Observational Sampling

NEON field scientists collect a broad variety of observations and samples at terrestrial and aquatic field sites at regular intervals throughout the year. The data and samples collected by NEON’s Terrestrial Observation System (TOS) and Aquatic Observation System (AOS) are standardized but the systems vary slightly by field site type.

Combined with automated instrument measurements and airborne remote sensing data surveys, NEON’s observational data and archived samples provide an unprecedented opportunity to study ecosystem-level change over time. Where logistically possible, NEON colocates aquatic sites with terrestrial sites to support understanding of linkages across atmospheric, terrestrial and aquatic ecosystems. Please note, that we must obtain research permits from our field site hosts to conduct all our field observations, and there are instances when a site host may restrict us from conducting a specific observation. You may visit any field site page on our website to discover the specific list of observations collected at that site.

Observational Sampling at Terrestrial Field Sites

NEON project scientists carefully place observational sampling plots across each terrestrial site, within key identified vegetation types, to capture site heterogeneity and support site-wide characterization of organismal dynamics. NEON also samples organisms within the tower footprint to detect connectivity between organismal data and flux tower measurements. Sampling methods are standardized to ensure comparable data across NEON sites and between vegetation types. The TOS system includes sampling of terrestrial organisms, biogeochemical measurements, and physical soil data collection:

Terrestrial Organisms

Sampling focuses on sentinel taxa, which are sensitive organisms that indicate the health of an ecosystem and provide data relevant to public health. Changes in community dynamics of sentinel taxa affect ecological processes, such as disease transmission rates, agricultural pest control, and ecosystem structure and function.

Soil Microbes

  • Soil microbe biomass
  • Soil microbe community composition
  • Soil microbe group abundances

Terrestrial Plants

  • Plant phenology observations
  • Plant presence and percent cover
  • Digital hemispheric photos of plot vegetation
  • Herbaceous clip harvest
  • Litterfall and fine woody debris sampling
  • Non-herbaceous perennial vegetation structure
  • Root sampling (Megapit)
  • Root sampling tower plots
  • Woody plant vegetation structure
  • Coarse downed wood bulk density sampling
  • Coarse downed wood log survey

Birds & Small Mammals

  • Breeding landbird point counts
  • Small mammal box trapping

Ticks, Mosquitoes and Ground Beetles

  • Ticks sampled using drag cloths
  • Mosquitoes sampled from CO2 traps
  • Ground beetles sampled from pitfall traps


  • Rodent-borne pathogen status
  • Tick-borne pathogen status
  • Mosquito-borne pathogen status

DNA & Meta-Barcode Sequences

  • Small mammal DNA barcodes
  • Mosquito DNA barcodes
  • Ground beetle DNA barcodes
  • Soil microbe marker genes
  • Soil microbe metagenomes


  • Soil chemical properties (Distributed initial characterization)
  • Soil chemical properties (Distributed periodic)
  • Soil inorganic nitrogen pools and transformations
  • Soil stable isotopes (Distributed periodic)
  • Plant foliar physical and chemical properties
  • Plant foliar stable isotopes
  • Litter chemical properties
  • Litter stable isotopes
  • Root chemical properties
  • Root stable isotopes

Physical - Soils

  • Soil physical properties (Distributed initial characterization)
  • Soil physical properties (Distributed periodic)

Observational Sampling at Aquatic Field Sites

At each aquatic field site, NEON’s aquatic observations characterize channel and lake morphology, organism abundance and diversity, seasonal climatic and hydrologic changes, and riparian phenology. These data complement aquatic sensor data that capture hydrologic conditions and surface water and groundwater quality, as well as local atmospheric conditions and airborne remote sensing survey data. Sampling methods are standardized to ensure comparable data across NEON field sites, however data collection may vary based on whether a site is at a stream, river or lake. The AOS system includes sampling of aquatic organisms, biogeochemical measurements, and physical aquatic data collection:

Aquatic Organisms

Sampling focuses on organisms that indicate the health of an ecosystem. Changes in community dynamics of these organisms can indicate how natural and man-made environmental pressures affect ecosystems such as changing climates, agricultural runoff, invasives species, and storm surges and droughts.

Aquatic Plants & Microalgae

  • Aquatic plant bryophyte macroalgae clip harvest
  • Aquatic plant, bryophyte, lichen, and macroalgae point counts in wadeable streams
  • Periphyton, seston, and phytoplankton collection

Aquatic Microbes

  • Benthic microbe community composition
  • Benthic microbe group abundances
  • Surface water microbe cell count
  • Surface water microbe community composition
  • Surface water microbe group abundances

Macroinvertebrates & Zooplankton

  • Macroinvertebrate collection
  • Zooplankton collection


  • Fish electrofishing, gill netting, and fyke netting counts

DNA & Meta-Barcode Sequences

  • Benthic microbe marker genes
  • Benthic microbe metagenomes
  • Surface water microbe marker genes
  • Surface water microbe metagenomes
  • Fish DNA barcodes
  • Macroinvertebrate DNA metabarcodes
  • Zooplankton DNA metabarcodes


  • Aquatic plant bryophyte chemical properties
  • Periphyton, seston, and phytoplankton chemical properties
  • Sediment chemical properties
  • Chemical properties of groundwater
  • Chemical properties of surface water
  • Stable isotope concentrations in groundwater
  • Stable isotope concentrations in surface waters
  • Dissolved gases in surface water
  • Reaeration field and lab collection

Aquatic Physical

  • Riparian composition and structure
  • Riparian vegetation % cover
  • Morphology maps (streams)
  • Bathymetric maps (lakes and rivers)
  • Sediment physical properties
  • Salt-based stream discharge
  • Stream discharge field collection
  • Depth profile at specific depths
  • Secchi depth

Curious about what samples are processed and archived? Visit our Archival Samples Catalog.

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