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

Abstract

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.

Disturbance Alters the Relative Importance of Topographic and Biogeochemical Controls on Microbial Activity in Temperate Montane Forests

“…The pH of unburned soils was more acidic due to organic matter inputs from pine trees, whereas soils from burned forests were more alkaline but also had higher range in pH likely due to differences in burn severity (Figures 2e and 4). Soil pH represents a well-known descriptor of microbial community composition at landscape and biome scales [85][86][87]. Field observations of ash depth, a proxy for burn intensity was positively correlated with pH (r = 0.7, p < 0.05) and patterns of litter depth were also consistent with this interpretation ( Figure A3).…”

Microbial diversity and biogeography in Arctic soils

“…pH and vegetation are the main known drivers of worldwide microbial communities, and Arctic microbial communities are no exception. However, other factors may be involved, as studies of worldwide soils have demonstrated the impact of salinity (Lozupone and Knight, ), moisture content (Dimitriu and Grayston, ) and C:N ratio (Docherty et al ., ) on microbial communities. Other factors may include temperature, ice formation/duration, light, altitude, soil age and texture, nutrient and elemental composition, water availability or pollution.…”

“…Environmental influence pH. pH has been identified as the main factor driving bacterial diversity in many soil studies (Fierer and Jackson, 2006;Rousk et al, 2010;Griffiths et al, 2011;Chong et al, 2012;Docherty et al, 2015), including in Arctic soils (Chu et al, 2010;Siciliano et al, 2014). Some taxon abundances are closely correlated with soil pH, notably the Acidobacteria (Lauber et al, 2009;Rousk et al, 2010).…”

Structural and Functional Responses of Soil Microbial Communities to Biodegradable Plastic Film Mulching in Two Agroecosystems

“…This corresponds with higher pH and saturated K in TN and higher soil organic matter and soil moisture in WA. Both pH and water content are major edaphic factors that influence temporal and spatial variation in soil microbial communities (44, 46). Changes in soil physicochemical properties and different climates and soil types between TN and WA could explain such locational differences.…”