These datasets are not necessarily representative of the long-term standardized data otherwise available on the NEON data portal. Prototype data are provided as downloadable zip files.

Optimization of a gas sampling system for measuring eddy-covariance fluxes of H2O and CO2, 2013 Atmosphere
Enclosed infrared gas analysers utilize a gas sampling system, which can substantially increase spectral corrections for eddy-covariance applications. Here, we show that a requirements-based design can reduce high-frequency attenuation for H2O by ≈3/4, with the remaining flux correction not exceeding 3%. The resulting gas sampling system can be used across a wide range of eco-climates and site layouts, and enables more automated and comparable eddy-covariance data processing across sites.
Science theme:
Atmosphere  
Locations:
Niwot Ridge Mountain Research Station (D13; CO; NIWO)  
Time range:
2013-2013
Abstract:
Several initiatives are currently emerging to observe the exchange of energy and matter between the earth''s surface and atmosphere standardized over larger space and time domains. For example, the National Ecological Observatory Network (NEON) and the Integrated Carbon Observing System (ICOS) will provide the ability of unbiased ecological inference across eco-climatic zones and decades by deploying highly scalable and robust instruments and data processing. In the construction of these observatories, enclosed infrared gas analysers are widely employed for eddy-covariance applications. While these sensors represent a substantial improvement compared to their open- and closed-path predecessors, remaining high-frequency attenuation varies with site properties, and requires correction. Here, we show that the gas sampling system substantially contributes to high-frequency attenuation, which can be minimized by careful design. From laboratory tests we determine the frequency at which signal attenuation reaches 50 % for individual parts of the gas sampling system. For different models of rain caps and particulate filters, this frequency falls into ranges of 2.5–16.5 Hz for CO2, 2.4–14.3 Hz for H2O, and 8.3–21.8 Hz for CO2, 1.4–19.9 Hz for H2O, respectively. A short and thin stainless steel intake tube was found to not limit frequency response, with 50 % attenuation occurring at frequencies well above 10 Hz for both H2O and CO2. From field tests we found that heating the intake tube and particulate filter continuously with 4 W was effective, and reduced the occurrence of problematic relative humidity levels (RH > 60 %) by 50 % in the infrared gas analyser cell. No further improvement of H2O frequency response was found for heating in excess of 4 W. These laboratory and field tests were reconciled using resistor-capacitor theory, and NEON''s final gas sampling system was developed on this basis. The design consists of the stainless steel intake tube, a pleated mesh particulate filter, and a low-volume rain cap in combination with 4 W of heating and insulation. In comparison to the original design, this reduced the high-frequency attenuation for H2O by ≈ 3/4, and the remaining cospectral correction did not exceed 3 %, even at a very high relative humidity (95 %). This standardized design can be used across a wide range of eco-climates and site layouts, and maximizes practicability due to minimal flow resistance and maintenance needs. Furthermore, due to minimal high-frequency spectral loss, it supports the routine application of adaptive correction procedures, and enables more automated data processing across sites.
Methods:
A comprehensive field experiment under various environmental conditions was performed in July 2013 and July 2014 at the Niwot Ridge AmeriFlux site.
The test philosophy is that a GSS component has better performance where it results in less IRGA CO2 and/or H2O signal attenuation when used individually and when integrated with other GSS components. Initially nine different types of particulate filters were tested in the laboratory, and it was found that the Swagelok FW 2 μm stainless steel mesh filter (Swagelok, Solon, OH, U.S.A.) provided the most suitable characteristics. This filter was then integrated with three different types of rain caps (Figure 1) and two different intake tubes, and further tested under laboratory conditions.
Responsible Neon Team:
Terrestrial Instrumented Systems (TIS)  
Related data products:
NEON.DOM.SITE.DP3.00010.001; NEON.DOM.SITE.DP3.00009.001  
Related publications:
Metzger, S., Burba, G., Burns, S. P., Blanken, P. D., Li, J., Luo, H., and Zulueta, R. C.: Optimization of a gas sampling system for measuring eddy-covariance fluxes of H2O and CO2, Atmos. Meas. Tech. Discuss., 8, 10983-11028, doi:10.5194/amtd-8-10983-2015, 2015.  
Keywords:
atmospheric fluxes; water; carbon dioxide  
Dataset ID:
30d084e0-ff4d-4bbe-a527-6e4366c6e545
Additional Information
File size:
1.9 GB
File type:
DOCX, PDF, TXT, GHG, GZ  

