Kenneth H Nealson

Publications (102) View all

• Article: A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer.

  Shun'ichi Ishii, Shino Suzuki, Trina M Norden-Krichmar, Aaron Tenney, Patrick S G Chain, Matthew B Scholz, Kenneth H Nealson, Orianna Bretschger
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  ABSTRACT: Microbial respiration via extracellular electron transfer (EET) is a ubiquitous reaction that occurs throughout anoxic environments and is a driving force behind global biogeochemical cycling of metals. Here we identify specific EET-active microbes and genes in a diverse biofilm using an innovative approach to analyse the dynamic community-wide response to changing EET rates. We find that the most significant gene expression responses to applied EET stimuli occur in only two microbial groups, Desulfobulbaceae and Desulfuromonadales. Metagenomic analyses reveal high coverage draft genomes of these abundant and active microbes. Our metatranscriptomic results show known and unknown genes that are highly responsive to EET stimuli and associated with our identified draft genomes. This new approach yields a comprehensive image of functional microbes and genes related to EET activity in a diverse community, representing the next step towards unravelling complex microbial roles within a community and how microbes adapt to specific environmental stimuli.
  Nature Communications 03/2013; 4:1601. · 7.40 Impact Factor
• Article: Shewanella oneidensis MR-1 chemotaxis proteins and electron-transport chain components essential for congregation near insoluble electron acceptors.

  H Wayne Harris, Mohamed Y El-Naggar, Kenneth H Nealson
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  ABSTRACT: Shewanella oneidensis MR-1 cells utilize a behaviour response called electrokinesis to increase their speed in the vicinity of IEAs (insoluble electron acceptors), including manganese oxides, iron oxides and poised electrodes [Harris, El-Naggar, Bretschger, Ward, Romine, Obraztsova and Nealson (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 326-331]. However, it is not currently understood how bacteria remain in the vicinity of the IEA and accumulate both on the surface and in the surrounding medium. In the present paper, we provide results indicating that cells that have contacted the IEAs swim faster than those that have not recently made contact. In addition, fast-swimming cells exhibit an enhancement of swimming reversals leading to rapid non-random accumulation of cells on, and adjacent to, mineral particles. We call the observed accumulation near IEAs 'congregation'. Congregation is eliminated by the loss of a critical gene involved with EET (extracellular electron transport) (cymA, SO_4591) and is altered or eliminated in several deletion mutants of homologues of genes that are involved with chemotaxis or energy taxis in Escherichia coli. These genes include chemotactic signal transduction protein (cheA-3, SO_3207), methyl-accepting chemotaxis proteins with the Cache domain (mcp_cache, SO_2240) or the PAS (Per/Arnt/Sim) domain (mcp_pas, SO_1385). In the present paper, we report studies of S. oneidensis MR-1 that lend some insight into how microbes in this group can 'sense' the presence of a solid substrate such as a mineral surface, and maintain themselves in the vicinity of the mineral (i.e. via congregation), which may ultimately lead to attachment and biofilm formation.
  Biochemical Society Transactions 12/2012; 40(6):1167-77. · 3.71 Impact Factor
• Article: Adaptation of soil microbes during establishment of microbial fuel cell consortium fed with lactate.

  Hiroyuki Futamata, Orianna Bretschger, Andrea Cheung, Jinjun Kan, Rubaba Owen, Kenneth H Nealson
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  ABSTRACT: We report the development of microbial populations and changes in their electrochemical production during a 2-month study of a two-chamber microbial fuel cell (MFC). The original inoculum was taken from anaerobic enrichment cultures with soil as the inoculum, and lactate as the exogenous electron donor. Power density (PD), coulombic production (CP), and coulombic efficiency (CE) increased rapidly, reaching high values (320 mW m(-3), 65 Q, and 12.5%, respectively) in 12-16 days. Under these conditions, several major microbial taxa dominated the anode population. The medium solution in the cathode chamber decreased with aeration, resulting in a decrease in PD to 55 mW m(-3) at day 20. Refilling the cathode chamber around day 30 resulted in restoration of the PD, CP and CE to values equal to or greater than those previously observed. However, after the change in conditions, a marked change in community structure was observed, and high levels of acetate were seen in the anode chamber of the fuel cell for the first time. At day 35, a series of lactate concentrations were used, beginning with low levels and increasing to the 20 mM level originally used (day 46), the PD decreased but was stable at 150 mW m(-3) and the acetate concentration in the anode stabilized at about 35 mM. Under these conditions, new major population structures, which were closely related to Propionibacterium, Clostridium, and uncultured bacteria, were observed in the anode. These results suggested that the flexibility of community structure was important for sustainable electricity production.
  Journal of Bioscience and Bioengineering 08/2012; · 1.79 Impact Factor
• Article: Electricity generation coupled to oxidation of propionate in a microbial fuel cell

  Jae Kyung Jang, In Seop Chang, Hwa Yeon Hwang, Yeng Fung Choo, JiYoung Lee, Kyung Suk Cho, Byung Hong Kim, Kenneth H. Nealson
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  ABSTRACT: Propionate was used as fuel to enrich an electrochemically-active microbial consortium in a microbial fuel cell, and the bacterial consortium was analyzed by culture-independent methods including denaturing gradient gel electrophoresis (DGGE) of the 16S rDNA, and by fluorescent in situ hybridization (FISH). MFCs fed with propionate produced a current of 4.88±0.1mA stably on 100mg propionate/l as COD within 3weeks of the enrichment. When the MFCs were fed with H2-saturated fuel containing propionate, the current dropped to 3.82±0.07mA. The maximum current generated was up to 8.8mA when MFCs were fed with 200mg propionate/l as COD. The DGGE of 16S rDNA showed that propionate-enriched MFCs have a different bacterial population from that enriched with acetate and from the inoculum used for enrichment. The major member (42%) of the consortium was an unidentified bacterium followed by γ, β, and δ-proteobacteria.
  Biotechnology Letters 04/2012; 32(1):79-85. · 1.68 Impact Factor
• Article: Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

  Tatiana V. Karpinets, Anna Y. Obraztsova, Yanbing Wang, Denise D. Schmoyer, Guruprasad H. Kora, Byung H. Park, Margrethe H. Serres, Margaret F. Romine, Miriam L. Land, Terence B. Kothe, Jim K. Fredrickson, Kenneth H. Nealson, Edward C. Uberbacher
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  ABSTRACT: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1. KeywordsPhenotypic trait-Bacteria-Molecular mechanisms of cold tolerance- Shewanella -Protein families
  Functional and Integrative Genomics 04/2012; 10(1):97-110. · 2.84 Impact Factor