OceanWiki - User contributions [en]

Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)

2026-09-24T13:43:28Z

Rachel A Foster: /* Units & currency */

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User: Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' single-cell isotope analysis
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' µm
|-
| '''Temporal scale:''' hours–days
|-
| '''Units:''' isotope enrichment, uptake rates
|-
| '''Community captured:''' active single cells
|-
| '''Co-measurements:''' incubation time, tracer enrichment, temperature, nutrients
|}
</div>
<div style="clear:both"></div>

== Method Overview ==
Single-cell uptake methods combine stable isotope probing (SIP) with secondary ion mass spectrometry (SIMS) to quantify nutrient assimilation at the level of individual cells. In nitrogen fixation studies, samples are incubated with 15N2, followed by analysis using nanoSIMS or related platforms. Taxonomic or functional identity can be resolved using complementary labeling techniques such as CARD-FISH or CHIP-SIMS, enabling direct linkage between nitrogen uptake and specific microbial taxa or functional groups. These approaches provide quantitative, cell-specific measurements of nitrogen assimilation and metabolic activity.

== Output ==
* Single-cell isotope enrichment values
* Cell-specific nutrient uptake rates
* Taxon-resolved nitrogen assimilation
* Spatial patterns of isotope incorporation, e.g. mass spectrometry imaging

=== Scale of measurement ===
* Single-cell
* Quantitative
* Taxon-specific activity

=== Data generated ===
* NanoSIMS ion images (e.g., 12C14N- and 12C15N-)
* Isotopic ratio measurements (e.g., 15N/14N) in regions of interest (ROIs)
* Cell-specific uptake rate calculations
* Linked microscopy, hybridization images, and mass spectrometry images

=== Units & currency ===
* Atom percent 15N
* 15N/14N from 12C15N-/12C14N-
* Excess isotope enrichment
* fmol N cell−1 h−1
* Relative enrichment above natural abundance

=== Sample size ===
* Typically:
** 10–100 analyzed cells per sample (depends on SIMS platform; nanoSIMS is fewer, SIMS1280 ion probe is typically more)
** 3–10 samples per treatment
* Limited throughput relative to bulk methods

=== Repositories & databases ===

Single cell rates for many of the cyanobacterial diazotrophs are reported in the following database: <ref name="Shao_2024"> Shao Z., et al. (2023) Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation, Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023. </ref>

== Limitations ==
* Low throughput and high analytical cost
* Requires specialized instrumentation and expertise
* Incubation conditions may alter in situ activity
* Taxonomic identification depends on probe specificity and labeling efficiency

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

Protocols:
* 15N2 tracer incubation protocols
* CARD-FISH combined with nanoSIMS workflows
* CHIP-SIMS and SIP-SIMS sample preparation protocols
* Custom laboratory SOPs for fixation, hybridization, and nanoSIMS analysis

=== Common calculations/conversions ===
* Atom percent excess = measured atom % − natural abundance
* Single-cell uptake rate = (isotope enrichment × cellular N content) / incubation time
* Correction for tracer enrichment and dilution
* Scaling single-cell rates to community-level estimates (with caution)

== References ==

[[index.php?title=Category:Main Pages|Model types]]

Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)

2026-09-24T13:42:43Z

Rachel A Foster: /* Repositories & databases */

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User: Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' single-cell isotope analysis
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' µm
|-
| '''Temporal scale:''' hours–days
|-
| '''Units:''' isotope enrichment, uptake rates
|-
| '''Community captured:''' active single cells
|-
| '''Co-measurements:''' incubation time, tracer enrichment, temperature, nutrients
|}
</div>
<div style="clear:both"></div>

== Method Overview ==
Single-cell uptake methods combine stable isotope probing (SIP) with secondary ion mass spectrometry (SIMS) to quantify nutrient assimilation at the level of individual cells. In nitrogen fixation studies, samples are incubated with 15N2, followed by analysis using nanoSIMS or related platforms. Taxonomic or functional identity can be resolved using complementary labeling techniques such as CARD-FISH or CHIP-SIMS, enabling direct linkage between nitrogen uptake and specific microbial taxa or functional groups. These approaches provide quantitative, cell-specific measurements of nitrogen assimilation and metabolic activity.

