Beschreibung: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

Beschreibung: The concept of phytoplankton functional types has emerged as a useful approach to classifying phytoplankton. It finds many applications in addressing some serious contemporary issues facing science and society. Its use is not without challenges, however. As noted earlier, there is no universally-accepted set of functional types, and the types used have to be carefully selected to suit the particular problem being addressed. It is important that the sum total of all functional types matches all phytoplankton under consideration. For example, if in a biogeochemical study, we classify phytoplankton as silicifiers, calcifiers, DMS-producers and nitrogen fix- ers, then there is danger that the study may neglect phytoplankton that do not contribute in any significant way to those functions, but may nevertheless be a significant contributor to, say primary production. Such considerations often lead to the adoption of a category of “other phytoplankton” in models, with no clear defining traits assigned them, but that are nevertheless necessary to close budgets on phytoplankton processes. Since this group is a collection of all phytoplankton that defy classification according to a set of traits, it is difficult to model their physi- ological processes. Our understanding of the diverse functions of phytoplankton is still growing, and as we recognize more functions, there will be a need to balance the desire to incorporate the increasing number of functional types in models against observational challenges of identifying and mapping them adequately. Modelling approaches to dealing with increasing functional diversity have been proposed, for example, using the complex adaptive systems theory and system of infinite diversity, as in the work of Bruggemann and Kooijman (2007). But it is unlikely that remote-sensing approaches might be able to deal with anything but a few prominent functional types. As long as these challenges are explicitly addressed, the functional- type concept should continue to fill a real need to capture, in an economic fashion, the diversity in phytoplankton, and remote sensing should continue to be a useful tool to map them. Remote sensing of phytoplankton functional types is an emerging field, whose potential is not fully realised, nor its limitations clearly established. In this report, we provide an overview of progress to date, examine the advantages and limitations of various methods, and outline suggestions for further development. The overview provided in this chapter is intended to set the stage for detailed considerations of remote-sensing applications in later chapters. In the next chapter, we examine various in situ methods that exist for observing phytoplankton functional types, and how they relate to remote-sensing techniques. In the subsequent chapters, we review the theoretical and empirical bases for the existing and emerging remote-sensing approaches; assess knowledge about the limitations, assumptions, and likely accuracy or predictive skill of the approaches; provide some preliminary comparative analyses; and look towards future prospects with respect to algorithm development, validation studies, and new satellite mis- sions.

Beschreibung: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 93 (2012): 1547–1566, doi:10.1175/BAMS-D-11-00201.1.

Beschreibung: The Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission was recommended by the National Research Council's (NRC's) Earth Science Decadal Survey to measure tropospheric trace gases and aerosols and coastal ocean phytoplankton, water quality, and biogeochemistry from geostationary orbit, providing continuous observations within the field of view. To fulfill the mandate and address the challenge put forth by the NRC, two GEO-CAPE Science Working Groups (SWGs), representing the atmospheric composition and ocean color disciplines, have developed realistic science objectives using input drawn from several community workshops. The GEO-CAPE mission will take advantage of this revolutionary advance in temporal frequency for both of these disciplines. Multiple observations per day are required to explore the physical, chemical, and dynamical processes that determine tropospheric composition and air quality over spatial scales ranging from urban to continental, and over temporal scales ranging from diurnal to seasonal. Likewise, high-frequency satellite observations are critical to studying and quantifying biological, chemical, and physical processes within the coastal ocean. These observations are to be achieved from a vantage point near 95°–100°W, providing a complete view of North America as well as the adjacent oceans. The SWGs have also endorsed the concept of phased implementation using commercial satellites to reduce mission risk and cost. GEO-CAPE will join the global constellation of geostationary atmospheric chemistry and coastal ocean color sensors planned to be in orbit in the 2020 time frame.

Beschreibung: Funding for GEO-CAPE definition activities is provided by the Earth Science Division of the National Aeronautics and Space Administration.

Beschreibung: 2013-04-01

Beschreibung: Author Posting. © University of California Press and American Institute of Biological Sciences, 2013. This article is posted here by permission of University of California Press and American Institute of Biological Sciences for personal use, not for redistribution. The definitive version was published in BioScience 63 (2013): 350-361, doi:10.1525/bio.2013.63.5.8.

Beschreibung: Humans depend on diverse ocean ecosystems for food, jobs, and sustained well-being, yet many stressors threaten marine life. Extensive research has demonstrated that maintaining biodiversity promotes ocean health and service provision; therefore, monitoring the status and trends of marine biodiversity is important for effective ecosystem management. However, there is no systematic sustained program for evaluating ocean biodiversity. Coordinating existing monitoring and building a proactive marine biodiversity observation network will support efficient, economical resource management and conservation and should be a high priority. A synthesis of expert opinions suggests that, to be most effective, a marine biodiversity observation network should integrate biological levels, from genes to habitats; link biodiversity observations to abiotic environmental variables; site projects to incorporate environmental forcing and biogeography; and monitor adaptively to address emerging issues. We summarize examples illustrating how to leverage existing data and infrastructure to meet these goals.

