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

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

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

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

What is the metabolic state of the oligotrophic ocean? A debate

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Marine Science 5 (2013):525-533, doi:10.1146/annurev-marine-121211-172331.For more than a decade there has been controversy in oceanography regarding the metabolic state of the oligotrophic gyres of the open sea. Here we review background on this controversy, commenting on several issues to set the context for a moderated debate between two groups of scientists. In a companion paper, Williams et al (2013) take the view that the oligotrophic subtropical gyres of the global ocean exhibit a state of net autotrophy, that is, the gross primary production (GPP) exceeds community respiration (R), when averaged over some suitably extensive region and over a long duration. Duarte et al (2013) take the opposite view, that the oligotrophic subtropical gyres are net heterotrophic, with R exceeding the GPP. This idea -- that large, remote areas of the upper ocean could be net heterotrophic raises of host of fundamental scientific questions about the metabolic processes of photosynthesis and respiration that underlie ocean ecology and global biogeochemistry. The question remains unresolved, in part, because the net state is finely balanced between large opposing fluxes and most current measurements have large uncertainties. This challenging question must be studied against the background of large, anthropogenically-driven changes in ocean ecology and biogeochemistry Current trends of anthropogenic change make it an urgent problem to solve and also greatly complicate finding that solution.The authors acknowledge support from the U.S. National Science Foundation through the Center for Microbial Oceanography Research and Education (C-MORE), an NSF Science and Technology Center (EF-0424599), and NSF award OPP 0823101 (Palmer LTER) from the Antarctic Organisms and Ecosystems Program

Assessing sources and ages of organic matter supporting river and estuarine bacterial production: A multiple-isotope (D14C, d13C, and d15N) approach

We used radiocarbon (D14C) and stable isotopic (d13C, d15N) signatures of bacterial nucleic acids to estimate the sources and ages of organic matter (OM) assimilated by bacteria in the Hudson River and York River estuary. Dualisotope plots of D14C and d13C coupled with a three-source mixing model resolved the major OM sources supporting bacterial biomass production (BBP). However, overlap in the stable isotopic (d13C and d15N) values of potential source end members (i.e., terrestrial, freshwater phytoplankton, and marsh-derived) prohibited unequivocal source assignments for certain samples. In freshwater regions of the York, terrigenous material of relatively recent origin (i.e., decadal in age) accounted for the majority of OM assimilated by bacteria (49–83%). Marsh and freshwater planktonic material made up the other major source of OM, with 5–33% and 6–25% assimilated, respectively. In the mesohaline York, BBP was supported primarily by estuarine phytoplankton–derived OM during spring and summer (53–87%) and by marsh-derived OM during fall (as much as 83%). Isotopic signatures from higher salinity regions of the York suggested that BBP there was fueled predominantly by either estuarine phytoplankton-derived OM (July and November) or by material advected in from the Chesapeake Bay proper (October). In contrast to the York, BBP in the Hudson River estuary was subsidized by a greater portion (up to ;25%) of old (;24,000 yr BP) allochthonous OM, which was presumably derived from soils. These findings collectively suggest that bacterial metabolism and degradation in rivers and estuaries may profoundly alter the mean composition and age of OM during transport within these systems and before its export to the coastal ocean

Modeling the response of top-down control exerted by gelatinous carnivores on the Black Sea pelagic food web

Recent changes in structure and functioning of the interior Black Sea ecosystem are studied by a series of simulations using a one-dimensional, vertically resolved, coupled physical-biochemical model. The simulations are intended to provide a better understanding of how the pelagic food web structure responds to increasing grazing pressure by gelatinous carnivores (medusae Aurelia aurita and ctenophore Mnemiopsis leidyi) during the past 2 decades. The model is first shown to represent typical eutrophic ecosystem conditions of the late 1970s and early 1980s. This simulation reproduces reasonably well the observed planktonic food web structure at a particular location of the Black Sea for which a year-long data set is available from 1978. Additional simulations are performed to explore the role of the Mnemiopsis-dominated ecosystem in the late 1980s. They are also validated by extended observations from specific years. The results indicate that the population outbreaks of the gelatinous species, either Aurelia or Mnemiopsis, reduce mesozooplankton grazing and lead to increased phytoplankton blooms as observed throughout the 1980s and 1990s in the Black Sea. The peaks of phytoplankton, mesozooplankton, Noctiluca, and gelatinous predator biomass distributions march sequentially as a result of prey-predator interactions. The late winter diatom bloom and a subsequent increase in mesozooplankton stocks are robust features common to all simulations. The autotrophs and heterotrophs, however, have different responses during the rest of the year, depending on the nature of grazing pressure exerted by the gelatinous predators. In the presence of Mnemiopsis, phytoplankton have additional distinct and pronounced bloom episodes during the spring and summer seasons. These events appear with a 2 month time shift in the ecosystem prior to introduction of Mnemiopsis

Long-term studies of the marine ecosystem along the west Antarctic Peninsula

Author Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 55 (2008): 1945-1948, doi:10.1016/j.dsr2.2008.05.014.Articles in this volume focus on longer-term studies of the marine ecosystem of the continental shelf west of the Antarctic Peninsula, principally by the Palmer, Antarctica Long- Term Ecological Research project (Ross et al., 1996; Ducklow et al., 2007). There is a rich history of oceanographic and ecological research in the Bellingshausen Sea region and on the continental shelf dating back to the 19th and early 20th centuries (El-Sayed, 1996). The modern era of scientific research started with the British Discovery Investigations of 1925-37 (Hardy, 1967), and included classic studies of phytoplankton (Hart, 1934) and krill (Marr, 1962). Hart’s report presciently suggested primary producers could be limited by iron availability. El-Sayed (1996) dissects the subsequent history of oceanographic research up to the advent of the Southern Ocean GLOBEC (Hofmann et al., 2001; Hofmann et al., 2004) and JGOFS (Anderson and Smith Jr., 2001) programs. The period from the 1970’s to the mid-90’s was dominated by expeditionary and process-level studies of particular regions and processes extending over a few seasons to a few years at most. The Research on Antarctic Coastal Ecosystem Rates (RACER) Program (Huntley et al., 1991; Karl, 1991) is the outstanding example of this mode of research, having focused on determination of key rate processes as a new approach to understanding ecosystem dynamics (Karl et al., 1991a; Karl et al., 1991b). RACER was a direct predecessor and major influence on Palmer LTER, GLOBEC and JGOFS. What was lacking in Antarctic waters, as in most other regions and ocean provinces were sustained, long-term observations of a variety of ocean properties and rates, conducted in the context of hypothesis-driven, experimental science (Ducklow et al., 2008a). The creation of the US LTER Network in 1980 (Magnuson, 1990) made this possible.Observations reported in this volume were supported by NSF Grants OPP-90-11927 and OPP- 96-32763 to the University of California-Santa Barbara and OPP-02-17282 to the Virginia Institute of Marine Science