NanoSIMS Reveals Microbial Role in Ocean Carbon and Nitrogen Cycles

The Application

Understanding the metabolic activity of individual microbial cells is essential for advancing environmental science, microbial ecology, and oceanography. By tracing nutrient assimilation at the singlecell level, researchers can uncover how microbes drive global biogeochemical cycles, interact with their environment, and contribute to ecosystem function—whether in oceans, soils, sediments, or extreme habitats.

The Challenge

Environmental microbial communities are highly diverse, dynamic, and largely uncultivable. Conventional bulk-scale and culture based approaches cannot uncover the metabolic behavior of rare, lowactivity, or taxonomically distinct microorganisms. To study these systems effectively, scientists need a method that can detect isotope labeled substrates at submicron resolution, directly link metabolic activity to specific phylogenetic identities, resolve cell-to-cell heterogeneity within complex communities, and capture true in situ ecophysiology without cultivation. Without such capabilities, achieving precise, cell level insight into microbial function and interactions remains difficult.

Our Unique Solution

Based on the SIMS technique, CAMECA’s NanoSIMS-HR uniquely bridges the gap between metabolic measurement and microbial identification. By combining high-resolution isotopic imaging (¹³C, ¹⁵N, and others) with phylogenetic labeling techniques, it allows researchers to:

• Track labeled nutrient uptake directly within individual microbial cells
• Map metabolic activity across diverse communities with nanometer precision
• Analyze even rare or slow growing microbes that cannot be cultured
• Deliver quantitative, spatially resolved insights into microbial ecophysiology

This NanoSIMS-HR integrated capability is unmatched by any other analytical platform—providing powerful, correlative analysis that links “who is there” to “what they are doing.”

Case Study

The study investigates how ocean warming affects carbon and nitrogen exchanges between marine phytoplankton and heterotrophic bacteria. Using NanoSIMS, researchers were able to precisely quantify singlecell uptake of ¹³C and ¹⁵N tracers in both free living microbes and physically attached phytoplankton–bacteria consortia (Figure).

NanoSIMS images and comparison between 13C and 15 N isotopic enrichment for all analyzed microbial cells incubated with 13C bicarbonate and 15 N leucine (dashed lines = isotope natural abundances). Each dot represents one cell, with enrichment obtained from the defined region of interest in the NanoSIMS images. Arrows show identified heterotrophs (left) and one autotroph (right).

From: Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment. N. Arandia-Gorostidi et al. The ISME Journal.

Best-fit product: CAMECA NanoSIMS-HR

The NanoSIMS-HR is the industry-leading instrument for single-cell isotope analysis. Engineered for ultimate sensitivity and spatial resolution, it offers:

• Imaging capabilities with down to 30 nm lateral resolution
• Multi-collection of up to seven masses simultaneously
• Excellent sensitivity for biologically relevant species
• Robust performance for complex environmental and oceanographic samples

Its proven track record in microbial ecology makes the NanoSIMS-HR the reference tool for researchers studying nutrient cycling, symbiosis, and microbial interactions at the most fundamental level.

Learn More

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