Beschreibung: Author Posting. © The Oceanography Society, 2014. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 27, no. 2 (2014): 18-23, doi:10.5670/oceanog.2014.56.

Beschreibung: Continental shelves and the waters overlying them support numerous industries as diverse as tourism and recreation, energy extraction, fisheries, transportation, and applications of marine bio-molecules (e.g., agribusiness, food processing, pharmaceuticals). Although these shelf ecosystems exhibit impacts of climate change and increased human use of resources (Halpern et al., 2012; IPCC, 2013, 2014; Melillo et al., 2014), there are currently no standardized metrics for assessing changes in ecological function in the coastal ocean. Here, we argue that it is possible to monitor vital signs of ecosystem function by focusing on the lowest levels of the ocean food web. Establishment of biodiversity, biomass, and primary productivity baselines and continuous evaluation of changes in biological resources in these economically and ecologically valuable regions requires an internationally coordinated monitoring effort that fully integrates natural, social, and economic sciences to jointly identify problems and design solutions. Such an ocean observing network is needed to protect the livelihoods of coastal communities in the context of the goals of the Future Earth program (Mooney et al., 2013) and of the Intergovernmental Platform on Biodiversity and Ecosystem Services (http://www.ipbes.net). The tools needed to initiate these assessments are available today.

Beschreibung: AEW and RML have been supported by C-MORE (NSF) and the Gordon and Betty Moore and Alfred P. Sloan Foundations. FMK and EM have been supported by NASA, NOAA, NSF, and EPA. FPC was supported by the David and Lucile Packard Foundation and NASA. HMS was supported by NASA and the Gordon and Betty Moore Foundation. EMJ received support from NOAA. MB received support from the NSF. MTK and SCD acknowledge support from C-MORE (NSF). MWL was supported by NSF and NASA. WMB was supported by NASA and NSF.

Beschreibung: Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): C03026, doi:10.1029/2003JC001977.

Beschreibung: We used budgets of absorption (a), scattering (b), and backscattering (bb) for particles and chromophoric dissolved organic matter (CDOM) to investigate sources of seasonal variations in apparent optical properties (AOPs) of New England continental shelf surface waters. Spectral a, b, and bb budgets for particles were estimated from flow cytometric measurements of eukaryotic pico/nanophytoplankton, Synechococcus, heterotrophic prokaryotes, detritus, and minerals; AOPs were modeled with Hydrolight radiative transfer software. For late summer and spring, our modeled values of the diffuse attenuation coefficient (Kd) and remote sensing reflectance (Rrs) were on average within 15% and 9%, respectively, of independent measurements. This close agreement allowed us to examine how different seawater constituents contributed to AOP variability. Higher values of Kd in the spring, compared to summer, were due to higher absorption by eukaryotic phytoplankton (aeuk) and CDOM (aCDOM), which coincided with higher nutrient levels and less stratified conditions than in the summer. Differences in the spectral shape of Rrs between the seasons were caused by a combination of differences in aeuk, aCDOM, and bb from non-phytoplankton particles (minerals and detritus combined). For non-phytoplankton bb the major seasonal difference was a higher inverse wavelength dependence in the summer due to the effects of small organic detritus. We applied two semianalytical ocean color models to our data, in order to evaluate whether the assumptions and parameterizations inherent in these models are applicable for New England shelf waters. We show how differences between observed and modeled chlorophyll a specific phytoplankton absorption, aCDOM, and non-phytoplankton bb cause errors in chlorophyll a concentration and IOPs retrieved from reflectance inversion models.

Beschreibung: Financial support was provided by ONR grants N00014-95-1-0333 and N00014-96-1-0965 (H. Sosik and R. Olson), NASA grants NAGW- 517, NAG5-7538, and NAG5-8868, and a NASA Earth System Science Fellowship (R. Green).

Beschreibung: Author Posting. © The Oceanography Society, 2014. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 27, no. 1 (2014): 222–235, doi:10.5670/oceanog.2014.26.

Beschreibung: One of the most dramatic large-scale features in the ocean is the seasonal greening of the North Atlantic in spring and summer due to the accumulation of phytoplankton biomass in the surface layer. In 1953, Harald Ulrik Sverdrup hypothesized a now canonical mechanism for the development and timing of phytoplankton blooms in the North Atlantic. Over the next 60 years, Sverdrup's Critical Depth Hypothesis spurred progress in understanding of bloom dynamics and offered a valuable theoretical framework on which to build. In reviewing 60 years of literature, the authors trace the development of modern bloom initiation hypotheses, highlighting three case studies that illuminate the complexity, including both catalysts and impediments, of scientific progress in the wake of Sverdrup's hypothesis. Most notably, these cases demonstrate that the evolution of our understanding of phytoplankton blooms was paced by access not only to technology but also to concurrent insights from several disciplines. This exploration of the trajectories and successes in bloom studies highlights the need for expanding interdisciplinary collaborations to address the complexity of phytoplankton bloom dynamics.

