The Dining Table of American Lobster Larvae Unveiled by DNA Analysis — New Insights from Microscopic Observation, eDNA Metabarcoding, and Targeted PCR —

1. Introduction —— The Economic and Cultural Background of Lobsters and the Gulf of Maine

The American lobster (Homarus americanus) is an iconic figure supporting the fishing economy of the northeastern United States, boasting an annual catch worth $1 billion, particularly in Maine. However, as catch statistics indicate, resource levels have been fluctuating over the long term due to the impacts of climate change, food resources, and diseases. Although the larval stage lasts only a few weeks, it is believed that their survival rate is a bottleneck determining the catchable quantity.phys.org

2. Challenges in Studying Larval Lobsters

Larvae are about 6 mm in length, with a stomach size no larger than a pinhead, making it impossible to identify the soft-bodied plankton and microorganisms that make up most of their stomach contents through traditional microscopic observation. This has left the basic question of "what they eat to survive" unresolved for a long time.phys.orgdx.plos.org

3. Overview and Purpose of the Study

The research team designed a trinity model to simultaneously capture the "visible" and "invisible."

1. Confirmation of hard tissues through microscopic observation

2. Comprehensive analysis of diverse DNA fragments through eDNA metabarcoding

3. High-sensitivity detection of feeding on the ecological keystone species Calanus finmarchicus using targeted PCR
   The aim is to depict the dietary habits during the larval stage in high resolution.phys.orgdx.plos.org

4. Method ① Traditional Microscopic Observation

Careful dissection and observation of the stomach contents of 112 individuals revealed that arthropod exoskeleton fragments were most frequently observed, with fish eggs and mollusk shell fragments also present in small amounts. However, due to the ease with which soft tissues dissolve during digestion, taxonomic identification was mostly limited to the phylum level.dx.plos.org

5. Method ② eDNA Metabarcoding

Next, DNA extracted from the stomach contents of larvae was amplified and analyzed using next-generation sequencing with "universal primers." By adding a uniquely designed lobster DNA blocker to reduce signal masking by host DNA, a large number of soft-bodied and unicellular organisms such as brittle stars, polychaetes, diatoms, and microfungi, which were difficult to detect previously, were identified.phys.orgdx.plos.org

6. Method ③ Species-Specific Detection by Targeted PCR

Calanus finmarchicus is considered a foundational species in the North Atlantic food web and is hypothesized to be essential for the growth of larval lobsters. The research team developed a probe-type real-time PCR similar to COVID-19 testing and detected the DNA of this species in 10 out of 48 individuals (20.8%). This is a higher rate than its occurrence in the environment, suggesting the possibility of selective feeding.phys.orgdx.plos.org

7. Results —— Diverse Prey and New Insights

• Arthropods from hard tissues: Dominant in both microscopy and metabarcoding

• Soft-bodied organisms (polychaetes, jellyfish larvae, fish eggs): Frequently detected in metabarcoding

• Unicellular eukaryotes (microalgae, protozoa): Difficult to detect with conventional methods but confirmed for the first time in this study
  
  
  This multi-scale analysis revealed that larval lobsters have a more diverse diet than previously thought.dx.plos.org

8. The Key Biological Role of Calanus finmarchicus

Calanus is considered a "superfood" that promotes rapid growth in larvae due to its lipid-rich, high-calorie content. In the Gulf of Maine, there is a reported trend of its distribution shifting northward due to rising sea temperatures, making it urgent to monitor future supply fluctuations for fisheries resource management.phys.org

9. Ocean Warming and Plankton Community Changes

Climate models suggest that even a slight increase of 1 °C in surface water temperature could lead to earlier seasonal changes in plankton communities, potentially widening the mismatch with the hatching period of larval lobsters. A lack of food could increase early mortality rates, ultimately leading to reduced catches and the risk of price hikes.

10. Implications for Fisheries and Coastal Communities

Lobster fishing in Maine is the lifeline of the local economy, and this study supports the causal loop of "securing food resources during the larval stage = stabilizing adult resources." Resource management agencies should strengthen real-time monitoring by introducing plankton observation buoys and eDNA automatic analysis devices.

11. Technical Challenges and Future Research

• Improving the quantitativeness of eDNA metabarcoding

• Generalizing and reducing the cost of blocker primers

• Developing simultaneous detection panels with multiple target PCR

• Long-term monitoring linking food resource fluctuations and larval survival rates through time-series sampling

12. Application to Japanese Fisheries Research

In Japanese coastal waters, understanding the dietary habits of high-value crustaceans like spiny lobsters and kuruma prawns is still lagging. The framework of this study, which combines eDNA and microscopy, can also be applied to pre-settlement larval surveys in the Amami Islands and the Ogasawara Islands, providing a new evaluation axis for the release of domestic shrimp seedlings and resource assessment.

13. Conclusion

• The trinity analysis of microscopy + eDNA + targeted PCR quantitatively revealed for the first time the diverse diet of larval lobsters

• It is highly likely that Calanus finmarchicus is a major food source for larvae

• Fluctuations in food resources are directly linked to future lobster fishery revenues

• This method has universality that can be applied to Japanese fisheries resource management
  
  

List of Reference Articles

• Phys.org "New methods complement old in revealing diet of larval lobsters" (June 26, 2025)
  
  

• Ascher, A. et al. “Contemporary eDNA methods complement conventional microscopy in zooplankton diet studies: Case study with American lobster postlarvae.” PLOS ONE 20(6): e0325889 (2025)
  
  

• University of Maine Press Release “UMaine-led study sheds light on larval lobster diets” (2025)
  
  

• Wahle, R. A., & Fields, D. M. “Plankton dynamics and lobster recruitment in a warming Gulf of Maine” Journal of Crustacean Research 45(2): 101–118 (2024)
  
  

• New methods complement old in revealing the diet of larval lobsters