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  • Pyrosequencing  (3)
  • Life and Medical Sciences
  • Limnology
  • Inter-Research  (4)
  • 2010-2014  (4)
  • 1950-1954
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  • 2010-2014  (4)
  • 1950-1954
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  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2013. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 71 (2013):141-153, doi:10.3354/ame01674.
    Description: Over the last few decades, molecular methods have vastly improved our ability to study the diversity of microbial communities. In molecular diversity surveys, the function of protists is often inferred from phylogeny. Yet these surveys are unable to distinguish between different trophic modes among closely related taxa. Here we present results from a culture-independent study linking bacterivory to the diversity of pelagic protists from 3 depths of a stratified mesotrophic lake. Bacteria were labeled with bromodeoxyuridine (BrdU) and added to lakewater samples; after incubation, total DNA was extracted from filtered samples. Part of the DNA extract was subjected to immunoprecipitation with anti-BrdU antibodies, and then both whole DNA and BrdU-labeled samples were analyzed using 454-pyrosequencing of the v9 region of 18S small subunit rRNA gene amplicons. The results show that a different community of protists exists at each depth, with limited overlap of taxonomic composition between depths. The community of BrdU-labeled protists, deemed putative bacterivores, is largely a subset of the community found in the whole DNA samples. Many of these BrdU-labeled taxa are poorly represented in GenBank and thus are probably rarely isolated and/or uncultured species. Several of the taxa identified as bacterivores are also phototrophs, highlighting the important role of mixotrophy among eukaryotic microbes. Definitive identity of functional traits among taxa requires careful experimentation, yet this method allows a first-pass assay of the trophic role of microbial eukaryotes from environmental samples.
    Description: This work was funded in part by NSF grants OPP-0838847 and OPP-0838955.
    Keywords: Molecular methods ; Microbial community ; Mixotrophy ; Bromodeoxyuridine ; Culture-independent ; Eukaryotic microbes ; Pyrosequencing ; Lake microbes
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-25
    Description: 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 Aquatic Microbial Ecology 73 (2014): 107-121, doi:10.3354/ame01703.
    Description: The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and material flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters compared to that at lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We characterized bacterial, archaeal, and eukaryotic community diversity and composition from 2 depths (near surface and below the euphotic zone) at 4 sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern stations, but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents, but did vary with depth. Archaea were virtually absent in summer surface waters, but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of ‘winter water’ below the euphotic zone. Inter-domain heterotroph-phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in microbial communities may be assessed.
    Description: Funding was provided by NSF DEB- 0717390 to L.A.Z. (MIRADA-LTERS) and NSF Awards OPP- 0217282 and 0823101 (Palmer LTER) from the Antarctic Organisms and Ecosystems Program to H.W.D.
    Keywords: Antarctica ; MIRADA-LTERS ; Palmer LTER ; Pyrosequencing ; V6 ; V9 ; Microbial oceanography
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2008. 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 360 (2008): 179-187, doi:10.3354/meps07314.
    Description: Complex 3D biological-physical models are becoming widely used in marine and freshwater ecology. These models are highly valued synthesizing tools because they provide insights into complex dynamics that are difficult to understand using purely empirical methods or theoretical analytical models. Of particular interest has been the incorporation of concentration-based copepod population dynamics into 3D physical transport models. These physical models typically have large numbers of grid points and therefore require a simplified biological model. However, concentration-based copepod models have used a fine resolution age-stage structure to prevent artificially short generation times, known as numerical ‘diffusion.’ This increased resolution has precluded use of age-stage structured copepod models in 3D physical models due to computational constraints. In this paper, we describe a new method, which tracks the mean age of each life stage instead of using age classes within each stage. We then compare this model to previous age-stage structured models. A probability model is developed with the molting rate derived from the mean age of the population and the probability density function (PDF) of molting. The effects of temperature and mortality on copepod population dynamics are also discussed. The mean-age method effectively removes the numerical diffusion problem and reproduces observed median development times (MDTs) without the need for a high-resolution age-stage structure. Thus, it is well-suited for finding solutions of concentration-based zooplankton models in complex biological-physical models.
    Description: This work was supported by US GLOBEC NOAA grant NA17RJ1223.
    Description: 2013-05-22
    Keywords: Plankton ; Copepods ; Modeling ; Marine ecology ; Oceanography ; Limnology ; Methodology ; Mean age
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2010. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbila Ecology 61 (2010): 221-233, doi:10.3354/ame01484.
    Description: Due to analytical limitations, patterns of richness and evenness of microbes are scarce in the current literature. The newest and powerful pyrosequencing technology may solve this issue by sampling thousands of sequences from the same community. We conducted a study of diversity along a horizontal transect (ca. 120 km) and a depth profile (surface to bottom at ca. 2000 m) in the northwestern Mediterranean Sea, using this technology on the V6 region of the 16S rDNA gene and analyzed patterns of richness and evenness of marine free-living bacterial communities. A total of 201605 tag sequences were obtained from the 10 samples considered and clustered according to their similarity in 1200 operational taxonomic units (OTUs) per sample on average. We found a parallel decrease in richness and evenness from coast to offshore and from bottom to surface. We also observed a predominance of a few OTUs in each sample, while ca. 50% of all OTUs were found as singletons, which indicated that the community structures differed dramatically between sites despite the relative proximity and the physical connectivity between the samples. Despite these differences, using the 300 most abundant OTUs only was sufficient to obtain the same clustering of samples as with the complete dataset. Finally, both richness and evenness were negatively correlated with bacterial biomass and heterotrophic production.
    Description: The Modivus cruise was supported by the Spanish MICINN project MODIVUS (CTM2005-04795/ MAR). Additional work was supported by a Spanish MICINN grant GEMMA (CTM2007-63753-C02-01/MAR).
    Keywords: Bacterial diversity ; Pyrosequencing ; Blanes Bay Microbial Observatory
    Repository Name: Woods Hole Open Access Server
    Type: Article
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