Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

• Published in: PloS one Vol. 10; no. 11; p. e0135352
• Main Authors: Docherty, Kathryn M, Borton, Hannah M, Espinosa, Noelle, Gebhardt, Martha, Gil-Loaiza, Juliana, Gutknecht, Jessica L M, Maes, Patrick W, Mott, Brendon M, Parnell, John Jacob, Purdy, Gayle, Rodrigues, Pedro A P, Stanish, Lee F, Walser, Olivia N, Gallery, Rachel E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04-11-2015; Public Library of Science (PLoS)
• Subjects: Acidobacteria - genetics; Alaska; Bacteria - genetics; Carbon; Cation exchange; Cation exchanging; Classrooms; Climate Change; Climate effects; Collaboration; Colleges & universities; Communities; Community composition; Community structure; Coniferous forests; Data analysis; Data processing; Data retrieval; Datasets; DNA, Bacterial - isolation & purification; Ecological monitoring; Ecology; Ecosystem; Ecosystems; Environmental changes; Fatty acids; Fatty Acids - analysis; Florida; Forest communities; Forests; Gene sequencing; Genetic diversity; Grasslands; Hawaii; Influence; Interdisciplinary aspects; Lipids - analysis; Microbial activity; Microbiomes; Microorganisms; Model testing; Moisture content; Natural resources; Neon; Observatories; Phospholipids; RNA, Ribosomal, 16S - analysis; rRNA 16S; Science; Seasonal variations; Seasons; Soil - chemistry; Soil analysis; Soil environment; Soil Microbiology; Soil microorganisms; Soil structure; Soil temperature; Soil water; Soil water storage; Storage temperature; Subgroups; Taiga; Temperature; Temporal variability; Transformation; Tropical forests; Utah; Variability; Water content; United States > US; Kalamazoo Michigan; Colorado; Arizona; Michigan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0135352

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent 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 phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences 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. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.