== Output ==
* Single-cell isotope enrichment values
* Cell-specific nutrient uptake rates
* Taxon-resolved nitrogen assimilation
* Spatial patterns of isotope incorporation, e.g. mass spectrometry imaging

=== Scale of measurement ===
* Single-cell
* Quantitative
* Taxon-specific activity

=== Data generated ===
* NanoSIMS ion images (e.g., 12C14N- and 12C15N-)
* Isotopic ratio measurements (e.g., 15N/14N) in regions of interest (ROIs)
* Cell-specific uptake rate calculations
* Linked microscopy, hybridization images, and mass spectrometry images

=== Units & currency ===
* Atom percent 15N
* 15N/14N from (12C15N-/12C14N-)
* Excess isotope enrichment
* fmol N cell−1 h−1
* Relative enrichment above natural abundance

=== Sample size ===
* Typically:
** 10–100 analyzed cells per sample (depends on SIMS platform; nanoSIMS is fewer, SIMS1280 ion probe is typically more)
** 3–10 samples per treatment
* Limited throughput relative to bulk methods

=== Repositories & databases ===

Single cell rates for many of the cyanobacterial diazotrophs are reported in the following database: <ref name="Shao_2024"> Shao Z., et al. (2023) Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation, Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023. </ref>

== Limitations ==
* Low throughput and high analytical cost
* Requires specialized instrumentation and expertise
* Incubation conditions may alter in situ activity
* Taxonomic identification depends on probe specificity and labeling efficiency

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

Protocols:
* 15N2 tracer incubation protocols
* CARD-FISH combined with nanoSIMS workflows
* CHIP-SIMS and SIP-SIMS sample preparation protocols
* Custom laboratory SOPs for fixation, hybridization, and nanoSIMS analysis

=== Common calculations/conversions ===
* Atom percent excess = measured atom % − natural abundance
* Single-cell uptake rate = (isotope enrichment × cellular N content) / incubation time
* Correction for tracer enrichment and dilution
* Scaling single-cell rates to community-level estimates (with caution)

== References ==

[[index.php?title=Category:Main Pages|Model types]]

Bulk uptake 15N2

2026-09-24T13:40:45Z

Rachel A Foster: /* Repositories & databases */

{{DISPLAYTITLE:Bulk uptake 15N2}}
{{BreadcrumbsNFixation}}

{{BreadcrumbsPrimaryProduction}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! N2 fixation (bulk 15N2)
|-
| '''Approach:''' 15N2 stable isotope tracer uptake
|-
| '''Context:''' incubation, ''in situ''
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to one day
|-
| '''Units:''' nmol N L-1 d-1; µmol N m-2 d-1 (depth-integrated)
|-
| '''Community captured:''' bulk, size-fractionated
|-
| '''Co-measurements:''' background δ15N (PON), 15N2 enrichment of dissolved phase; can couple with 13CO2 uptake
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

15N2 gas is dissolved into seawater and added to incubation bottles, labelling the dissolved N2 pool. Diazotrophic microorganisms fix the labelled N2, incorporating 15N into their biomass. After incubation, the particulate fraction is collected on pre-combusted GF/F filters; the 15N enrichment in particulate nitrogen (PN) is measured by EA-IRMS. The N2 fixation rate is calculated from the 15N excess in PN relative to the 15N enrichment of the dissolved N2 pool, measured by MIMS or GC-IRMS<ref name="Montoya1996">Montoya, J. P., Voss, M., Kähler, P., & Capone, D. G. (1996). A simple, high-precision, high-sensitivity tracer assay for N2 fixation. ''Applied and Environmental Microbiology'', 62(3), 986–993. https://doi.org/10.1128/aem.62.3.986-993.1996</ref>.

