Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils

<div><p>Background</p><p>Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far.</p> <p>Methodology/Principal Findings</p><p>In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the <i>nif</i>H gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher <i>nifH</i> gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from <i>nif</i>H gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the <i>nifH</i> gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan <i>nif</i>H species (present throughout the season) were affiliated with <i>Bradyrhizobium</i>, <i>Azospirillum</i> and <i>Methylocistis</i>, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for <i>Paenibacilus and Burkholderia.</i></p> <p>Conclusions</p><p>Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.</p>