Harvard Forest

Data Archive

HF438

Effect of Warming on Thermal Adaptation of Soil Microbial Growth Traits at Harvard Forest 2013-2023

Related Publications

Data

• hf438-01: raw growth curve data (preview)

Overview

• Lead: Kristen DeAngelis
• Investigators: Ashley Eng
• Contact: Information Manager
• Start date: 2013
• End date: 2023
• Status: complete
• Location: Prospect Hill Tract (Harvard Forest)
• Latitude: +42.54 degrees
• Longitude: -72.18 degrees
• Elevation: 365 meter
• Datum: WGS84
• Taxa: Alphaproteobacteria
• Release date: 2023
• Language: English
• EML file: knb-lter-hfr.438.2
• DOI: digital object identifier
• EDI: data package
• DataONE: data package
• Related links:
• Study type: short-term measurement
• Research topic: physiological ecology, population dynamics and species interactions
• LTER core area: population studies
• Keywords: bacteria, climate change, growth, microbes, soil, soil warming
• Abstract:

  Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5ºC above ambient temperature with unheated controls for thirty years. We hypothesized that Alphaproteobacteria from warmed plots have (1) less temperature sensitive growth rates; (2) higher optimum growth temperatures; and (3) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22-37ºC in 2-3ºC increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range.

• Methods:

  Bacteria were isolated from soils and cryopreserved at -80ºC. Isolates were grown in 10% tryptic soy broth. Absorbance (optical density at 600 nm) was measured over time between 22-37ºC in increments of 2-3ºC. Model fitting and phylogenetic comparative methods were used to determine whether adaptation of temperature sensitivity of growth, optimum growth temperature, and maximum growth temperature occurred.

• Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

• Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

• Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210. Other funding: NSF grant DEB-1749206.

• Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

• License: Creative Commons Zero v1.0 Universal (CC0-1.0)

• Citation: DeAngelis K. 2023. Effect of Warming on Thermal Adaptation of Soil Microbial Growth Traits at Harvard Forest 2013-2023. Harvard Forest Data Archive: HF438 (v.2). Environmental Data Initiative: https://doi.org/10.6073/pasta/a06237e33d9e8c2d9a530c1349d319a8.

