#250papers

Throughout 2017 I’m committing to read #250papers. (This is not an exhaustive list and excludes quick read throughs focusing on figures/discussion. This list represents papers carefully read and summarized.) Dates and titles here:

  1. 1/2/17 – Charlop-Powers Z et al. (2016) Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversityPNAS 113(51):14811-14816. NYC parks harbor a large diversity of natural product NRP and PK biosynthetic gene clusters. Important natural products originally isolated from disparate sites spanning the globe are represented in urban soils from a single city.  
  2. 1/3/17 – Jones SE et al. (2017) Streptomyces exploration is triggered by fungal interactions and volatile signalseLife 6:e21738. In the presence of yeasts, some Streptomyces species differentiate from cononical static mycelia into highly motile explorer cells. This is triggered by low glucose conditions and high pH conditions. Explorer cells emit an alkaline VOC that raises media pH, and this signal can trigger physically distant Streptomyces cells to begin exploring. 
  3. 1/4/17 –  Tyc et al. (2016) The ecological role of volatile and soluble secondary metabolites produced by soil bacteriaTrends in Microbiol 
  4. 1/4/17- Kaltenpoth et al. (2016) Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISHISME J 10:527-531.
  5. 1/5/17 – D’Souza and Kost. (2016) Experimental evolution of metabolic dependency in bacteria. PLoS Genet 12(11):e1006364. When amino acids are available, auxotrophs emerge under strong positive selection. Auxotrophs also evolve in the absence of amino acids at lower rates. Negative frequency dependent-selection supports the stable coexistence of auxo- and proto- trophs.
  6. 1/6/17 – Smith et al. (2016) Cell morphology drives spatial patterning in microbial communitiesPNAS doi: 10.1073/pnas.1613007114. Cell morphology can drive spatial structure and influence the fitness landscape in mixed biofilm cultures.
  7. 1/9/17 – Shapiro BJ et al. (2016) Origins of pandemic Vibrio cholerae from environmental gene pools. Nat Microbiol 2: 16240. Virulence adaptive polymorphisms (VAPs) recombine in environmental V. cholerae gene pools, certain VAP combinations are enriched, and subsequent acquisition of virulence genes in these pre-adapted genomic background supports a transition to pathogenic phenotypes.
  8. 1/10/17 – Locey KJ et al. (2016) Microscale insight into microbial seed banksFront Microbiol doi: 10.3389/fmicb.2016.02040. Microbial seed banks can form in nutrient rich habitats, and these dynamics are influenced by microscale dispersal dynamics and spatial and resource complexity.
  9. 1/11/17 – Zaremba-Niedzwiedzka K et al. (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexityNature doi:10.1038/nature21031. Assembled genomes from the Norse god phyla (within the Asgard archaea superphylum) associate phylogenetically with eukaryotes and also encode many eukaryotic cell features, suggesting that the last common ancestor of archaea and eukaryotes possessed greater cellular complexity than previously thought.
  10. 1/20/17 – McFall-Ngai M, et al. (2013) Animals in a bacterial world, a new imperative for the life sciencesPNAS 110(9):3229-3236. Microbes and animals have evolved intimate relationships that dictate biological system functioning and ecosystem processes. 
  11. 1/24/17 – Erez et al. (2017) Communication between viruses guides lysis–lysogeny decisionsNature 0(0): doi:10.1038/nature21049 Bacillus phage use phage-specific small peptides to communicate to subsequent progeny about lytic or lysogenic decisions; after each infection round, AimP accumulates and eventually triggers lysogeny.
  12. 1/24/17 – Chewapreecha C, et al. (2017) Global and regional dissemination and evolution of Burkholderia pseudomalleiNature Microbiol  2: doi:10.1038/nmicrobiol.2016.263
  13. 1/17/2017 – Behie SW et al. (2017) Molecules to Ecosystems: Actinomycetes Natural Products In situ. Front Microbiol 7: doi: 10.3389/fmicb.2016.02149. Actinomycetes product a vast array natural products of important consequence from the host to the ecosystem level. In situ ecology of NPs will aid in discovery and production of novel NP for human use. 
  14. 1/17/17 – Soppa J. (2017) Polyploidy and community structure. Nature Microbiol 2: doi:10.1038/nmicrobiol.2016.261. Compositional analysis of microbial communities are sensitive to 16S rRNA copy number, which differs across taxa and also within a species under differing growth conditions.
  15. 1/23/17 – Popa O et al. (2017) Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. ISME J 11: 543-554. Gene exchange mediated by phages has important evolutionary consequences, but transduction is limited by genetic similarity as opposed to ecological co-occurrence. A substantial number of transduction event  are duplications, or autology.  
  16. 1/24/17 – Larkin and Martiny. (2017) Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. Environ Microbiol Rep doi:10.1111/1758-2229.12523 Microdiversity shapes the fundamental niche space and biogeography of microbial taxa; this diversity is generated through the Renaissance model (gaining new traits usually through HGT) or the Maestro model (improving a single trait usually through mutation).
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