Two labelling approaches are used: (1) direct injection of 15N2 gas bubbles followed by vigorous shaking and equilibration; and (2) the dissolution method, in which pre-dissolved 15N2-enriched water is injected, achieving more homogeneous labelling. The method can be coupled with 13CO2 uptake in the same incubation to simultaneously measure N2 fixation and carbon fixation by diazotrophs.

=== Scale of measurement ===

Each incubation provides a point measurement. Depth-integrated fixation rates are obtained by incubating bottles collected from multiple depths and integrating over the euphotic zone. Incubation duration is typically hours to one day.

=== Data generated ===

N2 fixation rates in nmol N L-1 d-1 or µmol N m-2 d-1 (depth-integrated). Rates can be size-fractionated (e.g., 0.2–10 µm versus > 10 µm) to attribute fixation to different diazotroph size classes (unicellular vs. filamentous). Fixed nitrogen can also be tracked into the dissolved organic nitrogen (DON) pool.

=== Units & currency ===

Units are nmol N L-1 d-1 or µmol N m-2 d-1. The currency is nitrogen.

=== Sample size ===

Typical samples are 1–5 L in volume per incubation.

=== Repositories & databases ===
Bulk data for 15N2 fixation rates are reported here:<ref name="Shao_2024"> Shao Z., et al. (2023) Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation, Earth Syst. Sci. Data, 15, 3673–3709, https://doi.org/10.5194/essd-15-3673-2023. </ref>

== Limitations ==

The 15N2 enrichment of the dissolved pool must be measured accurately; under-estimation of the 15N2 enrichment (e.g., due to incomplete equilibration of bubbles) leads to overestimation of fixation rates. Bubble injection produces heterogeneous enrichment across replicate bottles; the dissolution method mitigates this. Diazotroph community composition affects the timing of fixation: Crocosphaera fixes N2 primarily at night, UCYN-A primarily during the day. Bottle effects apply.

== Example Applications & Protocols ==

=== Classic examples ===
* Montoya et al. (1996) ''A simple, high-precision, high-sensitivity tracer assay for N2 fixation'' <ref name="Montoya1996" />
* Wilson et al. (2012) ''Comparative assessment of nitrogen fixation methodologies, conducted in the oligotrophic North Pacific Ocean'' <ref name="Wilson2012">Wilson, S. T., Böttjer, D., Church, M. J., & Karl, D. M. (2012). Comparative assessment of nitrogen fixation methodologies, conducted in the oligotrophic North Pacific Ocean. ''Applied and Environmental Microbiology'', 78(18), 6516–6523. https://doi.org/10.1128/AEM.01146-12</ref>
* Großkopf et al. (2012) ''Doubling of marine dinitrogen-fixation rates based on direct measurements'' <ref name="Großkopf2012">Großkopf, T., Mohr, W., Baustian, T., Schunck, H., Gill, D., Kuypers, M. M. M., Lavik, G., Schmitz, R. A., Wallace, D. W. R., & LaRoche, J. (2012). Doubling of marine dinitrogen-fixation rates based on direct measurements. ''Nature'', 488(7411), 361–364. https://doi.org/10.1038/nature11338</ref>

=== Recent applications ===
* Tschitschko et al. (2024) ''Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean'' <ref name="Tschitschko2024">Tschitschko, B., Landa, M., Cheung, S., Zheng, H., Williams, C. M., Vergin, K., Giovannoni, S. J., Rocap, G., & Lindell, D. (2024). Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean. ''Nature'', 630, 899–904. https://doi.org/10.1038/s41586-024-07495-w</ref>

=== Common calculations/conversions ===
* N2 fixation rate (nmol N L-1 d-1) = [(15NPN,final − 15NPN,initial) / (15NN2,dissolved − 15Nnatural)] × [PN] / incubation time.
* Depth-integrated rate (µmol N m-2 d-1) = ∫ rate(z) dz over the euphotic zone.

