Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula

Lin, Yan; Cassar, Nicolas; Marchetti, Adrian; Moreno, Carly M.; Ducklow, Hugh W.; Li, Zuchuan

doi:10.1038/s41598-017-14109-1

Cited by 23 publications

(34 citation statements)

References 73 publications

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“…Phaeocystis has previously been reported as a key component of POC export in polar waters (DiTullio et al ), as they have the ability to form aggregates that sink rapidly out of the mixed layer (Arrigo ). However, during our study this eukaryotic phytoplankton appeared to contribute little to carbon transfer efficiency, especially compared to its diatom counterparts as observed elsewhere in Antarctic waters (Lin et al ). The rapid export of Phaeocystis out of the euphotic zone is generally related to their enhanced production of transparent exopolymer polysaccharides (TEP; Passow et al ).…”

Section: Resultssupporting

confidence: 61%

Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles

Duret

Lampitt

Lam

2019

Limnology & Oceanography

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Suspended marine particles constitute most of the particulate organic matter pool in the oceans, thereby providing substantial substrates for heterotrophs, especially in the mesopelagic. Conversely, sinking particles are major contributors to carbon fluxes defining the strength of the biological carbon pump (BCP). This study is the first to investigate the differential influence of eukaryotic communities to suspended and sinking particles, using 18S rRNA gene sequencing on particles collected with a marine snow catcher in the mixed layer and upper mesopelagic of the Scotia Sea, Southern Ocean. In the upper mesopelagic, most eukaryotic phytoplankton sequences belonged to chain‐forming diatoms in sinking particles and to prymnesiophytes in suspended particles. This suggests that diatom‐enriched particles are more efficient in carbon transfer to the upper mesopelagic than those enriched in prymnesiophytes in the Scotia Sea, the latter more easily disintegrating into suspended particles. In the upper mesopelagic, copepods appeared most influential on sinking particles whereas soft‐tissue metazoan sequences contributed more to suspended particles. Heterotrophic protists and fungi communities were distinct between mixed layer and upper mesopelagic, implying that few protists ride along sinking particles. Furthermore, differences between predatory flagellates and radiolarians between suspended and sinking particles implied different ecological conditions between the two particles pools, and roles in the BCP. Molecular analyses of sinking and suspended particles constitute powerful diagnostic tools to study the eukaryotic influence on the BCP in a more holistic manner compared to classic carbon export studies focusing on sinking particles.

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Section: Resultssupporting

confidence: 61%

Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles

Duret

Lampitt

Lam

2019

Limnology & Oceanography

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“…gDNA standard stock solutions and dilution concentrations were measured using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). After spiking in internal standards, DNA extraction was performed as described previously (8).…”

Section: Methodsmentioning

confidence: 99%

“…PCRs were performed in triplicates for each sample. 18S rRNA gene PCR and library pooling were performed as described previously (8). 16S rRNA gene library construction was similar to that for 18S rRNA gene except that 2 U of Platinum Taq DNA high-fidelity polymerase (Invitrogen) was added to each reaction mixture, and the PCR annealing temperature was 60°C.…”

Section: Methodsmentioning

confidence: 99%

“…, TARA expeditions (3,4), the Malaspina 2010 Expedition (5), Ocean Sampling Day (6) and the Long Term Ecological Research (LTER) sites (Palmer, HOT, Tahiti, and other sites). These studies and other programs have revealed unprecedented microbial diversity and biogeographic patterns and have advanced our understanding of marine microbial ecology (7) and biogeochemistry (4,8).…”

Section: Census Of Marine Microbesmentioning

confidence: 99%

“…1A) using 16S and 18S rRNA gene amplicon sequencing combined with internal DNA standards. The large environmental gradients (e.g., coast versus open-ocean and open-water ice-covered regions) at the WAP lead to diverse and highly variable microbial communities (8,26), thereby providing an ideal stage to test the ISN. Below, we present the ISN method as applied to marine samples.…”

Section: Census Of Marine Microbesmentioning

confidence: 99%

See 2 more Smart Citations

Towards Quantitative Microbiome Community Profiling Using Internal Standards

Lin

Gifford

Ducklow

et al. 2019

Appl Environ Microbiol

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An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems. IMPORTANCE High-throughput-sequencing-based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative; it provides taxon counts only in relative abundances. In order to address this issue, we present a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking known amounts of internal DNA standards into each sample. We validated this method by comparing the calculated abundances to other independent estimates, including chemical markers (pigments) and total bacterial cell counts by flow cytometry. The internal standard approach allows us to quantitatively estimate and compare marine microbial community profiles, with important implications for linking environmental microbiomes to quantitative processes such as metabolic and biogeochemical rates.

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Low diversity of a key phytoplankton group along the West Antarctic Peninsula

Brown

Bowman

Lin

et al. 2021

Limnology & Oceanography

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The West Antarctic Peninsula (henceforth “Peninsula”) is experiencing rapid warming and melting that is impacting the regional marine food web. The primary phytoplankton groups along the Peninsula are diatoms and cryptophytes. Relative to diatoms, there has been little focus on regional cryptophytes, and thus our understanding of their diversity and ecology is limited, especially at the species level. This gap is important, as diatoms and cryptophytes play distinct roles in the regional marine food web and biogeochemistry. Here, we use a phylogenetic placement approach with 18S rRNA gene amplicon sequence variants to assess surface ocean cryptophyte diversity and its drivers at a high taxonomic resolution along the Peninsula. Data were collected over 5 years (2012–2016) during the regional research cruises of the Palmer Long‐Term Ecological Research program. Our results indicate that there are two major cryptophyte taxa along the Peninsula, consisting of distinct Geminigera spp., which in aggregate always comprise nearly 100% of the cryptophyte community (indicating low taxa evenness). The primary taxon dominates the cryptophyte community across all samples/years, which span a broad range of oceanographic conditions. A shift in cryptophyte community composition between a lower (higher) primary (secondary) taxon percentage is associated with distinct oceanographic conditions, including lower (higher) temperature, salinity, nutrients, and cryptophyte relative abundance (phytoplankton biomass and diatom relative abundance). These results emphasize the need for a full characterization of the ecology of these two taxa, as it is predicted that cryptophytes will increase along the Peninsula given projections of continued regional environmental change.

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Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula

Cited by 23 publications

References 73 publications

Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles

Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles

Towards Quantitative Microbiome Community Profiling Using Internal Standards

Low diversity of a key phytoplankton group along the West Antarctic Peninsula

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