The JGOFS North Atlantic Bloom Experiment: An overview

The North Atlantic Bloom Experiment (NABE) of JGOFS presents a unique opportunity and challenge to the data management community because of the diversity and large size of biogeochemical data sets collected. NABE was a pilot study for JGOFS and has also served as a pilot study within the U.S. NODC for management and archiving of the data sets. Here I present an overview to some of the scientific results of NABE, which will be published as an Introduction to a special volume of NABE results in Deep-Sea Research later this year. An overview of NABE data management is given elsewhere in the present report. This is the first collection of papers from the Joint Global Ocean Flux Study (JGOFS). Formed as an international program in 1987, JGOFS has four principal elements: modelling and data management, multidisciplinary regional process studies, a global survey of biogeochemical properties and long-term time series observatories. In 1989-1990 JGOFS conducted a pilot process study of the spring phytoplankton bloom, the North Atlantic Bloom Experiment (NABE). JGOFS decided to conduct a large scale, internationally-coordinated pilot study in the North Atlantic because of its proximity to the founding nations of the project, the size and predictability of the bloom and its fundamental impact on ocean bio-geochemistry (Billett et al., 1983; Watson and Whitfield, 1985; Pfannkuche, 1992). In 1989, six research vessels from Canada, Germany, The Netherlands, the United Kingdom and the USA and over 200 scientists and students from more than a dozen nations participated in NABE. Some of their initial results are reported in this volume

Ultrahigh bacterial production in a eutrophic subtropical Australian river : does viral lysis short-circuit the microbial loop?

Author Posting. © American Society of Limnology and Oceanography, 2011. This article is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 56 (2011): 1115-1129, doi:10.4319/lo.2011.56.3.1115.We studied trophic dynamics in a warm eutrophic subtropical river (Bremer River, Australia) to determine potential sources of dissolved organic carbon (DOC) and the fate of heterotrophic bacterial production. Sustained high rates of bacterial production suggested that the exogenous DOC was accessible (labile). Bacterial specific growth rates (0.2 h−1 to 1.8 h−1) were some of the highest measured for natural aquatic ecosystems, which is consistent with high respiration rates. Bacteria consumed 10 times more organic carbon than that supplied by the daily algal production, a result that implies that terrestrial sources of organic carbon were driving the high rates of bacterial production. Viruses (1011 L−1) were 10 times more abundant than bacteria; the viral to bacterial ratio ranged from 3.5 to 12 in the wet summer and 11 to 35 in the dry spring weather typical of eutrophic environments. Through a combination of high bacterial respiration and phage lysis, a continuous supply of terrestrial DOC was lost from the aquatic ecosystem in a CO2-vented bacterial–viral loop. Bacterial processing of DOC in subtropical rivers may be contributing disproportionately large amounts of CO2 to the global carbon cycle compared to temperate freshwater ecosystems.Thanks go to the Coastal Cooperative Research Centre and the Healthy Waterways Partnership for their funding

Single-cell physiological structure and growth rates of heterotrophic bacteria in a temperate estuary (Waquoit Bay, Massachusetts)

Author Posting. © American Society of Limnology and Oceanography, 2011. This article is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 56 (2011): 37-48, doi:10.4319/lo.2011.56.1.0037.Flow cytometric determinations of membrane integrity, nucleic acid content, and respiratory activity were combined with dilution cultures in Waquoit Bay Estuary (Massachusetts) to estimate specific growth rates of total, live, high (HNA), and low (LNA) nucleic acid content and actively respiring (CTC+) cells. Bacterial abundance ranged from 106 to 107 cells mL-1, with live cells generally contributing > 85% to total numbers, 42-82% HNA cells, and 3-36% CTC+ cells. Specific growth rates (µ) from all physiological groups were positively correlated, but they showed different temperature dependences, with activation energies ranging from 0.28 (live) to 0.97 eV (LNA). The µ values of live cells (0.14-2.40 d-1) were similar to those of total bacteria (0.06-1.53 d-1). LNA bacteria were not dormant but showed positive growth in most experiments, although HNA cells greatly outgrew LNA cells (µ ranges of 0.28-2.26 d-1 vs. 0-0.69 d-1), and CTC+ cells showed the highest values (0.12-2.65 d-1). Positive correlations of HNA bacteria µ with total and phytoplankton-derived dissolved organic carbon support the previously hypothesized strong bottom-up control of HNA cells. Bacterial production estimated from leucine incorporation and empirical conversion factors agreed well with estimates based on growth rates. HNA cells were always responsible for the largest share of bacterial production in the estuary. The contribution of CTC+ cells significantly increased with temperature in the 7-27°C range, reaching values of 40% at temperatures higher than 20°C.This study was supported by the Spanish Ministry of Science and Innovation (MICINN) sabbatical stay program (to X.A.G.M.), National Science Foundation Office of Polar Programs grant 0823101 to H.W.D., and by the Marine Biological Laboratory

