Sampling, preservation, enumeration and biomass of marine protozooplankton

Gifford, Dian J.; Caron, David A.

doi:10.1016/b978-012327645-2/50006-2

Cited by 86 publications

(68 citation statements)

References 95 publications

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“…Specimens were identified to the level of order and enumerated. An average of 960 individuals were counted per sample and we estimated an enumeration error of 6.4 % (Gifford and Caron, 2000). The category copepod nauplii comprised a mix of calanoid, cyclopoid, and poecilostomatoid copepods.…”

Section: Zooplankton Sampling and Processingmentioning

confidence: 99%

Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

et al. 2016

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Abstract. In oligotrophic tropical and subtropical oceans, where strong stratification can limit the replenishment of surface nitrate, dinitrogen (N 2 ) fixation by diazotrophs can represent a significant source of nitrogen (N) for primary production. The VAHINE (VAriability of vertical and tropHIc transfer of fixed N 2 in the south-wEst Pacific) experiment was designed to examine the fate of diazotroph-derived nitrogen (DDN) in such ecosystems. In austral summer 2013, three large (∼ 50 m 3 ) in situ mesocosms were deployed for 23 days in the New Caledonia lagoon, an ecosystem that typifies the low-nutrient, low-chlorophyll environment, to stimulate diazotroph production. The zooplankton component of the study aimed to measure the incorporation of DDN into zooplankton biomass, and assess the role of direct diazotroph grazing by zooplankton as a DDN uptake pathway. Inside the mesocosms, the diatom-diazotroph association (DDA) het-1 predominated during days 5-15 while the unicellular diazotrophic cyanobacteria UCYN-C predominated during days 15-23. A Trichodesmium bloom was observed in the lagoon (outside the mesocosms) towards the end of the experiment. The zooplankton community was dominated by copepods (63 % of total abundance) for the duration of the experiment. Using two-source N isotope mixing models we estimated a mean ∼ 28 % contribution of DDN to zooplankton nitrogen biomass at the start of the experiment, indicating that the natural summer peak of N 2 fixation in the lagoon was already contributing significantly to the zooplankton. Stimulation of N 2 fixation in the mesocosms corresponded with a generally low-level enhancement of DDN contribution to zooplankton nitrogen biomass, but with a peak of ∼ 73 % in mesocosm 1 following the UCYN-C bloom. qPCR analysis targeting four of the common diazotroph groups present in the mesocosms (Trichodesmium, het-1, het-2, UCYN-C) demonstrated that all four were ingested by copepod grazers, and that their abundance in copepod stomachs generally corresponded with their in situ abundance. 15 N 2 labelled grazing experiments therefore provided evidence for direct ingestion and assimilation of UCYN-C-derived N by the zooplankton, but not for het-1 and Trichodesmium, supporting an important role of secondary pathways of DDN to the zooplankton for the latter groups, i.e. DDN contributions to the dissolved N pool and uptake by nondiazotrophs. This study appears to provide the first evidence of direct UCYN-C grazing by zooplankton, and indicates that UCYN-C-derived N contributesPublished by Copernicus Publications on behalf of the European Geosciences Union.

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Section: Zooplankton Sampling and Processingmentioning

confidence: 99%

Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

et al. 2016

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“…Microplankton samples were processed and analyzed according to Gifford and Caron (2000) and carbon content was calculated according to Putt and Stoecker (1989) for ciliates and Lessard (1991) for heterotrophic dinoflagellates.…”

Section: 2microzooplanktonmentioning

confidence: 99%

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

Steele

Collie

Bisagni

et al. 2007

Progress in Oceanography

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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 pelagicbenthic 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 1 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, 1963This decade, -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.

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“…It is therefore no coincidence that attempts to analyze the DNA sequence from preserved microplankton samples focused mainly on alveolate taxa, i.e., organisms presumably with a high copy number of the SSU rRNA gene (dinoflagellates [5,11,13,29]; ciliates [9]). Still, despite the presumably high gene copy number in the alveolates investigated so far, success with field samples is usually low.Among the most common fixatives for microalgae and protists are formaldehyde and Lugol's iodine solution (12,20,32). Formaldehyde-preserved samples are generally problematic for molecular analyses, as formaldehyde may cause severe cell loss (e.g., reference 20 and references therein).…”

mentioning

confidence: 99%

“…Among the most common fixatives for microalgae and protists are formaldehyde and Lugol's iodine solution (12,20,32). Formaldehyde-preserved samples are generally problematic for molecular analyses, as formaldehyde may cause severe cell loss (e.g., reference 20 and references therein).…”

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Improved Methodology for Identification of Protists and Microalgae from Plankton Samples Preserved in Lugol's Iodine Solution: Combining Microscopic Analysis with Single-Cell PCR

Auinger

Pfandl

Boenigk

2008

Appl Environ Microbiol

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Here we introduce a method for quantitative analysis of planktonic protists and microalgae from preserved field samples combining morphological and small-subunit (SSU) rRNA gene sequence analysis. We linked a microscopic screening with PCR of single cells using field samples preserved with Lugol's iodine solution. Cells possessing a rigid cell wall were incubated with Viscozyme and subsequently with proteinase K for cell disruption; this was unnecessary for fragile cells. The addition of sodium thiosulfate to the PCR tube considerably decreased the inhibiting effect of the fixative (iodine) on the PCR and thus allowed for successful single-cell PCR even of long DNA fragments (up to as many as 3,000 base pairs). We further applied the protocol to investigate the dominant SSU rRNA genotypes in distinct flagellate morphospecies originating from different samples. We hypothesized that despite the morphological similarity, protist morphospecies in different habitats or sampled during different seasons are represented by different genotypes. Our results indicate species-specific differences: the two species Ochromonas sp. and Dinobryon divergens were represented by several different genotypes each, and for the latter species, the dominating genotype differed with habitat. In contrast, Dinobryon pediforme, Dinobryon bavaricum, and Synura sphagnicola were exclusively represented by a single genotype each, and the respective genotype was the same in different samples. In summary, our results highlight the significance of molecular variation within protist morphospecies.Linking a specific protist or microalgal small-subunit (SSU) rRNA gene sequence from environmental surveys to a specific morphotype is often problematic. Molecular surveys do not usually provide any information on the morphology of the organism (see references 19, 25, and 27 but compare with reference 10), whereas morphological surveys concentrate on preserved samples, which are usually not considered for molecular analyses (7). One main way to overcome these problems is to link sequence analysis with morphological investigations from preserved plankton samples on a per cell basis.Successful sequence analysis has already been demonstrated for preserved specimens, but it has various shortcomings. Most methods either require relatively large amounts of template DNA (i.e., cultured material, preserved tissues, or environmental DNA collected on filters or by centrifugation [18]) or amplification is limited to short fragments or both (2, 4, 6). It is therefore no coincidence that attempts to analyze the DNA sequence from preserved microplankton samples focused mainly on alveolate taxa, i.e., organisms presumably with a high copy number of the SSU rRNA gene (dinoflagellates [5,11,13,29]; ciliates [9]). Still, despite the presumably high gene copy number in the alveolates investigated so far, success with field samples is usually low.Among the most common fixatives for microalgae and protists are formaldehyde and Lugol's iodine solution (12,20,32). Formaldehyde-p...

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Sampling, preservation, enumeration and biomass of marine protozooplankton

Cited by 86 publications

References 95 publications

Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

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

Improved Methodology for Identification of Protists and Microalgae from Plankton Samples Preserved in Lugol's Iodine Solution: Combining Microscopic Analysis with Single-Cell PCR

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