Detailed Metadata

hf438-01: raw growth curve data

1. runID: run identifier
2. day: day on which optical density at 600 nm reading bacterial liquid cultures in 96-well plate was taken (unit: dimensionless / missing value: NA)
3. hour: hour at which optical density at 600 nm reading bacterial liquid cultures in 96-well plate was taken (unit: dimensionless / missing value: NA)
4. minute: minute at which optical density at 600 nm reading bacterial liquid cultures in 96-well plate was taken (unit: dimensionless / missing value: NA)
5. second: second at which optical density at 600 nm reading bacterial liquid cultures in 96-well plate was taken (unit: dimensionless / missing value: NA)
6. temperature_C: temperature of plate reader at each time point (unit: celsius / missing value: NA)
7. A1: optical density at 600 nm of well A1 (unit: dimensionless / missing value: NA)
8. A2: optical density at 600 nm of well A2 (unit: dimensionless / missing value: NA)
9. A3: optical density at 600 nm of well A3 (unit: dimensionless / missing value: NA)
10. A4: optical density at 600 nm of well A4 (unit: dimensionless / missing value: NA)
11. A5: optical density at 600 nm of well A5 (unit: dimensionless / missing value: NA)
12. A6: optical density at 600 nm of well A6 (unit: dimensionless / missing value: NA)
13. A7: optical density at 600 nm of well A7 (unit: dimensionless / missing value: NA)
14. A8: optical density at 600 nm of well A8 (unit: dimensionless / missing value: NA)
15. A9: optical density at 600 nm of well A9 (unit: dimensionless / missing value: NA)
16. A10: optical density at 600 nm of well A10 (unit: dimensionless / missing value: NA)
17. A11: optical density at 600 nm of well A11 (unit: dimensionless / missing value: NA)
18. A12: optical density at 600 nm of well A12 (unit: dimensionless / missing value: NA)
19. B1: optical density at 600 nm of well B1 (unit: dimensionless / missing value: NA)
20. B2: optical density at 600 nm of well B2 (unit: dimensionless / missing value: NA)
21. B3: optical density at 600 nm of well B3 (unit: dimensionless / missing value: NA)
22. B4: optical density at 600 nm of well B4 (unit: dimensionless / missing value: NA)
23. B5: optical density at 600 nm of well B5 (unit: dimensionless / missing value: NA)
24. B6: optical density at 600 nm of well B6 (unit: dimensionless / missing value: NA)
25. B7: optical density at 600 nm of well B7 (unit: dimensionless / missing value: NA)
26. B8: optical density at 600 nm of well B8 (unit: dimensionless / missing value: NA)
27. B9: optical density at 600 nm of well B9 (unit: dimensionless / missing value: NA)
28. B10: optical density at 600 nm of well B10 (unit: dimensionless / missing value: NA)
29. B11: optical density at 600 nm of well B11 (unit: dimensionless / missing value: NA)
30. B12: optical density at 600 nm of well B12 (unit: dimensionless / missing value: NA)
31. C1: optical density at 600 nm of well C1 (unit: dimensionless / missing value: NA)
32. C2: optical density at 600 nm of well C2 (unit: dimensionless / missing value: NA)
33. C3: optical density at 600 nm of well C3 (unit: dimensionless / missing value: NA)
34. C4: optical density at 600 nm of well C4 (unit: dimensionless / missing value: NA)
35. C5: optical density at 600 nm of well C5 (unit: dimensionless / missing value: NA)
36. C6: optical density at 600 nm of well C6 (unit: dimensionless / missing value: NA)
37. C7: optical density at 600 nm of well C7 (unit: dimensionless / missing value: NA)
38. C8: optical density at 600 nm of well C8 (unit: dimensionless / missing value: NA)
39. C9: optical density at 600 nm of well C9 (unit: dimensionless / missing value: NA)
40. C10: optical density at 600 nm of well C10 (unit: dimensionless / missing value: NA)
41. C11: optical density at 600 nm of well C11 (unit: dimensionless / missing value: NA)
42. C12: optical density at 600 nm of well C12 (unit: dimensionless / missing value: NA)
43. D1: optical density at 600 nm of well D1 (unit: dimensionless / missing value: NA)
44. D2: optical density at 600 nm of well D2 (unit: dimensionless / missing value: NA)
45. D3: optical density at 600 nm of well D3 (unit: dimensionless / missing value: NA)
46. D4: optical density at 600 nm of well D4 (unit: dimensionless / missing value: NA)
47. D5: optical density at 600 nm of well D5 (unit: dimensionless / missing value: NA)
48. D6: optical density at 600 nm of well D6 (unit: dimensionless / missing value: NA)
49. D7: optical density at 600 nm of well D7 (unit: dimensionless / missing value: NA)
50. D8: optical density at 600 nm of well D8 (unit: dimensionless / missing value: NA)