Seasonal succession of free-living bacterial communities in coastal waters of the Western Antarctic Peninsula

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR

Two decades of inorganic carbon dynamics along the West Antarctic Peninsula

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 12 (2015): 6761-6779, doi:10.5194/bg-12-6761-2015.We present 20 years of seawater inorganic carbon measurements collected along the western shelf and slope of the Antarctic Peninsula. Water column observations from summertime cruises and seasonal surface underway pCO2 measurements provide unique insights into the spatial, seasonal, and interannual variability in this dynamic system. Discrete measurements from depths > 2000 m align well with World Ocean Circulation Experiment observations across the time series and underline the consistency of the data set. Surface total alkalinity and dissolved inorganic carbon data showed large spatial gradients, with a concomitant wide range of Ωarag (< 1 up to 3.9). This spatial variability was mainly driven by increasing influence of biological productivity towards the southern end of the sampling grid and meltwater input along the coast towards the northern end. Large inorganic carbon drawdown through biological production in summer caused high near-shore Ωarag despite glacial and sea-ice meltwater input. In support of previous studies, we observed Redfield behavior of regional C / N nutrient utilization, while the C / P (80.5 ± 2.5) and N / P (11.7 ± 0.3) molar ratios were significantly lower than the Redfield elemental stoichiometric values. Seasonal salinity-based predictions of Ωarag suggest that surface waters remained mostly supersaturated with regard to aragonite throughout the study. However, more than 20 % of the predictions for winters and springs between 1999 and 2013 resulted in Ωarag < 1.2. Such low levels of Ωarag may have implications for important organisms such as pteropods. Even though we did not detect any statistically significant long-term trends, the combination of on\-going ocean acidification and freshwater input may soon induce more unfavorable conditions than the ecosystem experiences today.We gladly acknowledge support from the National Science Foundation Polar Programs (NSF OPP-90-11927, OPP-96-32763, OPP-02-17282, OPP-08-23101, and PLR-1440435). T. Takahashi and the Ship of Opportunity Observation Program (SOOP) were supported by a grant (NA10OAR4320143) from the United States NOAA

Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

Taxonomic marker gene studies, such as the 16S rRNA gene, have been used to successfully explore microbial diversity in a variety of marine, terrestrial, and host environments. For some of these environments long term sampling programs are beginning to build a historical record of microbial community structure. Although these 16S rRNA gene datasets do not intrinsically provide information on microbial metabolism or ecosystem function, this information can be developed by identifying metabolisms associated with related, phenotyped strains. Here we introduce the concept of metabolic inference; the systematic prediction of metabolism from phylogeny, and describe a complete pipeline for predicting the metabolic pathways likely to be found in a collection of 16S rRNA gene phylotypes. This framework includes a mechanism for assigning confidence to each metabolic inference that is based on a novel method for evaluating genomic plasticity. We applied this framework to 16S rRNA gene libraries from the West Antarctic Peninsula marine environment, including surface and deep summer samples and surface winter samples. Using statistical methods commonly applied to community ecology data we found that metabolic structure differed between summer surface and winter and deep samples, comparable to an analysis of community structure by 16S rRNA gene phylotypes. While taxonomic variance between samples was primarily driven by low abundance taxa, metabolic variance was attributable to both high and low abundance pathways. This suggests that clades with a high degree of functional redundancy can occupy distinct adjacent niches. Overall our findings demonstrate that inferred metabolism can be used in place of taxonomy to describe the structure of microbial communities. Coupling metabolic inference with targeted metagenomics and an improved collection of completed genomes could be a powerful way to analyze microbial communities in a high-throughput manner that provides direct access to metabolic and ecosystem function

