Background Group II introns are mobile retroelements, capable of invading new sites in DNA. They are self-splicing ribozymes that complex with an intron-encoded protein to form a ribonucleoprotein that targets DNA after splicing. These molecules can invade DNA site-specifically, through a process known as retrohoming, or can invade ectopic sites through retrotransposition. Retrotransposition, in particular, can be strongly influenced by both environmental and cellular factors. Results To investigate host factors that influence retrotransposition, we performed random insertional mutagenesis using the IS S1 transposon to generate a library of over 1000 mutants in Lactococcus lactis , the native host of the Ll.LtrB group II intron. By screening this library, we identified 92 mutants with increased retrotransposition frequencies (RTP-ups). We found that mutations in amino acid transport and metabolism tended to have increased retrotransposition frequencies. We further explored a subset of these RTP-up mutants, the most striking of which is a mutant in the ribosomal RNA methyltransferase rlmH, which exhibited a reproducible 20-fold increase in retrotransposition frequency. In vitro and in vivo experiments revealed that ribosomes in the rlmH mutant were defective in the m3Ψ modification and exhibited reduced binding to the intron RNA. Conclusions Taken together, our results reinforce the importance of the native host organism in regulating group II intron retrotransposition. In particular, the evidence from the rlmH mutant suggests a role for ribosome modification in limiting rampant retrotransposition.

Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.

Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into B. anthracis evolution.

Agricultural drought in the U.S. Corn Belt region (CBR) has tremendous global socioeconomic implications. Unfortunately, the weather and climate factors that contribute to transition events toward or away from such droughts are poorly understood. This study applies composite, trajectory clusters, and a vertically integrated moisture budget to understand the phenomena that influence transition events that evolve over 20 and 60 days as modulated by interannual, intraseasonal, and synoptic-time-scale variability during May-August over the CBR. Results show that a shift in the low-frequency base state does not explain onset or decay of the 20- or 60-day drought transition cases. Instead, amplification of an intraseasonal Rossby wave train across the Pacific Ocean into North America, which occurs coincident with intraseasonal tropical convection on its equatorward side, triggers the transition. Trajectory analysis reveals similar source regions for air parcels associated with drought development and breakdown, but with a shift toward more parcels originating over the Gulf of Mexico during transitions away from drought. Finally, the vertically integrated moisture budget shows that advection and convergence of moisture on intraseasonal time scales dominates during these transitions. These results demonstrate that weather events are the primary driver of agricultural drought transitions occurring over 20 and 60 days.

The prediction of drought onset and decay in the U.S. Corn Belt region (CBR) on seasonal-to-subseasonal time scales has not been well studied. This study utilizes the subseasonal-to-seasonal prediction archive to assess model errors in large-scale circulation patterns associated with agricultural drought transition periods, targeting models used by the European Centre for Medium-Range Forecasts, National Centers for Environmental Prediction, and Australian Bureau of Meteorology. An analysis of the seasonal cycle of bias for geopotential anomalies at 200 hPa and net radiation at the top of the atmosphere in each model is presented and used to subtract the long-term bias from each model. Model fields are decomposed into three spectral bands-low frequency (periods > 100 days), intraseasonal (periods 20-100 days), and synoptic (periods < 20 days)-to demonstrate each model's ability to predict patterns associated with agricultural drought transition periods in each band. Results demonstrate that ECMWF and NCEP struggle in predicting the large-scale circulation patterns associated with 20-day agricultural drought and onset transitions, but are more skillful in predicting the patterns associated with 60-day agricultural drought onset and decay events at reforecast hour lead window 360-480 (F360-F480). BoM was not skillful in predicting the circulation patterns associated with either type of drought transition. Results also demonstrate that the errors associated with these events are no worse than historical errors for the target study period.