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Citation: National Ecological Observatory Network. 2016. Optimization of a gas sampling system for measuring eddy-covariance fluxes of H2O and CO2, 2013. Downloaded from data.neonscience.org on April, 30, 2017

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Data Hosted by NEON

NEON_Metzger_etal_2015_GasSamplingSystem.zip

Soil microbe prototype 16S sequence data, 2009-2010 Organisms, Populations, and Communities
Bacterial sequencing metadata and sequence accession numbers from 2009-2010 sampling efforts in AK, HI, UT, and FL
Science theme:
Organisms, Populations, and Communities  
Locations:
Caribou Creek-Poker Flats Watershed (D19; AK; ); Laupahoehoe (D20; HI; ); Onaqui (D15; UT; ); Ordway-Swisher Biological Station (D03; FL; )  
Time range:
2009-2010
Abstract:
Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal etxent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and PLFA composition across four biomes. In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available NEON data that quantify diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominantly influenced by pH, soil water content, and cation exchange capacity. Temporal differences between profiling methods may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions.
Methods:
This study took place in soil habitats at four NEON domains. The sampling locations differ greatly in climatic and physico-chemical characteristics in order to capture the range of soil conditions that will be encountered at NEON sites.
408 soil samples were collected at 4-5 time points during a year from four sites with different levels of intra-annual variability in temperature and precipitation. Samples were collected within a gride measuring 160x320 m divided into eigth 80x80 m cells. Soil cores were 7.5 cm in diameter and sampled from 0-10cm depth. Sub-sets of the three cores corresponding to each cell were combined for a composite sample representative of each cell. Core samples were homogenized, sieved through a 2 mm mesh, and either air-dried or frozen at -80 degrees celcius for downstream analyses. Air-dried samples were analyzed for a suite of biogeochemical measurements.
Responsible Neon Team:
Terrestrial Observational Systems (TOS)  
Related data products:
NEON.DOM.SITE.DP1.10108.001  
Related publications:
Docherty, Kathryn M., Hannah M. Borton, Noelle Espinosa, Martha Gebhardt, Juliana Gil-Loaiza, Jessica LM Gutknecht, Patrick W. Maes, et al. 2015. “Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes.” PloS One 10 (11): e0135352.  
Keywords:
marker gene sequences; soil microbes; microbial ecology  
Dataset ID:
bfe3bcf1-558a-49d0-a90a-9ed4ff3717d0
Additional Information
File size:
55.6 MB
File type:
CSV, TXT, ZIP, FASTQ  

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Citation: National Ecological Observatory Network. 2016. Soil microbe prototype 16S sequence data, 2009-2010. Downloaded from data.neonscience.org on April, 30, 2017

