Bacterial adaptation strategies and interactions in different soil habitats

Abstract

Bacterial communities are important in soil ecosystem functioning, particularly due to their role in soil formation, plant production and biogeochemical processes. The close and complex interplay between soil biotic and abiotic properties of soil and bacteria has major implications for agriculture, environmental and human health. In order to gain further insights into bacterial functions and specific interactions which mediate bacterial community development in various niches of natural temperate grasslands, culture dependent and independent approaches were employed in the present study. For bacterial communities in the rhizosphere, an overwhelming effect of soil type on rhizosphere bacterial communities was determined, significantly surpassing the influence of plants. Plant species seem to influence bacterial communities to a limited degree through differences in composition of root exudates, selecting for distinct bacterial groups. For bacteria colonizing soil minerals de novo, mineral properties were identified as the major driver of bacterial community composition compared to the effect of different carbon sources available. Minerals provide a selective environment which counteracts the homogenising effects of dispersal, enabling the establishment of adapted bacterial communities which develop consistent temporal patterns of successional change. The lack of knowledge on bacterial functions and ecological relevance at high taxonomic resolution is only resolved with bacterial cultivation and isolation. Therefore, different cultivation approaches were applied in order to retrieve novel, relevant representatives of oligotrophic soil bacteria. Indeed, a large number of novel bacterial isolates could be retrieved, many belonging to underexplored lineages which likely harbour novel traits and functions. This study provides a deepened understanding of the drivers of bacterial community composition and function in distinct niches of soil ecosystems and thereby improves our understanding of the role of bacteria in the process of soil formation and in the association with higher organisms.