We will be offering an R workshop December 18-20, 2019. Learn more.

Soil

From mothur
Jump to: navigation, search

Here is a link to NCBI definition page for the soil package.

Required

sample_name

This is your group name. Mothur will fill this in for you, thanks mom!

description

Description of sample

sample_title

The title for your sample.

format: {text} 

seq_methods

The free form descriptions of methods used to create the sequencing library.

format: {text}

organism

You must choose this from the NCBI's list found here. This is controlled vocabulary. Your choices are: activated carbon metagenome, activated sludge metagenome, air metagenome, anaerobic digester metagenome, ant fungus garden metagenome, aquatic metagenome, activated carbon metagenome, activated sludge metagenome, beach sand metagenome, biofilm metagenome, biofilter metagenome, biogas fermenter metagenome, bioreactor metagenome, bioreactor sludge metagenome, clinical metagenome, coal metagenome, compost metagenome, dust metagenome, fermentation metagenome, food fermentation metagenome, food metagenome, freshwater metagenome, freshwater sediment metagenome, groundwater metagenome, halite metagenome, hot springs metagenome, hydrocarbon metagenome, hydrothermal vent metagenome, hypersaline lake metagenome, ice metagenome, indoor metagenome, industrial waste metagenome, mangrove metagenome, marine metagenome, marine sediment metagenome, microbial mat metagenome, mine drainage metagenome, mixed culture metagenome, oil production facility metagenome, paper pulp metagenome, permafrost metagenome, plastisphere metagenome, power plant metagenome, retting rhizosphere metagenome, rock metagenome, salt lake metagenome, saltern metagenome, sediment metagenome, snow metagenome, soil metagenome, stromatolite metagenome, terrestrial metagenome, tomb wall metagenome, wastewater metagenome, wetland metagenome, whale fall metagenome, algae metagenome, ant metagenome, bat metagenome, beetle metagenome, bovine gut metagenome, bovine metagenome, chicken gut metagenome, coral metagenome, echinoderm metagenome, endophyte metagenome, epibiont metagenome, fish metagenome, fossil metagenome, gill metagenome, gut metagenome, honeybee metagenome, human gut metagenome, human lung metagenome, human metagenome, human nasal/pharyngeal metagenome, human oral metagenome, human skin metagenome, insect gut metagenome, insect metagenome, mollusc metagenome, mosquito metagenome, mouse gut metagenome, mouse metagenome, mouse skin metagenome, nematode metagenome, oral metagenome, phyllosphere metagenome, pig metagenome, plant metagenome, primate metagenome, rat metagenome, root metagenome, sea squirt metagenome, seed metagenome, shoot metagenome, skin metagenome, snake metagenome, sponge metagenome, stomach metagenome, symbiont metagenome, termite gut metagenome, termite metagenome, upper respiratory tract metagenome, urine metagenome, viral metagenome, wallaby gut metagenome, wasp metagenome, synthetic metagenome, metagenome. You can modify your choice after submission.

collection_date

Date of sampling, in \"DD-Mmm-YYYY\", \"Mmm-YYYY\" or \"YYYY\" format (single instance, eg., 05-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard \"YYYY-mm-dd\" or \"YYYY-mm-ddThh:mm:ss\" (eg. 1990-11-05 or 1990-11-05T14:41:36)

format: {timestamp}

env_biome

Major class of ecologically similar communities of plants, animals, and other organisms (eg., desert, coral reef).

format: {term}

env_feature

Geographical environmental feature (eg., harbor, lake).

format: {term}

geo_loc_name

Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg \"Canada: Vancouver\" or \"Germany: halfway down Zugspitze, Alps\".

format: {term}:{term}:{text}

lat_lon

The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format \"d[d.dddd] N|S d[dd.dddd] W|E\", eg, 38.98 N 77.11 W.

format: {float} {float}

env_material

The matter displaced by the sample (eg., air, soil, water).

format: {term}

depth

Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.

format: {float} m

elev

The elevation of the sampling site as measured by the vertical distance from mean sea level.

format: {float} {unit}

Optional

agrochem_addition

The addition of fertilizers, pesticides, etc. - amount and time of applications.

format: {text};{float} {unit};{timestamp}

al_sat

The aluminum saturation (esp. for tropical soils).

format: {float} {unit}

al_sat_meth

The reference or method used in determining Al saturation.

format: {PMID|DOI|URL}

ammonium

The concentration of ammonium.

format: {float} {unit}

altitude

The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

format: {float} m

annual_season_precpt

The mean annual and seasonal precipitation (mm).

format: {float} {unit}

annual_season_temp

The mean annual and seasonal temperature (oC).

format: {float} {unit}

crop_rotation

Whether or not crop is rotated, and if yes, rotation schedule.

format: {boolean};Rn/{timestamp}/{period}

cur_land_use

The present state of sample sitel.

