Global patterns of marine plankton through imaging and DNA sequencing | 9am PT Thu, Dec 5, 2024

[Grigory Bronevetsky]

Modeling Talks

Global patterns of marine plankton through imaging and DNA sequencing Juan J Pierella Karlusich, MIT Thu, Dec 5 | 9am PT Meet | Youtube Stream Hi all, The presentation will be via Meet and all questions will be addressed there. If you cannot attend live, the event will be recorded and can be found afterward at https://sites.google.com/modelingtalks.org/entry/global-patterns-of-marine-plankton-through-imaging-and-dna-sequencing More information on previous and future talks: https://sites.google.com/modelingtalks.org/entry/home Abstract: Marine plankton—viruses, bacteria, and micro eukaryotes—make up over two-thirds of ocean biomass, performing photosynthesis on par with land plants, sequestering carbon, and supporting the ocean food web. However, they are increasingly impacted by human activities such as greenhouse gas emissions and pollution, with cascading effects on fisheries and aquaculture.  DNA sequencing from seawater samples enables high-resolution analysis of microbial species and functions, revealing rare species and adaptive mechanisms across environmental gradients. Yet, challenges remain due to reference database gaps and variability in gene copy numbers. High-throughput imaging, applied in situ or on collected seawater samples, provides rapid enumeration and phenotypic data for plankton but requires extensive annotated datasets for machine learning classifiers. Meanwhile, satellite remote sensing estimates plankton distributions but lacks taxonomic resolution and subsurface insights.  Integrating DNA sequencing, imaging, and remote sensing offers new insights into how marine plankton respond to environmental changes, shedding light on the impacts of global change and human activities on ocean ecosystems. Bio: Postdoctoral researcher in Sergey Ovchinnikov’s lab at the Department of Biology of MIT.

[Grigory Bronevetsky]

Recording: https://www.youtube.com/live/lOtLPhkxWdc

Slides: https://drive.google.com/file/d/1WhbgpgrNF3uDXpLzNHTss2OKmRbroByo/view?usp=sharing

Summary:

• Focus: analyzing dynamics of marine plankton at ocean scale using diverse datasets

• Plankton: viruses, bacteria, algae, plants, fungi (diverse sizes, morphology)

• 60% of ocean biomass

• 50% of global photosynthesis

• Basis of marine food systems

• Biological C pump: sinking organisms are stored long-term in deep ocean

• Data

• Challenging to measure due to diverse sizes & biologies

• Tara Ocean expeditions 2009-2013: https://fondationtaraocean.org/en/expedition/tara-oceans

• Serial filtration of ocean water to collect plankton at different sizes

• Smaller organisms are more abundant than larger ones (need to process more sea water to find them)

• Organisms and their DNA/RNA was collected from filters and analyzed

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• Molecular data

• Environmental parameters

• High throughput imaging

• Analysis: Nitrogen fixer organisms

• Ocean N is limited

• Some organisms can capture N and their presence affects other organisms’ growth

• Huge lifestyle variation: free-living, aggregates, symbiants

• Results of environmental DNA measure the distribution of nitrogen fixers: 

• More larger organisms than smaller

• Majority is cyanobacteria (e.g. Trichodesmium)

• Smaller fixers are spread more broadly across environments (including the Arctoc) and are more diverse

• Imaging data

• 2M images collected: microscope images of organisms, colonotes and symbiants

• Random Forest model to predict N fixers in images

• Helps 

• Identify new hotspots of N fixers (e.g. in Indian ocean)

• Understand the lifecycle dynamics of these organisms

• Support future efforts to design these interactions (e.g. fertilize ocean crops using N2 fixers)

• In the future can integrate with satellite imagery to detect blooms of N2 fixers

• Analysis: marine phytoplankton

• Very Diverse: Synechococcus, Diatoms, Prochlorococcus, Chlorophytes, Dinoflagellates, Haptophytes (bacteria, eucaryotes)

• Using 

• Metagenomic analysis of DNA of photosynthetic gene psbO

• More accurate than PCR analysis of rRNS (Ribosomal RNA)

• Enables analysis of phytoplankton populations in samples collected across the world

• Among small organisms high abundance of prokaryotes

• Among larger organisms more eukaryotes and symbiotic & colony cyanobacteria, still many prokaryotes

• The psbO gene is a good market for molecular-based evaluation of phytoplankton communities

• Satellite remote sensing of phytoplankton groups

• Used psbO marker