@article{sheng_baars_guo_whitham_srivastava_dong_2023, title={Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation}, volume={4}, ISSN={["1520-5851"]}, url={https://doi.org/10.1021/acs.est.3c01371}, DOI={10.1021/acs.est.3c01371}, abstractNote={Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Sheng, Yizhi and Baars, Oliver and Guo, Dongyi and Whitham, Jason and Srivastava, Shreya and Dong, Hailiang}, year={2023}, month={Apr} }
 @article{zwilling_whitham_zambrano_pifano_grunden_jameel_venditti_gonzalez_2023, title={Survivability of Salmonella Typhimurium (ATCC 14208) and Listeria innocua (ATCC 51742) on lignocellulosic materials for paper packaging}, volume={9}, ISSN={["2405-8440"]}, url={https://doi.org/10.1016/j.heliyon.2023.e14122}, DOI={10.1016/j.heliyon.2023.e14122}, abstractNote={Lignocellulosic materials are widely used for food packaging due to their renewable and biodegradable nature. However, their porous and absorptive properties can lead to the uptake and retention of bacteria during food processing, transportation, and storage, which pose a potential risk for outbreaks of foodborne disease. Thus, it is of great importance to understand how bacteria proliferate and survive on lignocellulosic surfaces. The aim of this research was to compare the growth and survivability of Salmonella Typhimurium and Listeria innocua on bleached and unbleached paper packaging materials. Two different paper materials were fabricated to simulate linerboard from fully bleached and unbleached market pulps and inoculated with each bacterium at high bacterial loads (107 CFU). The bacteria propagated during the first 48 h of incubation and persisted at very high levels (>107 CFU/cm2) for 40 days for all paper and bacterium types. However, the unbleached paper allowed for a greater degree of bacterial growth to occur compared to bleached paper, suspected to be due to the more hydrophobic nature of the unbleached, lignin-containing fibers. Several other considerations may also alter the behavior of bacteria on lignocellulosic materials, such as storage conditions, nutrient availability, and chemical composition of the fibers.}, number={3}, journal={HELIYON}, author={Zwilling, Jacob D. and Whitham, Jason and Zambrano, Franklin and Pifano, Alonzo and Grunden, Amy and Jameel, Hasan and Venditti, Richard and Gonzalez, Ronalds}, year={2023}, month={Mar} }
 @article{whitham_grunden_2023, title={Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis}, volume={18}, ISSN={["2212-392X"]}, DOI={10.2174/1574893618666230227145952}, abstractNote={
Background:
Investigators using metagenomic sequencing to study microbiomes often
trim and decontaminate reads without knowing their effect on downstream analyses.


Objective:
This study was designed to evaluate the impacts JGI trimming and decontamination procedures
have on assembly and binning metrics, placement of MAGs into species trees, and functional
profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive
trimming impacts these binning metrics.


Methods:
Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different
combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk.
Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to
evaluate the effects of trimming and decontamination on downstream analyses.


Results:
We found that JGI trimmed and decontaminated reads had significant impacts on assembly
and binning metrics compared to raw reads, including significantly higher total contig counts, more
contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies,
and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also
found that differences in the placement of MAGs in species trees increased with decreasing completeness
and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly
reduce MAG counts.


Conclusion:
Trimming and decontamination of metagenomics reads prior to assembly can change an
investigator’s answer to the questions, “Who is there and what are they doing?” However, mild trimming
and decontamination of metagenomic reads with high-quality scores are recommended for removing
sample processing and sequencing artifacts.
}, number={5}, journal={CURRENT BIOINFORMATICS}, author={Whitham, Jason M. and Grunden, Amy M.}, year={2023}, pages={428–439} }
 @article{dow_wood-charlson_biller_paustian_schirmer_sheik_whitham_krebs_goller_allen_et al._2021, title={Bioinformatic Teaching Resources - For Educators, by Educators - Using KBase, a Free, User-Friendly, Open Source Platform}, volume={6}, ISSN={["2504-284X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85118243633&partnerID=MN8TOARS}, DOI={10.3389/feduc.2021.711535}, abstractNote={Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.}, journal={FRONTIERS IN EDUCATION}, author={Dow, Ellen G. and Wood-Charlson, Elisha M. and Biller, Steven J. and Paustian, Timothy and Schirmer, Aaron and Sheik, Cody S. and Whitham, Jason M. and Krebs, Rose and Goller, Carlos C. and Allen, Benjamin and et al.}, year={2021}, month={Oct} }