on the basis of strong and coherent variations in thermocline depth, wind‐driven upwelling and light, but changes associated with the second mode are more subtle and complex. Equatorial temperature profiles indicate that the warming is confined to the mixed layer and that changes in thermocline depth are small. The biological changes associated with the second mode may be driven by a combination of weak perturbations to vertical nutrient supply and the strength of subtropical gyres. In the western tropical Pacific, the site of some of the strongest perturbations, the biological changes can be associated with the occurrence and thickness of barrier layers and to island effects downstream of the Kiribati Islands. Globally integrated impacts of the second mode are much weaker than those associated with the traditional ENSO. During the positive phase, chlorophyll is strongly enhanced in the tropics and weakly enhanced at the global scale in sharp contrast to traditional El Niño effects. The analysis improves our understanding of global‐scale physical and biological coupling associated with the so‐called El Niño Modoki and the NPGO. The second global EOF mode in physics and biology is related to ENSO ModokiThe integrated global‐scale impacts of this mode and ENSO Modoki are very weakMain drivers of biological variability are circulation and barrier layer changes

Inorganic polyphosphate (polyP) is a biopolymer of tens or hundreds of phosphate (Pi) residues linked by highenergy phosphoanhydride bonds. PolyP has been studied mainly in prokaryotes but it is present in all species of the three domains of life. In bacteria, polyP and its processing enzymes play important roles in cellular metabolism as well as in pathogenesis. The genomes of many bacterial species, including pathogens, encode orthologs of the main polyPsynthesizing enzyme, PPK1. This enzyme has been studied in E. coli and its metabolic inhibitors have been reported. The high degree of identity between the PPK1 orthologs in some of the major pathogenic species has prompted the knockout of their ppk1 genes to determine the dependence of virulence on polyP. Although viable, mutants lacking the ppk1 gene have reduced levels of polyP and exhibit multiple structural, functional and virulence defects. The emergence of multi-drug resistant (MDR) bacteria is the result of antibiotic overuse. Therefore, novel approaches are much needed to tackle them. One of these combines the reduction of bacterial virulence while simultaneously increasing susceptibility to host defenses instead of killing the pathogen. Considering that no PPK1 orthologs have been identified in higher-order eukaryotes, PPK1 exhibits an enormous potential as a novel target for antimicrobial drug design. In this review we focus on the current state of the art regarding polyP deficiency in pathogenic bacteria and attempts to design inhibitors targeting enzymes responsible for the synthesis of polyP in bacteria.

Marine photosynthetic plankton are responsible for approximately 50 petagrams (1015) of carbon per year of net primary production, an amount equivalent to that on land. This primary production supports essentially all life in the oceans and profoundly affects global biogeochemical cycles and climate. This review discusses the general distribution of primary production in the sea, the processes that regulate this distribution, and how marine primary production is sensitive to climate variability and change. Statistical modes of ocean variability and their characteristic interannual to multi-decadal timescales over the last century are described. Recent in situ and satellite time-series of primary production can be clearly linked to interannual ocean variability. Global marine primary production appears to have increased over the past several decades in association with multi-decadal variations. A paleoclimate record extends discussion to the centennial scale, providing contrasting insights into how marine primary production might vary in the future.

