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      Evidence of Spatial Homogeneity in an Electromethanogenic Cathodic Microbial Community

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          Abstract

          Microbial electrosynthesis (MES) has been gaining considerable interest as the next step in the evolution of microbial electrochemical technologies. Understanding the niche biocathode environment and microbial community is critical for further developing this technology as the biocathode is key to product formation and efficiency. MES is generally operated to enrich a specific functional group (e.g., methanogens or homoacetogens) from a mixed-culture inoculum. However, due to differences in H 2 and CO 2 availability across the cathode surface, competition and syntrophy may lead to overall variability and significant beta-diversity within and between replicate reactors, which can affect performance reproducibility. Therefore, this study aimed to investigate the distribution and potential spatial variability of the microbial communities in MES methanogenic biocathodes. Triplicate methanogenic biocathodes were enriched in microbial electrolysis cells for 5 months at an applied voltage of 0.7 V. They were then transferred to triplicate dual-chambered MES reactors and operated at -1.0 V vs. Ag/AgCl for six batches. At the end of the experiment, triplicate samples were taken at different positions (top, center, bottom) from each biocathode for a total of nine samples for total biomass protein analysis and 16S rRNA gene amplicon sequencing. Microbial community analyses showed that the biocathodes were highly enriched with methanogens, especially the hydrogenotrophic methanogen family Methanobacteriaceae, Methanobacterium sp., and the mixotrophic Methanosarcina sp., with an overall core community representing > 97% of sequence reads in all samples. There was no statistically significant spatial variability ( p > 0.05) observed in the distribution of these communities within and between the reactors. These results suggest deterministic community assembly and indicate the reproducibility of electromethanogenic biocathode communities, with implications for larger-scale reactors.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            FLASH: fast length adjustment of short reads to improve genome assemblies.

            Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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              The ecology and biotechnology of sulphate-reducing bacteria.

              Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that use sulphate as a terminal electron acceptor in, for example, the degradation of organic compounds. They are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. SRB can cause a serious problem for industries, such as the offshore oil industry, because of the production of sulphide, which is highly reactive, corrosive and toxic. However, these organisms can also be beneficial by removing sulphate and heavy metals from waste streams. Although SRB have been studied for more than a century, it is only with the recent emergence of new molecular biological and genomic techniques that we have begun to obtain detailed information on their way of life.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                31 July 2019
                2019
                : 10
                : 1747
                Affiliations
                Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center, King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
                Author notes

                Edited by: Jorge Rodríguez, Khalifa University, United Arab Emirates

                Reviewed by: Anthony P. Malanoski, United States Naval Research Laboratory, United States; Guangli Liu, Sun Yat-sen University, China

                *Correspondence: Pascal E. Saikaly, pascal.saikaly@ 123456kaust.edu.sa

                This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2019.01747
                6685142
                915077df-81c8-497b-913c-e8340043a703
                Copyright © 2019 Ragab, Katuri, Ali and Saikaly.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 16 May 2019
                : 15 July 2019
                Page count
                Figures: 8, Tables: 0, Equations: 6, References: 69, Pages: 15, Words: 0
                Funding
                Funded by: King Abdullah University of Science and Technology 10.13039/501100004052
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                electromethanogenesis,spatial variability,co2 reduction,biocathode,microbial community assembly

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