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Data Hosted by NEON

NEON_MicrobePrototypeData-2009-2010.zip

Data Hosted Externally

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http://www.ncbi.nlm.nih.gov/bioproject/288822
NEON prototype data: beetle pitfall collections from CPER in 2008 Organisms, Populations, and Communities
NEON ground beetle sampling will improve our understanding of the distribution, ecology and evolution of ground beetles in both wildland and human-dominated landscapes at a very wide scale over several decades. NEON ground beetle data will have added value through active collocation at the plot and site level with other NEON data (e.g., plant productivity and diversity, rodent density, temperature, precipitation and hundreds of other NEON data products).
Science theme:
Organisms, Populations, and Communities  
Locations:
Central Plains Experimental Range (D10; CO; CPER; [40.839, -104.725])  
Time range:
2008-2008
Abstract:
Ground beetles have been extensively used as indicator species of arthropod biodiversity, environmental change, land use and land management. The ground beetle family is large, widespread, and associated with the ground layer, rather than any particular plant community, ensuring that some ground beetles are present in virtually all terrestrial habitats over the entire extent of the observatory. The family is rich in species, abundant in individuals and well known taxonomically. In addition, ground beetles are sensitive to environmental conditions and form well-defined richness gradients. This prototype data allowed for lessons learned about the implementation of beetle sampling and protocol design.
Methods:
The Central Plains Experimental Range (CPER) is located at the western edge of the Pawnee National Grasslands in Colorado, 19 kilometers northeast of Nunn, Colorado. The elevation ranges between 1,500-1,700 meters. This prototype effort was implemented at alternative plot locations to the operational ones listed on the data portal. GPS coordinates of each plot are recorded.
Ground beetles have been extensively used as indicator species of arthropod biodiversity, environmental change, land use and land management. To implement a sampling regime that measures the abundance and diversity of this indicator, we conducted initial prototype sampling. For this prototype effort, we set out 6 pitfall traps at each of 8 plot locations within the Central Plains Experimental Range site in 2008. Two collections were performed at each trap. The interval of collection for each trap was approximately 2 weeks. Refer to NEON.DOC.000909 for more details on the operational beetle sampling effort.
Responsible Neon Team:
Terrestrial Observational Systems (TOS)  
Related data products:
NEON.DOM.SITE.DP1.10022.001; NEON.DOM.SITE.DP1.10020.001  
Related publications:
 
Keywords:
diversity; abundance; beetles  
Dataset ID:
f136909d-8454-429f-8a68-7756197f8089
Additional Information
File size:
25.9 kB
File type:
xlsx  

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Citation: National Ecological Observatory Network. 2016. NEON prototype data: beetle pitfall collections from CPER in 2008. Downloaded from data.neonscience.org on April, 30, 2017

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Data Hosted by NEON

NEONbeetle2008CPER.zip

eddy4R: A community-extensible processing, analysis and modelling framework for eddy-covariance data Atmosphere
Computational compatibility is one of the current challenges for eddy covariance (EC) tower networks in informing regional and continental scale processes. To resolve this issue, by adopting a Development and Systems Operation (DevOps) philosophy, NEON developed a data product process framework that allows the scalable, portable, and extensible integration of raw measurement hierarchies and geoscientific analyses in a single, open-source, distributed processing environment.
Science theme:
Atmosphere  
Locations:
The Smithsonian Environmental Research Center (D02; MD; SERC; [38.890, -76.560])  
Time range:
2016-2016
Abstract:
This study presents the systematic development of an open-source, flexible and modular eddy-covariance (EC) data processing framework. This is achieved through adopting a Development and Systems Operation (DevOps) philosophy, building on the eddy4R family of EC code packages in the R Language for Statistical Computing as foundation. These packages are community-developed via the GitHub distributed version control system and wrapped into a portable and reproducible Docker filesystem that is independent of the underlying host operating system. The HDF5 hierarchical data format then provides a streamlined mechanism for highly compressed and fully self-documented data ingest and output. This framework is applicable beyond EC, and more generally builds the capacity to deploy complex algorithms developed by scientists in an efficient and scalable manner. In addition, modularity permits meeting project milestones while retaining extensibility with time. The efficiency and consistency of this framework is demonstrated in the form of three application examples. These include tower EC data from first instruments installed at a National Ecological Observatory (NEON) field site, aircraft flux measurements in combination with remote sensing data, as well as a software intercomparison. In conjunction with this study, the first two eddy4R packages and simple NEON EC data products are released publicly. While this proof-of-concept represents a significant advance, substantial work remains to arrive at the automated framework needed for the streaming generation of science-grade EC fluxes.
Methods:
EC tower data from the Smithsonian Environmental Research Center (SERC) in Edgewater, MD, USA are used to demonstrate the capability of eddy4R in this manuscript. SERC is located on the Rhode and West Rivers, and hosts the NEON SERC tower (38°53'24.29" N, 76°33'36.04" W; 30 m a.s.l.). The ecosystem at SERC is a closed-canopy hardwood deciduous forest dominated by tulip popular, oak and ash, with a mean canopy height of approximately 38 m.
By adopting a DevOps philosophy, the data product process frame work developed by NEON includes git-distributed version controlled scientific algorithms and a modular family of open-source R packages (eddy4R), the Hierarchical Data Format (HDF5) data input and output for efficient, self-describing, as well as Docker images to guarantee the same performance regardless of the compute environment.
Responsible Neon Team:
Terrestrial Instrumented Systems (TIS)  
Related data products:
NEON.DOM.SITE.DP1.00010.001; NEON.DOM.SITE.DP1.00007.001; NEON.DOM.SITE.DP1.00034.001; NEON.DOM.SITE.DP1.00035.001  
Related publications:
 