Beschreibung: Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 1572-1578, doi:10.4319/lo.2012.57.5.1572.

Beschreibung: We used a time-lapse imaging approach to examine cell division in the marine centric diatom Ditylum brightwellii and observed that daughter cells who inherited their parents' hypothecal frustule half were more likely to divide before their sisters. This is consistent with observations in Escherichia coli of a bias between sister cells, where faster growth in one sister is thought to arise from its inheriting parental material with less oxidative damage. We also observed that hypothecal sisters in D. brightwellii were more likely to inherit a greater proportion of their parents' cellular material, similar to what has been seen in E. coli. We found a statistically significant correlation between the amount of parental material inherited by a hypothecal daughter and its relative division rate, indicating that this extra material inherited by the hypothecal daughter plays a role in its more rapid division. Furthermore, the intercept in this regression was greater than zero, indicating that other factors, such as differences in the quality of inherited material, also play a role. This similarity between two taxonomically distant microbes suggests that favoritism toward one daughter might occur broadly among unicellular organisms that reproduce asexually by binary fission. Such a bias in cell division might be advantageous, given model predictions that show that favoring one daughter at the expense of the other can result in higher population growth rates, increasing the chance that a cell's genotype will survive compared to a model where the daughters divide at equal rates.

Beschreibung: This research was funded in part by the Woods Hole Oceanographic Institution through an Ocean Life Institute Postdoctoral Scholarship to S.R.L. and by support to R.J.O. and H.M.S. from the Gordon and Betty Moore Foundation.

Beschreibung: Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography: Methods 10 (2012): 278-288, doi:10.4319/lom.2012.10.278.

Beschreibung: We describe and evaluate an algorithm that uses a distance map to automatically calculate the biovolume of a planktonic organism from its two-dimensional boundary. Compared with existing approaches, this algorithm dramatically increases the speed and accuracy of biomass estimates from plankton images, and is thus especially suited for use with automated cell imaging technologies that produce large quantities of data. The algorithm operates on a two-dimensional image processed to identify organism boundaries. First, the distance of each interior pixel to the nearest boundary is calculated; next these same distances are assumed to apply for projection in the third dimension; and finally the resulting volume is adjusted by a multiplicative factor assuming locally circular cross-sections in the third dimension. Other cross-sectional shape factors can be applied as needed. In this way, the simple, computationally efficient, volume calculation can be refined to include taxon-specific shape information if available. We show that compared to traditional manual microscopic analysis, the distance map algorithm is unbiased and accurate (mean difference = -0.25%, standard deviation = 17%) for a range of cell morphologies, including those with concave boundaries that deviate from simple geometric shapes and whose volumes are not well represented by a solid of revolution around a single axis. Automated calculation of cell volumes can now be implemented with a combination of this new distance map algorithm for complex shapes and the solid of revolution approach for simple shapes, with an automated decision criterion to choose the appropriate approach for each image.

Beschreibung: This research was supported by grants (to HMS) from the Gordon and Betty Moore Foundation and NASA’s Ocean Biology and Biogeochemistry program, and a Woods Hole Oceanographic Institution Summer Student Fellow award (to EAM).

Beschreibung: Author Posting. © Inter-Research, 2014. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 503 (2014): 1-10, doi:10.3354/meps10784.

Beschreibung: Plankton images collected by Imaging FlowCytobot from 2006 to 2013 at the Martha’s Vineyard Coastal Observatory (Massachusetts, USA) were used to identify and quantify the occurrence of the diatom Guinardia delicatula and of a parasite that seems specific to this host. We observed infection with morphological stages that appear similar to the parasite Cryothecomonas aestivalis. Our results show that events during which infection rates exceed 10% are recurrent on the New England Shelf and suggest that the parasites are an important source of host mortality. We document a significant negative relationship between bloom magnitude and parasite infection rate, supporting the hypothesis that the parasites play a major role in controlling blooms. While G. delicatula is observed during all seasons, the infecting stages of the parasite are abundant only when water temperature is above 4°C. The anomalously warm water and small G. delicatula bloom during the winter of 2012 provided evidence that parasites can be active through winter if temperatures remain relatively high. As climate change continues, winter periods of water below 4°C may shorten or disappear in this region, suggesting that parasite effects on species such as G. delicatula may increase, with immediate impacts on their population dynamics.

Beschreibung: This work was supported by grants from NSF’s Ocean Technology and Interdisciplinary Coordination program, NASA’s Ocean Biology and Biogeochemistry program and Biodiversity and Ecological Forecasting program, the Gordon and Betty Moore Foundation, and the National Ocean Partnership Program.