Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect

Balancing end-to-end budgets of the Georges Bank ecosystem

Author Posting. © Elsevier, 2007. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 74 (2007): 423-448, doi:10.1016/j.pocean.2007.05.003.Oceanographic regimes on the continental shelf display a great range in the time scales of physical exchange, biochemical processes and trophic transfers. The close surface-to-seabed physical coupling at intermediate scales of weeks to months means that the open ocean simplification to a purely pelagic food web is inadequate. Top-down trophic depictions, starting from the fish populations, are insufficient to constrain a system involving extensive nutrient recycling at lower trophic levels and subject to physical forcing as well as fishing. These pelagic-benthic interactions are found on all continental shelves but are particularly important on the relatively shallow Georges Bank in the northwest Atlantic. We have generated budgets for the lower food web for three physical regimes (well mixed, transitional and stratified) and for three seasons (spring, summer and fall/winter). The calculations show that vertical mixing and lateral exchange between the three regimes are important for zooplankton production as well as for nutrient input. Benthic suspension feeders are an additional critical pathway for transfers to higher trophic levels. Estimates of production by mesozooplankton, benthic suspension feeders and deposit feeders, derived primarily from data collected during the GLOBEC years of 1995-1999, provide input to an upper food web. Diets of commercial fish populations are used to calculate food requirements in three fish categories, planktivores, benthivores and piscivores, for four decades, 1963-2002, between which there were major changes in the fish communities. Comparisons of inputs from the lower web with fish energetic requirements for plankton and benthos indicate that we obtained reasonable agreement for the last three decades, 1973 to 2002. However, for the first decade, the fish food requirements were significantly less than the inputs. This decade, 1963-1972, corresponds to a period characterized by a strong Labrador Current and lower nitrate levels at the shelf edge, demonstrating how strong bottom-up physical forcing may determine overall fish yields.The research was done under the aegis of the U.S.-GLOBEC Northwest Atlantic Georges Bank Study, a program sponsored jointly by the U.S. National Science Foundation and the U.S. National Oceanic and Atmospheric Administration. We acknowledge NOAA-CICOR award NA17RJ1233 (J.H. Steele), NSF awards OCE0217399 (D.J. Gifford), OCE0217122 (J.J. Bisagni) and OCE0217257 (M.E. Sieracki). W.T. Stockhausen was supported by the NOAA Sponsored Coastal Ocean Research Program

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Major contribution of diatom resting spores to vertical flux in the sub-polar North Atlantic

The mass sinking of phytoplankton cells following blooms is an important source of carbon to the ocean's interior, with some species contributing more to the flux of particulate organic carbon (POC) than others. During the 2008 North Atlantic Bloom Experiment in the Iceland Basin, we examined plankton community composition from surface waters and from sediment traps at depths down to 750 m. Samples collected with neutrally buoyant Lagrangian sediment traps captured a major flux event. Diatoms comprised ≥99% of cell flux into the sediment traps, with vegetative cells and resting spores of the genus Chaetoceros contributing 50–95% of cell flux. Resting spores of one species, identified as Chaetoceros aff. diadema, were dominant, comprising 35–92% of cell flux. The flux of resting spores ranged from 2 to 63 mg C m−2 day−1 and was significantly correlated with POC flux (p=0.003). Over the course of 10 days, the flux of resting spores increased by 26 fold, suggesting that the cells sank en masse, possibly in aggregates. In contrast, vegetative cells of C. aff. diadema sampled from surface waters during the period preceding the flux event generally comprised <1% of the diatom community and never exceeded 5.2%. Resting spores of C. aff. diadema were rarely observed in surface waters but their concentrations increased with depth (to 200 m) below the mixed layer. This increase in resting spore abundance, coupled with increased dissolved silicic acid concentrations at depth, suggest that the morphological changes associated with spore formation may have occurred in the mesopelagic zone, while cells were sinking. The values of variable fluorescence (Fv/Fm) measured on sediment trap material dominated by resting spores were among the highest values measured in the study area at any depth. This, in combination with the rapid germination of resting spores in ship-board incubations, suggests that vegetative cells were not physiologically stressed during spore formation. The degradation-resistant, heavily silicified resting spore valves explain the high relative contribution of C. aff. diadema resting spores to total plankton carbon at depth. These data emphasize the ephemeral nature of organic carbon flux events in the open ocean and highlight how non-dominant species and transient life stages can contribute more to carbon flux than their more abundant counterparts

Rapid growth rates of aerobic anoxygenic phototrophs in the ocean

We analysed bacteriochlorophyll diel changes to assess growth rates of aerobic anoxygenic phototrophs in the euphotic zone across the Atlantic Ocean. The survey performed during Atlantic Meridional Transect cruise 16 has shown that bacteriochlorophyll in the North Atlantic Gyre cycles at rates of 0.91–1.08 day1 and in the South Atlantic at rates of 0.72–0.89 day1. In contrast, in the more productive equatorial region and North Atlantic it cycled at rates of up to 2.13 day1. These results suggest that bacteriochlorophyll-containing bacteria in the euphotic zone of the oligotrophic gyres grow at rates of about one division per day and in the more productive regions up to three divisions per day. This is in striking contrast with the relatively slow growth rates of the total bacterial community. Thus, aerobic anoxygenic phototrophs appear to be a very dynamic part of the marine microbial community and due to their rapid growth, they are likely to be larger sinks for dissolved organic matter than their abundance alone would predict.<br/

RAPID: Research on Automated Plankton Identification

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