== References ==

[[Category:Main Pages|Model types]]

Bulk uptake 15N2

2026-09-24T13:35:01Z

Rachel A Foster: /* Repositories & databases */

{{DISPLAYTITLE:Bulk uptake 15N2}}
{{BreadcrumbsNFixation}}

{{BreadcrumbsPrimaryProduction}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
----

__TOC__
<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! N2 fixation (bulk 15N2)
|-
| '''Approach:''' 15N2 stable isotope tracer uptake
|-
| '''Context:''' incubation, ''in situ''
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to one day
|-
| '''Units:''' nmol N L-1 d-1; µmol N m-2 d-1 (depth-integrated)
|-
| '''Community captured:''' bulk, size-fractionated
|-
| '''Co-measurements:''' background δ15N (PON), 15N2 enrichment of dissolved phase; can couple with 13CO2 uptake
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

15N2 gas is dissolved into seawater and added to incubation bottles, labelling the dissolved N2 pool. Diazotrophic microorganisms fix the labelled N2, incorporating 15N into their biomass. After incubation, the particulate fraction is collected on pre-combusted GF/F filters; the 15N enrichment in particulate nitrogen (PN) is measured by EA-IRMS. The N2 fixation rate is calculated from the 15N excess in PN relative to the 15N enrichment of the dissolved N2 pool, measured by MIMS or GC-IRMS<ref name="Montoya1996">Montoya, J. P., Voss, M., Kähler, P., & Capone, D. G. (1996). A simple, high-precision, high-sensitivity tracer assay for N2 fixation. ''Applied and Environmental Microbiology'', 62(3), 986–993. https://doi.org/10.1128/aem.62.3.986-993.1996</ref>.

Two labelling approaches are used: (1) direct injection of 15N2 gas bubbles followed by vigorous shaking and equilibration; and (2) the dissolution method, in which pre-dissolved 15N2-enriched water is injected, achieving more homogeneous labelling. The method can be coupled with 13CO2 uptake in the same incubation to simultaneously measure N2 fixation and carbon fixation by diazotrophs.

=== Scale of measurement ===

Each incubation provides a point measurement. Depth-integrated fixation rates are obtained by incubating bottles collected from multiple depths and integrating over the euphotic zone. Incubation duration is typically hours to one day.

=== Data generated ===

N2 fixation rates in nmol N L-1 d-1 or µmol N m-2 d-1 (depth-integrated). Rates can be size-fractionated (e.g., 0.2–10 µm versus > 10 µm) to attribute fixation to different diazotroph size classes (unicellular vs. filamentous). Fixed nitrogen can also be tracked into the dissolved organic nitrogen (DON) pool.

=== Units & currency ===

Units are nmol N L-1 d-1 or µmol N m-2 d-1. The currency is nitrogen.

=== Sample size ===

Typical samples are 1–5 L in volume per incubation.

=== Repositories & databases ===
Bulk data for 15N2 fixation rates are reported here:

== Limitations ==

The 15N2 enrichment of the dissolved pool must be measured accurately; under-estimation of the 15N2 enrichment (e.g., due to incomplete equilibration of bubbles) leads to overestimation of fixation rates. Bubble injection produces heterogeneous enrichment across replicate bottles; the dissolution method mitigates this. Diazotroph community composition affects the timing of fixation: Crocosphaera fixes N2 primarily at night, UCYN-A primarily during the day. Bottle effects apply.

