Biology subjects

Day, L. A.

Publications and source records attributed to Day, L. A..

4 recordsLinked to original sources

bioRxiv2025

Terrestrial Organic Matter Amplifies Methane Emissions Across Sediments of the Mississippi River Headwaters

Terrestrial organic matter (tOM) plays a critical role in aquatic ecosystems, influencing carbon processes and greenhouse gas emissions. Here, we investigate the impact of tOM on methane production in littoral and pelagic sediments from the Mississippi River headwaters using a microcosm approach. Contrary to our expectations, tOM addition universally increased methane production across lentic sediments, with no significant difference between littoral and pelagic zones. Methane production was influenced by select sediment microorganisms, primarily methanogens and lignocellulose degrading bacteria, which responded similarly across different sediment habitats. The study highlights the role of cytochrome-containing methanogens and their syntrophic relationships with fermentative bacteria, emphasizing the significance of microbial community structure in sediment methane dynamics. Our findings suggest that increasing tOM loads to freshwater systems could have broader implications for methane emissions, driven by specific microbial interactions. Author Contribution StatementHMS and TLH conceived the study and obtained the funds. HMS led fieldwork and microcosm set-up. HMS and LAD analyzed gas samples and HMS performed the data analysis and graphical representation of the results. HMS wrote the first draft of the manuscript, and all authors contributed significantly to the preparation of the final draft. Scientific Significance StatementAs human activities and climate change increase the amount of organic material entering lakes and rivers, understanding the effects this has on greenhouse gas emissions is crucial. Our study reveals that adding terrestrial organic matter to freshwater sediments universally boosts methane production, a potent greenhouse gas. Through the exploration of microbial communities responsible for this process, our research highlights how changes in terrestrial organic matter export to aquatic systems could increase methane emissions from sediments. Data Availability StatementAdditional Supporting Information can be found in the online version of this article, including an extended version of methods and supplementary tables. Sequencing data associated with this paper is available on NCBI, BioProject PRJNA1164797.

ecology↗

bioRxiv2024

Improving the annotation of amino acid biosynthesis pathways: GapMind 2024

We previously described GapMind, an automated web-based tool for annotating amino acid biosynthesis pathways in bacterial and archaeal genomes. We used GapMind to identify gaps in biosynthetic pathways and systematically used comparative genomics and high-throughput genetics to identify candidate genes to fill these gaps. We confirmed the activity of ten of the proposed enzymes by using cross-species complementation assays. Highlights include a novel route to glycine, two families that can replace phosphoserine phosphatase, an alternative N-succinyl-L,L-diaminopimelate desuccinylase, an alternative N-acetylornithine deacetylase, and a bifunctional MetB/MetC. We updated GapMind to include these additional enzymes. Across 208 prokaryotes that have high-quality genomes and can grow in minimal media, the average number of unexplained missing steps or gaps in amino acid biosynthesis dropped from 1.4 per genome to 0.7 per genome. The majority of remaining gaps involve the gain or loss of phosphate groups.

microbiology↗

bioRxiv2024

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly-barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we provide the first evidence that M. maripaludis can utilize the nitrogen sources L-glutamine, D-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP, group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale dataset that can be used as a resource to further understand gene function and metabolism in the archaeal domain. Significance StatementArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly-barcoded transposon libraries (RB-TnSeq) to the model archaeon Methanococcus maripaludis. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This dataset encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy; thus, providing an extensive dataset for the archaeal community to mine for characterizing additional genes of unknown function.

microbiology↗

bioRxiv2022

Random transposon mutagenesis identifies genes essential for transformation in naturally competent archaea

Natural transformation, the process whereby a cell acquires DNA directly from the environment, is an important driver of evolution in microbial populations. While transformation is well characterized in bacteria, relatively little is known about this process in archaea. Here, we leverage an optimized method to generate transposon mutants in Methanococcus maripaludis to screen for genes essential to natural transformation. A screen of 5,376 mutant strains identified 25 candidate genes. Among these are genes encoding components of the type IV-like pilus, transcription/translation associated genes, putative membrane bound transport proteins, and genes of unknown function. Interestingly, similar genes were identified regardless of whether replicating or integrating plasmids were provided as substrate for transformation. Using allelic replacement mutagenesis, we confirmed that several genes identified in these screens are essential for transformation. Finally, we identified a homolog of a membrane bound substrate transporter in Methanoculleus thermophilus and verified its importance using allelic replacement mutagenesis, suggesting a conserved mechanism for DNA transfer in multiple archaea. These data provide an initial catalog of genes important for transformation in the archaea and can inform efforts to understand gene flow in this domain. ImportanceHorizontal gene transfer (HGT) is an important driver of evolution in microbial populations. One of the primary ways microorganisms acquire genetic material through HGT is transformation, the direct uptake of DNA from the environment. While transformation is well-studied in bacteria, little is known about this process in archaea. Using a random mutagenesis screen to identify components of the archaeal transformation pathway, we identify a catalog of genes important to transformation in Methanococcus maripaludis and show that a subset of these genes is functionally conserved across diverse archaea. This is a key step in understanding mechanisms of gene flow in natural populations, and identification of the DNA uptake system will assist in establishing new model genetic systems for studying the archaea.

microbiology↗