Biology subjects

Nealson, K. H.

Publications and source records attributed to Nealson, K. H..

3 recordsLinked to original sources

bioRxiv2019

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms, and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earths crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and the associated surge in publicly-available sequence data has now made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition and utilization in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) that is based on genes related to iron acquisition, storage, and reduction/oxidation. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate the provided datasets with respect to iron-related genes and gene clusters. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenies database will be maintained and continually-updated as new genetic markers are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

bioinformatics↗

bioRxiv2019

Basicity of N5 in semiquinone enhances the rate of respiratory electron outflow in Shewanella oneidensis MR-1

Extracellular electron transport (EET) occurs in environmental iron-reducing bacteria and is mediated by an outer membrane multi-heme cytochrome complex (Cyts). It has critical implications for global mineral cycling and electrochemical microbial catalysis. The rate of EET mediated by multiple heme redox centers significantly increases in the presence of flavins and quinones. Their electron free energy does not entirely account for the fact that differential effects on EET rate enhancement vary significantly by factors [≥]100. Here, we report on whole-cell electrochemical analysis of Shewanella oneidensis MR-1 using six flavin analogs and four quinones. We demonstrated that protonation of the nitrogen atom at position 5 (N5) of the isoalloxazine ring is essential for electron outflow acceleration as a bound non-covalent cofactor of Cyts. EET mediated by Cyts was accelerated at a rate dependent on pKa(N5). The EET rate largely decreased in response to the addition of deuterated water (D2O), while low concentration of D2O (4 %) had little impact on electron free energy difference of the heme and non-covalent bound cofactors, strongly suggesting that the protonation of N5 limits the rate of EET. Our findings directly link EET kinetics to proton transport reaction via N5 and provide a basis for the development of novel strategies for controlling EET-associated biological reactions.\n\nSignificance statementThe potential of various small molecules such as flavins and quinones to enhance the rate of extracellular electron transport (EET) has been exploited to develop environmental energy conversion systems. Flavins and quinones have similar molecular structures but their abilities to enhance EET vary by >100x in Shewanella oneidensis MR-1. These large differences are inconsistent with conventional models, which rely on redox potentials or diffusion constant of shuttling electron mediators. In this study, we demonstrated that the basicity of the nitrogen atom of the isoalloxazine ring (N5) enhances the rate of electron outflow when a flavin or quinone is a non-covalent cofactor of S. oneidensis MR-1 outer membrane c-type cytochromes.

biochemistry↗

bioRxiv2018

A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation.

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type species and non-type species. More than 750 genomes representing type strains of species from 10 different phyla, and 19 different taxonomic orders/families in Gram-positive/negative, bacterial and archaeal lineages were tested. Overall, all 19 analyzed taxa conserved significant genomic differences between members of a genus and type species of other genera in the same taxonomic family. Bacillus, Flavobacterium, Hydrogenovibrio, Lactococcus, Methanosarcina, Thiomicrorhabdus, Thiomicrospira, Shewanella, and Vibrio are discussed in detail. Less than 1% of the type strains analyzed need reclassification, highlighting that the adoption of the 16S rRNA gene as a taxonomic marker has provided consistency to the classification of microorganisms in recent decades. One exception to this is the genus Bacillus with 61% of type strains needing reclassification, including the human pathogens B. cereus and B. anthracis. The results provide a first line of evidence that the combination of genomic indices provides appropriate resolution to effectively demarcate genera within the current taxonomic framework that is based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of genera. Altogether, these results show that a distinct difference between distant relatives and close relatives at the genome level (i.e., genomic coherence) is an emergent property of genera in Bacteria and Archaea.

microbiology↗