@article{wu_piedade_moore_harrison_martins_bidle_polson_sakowski_nissimov_dums_et al._2023, title={Ubiquitous, B<sub>12</sub>-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean}, volume={3}, ISSN={["2730-6151"]}, DOI={10.1038/s43705-023-00306-9}, abstractNote={Abstract Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B 12 -dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling–downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral–host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.}, number={1}, journal={ISME COMMUNICATIONS}, author={Wu, Ling-Yi and Piedade, Goncalo J. and Moore, Ryan M. and Harrison, Amelia O. and Martins, Ana M. and Bidle, Kay D. and Polson, Shawn W. and Sakowski, Eric G. and Nissimov, Jozef I. and Dums, Jacob T. and et al.}, year={2023}, month={Oct} }
 @article{ladin_ferrell_dums_moore_levia_shriver_d'amico_trammell_setubal_wommack_2021, title={Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems}, volume={11}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-80602-9}, abstractNote={Abstract We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Ladin, Zachary S. and Ferrell, Barbra and Dums, Jacob T. and Moore, Ryan M. and Levia, Delphis F. and Shriver, W. Gregory and D'Amico, Vincent and Trammell, Tara L. E. and Setubal, Joao Carlos and Wommack, K. Eric}, year={2021}, month={Jan} }
 @article{dums_murphree_vasani_young_sederoff_2018, title={Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented With Ammonium Derived From Glutamine}, volume={5}, ISSN={["2296-7745"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052906510&partnerID=MN8TOARS}, DOI={10.3389/fmars.2018.00311}, abstractNote={Algal biofuel production requires an input of synthetic nitrogen fertilizer. Fertilizer synthesized via the Haber-Bosch process produces CO2 as a waste byproduct and represents a substantial financial and energy investment. Reliance on synthetic fertilizer attenuates the environmental significance and economic viability of algae production systems. To lower fertilizer input, the waste streams of algal production systems can be recycled to provide alternative sources of nitrogen such as amino acids to the algae. The halophytic green alga Dunaliella viridis can use ammonium (NH4+) derived from the abiotic degradation of amino acids, and previously, supplementation of NH4+ from glutamine degradation was shown to support acceptable levels of growth and increased neutral lipid production compared to nitrate. To understand the effect of glutamine-released NH4+ on algae growth and physiology, metabolite levels, growth parameters, and transcript profiles of D. viridis cultures were observed in a time course after transition from media containing nitrate as a sole N source to medium containing glutamine, glutamate, or a N-depleted medium. Growth parameters were similar between glutamine (NH4+) and nitrate supplemented cultures, however, metabolite data showed that the glutamine supplemented cultures (NH4+) more closely resembled cultures under nitrogen starvation (N-depleted and glutamate supplementation). Neutral lipid accumulation was the same in nitrate and glutamine-derived NH4+ cultures. However, glutamine-derived NH4+ caused a transcriptional response in the immediate hours after inoculation of the culture. The strong initial response of cultures to NH4+ changed over the course of days to closely resemble that of nitrogen starvation. These observations suggest that release of NH4+ from glutamine was sufficient to maintain growth, but not high enough to trigger a cell transition to a nitrogen replete state. Comparative transcript profiling of the nitrogen-starved and nitrate-supplied cultures show an overall downregulation of fatty acid synthesis and a shift to starch synthesis and accumulation. The results indicate that a continuous, amino acid derived slow release of NH4+ to algae cultures could reduce the amount of synthetic nitrogen needed for growth, but optimization is needed to balance nitrogen starvation and cell division.}, number={AUG}, journal={FRONTIERS IN MARINE SCIENCE}, author={Dums, Jacob and Murphree, Colin and Vasani, Naresh and Young, Danielle and Sederoff, Heike}, year={2018}, month={Aug} }
 @article{murphree_dums_jain_zhao_young_khoshnoodi_tikunov_macdonald_pilot_sederoff_et al._2017, title={Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth}, volume={8}, ISSN={["1664-462X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021390666&partnerID=MN8TOARS}, DOI={10.3389/fpls.2017.00847}, abstractNote={Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Murphree, C. A. and Dums, J. T. and Jain, S. K. and Zhao, C. S. and Young, D. Y. and Khoshnoodi, N. and Tikunov, A. and Macdonald, J. and Pilot, G. and Sederoff, Heike and et al.}, year={2017}, month={May} }
 @article{srirangan_sauer_howard_dvora_dums_backman_sederoff_2015, title={Interaction of Temperature and Photoperiod Increases Growth and Oil Content in the Marine Microalgae Dunaliella viridis}, volume={10}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84930682335&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0127562}, abstractNote={Eukaryotic marine microalgae like Dunaliella spp. have great potential as a feedstock for liquid transportation fuels because they grow fast and can accumulate high levels of triacylgycerides with little need for fresh water or land. Their growth rates vary between species and are dependent on environmental conditions. The cell cycle, starch and triacylglycerol accumulation are controlled by the diurnal light:dark cycle. Storage compounds like starch and triacylglycerol accumulate in the light when CO2 fixation rates exceed the need of assimilated carbon and energy for cell maintenance and division during the dark phase. To delineate environmental effects, we analyzed cell division rates, metabolism and transcriptional regulation in Dunaliella viridis in response to changes in light duration and growth temperatures. Its rate of cell division was increased under continuous light conditions, while a shift in temperature from 25°C to 35°C did not significantly affect the cell division rate, but increased the triacylglycerol content per cell several-fold under continuous light. The amount of saturated fatty acids in triacylglycerol fraction was more responsive to an increase in temperature than to a change in the light regime. Detailed fatty acid profiles showed that Dunaliella viridis incorporated lauric acid (C12:0) into triacylglycerol after 24 hours under continuous light. Transcriptome analysis identified potential regulators involved in the light and temperature-induced lipid accumulation in Dunaliella viridis.}, number={5}, journal={PLOS ONE}, author={Srirangan, Soundarya and Sauer, Marie-Laure and Howard, Brian and Dvora, Mia and Dums, Jacob and Backman, Patrick and Sederoff, Heike}, year={2015}, month={May} }