Diversity, dynamic and abundance of Geobacteraceae species in paddy soil following slurry incubation

Abstract

Microbially-mediated Fe(III) reduction is of environmental significance in wetland ecosystems such as rice fields. Despite a number of incubation experiments showing the dynamic structure and activity of microbial communities in rice paddy soils amended with different substrates, little is known regarding the succession of Fe(III)-reducing bacterial populations in non-amended, natural paddy soils upon flooding. In this study, a 30-d laboratory incubation experiment was conducted to examine the diversity, dynamic and abundance of representative Fe(III)-reducing bacterial family Geobacteraceae in anaerobic natural paddy soil slurry incubations. The Logistic model showed that the microbial Fe(III) reduction rate in paddy slurry reached the highest level (1.36 mg g−1 d−1) after 3.3-d flooding, and the accumulated Fe(II) level stabilized at 8.14 mg g−1 on day 20. Quantitative, real-time PCR assay showed that the absolute abundances of Geobacteraceae and total bacterial populations varied in similar trends. Both decreased from day 1–10 and peaked on day 20 (13.98 × 106 and 5.29 × 108 copies of 16S rDNA g−1 dry soil, respectively), followed by large decreases on day 30 (1.94 × 106 and 0.62 × 108 copies of 16S rDNA g−1 dry soil, respectively). The relative abundance of Geobacteraceae, i.e., the proportion of Geobacteraceae to total bacteria reached the highest level (∼4%) following 5-d flooding, and then slightly fluctuated at 2.6%–3.9% till the end of the experiment. Clone library construction and sequencing analysis showed that the Geobacteraceae mainly consisted of Geobacter spp. which promoted bacterial Fe(III) reduction in paddy slurries upon flooding. UniFrac principal coordinate analysis revealed the succession of Geobacteraceae species, with the highest diversity observed in the initial stage (1 h–1 d) and the dominant successional members in the late stage (20–30 d). These results indicated that Geobacteraceae species contributed to Fe(III) reduction in flood paddy soils, and that the structure of Geobacteraceae population was maintained through the common occurrence of generalized species and the succession of specialized species.