Concentrations and uptake of neutral monosaccharides along 14°W in the equatorial Pacific: Contribution of glucose to heterotrophic bacterial activity and the DOM flux

We examined concentrations and uptake of dissolved neutral monosaccharides (DNMS) in order to determine the contribution of DNMS to heterotrophic bacterial production and to the flux of dissolved organic matler (DOM) in the equatorial Pacific. DNMS concentrations were greater during El Niño‐affected months of February–April 1992 than during August–October 1992; in contrast, glucose turnover was the opposite— turnover was faster in August–October than in February–April. The variation in sugar concentrations and turnover probably resulted from El Niño‐induced changes in primary production; as El Niño waned primary production increased, which appeared to stimulate bacterial activity, especially glucose turnover, that in turn forced down DNMS concentrations. In all months, however, DNMS concentrations were low, especially compared with total dissolved organic carbon concentrations (\u3c1%). Glucose was the dominant neutral monosaccharide and alone supported 15–47% of bacterial production. Other monosaccharides apparently did not support much bacterial growth; concentrations of other sugars were low, as probably was turnover. Respiration of glucose (30–60% of uptake) and mannose (60–90%) was relatively high, suggesting that DNMS supported a large fraction of bacterial respiration as well as biomass production. These results point to the importance of DNMS and glucose in particular in supporting bacterial growth and in contributing to the flux of labile DOM

The microbial loop concept: A history, 1930–1974

The microbial loop as a leading concept in marine microbiology gained wide recognition in the 1980s, but it has roots extending back to the 1930s when microbiologists first began to take a more dynamic approach to investigating the roles of bacteria in ocean food webs and biogeochemical cycles. Here we present a history of the microbial loop concept with emphasis on the period starting in 1930, when marine bacteriologists in Russia and the West began to study explicitly the roles of marine bacteria in the sea. Selman Waksman at Woods Hole and Claude ZoBell at La Jolla relied on colony counts on agar plates as the basis of their work. We suggest that failure to accept direct microscopic evidence of high numbers of bacteria in seawater retarded conceptual development in the West well into the 1970s. Easterners pioneered direct count and radioisotopic techniques and created a dynamic marine microbiology integrating bacteria as important components of marine food webs by the 1960s. Yurii Sorokin and colleagues carried out extensive experimental studies of bacteria as food for marine grazers and provided data for Mikhail Vinogradov and his group to write the first numerical simulation models of ocean ecosystems incorporating microbial components. It had little impact on the Western modeling community, as other Russian work of the times. In spite of continuing technical shortcomings in the field, Lawrence Pomeroy constructed a new conceptual model, providing a synthesis pointing the way toward a modern view of marine microbial ecology that finally matured technically and conceptually in the West in the early 1980s

Introduction to the special issue on Antarctic oceanography in a changing world

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 3 (2012): 14-17, doi:10.5670/oceanog.2012.68."Antarctic Oceanography in a Changing World" commemorates the twentieth anniversary of the commissioning of Research Vessel Icebreaker (RVIB) Nathaniel B. Palmer and the fifteenth anniversary of Antarctic Research and Supply Vessel (ARSV) Laurence M. Gould. The addition of these two Antarctic research vessels to the US fleet in the 1990s ushered in a new era of Antarctic oceanographic research for US scientists and their international collaborators. Although several US Coast Guard icebreakers in the Arctic and Antarctic waters conduct oceanographic research, their primary mission is icebreaking to facilitate access to land-based stations. The Palmer was, and remains to this day, the first and only purpose-built US research icebreaker in Antarctic service and has been serving sea-going scientists in all areas of Antarctica's seas for two decades. The Gould has afforded reliable year-round access to Palmer Station and has conducted oceanographic research in the Antarctic Peninsula area since 1997