@article {3134, title = {Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange.}, journal = {Environ Microbiol Rep}, volume = {5}, year = {2013}, month = {2013 Dec}, pages = {904-10}, abstract = {

Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G. sulfurreducens via DIET, were established with a citrate synthase-deficient G. sulfurreducens strain that can receive electrons for respiration through DIET only. In a medium with ethanol as the electron donor and fumarate as the electron acceptor, co-cultures with the citrate synthase-deficient G. sulfurreducens strain metabolized ethanol as fast as co-cultures with wild-type, but the acetate that G. metallireducens generated from ethanol oxidation accumulated. The lack of acetate metabolism resulted in less fumarate reduction and lower cell abundance of G. sulfurreducens. RNAseq analysis of transcript abundance was consistent with a lack of acetate metabolism in G. sulfurreducens and revealed gene expression levels for the uptake hydrogenase, formate dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration.

}, keywords = {Acetates, Anaerobiosis, Citrate (si)-Synthase, Cytochrome c Group, Electron Transport, Electrons, Energy Metabolism, Ethanol, Fimbriae, Bacterial, Formate Dehydrogenases, Fumarates, Geobacter, Oxidation-Reduction}, issn = {1758-2229}, doi = {10.1111/1758-2229.12093}, author = {Shrestha, Pravin Malla and Rotaru, Amelia-Elena and Aklujkar, Muktak and Liu, Fanghua and Shrestha, Minita and Summers, Zarath M and Malvankar, Nikhil and Flores, Dan Carlo and Lovley, Derek R} } @article {3141, title = {When is a microbial culture "pure"? Persistent cryptic contaminant escapes detection even with deep genome sequencing.}, journal = {mBio}, volume = {4}, year = {2013}, month = {2013 Mar 12}, pages = {e00591-12}, abstract = {

UNLABELLED: Geobacter sulfurreducens strain KN400 was recovered in previous studies in which a culture of the DL1 strain of G. sulfurreducens served as the inoculum in investigations of microbial current production at low anode potentials (-400 mV versus Ag/AgCl). Differences in the genome sequences of KN400 and DL1 were too great to have arisen from adaptive evolution during growth on the anode. Previous deep sequencing (80-fold coverage) of the DL1 culture failed to detect sequences specific to KN400, suggesting that KN400 was an external contaminant inadvertently introduced into the anode culturing system. In order to evaluate this further, a portion of the gene for OmcS, a c-type cytochrome that both KN400 and DL1 possess, was amplified from the DL1 culture. HiSeq-2000 Illumina sequencing of the PCR product detected the KN400 sequence, which differs from the DL1 sequence at 14 bp, at a frequency of ca. 1 in 10(5) copies of the DL1 sequence. A similar low frequency of KN400 was detected with quantitative PCR of a KN400-specific gene. KN400 persisted at this frequency after intensive restreaking of isolated colonies from the DL1 culture. However, a culture in which KN400 could no longer be detected was obtained by serial dilution to extinction in liquid medium. The KN400-free culture could not grow on an anode poised at -400 mV. Thus, KN400 cryptically persisted in the culture dominated by DL1 for more than a decade, undetected by even deep whole-genome sequencing, and was only fortuitously uncovered by the unnatural selection pressure of growth on a low-potential electrode.

IMPORTANCE: Repeated streaking of isolated colonies on solidified medium remains a common strategy for obtaining pure cultures, especially of difficult-to-cultivate microorganisms such as strict anaerobes. The results presented here demonstrate that verifying the purity of cultures obtained in this manner may be difficult because extremely rare variants can persist, undetectable with even deep genomic DNA sequencing. The only way to ensure that a culture is pure is to cultivate it from an initial single cell, which may be technically difficult for many environmentally significant microbes.

}, keywords = {Coinfection, Electrodes, Genes, Bacterial, Genotype, Geobacter, High-Throughput Nucleotide Sequencing, Microbial Interactions, Polymerase Chain Reaction}, issn = {2150-7511}, doi = {10.1128/mBio.00591-12}, author = {Shrestha, Pravin Malla and Nevin, Kelly P and Shrestha, Minita and Lovley, Derek R} }