== Example Applications & Protocols ==

=== Classic examples ===
* Montoya et al. (1996) ''A simple, high-precision, high-sensitivity tracer assay for N2 fixation'' <ref name="Montoya1996" />
* Wilson et al. (2012) ''Comparative assessment of nitrogen fixation methodologies, conducted in the oligotrophic North Pacific Ocean'' <ref name="Wilson2012">Wilson, S. T., Böttjer, D., Church, M. J., & Karl, D. M. (2012). Comparative assessment of nitrogen fixation methodologies, conducted in the oligotrophic North Pacific Ocean. ''Applied and Environmental Microbiology'', 78(18), 6516–6523. https://doi.org/10.1128/AEM.01146-12</ref>
* Großkopf et al. (2012) ''Doubling of marine dinitrogen-fixation rates based on direct measurements'' <ref name="Großkopf2012">Großkopf, T., Mohr, W., Baustian, T., Schunck, H., Gill, D., Kuypers, M. M. M., Lavik, G., Schmitz, R. A., Wallace, D. W. R., & LaRoche, J. (2012). Doubling of marine dinitrogen-fixation rates based on direct measurements. ''Nature'', 488(7411), 361–364. https://doi.org/10.1038/nature11338</ref>

=== Recent applications ===
* Tschitschko et al. (2024) ''Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean'' <ref name="Tschitschko2024">Tschitschko, B., Landa, M., Cheung, S., Zheng, H., Williams, C. M., Vergin, K., Giovannoni, S. J., Rocap, G., & Lindell, D. (2024). Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean. ''Nature'', 630, 899–904. https://doi.org/10.1038/s41586-024-07495-w</ref>

=== Common calculations/conversions ===
* N2 fixation rate (nmol N L-1 d-1) = [(15NPN,final − 15NPN,initial) / (15NN2,dissolved − 15Nnatural)] × [PN] / incubation time.
* Depth-integrated rate (µmol N m-2 d-1) = ∫ rate(z) dz over the euphotic zone.

== References ==

[[Category:Main Pages|Model types]]

Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)

2026-09-24T13:29:10Z

Rachel A Foster:

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User: Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' single-cell isotope analysis
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' µm
|-
| '''Temporal scale:''' hours–days
|-
| '''Units:''' isotope enrichment, uptake rates
|-
| '''Community captured:''' active single cells
|-
| '''Co-measurements:''' incubation time, tracer enrichment, temperature, nutrients
|}
</div>
<div style="clear:both"></div>

== Method Overview ==
Single-cell uptake methods combine stable isotope probing (SIP) with secondary ion mass spectrometry (SIMS) to quantify nutrient assimilation at the level of individual cells. In nitrogen fixation studies, samples are incubated with 15N2, followed by analysis using nanoSIMS or related platforms. Taxonomic or functional identity can be resolved using complementary labeling techniques such as CARD-FISH or CHIP-SIMS, enabling direct linkage between nitrogen uptake and specific microbial taxa or functional groups. These approaches provide quantitative, cell-specific measurements of nitrogen assimilation and metabolic activity.

== Output ==
* Single-cell isotope enrichment values
* Cell-specific nutrient uptake rates
* Taxon-resolved nitrogen assimilation
* Spatial patterns of isotope incorporation, e.g. mass spectrometry imaging

=== Scale of measurement ===
* Single-cell
* Quantitative
* Taxon-specific activity

=== Data generated ===
* NanoSIMS ion images (e.g., 12C14N- and 12C15N-)
* Isotopic ratio measurements (e.g., 15N/14N) in regions of interest (ROIs)
* Cell-specific uptake rate calculations
* Linked microscopy, hybridization images, and mass spectrometry images

=== Units & currency ===
* Atom percent 15N
* 15N/14N from (12C15N-/12C14N-)
* Excess isotope enrichment
* fmol N cell−1 h−1
* Relative enrichment above natural abundance

=== Sample size ===
* Typically:
** 10–100 analyzed cells per sample (depends on SIMS platform; nanoSIMS is fewer, SIMS1280 ion probe is typically more)
** 3–10 samples per treatment
* Limited throughput relative to bulk methods

