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.
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
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