51. D9: optical density at 600 nm of well D9 (unit: dimensionless / missing value: NA)
52. D10: optical density at 600 nm of well D10 (unit: dimensionless / missing value: NA)
53. D11: optical density at 600 nm of well D11 (unit: dimensionless / missing value: NA)
54. D12: optical density at 600 nm of well D12 (unit: dimensionless / missing value: NA)
55. E1: optical density at 600 nm of well E1 (unit: dimensionless / missing value: NA)
56. E2: optical density at 600 nm of well E2 (unit: dimensionless / missing value: NA)
57. E3: optical density at 600 nm of well E3 (unit: dimensionless / missing value: NA)
58. E4: optical density at 600 nm of well E4 (unit: dimensionless / missing value: NA)
59. E5: optical density at 600 nm of well E5 (unit: dimensionless / missing value: NA)
60. E6: optical density at 600 nm of well E6 (unit: dimensionless / missing value: NA)
61. E7: optical density at 600 nm of well E7 (unit: dimensionless / missing value: NA)
62. E8: optical density at 600 nm of well E8 (unit: dimensionless / missing value: NA)
63. E9: optical density at 600 nm of well E9 (unit: dimensionless / missing value: NA)
64. E10: optical density at 600 nm of well E10 (unit: dimensionless / missing value: NA)
65. E11: optical density at 600 nm of well E11 (unit: dimensionless / missing value: NA)
66. E12: optical density at 600 nm of well E12 (unit: dimensionless / missing value: NA)
67. F1: optical density at 600 nm of well F1 (unit: dimensionless / missing value: NA)
68. F2: optical density at 600 nm of well F2 (unit: dimensionless / missing value: NA)
69. F3: optical density at 600 nm of well F3 (unit: dimensionless / missing value: NA)
70. F4: optical density at 600 nm of well F4 (unit: dimensionless / missing value: NA)
71. F5: optical density at 600 nm of well F5 (unit: dimensionless / missing value: NA)
72. F6: optical density at 600 nm of well F6 (unit: dimensionless / missing value: NA)
73. F7: optical density at 600 nm of well F7 (unit: dimensionless / missing value: NA)
74. F8: optical density at 600 nm of well F8 (unit: dimensionless / missing value: NA)
75. F9: optical density at 600 nm of well F9 (unit: dimensionless / missing value: NA)
76. F10: optical density at 600 nm of well F10 (unit: dimensionless / missing value: NA)
77. F11: optical density at 600 nm of well F11 (unit: dimensionless / missing value: NA)
78. F12: optical density at 600 nm of well F12 (unit: dimensionless / missing value: NA)
79. G1: optical density at 600 nm of well G1 (unit: dimensionless / missing value: NA)
80. G2: optical density at 600 nm of well G2 (unit: dimensionless / missing value: NA)
81. G3: optical density at 600 nm of well G3 (unit: dimensionless / missing value: NA)
82. G4: optical density at 600 nm of well G4 (unit: dimensionless / missing value: NA)
83. G5: optical density at 600 nm of well G5 (unit: dimensionless / missing value: NA)
84. G6: optical density at 600 nm of well G6 (unit: dimensionless / missing value: NA)
85. G7: optical density at 600 nm of well G7 (unit: dimensionless / missing value: NA)
86. G8: optical density at 600 nm of well G8 (unit: dimensionless / missing value: NA)
87. G9: optical density at 600 nm of well G9 (unit: dimensionless / missing value: NA)
88. G10: optical density at 600 nm of well G10 (unit: dimensionless / missing value: NA)
89. G11: optical density at 600 nm of well G11 (unit: dimensionless / missing value: NA)
90. G12: optical density at 600 nm of well G12 (unit: dimensionless / missing value: NA)
91. H1: optical density at 600 nm of well H1 (unit: dimensionless / missing value: NA)
92. H2: optical density at 600 nm of well H2 (unit: dimensionless / missing value: NA)
93. H3: optical density at 600 nm of well H3 (unit: dimensionless / missing value: NA)
94. H4: optical density at 600 nm of well H4 (unit: dimensionless / missing value: NA)
95. H5: optical density at 600 nm of well H5 (unit: dimensionless / missing value: NA)
96. H6: optical density at 600 nm of well H6 (unit: dimensionless / missing value: NA)
97. H7: optical density at 600 nm of well H7 (unit: dimensionless / missing value: NA)
98. H8: optical density at 600 nm of well H8 (unit: dimensionless / missing value: NA)
99. H9: optical density at 600 nm of well H9 (unit: dimensionless / missing value: NA)
100. H10: optical density at 600 nm of well H10 (unit: dimensionless / missing value: NA)
101. H11: optical density at 600 nm of well H11 (unit: dimensionless / missing value: NA)
102. H12: optical density at 600 nm of well H12 (unit: dimensionless / missing value: NA)