Research Article Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells Irina V. Khilyas, 1 Anatoly A. Sorokin, 2,3 Larisa Kiseleva, 4 David J. W. Simpson, 4 V. Fedorovich, 4 Margarita R. Sharipova, 1 Mami Kainuma, 4 Michael F. Cohen, 4,5 and Igor Goryanin 4,6,7 1 Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia 2 Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia 3 Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia 4 Biological Systems Unit, Okinawa Institute of Science and Technology, Okinawa, Japan 5 Department of Biology, Sonoma State University, Rohnert Park, CA, USA 6 School of Informatics, University of Edinburgh, Edinburgh, UK 7 Tianjin Institute of Industrial Biotechnology, Tianjin, China Correspondence should be addressed to Irina V. Khilyas; irina.khilyas@gmail.com Received 24 April 2017; Accepted 15 August 2017; Published 12 October 2017 Academic Editor: Ravinder Malik Copyright © 2017 Irina V. Khilyas et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bioelectrochemical systems such as microbial fuel cells (MFCs) are promising new technologies for efcient removal of organic compounds from industrial wastewaters, including that generated from swine farming. We inoculated two pairs of laboratory-scale MFCs with sludge granules from a beer wastewater-treating anaerobic digester (IGBS) or from sludge taken from the bottom of a tank receiving swine wastewater (SS). Te SS-inoculated MFC outperformed the IGBS-inoculated MFC with regard to COD and VFA removal and electricity production. Using a metagenomic approach, we describe the microbial diversity of the MFC planktonic and anodic communities derived from the diferent inocula. Proteobacteria (mostly Deltaproteobacteria) became the predominant phylum in both MFC anodic communities with amplifcation of the electrogenic genus Geobacter being the most pronounced. Eight dominant and three minor species of Geobacter were found in both MFC anodic communities. Te anodic communities of the SS- inoculated MFCs had a higher proportion of Clostridium and Bacteroides relative to those of the IGBS-inoculated MFCs, which were enriched with Pelobacter. Te archaeal populations of the SS- and IGBS-inoculated MFCs were dominated by Methanosarcina barkeri and Methanothermobacter thermautotrophicus, respectively. Our results show a long-term infuence of inoculum type on the performance and microbial community composition of swine wastewater-treating MFCs. 1. Introduction Livestock farming constitutes an important agricultural sec- tor of many countries but produces considerable amounts of organic wastes that require proper treatment and dis- posal. Te rapidly growing pig farming industry generates high-strength wastewater containing organic compounds, ammonia, phosphates, odorous gases, suspended solids, and pathogens [1]. Treating swine wastewater is especially difcult where land is limited and pig farming facilities occur in close proximity to population centers, such as in Okinawa, Japan. Te lack of available land for application of swine wastewater (SW) as a fertilizer and potential for contamination of surface and ground water sources underscore the need to employ thorough treatment of SW. Common methods of treating SW include aerobic oxi- dation ponds, lagoons, anaerobic digestion, and constructed wetlands [2]. Bioelectrochemical systems such as microbial fuel cells (MFCs) are promising new technologies for efcient removal of organic compounds in wastewaters. Inside the Hindawi Scientifica Volume 2017, Article ID 7616359, 10 pages https://doi.org/10.1155/2017/7616359