=== Repositories & databases ===

== Limitations ==
* Low throughput and high analytical cost
* Requires specialized instrumentation and expertise
* Incubation conditions may alter in situ activity
* Taxonomic identification depends on probe specificity and labeling efficiency

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

Protocols:
* 15N2 tracer incubation protocols
* CARD-FISH combined with nanoSIMS workflows
* CHIP-SIMS and SIP-SIMS sample preparation protocols
* Custom laboratory SOPs for fixation, hybridization, and nanoSIMS analysis

=== Common calculations/conversions ===
* Atom percent excess = measured atom % − natural abundance
* Single-cell uptake rate = (isotope enrichment × cellular N content) / incubation time
* Correction for tracer enrichment and dilution
* Scaling single-cell rates to community-level estimates (with caution)

== References ==

[[index.php?title=Category:Main Pages|Model types]]

Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)

2026-09-24T13:24:58Z

Rachel A Foster: /* Output */

{{BreadcrumbsNFixation}}

* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User: Chreaa|Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' single-cell isotope analysis
|-
| '''Context:''' incubation
|-
| '''Spatial scale:''' µm
|-
| '''Temporal scale:''' hours–days
|-
| '''Units:''' isotope enrichment, uptake rates
|-
| '''Community captured:''' active single cells
|-
| '''Co-measurements:''' incubation time, tracer enrichment, temperature, nutrients
|}
</div>
<div style="clear:both"></div>

== Method Overview ==
Single-cell uptake methods combine stable isotope probing (SIP) with secondary ion mass spectrometry (SIMS) to quantify nutrient assimilation at the level of individual cells. In nitrogen fixation studies, samples are incubated with 15N2, followed by analysis using nanoSIMS or related platforms. Taxonomic or functional identity can be resolved using complementary labeling techniques such as CARD-FISH or CHIP-SIMS, enabling direct linkage between nitrogen uptake and specific microbial taxa or functional groups. These approaches provide quantitative, cell-specific measurements of nitrogen assimilation and metabolic activity.

== Output ==
* Single-cell isotope enrichment values
* Cell-specific nutrient uptake rates
* Taxon-resolved nitrogen assimilation
* Spatial patterns of isotope incorporation, e.g. mass spectrometry imaging

=== Scale of measurement ===
* Single-cell
* Quantitative
* Taxon-specific activity

=== Data generated ===
* NanoSIMS ion images (e.g., 12C14N-, and 12C15N-)
* Isotopic ratio measurements (e.g., 15N/14N) in regions of interest (ROIs)
* Cell-specific uptake rate calculations
* Linked microscopy, hybridization images, and mass spectrometry images

=== Units & currency ===
* Atom percent 15N
* 15N/14N from (12C15N-/12C14N-)
* Excess isotope enrichment
* fmol N cell−1 h−1
* Relative enrichment above natural abundance

=== Sample size ===
* Typically:
** 10–100 analyzed cells per sample (depends on SIMS platform; nanoSIMS is fewer, SIMS1280 ion probe is typically more)
** 3–10 samples per treatment
* Limited throughput relative to bulk methods

=== Repositories & databases ===

== Limitations ==
* Low throughput and high analytical cost
* Requires specialized instrumentation and expertise
* Incubation conditions may alter in situ activity
* Taxonomic identification depends on probe specificity and labeling efficiency

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

Protocols:
* 15N2 tracer incubation protocols
* CARD-FISH combined with nanoSIMS workflows
* CHIP-SIMS and SIP-SIMS sample preparation protocols
* Custom laboratory SOPs for fixation, hybridization, and nanoSIMS analysis

=== Common calculations/conversions ===
* Atom percent excess = measured atom % − natural abundance
* Single-cell uptake rate = (isotope enrichment × cellular N content) / incubation time
* Correction for tracer enrichment and dilution
* Scaling single-cell rates to community-level estimates (with caution)

== References ==

[[index.php?title=Category:Main Pages|Model types]]