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1. Methane fluxes from tropical coastal lagoons surrounded by mangroves, Yucatán, Mexico: Methane Fluxes from Coastal Lagoons

   https://doi.org/10.1002/2017JG003761  

   Chuang, P.-C. ; Young, M. B. ; Dale, A. W. ; Miller, L. G. ; Herrera-Silveira, J. A. ; Paytan, A. ( May 2017 , Journal of Geophysical Research: Biogeosciences)
2. Local environmental conditions structured discrete fish assemblages in Arctic lagoons

   https://doi.org/10.1007/s00300-024-03239-8  

   Laske, Sarah M ; von_Biela, Vanessa R ; Stanek, Ashley E ; Dunton, Kenneth H ( June 2024 , Polar Biology)

   Rapid changes in sea ice extent and changes in freshwater inputs from land are rapidly changing the nature of Arctic estuarine ecosystems. In the Beaufort Sea, these nearshore habitats are known for their high productivity and mix of marine resident and diadromous fishes that have great subsistence value for Indigenous communities. There is, however, a lack of information on the spatial variation among Arctic nearshore fish communities as related to environmental drivers. In summers of 2017–2019, we sampled fishes in four estuarine ecosystems to assess community composition and relate fish abundance to temperature, salinity, and wind conditions. We found fish communities were heterogeneous over larger spatial extents with rivers forming fresh estuarine plumes that supported diadromous species (e.g., broad whitefishCoregonus nasus), while lagoons with reduced freshwater input and higher salinities were associated with marine species (e.g., saffron codEleginus gracilis). West–East directional winds accounted for up to 66% of the community variation, indicating importance of the wind-driven balance between fresh and marine water masses. Salinity and temperature accounted for up to 54% and 37% of the variation among lagoon communities, respectively. Recent sea ice declines provide more opportunity for wind to influence oceanographic conditions and biological communities. Current subsistence practices, future commercial fishing opportunities, and on-going oil and gas activities benefit from a better understanding of current fish community distributions. This work provides important data on fish spatial distributions and community composition, providing a basis for fish community response to changing climatic conditions and anthropogenic use.

    

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3. A Novel Assay for RNA Polymerase I Transcription Elongation Sheds Light on the Evolutionary Divergence of Eukaryotic RNA Polymerases

   https://doi.org/10.1021/acs.biochem.8b01256  

   Scull, Catherine E. ; Ingram, Zachariah M. ; Lucius, Aaron L. ; Schneider, David A. ( April 2019 , Biochemistry)
4. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons

   https://doi.org/10.3389/fmicb.2021.601901  

   Baker, Kristina D. ; Kellogg, Colleen T. ; McClelland, James W. ; Dunton, Kenneth H. ; Crump, Byron C. ( February 2021 , Frontiers in Microbiology)

   null (Ed.)

   In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic. 

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5. Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila

   https://doi.org/10.3390/genes13010057  

   Krinsky, Benjamin H. ; Arthur, Robert K. ; Xia, Shengqian ; Sosa, Dylan ; Arsala, Deanna ; White, Kevin P. ; Long, Manyuan ( January 2022 , Genes)

   Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in Drosophila, Zeus that unexpectedly diverged rapidly from its parent, Caf40, an extremely conserved component in the CCR4–NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-Seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we found a dynamic pattern in which Zeus binding rapidly coevolved with a previously unknown DNA motif, which we term Caf40 and Zeus-Associated Motif (CAZAM), under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Using CRISPR-Cas9-mediated gene knockout of Zeus and RNA-Seq, we found that Zeus regulated the expression of 661 differentially expressed genes (DEGs). Our results suggest that the evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic genome-wide evolutionary processes associated with new genes. 

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