format: [, 'cities', 'farmstead', 'industrial areas', 'roads/railroads', 'rock', 'sand', 'gravel', 'mudflats', 'salt flats', 'badlands', 'permanent snow or ice', 'saline seeps', 'mines/quarries', 'oil waste areas', 'small grains', 'row crops', 'vegetable crops', 'horticultural plants (e.g. tulips)', 'marshlands (grass,sedges,rushes)', 'tundra (mosses,lichens)', 'rangeland', 'pastureland (grasslands used for livestock grazing)', 'hayland', 'meadows (grasses,alfalfa,fescue,bromegrass,timothy)', 'shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)', 'successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)', 'shrub crops (blueberries,nursery ornamentals,filberts)', 'vine crops (grapes)', 'conifers (e.g. pine,spruce,fir,cypress)', 'hardwoods (e.g. oak,hickory,elm,aspen)', 'intermixed hardwood and conifers', 'tropical (e.g. mangrove,palms)', 'rainforest (evergreen forest receiving >406 cm annual rainfall)', 'swamp (permanent or semi-permanent water body dominated by woody plants)', 'crop trees (nuts,fruit,christmas trees,nursery trees)']

cur_vegetation

The vegetation classification from one or more standard classification systems, or agricultural crop.

format: {text}

cur_vegetation_meth

The reference or method used in vegetation classification.

format: {PMID|DOI|URL}

depth

Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples..

format: {float} m

drainage_class

The drainage classification from a standard system such as the USDA system.

format: [, 'very poorly', 'poorly', 'somewhat poorly', 'moderately well', 'well', 'excessively drained']

extreme_event

The unusual physical events that may have affected microbial populations.

format: {timestamp}

extreme_salinity

The measured salinity.

format: {float} {unit}

fao_class

The soil classification from the FAO World Reference Database for Soil Resources.

format: {term}

fire

The historical and/or physical evidence of fire.

format: {timestamp}

flooding

The historical and/or physical evidence of flooding.

format:  {timestamp}

heavy_metals

The heavy metals present and concentrationsany drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations.

format: {text};{float} {unit}

heavy_metals_meth

The reference or method used in determining heavy metals.

format: {PMID|DOI|URL}

horizon

The specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath.

format: [, 'O horizon', 'A horizon', 'E horizon', 'B horizon', 'C horizon', 'R layer', 'Permafrost']

horizon_meth

The reference or method used in determining the horizon.

format: {PMID|DOI|URL}

link_addit_analys

Links to additional analysis.

format: {PMID|DOI|URL}

link_class_info

The link to digitized soil maps or other soil classification information.

format: {PMID|DOI|URL}

link_climate_info

The link to climate resource.

format: {PMID|DOI|URL}

local_class

The soil classification based on local soil classification system.

format: {text} 

local_class_meth

The reference or method used in determining the local soil classification

format: {PMID|DOI|URL}

microbial_biomass

The the part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 µm. IF you keep this, you would need to have correction factors used for conversion to the final units, which should be mg C (or N)/kg soil)..

format: {float} {unit}

microbial_biomass_meth

The reference or method used in determining microbial biomass.

format: {PMID|DOI|URL}

ph

The pH measurement.

format: {float} {unit}

ph_meth

The reference or method used in determining pH.

format: {PMID|DOI|URL}

pool_dna_extracts

Were multiple DNA extractions mixed? how many?.

format: {boolean};{float} {unit}

previous_land_use

The previous land use and dates.

format: {text};{timestamp}

previous_land_use_meth

The reference or method used in determining previous land use and dates.

format: {PMID|DOI|URL}

profile_position

The cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas.

format: [, 'summit', 'shoulder', 'backslope', 'footslope', 'toeslope']

rel_to_oxygen

Aerobic or anaerobic

format: [, 'aerobe', 'anaerobe', 'facultative', 'microaerophilic', 'microanaerobe', 'obligate aerobe', 'obligate anaerobe']

salinity_meth

The reference or method used in determining salinity.

format: {PMID|DOI|URL}

samp_collect_device

Method or device employed for collecting sample

format: {text}

samp_mat_process

Processing applied to the sample during or after isolation.

format: {text|term}

samp_size

The sample size.

format: {float} {unit}

samp_weight_dna_ext

The weight (g) of soil processed.

format: {float} g

sieving

The collection design of pooled samples and/or sieve size and amount of sample sieved.

format: {{text}|{float} {unit}};{float} {unit}

slope_aspect

The the direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., NW or 315°. This measure provides an indication of sun and wind exposure that will influence soil .

format: {float} {unit}

slope_gradient

The commonly called \\u201cslope.\\u201d The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer.

format: {float} {unit}

soil_type

The soil series name or other lower-level classification.

format: {text} 

soil_type_meth

The reference or method used in determining soil series name or other lower-level classification.

format: {PMID|DOI|URL}

store_cond

Explain how and for how long the soil sample was stored before DNA extraction..

format: {text};{period}

texture

The the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.

format: {float} {unit}

texture_meth

The reference or method used in determining soil texture.

format: {PMID|DOI|URL}

tillage

The note method(s) used for tilling.

format: [, 'drill', 'cutting disc', 'ridge till', 'strip tillage', 'zonal tillage', 'chisel', 'tined', 'mouldboard', 'disc plough']

tot_n

The total nitrogen content of the soil Units of g N/kg soil.

format: {float} {unit}

tot_n_meth

The reference or method used in determining the total N.

format: {PMID|DOI|URL}

tot_org_c_meth

The reference or method used in determining total organic C.

format: {PMID|DOI|URL}

tot_org_carb

Definition for soil: total organic C content of the soil units of g C/kg soil. Definition otherwise: total organic carbon content.

format: {float} {unit}

water_content_soil

The water content (g/g or cm3/cm3).

format: {float} [g/g|cm3/cm3]

water_content_soil_meth

The reference or method used in determining the water content of soil.

format: {PMID|DOI|URL}

user_defined

You may create your own optional fields to describe your sample.