Results of Soil Metadata Survey for Microbial Studies

The purpose of this survey was to determine what data about soil is believed to be important to accompany microbial molecular data entered into major databases, e.g GenBank, EMBL, RDP. The value of this metadata is to enable a search of the data for particular features and for determining relationships among soil features and molecular data over more global data sets. We are surveying the soil biology community to gain this assessment and then will work with the Genomic Standards Consortium (GSC) and the Environmental Ontology Subgroup to ensure that soil data will be properly considered along with the metadata from other environments.

--an initiative of the Genomic Standards Consortium
and the new International Soil Metagenome
Consortium (Terragenome)


Download DRAFT data entry worksheet (Excel Template-10 NOV 09)
Special thanks to committee members:
George Kowalchuk, Netherlands Institute of Ecology and Free University of Amsterdam
David Myrold, Oregon State University, Crop and Soil Sciences
Cindy Nakatsu, Purdue University, Agriculture/Agronomy
Dawn Field, Oxford Centre of Ecology and Hydrology, Natural Environment Research Council
Christoph Tebbe, Federal Agricultural Research Centre, Institute of Agroecology
James Tiedje, Michigan State University, Center for Microbial Ecology
James Cole, Michigan State University, CME's Ribosomal Database Project

Soil Metadata Survey Report

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# Who
Checked
Req'd		 Tallied Responses March 10 to July 14
-- 105 unique IP responses --
(visit Comments page)		 Importance Difficulty
1 2 3 4   1 2 3 4  
Not
important
at all		 Minimally
important		 Moderately
important		 Very
important		 left
blank		 Easy to
obtain		 Moderately
easy		 Moderately
difficult		 Very
difficult
to obtain		 left
blank
  Chemical                    
73 pH (in water or Calcium chloride) 7 5 15 76 2 94 7 0 0 4
33 salinity/conductivity 5 30 37 27 6 54 30 7 0 14
68 total organic C 3 5 13 80 4 27 52 20 0 6
59 total N 3 11 21 66 4 28 44 25 1 7
28 nitrogen species (e.g., Nitrate, Ammonia) 3 24 40 32 6 11 40 40 6 8
33 total P 1 31 41 26 6 18 32 41 6 8
23 total S 5 39 37 16 8 12 27 43 11 12
18 Ca, Mg 7 42 35 11 10 13 43 35 3 11
9 carbonates 15 39 28 11 12 10 42 32 5 16
31 available carbon (e.g., DOC...) 1 16 43 37 8 9 34 44 7 11
15 carbon fractions (e.g., light, heavy, occluded, fulvic, humic acids) 5 41 31 17 11 2 6 36 48 13
16 mineralogy 8 26 41 11 19 5 17 34 32 17
18 pore space oxygen concentration 10 25 37 18 15 4 10 31 42 18
19 Eh (redox potential) 4 28 27 28 18 13 29 26 18 19
23 cation exchange capacity 5 30 42 13 15 13 32 41 4 15
10 base saturation 6 47 27 7 18 9 35 37 4 20
9 Al saturation 6 53 18 8 20 6 28 42 5 24
19 pollutants (e.g., solvents, heavy metals) 6 25 34 24 16 2 10 45 33 15
16 trace elements (e.g., metals: Fe, Mn, Cu...) 8 36 34 11 16 9 23 45 13 15
                       
  Physical                    
47 texture (granulometry) 5 16 23 50 11 30 38 22 1 14
10 aggregate stability 7 36 33 8 21 7 26 40 11 21
6 penetration resistance 17 46 14 7 21 20 35 19 6 25
23 soil structure 9 25 34 19 18 11 34 35 4 21
19 porosity 7 21 38 21 18 10 32 36 7 20
29 bulk density 7 27 28 29 14 29 38 20 2 16
16 water retention curve 8 23 34 20 20 4 21 35 20 25
15 field capacity 9 30 30 15 21 21 33 21 7 23
4 wilting coeffecient 17 36 21 6 25 6 28 28 14 29
7 infiltration capacity 8 41 25 8 23 11 24 32 14 24
25 slope, position 9 23 31 23 19 60 19 6 0 20
                       
  Biological                    
42 microbial biomass and its C,N,P 2 12 28 55 8 5 34 46 8 12
31 C/N ratio 4 11 28 50 12 30 35 20 5 15
19 respiration rate 3 25 39 26 12 13 34 33 9 16
18 N cycle rates (e.g., nitrification) 3 30 35 23 14 3 17 44 21 20
45 plant cover (native) 6 16 24 47 12 40 33 14 3 15
14 root biomass 3 30 31 23 18 8 19 37 20 21
21 enzymatic activities (e.g., dehydrogenases) 11 22 37 20 15 6 22 44 16 17
17 annual primary productivity of site 6 22 39 20 18 8 29 32 15 21
16 annual plant residue returned to soil 6 26 35 18 20 9 25 33 17 21
18 soil fauna (types, density) 5 34 31 18 17 5 10 34 38 18
13 earthworm activity or density 7 35 35 9 19 7 15 50 12 21
12 susceptibility to microbe immigration (water, dust, birds…) 12 33 33 9 18 4 18 32 31 20
                       
  Soil / Geological                    
67 soil type (classification) 7 5 23 62 8 33 43 13 1 15
58 horizon 7 8 24 52 14 42 37 5 0 21
23 drainage classification 8 27 34 19 17 23 42 16 3 21
24 parent rock material 8 32 30 22 13 25 41 18 2 19
14 water table (maximum and minimum annual depths) 11 31 32 15 16 12 21 37 17 18
19 degree of heterogeneity within sampled site 5 22 32 30 16 6 26 32 22 19
                       
  Geographical                    
66 latitude and longitude 7 6 18 65 9 86 7 1 0 11
63 elevation 7 8 24 56 10 81 9 2 0 13
                       
  Management                    
72 land use (e.g., urban, agriculture, forestry) 8 1 12 76 8 81 8 2 1 13
47 tillage (type) 7 14 20 53 11 70 18 3 1 13
54 crops (current, rotation) 6 9 23 58 9 73 15 4 1 12
21 crop yield 8 36 27 21 13 28 35 19 6 17
28 animal activity (e.g., feral pigs, grazing) 7 27 31 25 15 26 41 19 2 17
44 fertilizers (type and annual amount) 4 7 34 50 10 37 37 14 5 12
33 pesticides 4 14 31 41 15 28 34 21 6 16
38 historical data (e.g., previous land use) 7 10 34 45 9 11 31 38 13 12
28 fire 5 24 28 34 14 27 33 24 3 18
21 erosion 4 28 29 28 16 15 36 30 6 18
                       
  Climate                    
60 mean and seasonal rainfall 4 12 17 65 7 45 37 10 2 11
55 mean and seasonal temperatures 4 12 18 63 8 42 36 10 3 14
21 evapotransportation 6 28 40 17 14 9 29 43 7 17
14 global radiation 10 38 25 13 19 13 21 36 13 22
                       
  Sampling                    
76 depth 9 1 5 84 6 87 7 0 1 10
52 composite design 6 12 14 57 16 64 21 1 1 18
42 soil temperature at sampling 8 29 27 32 9 64 24 3 0 14
28 weather at sampling 12 35 31 17 10 77 11 2 1 14
50 moisture content at sampling 6 15 22 49 13 63 21 6 0 15
40 area represented by composite sample 5 18 26 41 15 50 29 5 1 20
60 weight of sample used for DNA extraction 7 10 17 62 9 76 13 2 0 14