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The first complete human genome

Sequences of the human genome have typically included gaps in repetitive regions of DNA. A combination of state-of-the-art technologies has now enabled researchers to generate the first complete human genome sequence. [Read More]

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Plant response to drought stress involves fungi and bacteria that live on and in plants and in the rhizosphere, yet the stability of these myco- and micro-biomes remains poorly understood. We investigate the resistance and resilience of fungi and bacteria to drought in an agricultural system using both community composition and microbial associations. Here we… [Read More]

RIViT-seq enables systematic identification of regulons of transcriptional machineries

Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here,… [Read More]

Microbes and Climate Change: a Research Prospectus for the Future

Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought,… [Read More]

Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers

Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five… [Read More]

Complete Genome Sequences of Two Phylogenetically Distinct Nitrospina Strains Isolated from the Atlantic and Pacific Oceans

The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis… [Read More]

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

BackgroundPhytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and… [Read More]

Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and… [Read More]

Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters

The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, ketoacids, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to… [Read More]