Keywords:
computing; continuous development; continuous integration; devOps; eddy4R; eddy-covariance; image; reproducibility; science code; Docker  
Dataset ID:
d0debf5e-5c66-40c6-8d3c-2a253911d8e6
Additional Information
File size:
712.3 MB
File type:
HDF5  

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Citation: National Ecological Observatory Network. 2017. eddy4R: A community-extensible processing, analysis and modelling framework for eddy-covariance data. Downloaded from data.neonscience.org on April, 30, 2017

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Data Hosted by NEON

NEON-SERC-field-test-data.zip

NEON prototype data: Co-located soil microbial and biogeochemical sampling from Harvard Forest, 2012 Organisms, Populations, and Communities Biogeochemistry
A goal of the NEON soil microbial ecology program is to capture microbial diversity across the U.S. This study evaluates the feasibility of employing a design of co-locating plant productivity and soil biogeochemistry measurements. This approach enables comparisons of microbial and plant diversity with biogeochemical and remote sensing data. These linkages across spatial scales are essential for scaling molecular measurements across the Observatory.
Science theme:
Organisms, Populations, and Communities; Biogeochemistry  
Locations:
Harvard Forest (D01; MA; HARV; [42.000, -72.000])  
Time range:
2012-2012
Abstract:
A goal of the NEON soil microbial ecology program is to capture microbial diversity across the U.S. This study evaluates the feasibility of employing a design of co-locating plant productivity and soil biogeochemistry measurements. The objectives of this prototype effort were to: 1. Evaluate a microbial sampling strategy that is co-located with plant productivity and soil biogeochemisty measurements; 2. Validate a protocol for determining soil microbial function using environmental transcriptomics; 3. Identify feedback links between microbial function, nutrient cycling, and plant productivity; and 4. Develop a strategy to scale extremes of spatial measurements (sub-micron to km-scale). If successful, this approach will enable comparisons of microbial and plant diversity with biogeochemical and remote sensing data. These linkages across spatial scales are essential for scaling molecular measurements across the Observatory.
Methods:
The Harvard Forest site is comprised of 3,750 acres of land and multiple research facilities. Representative habitats at Harvard Forest include northern, transition, and central forests; marshes, swamps, and conifer-dominated bogs; and forest plantations. The vegetation is typical of the Transition Hardwoods-White Pine-Hemlock region. The dominant vegetation is regenerating Eastern Deciduous temperate forest.
Soil samples were collected from 7/23/2012-7/27/2012 at the D1 Harvard forest site from randomly selected, pre-determined plots. Samples were collected for various analyses, including micronutrients, bulk density, and stable isotope analyses. Soil samples were separated into organic and mineral horizons For organic horizons, three 10x10 ‘brownies’ were taken at each sample site within 0.5m of each other and pooled into one sample. The sample was then placed in a labeled ziplock bag and placed in a cooler with ice packs. For mineral horizons, three soil cores were taken in the same locations as the three brownies with a slide hammer corer at each sample site and pooled together for each sample. The soil was pushed into a ziplock bag and homogenized, large rocks and roots were removed from the bag.
Responsible Neon Team:
Airborne Observation Platform (AOP) ; Aquatic Instrumented Systems (AIS) ; Terrestrial Observational Systems (TOS)  
Related data products:
 
Related publications:
 
Keywords:
soil microbes; microbial ecology; biogeochemistry  
Dataset ID:
9edb1594-24a9-4976-a8ef-2cfa0c9ffcb7
Additional Information
File size:
16 kB
File type:
CSV, TXT  

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Citation: National Ecological Observatory Network. 2017. NEON prototype data: Co-located soil microbial and biogeochemical sampling from Harvard Forest, 2012. Downloaded from data.neonscience.org on April, 30, 2017

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Data Hosted by NEON

NEON_HARV_SoilMicrobeBiogeochem_PrototypeData_2012.zip

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