Abstract
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.
Highlights
Soil microbial communities are recognized as being extremely diverse[1,2] and as the fabric that supports the diverse soil ecosystem functions upon which macroscopic organisms depend[3,4,5,6]
We assessed whether changes in diversity and community structure take place among the microbial communities inhabiting a 56 km long altitudinal transect across the central Atacama Desert
By applying Correspondence Analysis (CCA), we detected that taxonomic changes observed across the Talabre-Lejía Transect (TLT) were driven by a combination of pH and nutritional factors, which is consistent with the observation that changes of pH values among soil samples showed significant correlations with many nutritional variables (Supplementary information Table 1)
Summary
Soil microbial communities are recognized as being extremely diverse[1,2] and as the fabric that supports the diverse soil ecosystem functions upon which macroscopic organisms depend[3,4,5,6]. Recent studies of microbial communities have greatly benefited from the development of techniques to sequence ribosomal genes without the need for cultivation[7] These studies provide insights into the importance of environmental factors such as pH8,9, temperature[10] and relative humidity[11,12] in soil microbial structure and composition. L-GRAAL, the graph alignment method we used here to examine changes in network structure, overcomes general computational needs from previous approaches[16,17] while allowing for visual representation and interactive examination of important network attributes To our knowledge, this is the first time the method is applied to microbial systems biology, which by itself represents a significant advance in microbial network comparisons that expands from recent topological characterizations of co-occurrence networks[18], and provides a comprehensive way to understand topological shifts among members from two networks. We show here that this method provides a glimpse into the nature of the changes in microbial communities that can foster resistance and resilience to contrasting environmental conditions
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