In the California Current Ecosystem, krill represent a key link between primary production and higher trophic level species owing to their central position in the food web and tendency to form dense aggregations. However, the strongly advective circulation associated with coastal upwelling may decouple the timing, occurrence, and persistence of krill hotspots from phytoplankton biomass and nutrient sources. Results from a coupled physical‐biological model provide insights into fundamental mechanisms controlling the phenology of krill hotspots in the California Current Ecosystem, and their sensitivity to alongshore changes in coastal upwelling intensity. The simulation indicates that dynamics controlling krill hotspot formation, intensity, and persistence on seasonal and interannual timescales are strongly heterogeneous and related to alongshore variations in upwelling‐favorable winds, primary production, and ocean currents. Furthermore, regions promoting persistent krill hotspot formation coincide with increased observed abundance of top predators, indicating that the model resolves important ecosystem complexity and function. The California Current region off the west coast of North America is one of the four main upwelling systems of the World Ocean, and it supports a productive marine ecosystem including economically important fisheries. A numerical model representing the effects of ocean circulation on plankton dynamics is applied to explain how locally enhanced nutrient supply and transport by nearshore currents creates regions favoring the aggregation of krill, a key zooplankton species responsible for transferring energy between the base of the food web and marine predators. The two main conclusions from the study are that (1) the location, timing, and intensity of krill aggregations vary greatly both seasonally and from year to year and (2) regions of enhanced krill abundances in the model coincide with an increased observed presence of whales and seabirds, which suggest that these aggregations may support broader ecosystem hotspots. Krill hotspot formation and persistence are strongly heterogeneous in space and timeKrill hotspots are shaped by local upwelling variability and regional circulationKrill hotspots coincide with observed distributions of marine mammals and seabirds

A three‐dimensional physical‐biological model was used to study the dynamics of physical and biological processes in the central California Current System (CCS) from 1993 to 2016 and investigate its response to different climate modes. The variations of new production (NP) and nitrate fluxes in the central CCS showed robust seasonal and interannual variability. In the coastal upwelling region (0–150 km offshore), the variability of NPwas associated with both coastal upwelling and alongshore nitrate advection. In the coastal transition zone (150–300 km offshore), it was related to nitrate fluxes that were determined primarily by the physics rather than nitrate concentration, with vertical mixing and offshore transport being dominant factors. In the offshore oceanic region (California Current; 300–1,000 km offshore), nitrate concentrations played a more important role in the variations of nitrate fluxes, and the NPvariability was dominated by the nutrient supplies of vertical mixing and lateral transports. Although El Niño–Southern Oscillation can affect coastal upwelling, alongshore currents, and nitrate fluxes, the coastal NPresponded to El Niño–Southern Oscillation mostly in the frequencies of <1 and >6 years. Pacific Decadal Oscillation and North Pacific Gyre Oscillation may affect the CCS ecosystem through large‐scale winds and stratification, modifying the circulation in the upper layer and leading to changes in nitrate concentration and NP. The central California Current System (CCS) is one of the most productive ecosystems in the global ocean, because strong coastal upwelling brings a large amount of subsurface nutrients to the sunlit layer and supports abundant phytoplankton growth. Understanding the response of this system to varying physical forcing is of great importance in predicting how marine ecosystem will evolve with global change. By using a three‐dimensional model, this study demonstrates that biological properties in the central CCS show strong interannual variability. The dominant driver leading to this variability varies in different subregions moving from the coast to offshore. Over the CCS, climate variability can cause variations in surface wind, stratification, sea level, and circulations at different time scales, which contribute to changes in nutrient supply and phytoplankton production. The central CCS showed strong interannual variability from 1993 to 2016From the coast to offshore, dominant controlling mechanisms for NP variability changedENSO, PDO, and NPGO affected NP through different dynamics with different dominant frequencies

Coupled measurements of nitrate (NO3−), nitrogen (N), and oxygen (O) isotopic composition (δ15NNO3and δ18ONO3) were made in surface waters of Monterey Bay to investigate multiple N cycling processes occurring within surface waters. Profiles collected throughout the year at three sites exhibit a wide range of values, suggesting simultaneous and variable influence of both phytoplankton NO3−assimilation and nitrification within the euphotic zone. Specifically, increases in δ18ONO3were consistently greater than those in δ15NNO3. A coupled isotope steady state box model was used to estimate the amount of NO3−supplied by nitrification in surface waters relative to that supplied from deeper water. The model highlights the importance of the branching reaction during ammonium (NH4+) consumption, in which NH4+either serves as a substrate for regenerated production or for nitrification. Our observations indicate that a previously unrecognized proportion of nitrate‐based productivity, on average 15 to 27%, is supported by nitrification in surface waters and should not be considered new production. This work also highlights the need for a better understanding of isotope effects of NH4+oxidation, NH4+assimilation, and NO3−assimilation in marine environments.