Lab Publications

Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic …

Schmidt, J. M., Royalty, T. M., Lloyd, K. G., & Steen, A. D. (2021). Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea. Frontiers in Microbiology, 12, 702015.

Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in …

Steen, A. D. (2020). Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of "Omics". Frontiers in Marine Science, 7, 718.

Organic carbon in marine sediments is a critical component of the global carbon cycle, and its degradation influences a wide range of phenomena, including the magnitude of carbon sequestration over geologic timescales, the recycling of inorganic carbon and nutrients, the dissolution and …

LaRowe, D. E., Arndt, S., Bradley, J. A., & Steen, A. D. (2020). The fate of organic carbon in marine sediments - New insights from recent data and analysis. Earth-Science Reviews, 204, 103146.

Deep-sea sediments are populated by diverse microbial communities that derive their nutritional requirements from the degradation of organic matter. Extracellular hydrolytic enzymes play a key role in the survival of microbes by enabling them to access and degrade complex organic compounds that are …

Mahmoudi, N., et al., & Steen, A. D. (2020). Patterns in extracellular enzyme activity and microbial diversity in deep-sea Mediterranean sediments. Deep-Sea Research Part I, 103231.

This chapter is in Deep Carbon: Past to Present, Beth N. Orcutt, Isabelle Daniel, and Rajdeep Gupta, eds, to be published by Cambrdige University Press in October 2019.

Lang, S. Q., Osburn, M. R., & Steen, A. D. (2019). Carbon in the deep biosphere: forms, fates, and biogeochemical cycling. In B. N. Orcutt, I. Daniel, & R. Gupta (Eds.), Deep Carbon: Past to Present. Cambridge University Press.

Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does not have a close match in the database. In addition, each …

Royalty, T. M., & Steen, A. D. (2019). Unaligned Sequence Similarity Search Using Deep Learning. arXiv preprint arXiv:1909.06929.

Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy …

Royalty, T. M., & Steen, A. D. (2019). Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, NC. Applied and Environmental Microbiology.

We applied theoretical and simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short-read sequences. First, a coupon collector equation was proposed as an analytical model for …

Royalty, T. M., & Steen, A. D. (2019). Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes. mSphere, 4.

Oceanic oil-degrading bacteria produce copious amounts of exopolymeric substances (EPS) that facilitate their access to oil. The fate of EPS in the water column is in part determined by activities of heterotrophic microbes capable of utilizing EPS compounds as carbon and energy sources. To evaluate …

Ziervogel, K., et al., & Steen, A. D. (2019). Polysaccharide hydrolysis in the presence of oil and dispersants: Insights into potential degradation pathways of exopolymeric substances (EPS) from oil-degrading bacteria. Elementa: Science of the Anthropocene, 7, 371.

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that …

Steen, A. D., et al. (2019). High proportions of bacteria and archaea across most biomes remain uncultured. ISME Journal, 13, 3126–3130.

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, …

Bird, J. T., et al., & Steen, A. D. (2019). Uncultured microbial phyla suggest mechanisms for multi-thousand-year subsistence in Baltic Sea sediments. mBio, 10(2), e02376-18.

Geochemical models typically represent organic matter (OM) as consisting of multiple, independent pools of compounds, each accessed by microorganisms at different rates. However, recent findings indicate that organic compounds can interact within microbial metabolisms. The relevance of interactive …

Quigley, L. N. M., & Steen, A. D. (2019). Characterization of the Interactive Effects of Labile and Recalcitrant Organic Matter on Microbial Growth and Metabolism. Frontiers in Microbiology, 10, 493.

This study offers insight into the roles anodic and cathodic processes play in electrochemically activated persulfate (EAP) and screens EAP as a viable technique for ciprofloxacin degradation in wastewater. Sulfate radical formation at a boron-doped diamond (BDD) anode and persulfate activation at a …

Matzek, L. W., et al., & Steen, A. D. (2018). Understanding Electrochemically Activated Persulfate and Its Application to Ciprofloxacin Abatement. Environmental Science & Technology, 52(10), 5875–5883.

Proteins constitute a particularly bioavailable subset of organic carbon and nitrogen in aquatic environments but must be hydrolyzed by extracellular enzymes prior to being metabolized by microorganisms. Activities of extracellular peptidases (protein-degrading enzymes) have frequently been assayed …

Mullen, L., et al., & Steen, A. D. (2018). Potential Activities of Freshwater Exo- and Endo-Acting Extracellular Peptidases in East Tennessee and the Pocono Mountains. Frontiers in Microbiology, 9, 368.

Aquatic sediments harbour diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to …

Mahmoudi, N., et al., & Steen, A. D. (2017). Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria. Environmental Microbiology, 19(7), 2857–2866.

The “priming effect,” in which addition of labile substances changes the remineralization rate of recalcitrant organic matter, has been intensively studied in soils, but is less well-documented in aquatic systems. We investigated the extent to which additions of nutrients or labile organic carbon …

Steen, A. D., Quigley, L. N. M., & Buchan, A. (2016). Evidence for the Priming Effect in a Planktonic Estuarine Microbial Community. Frontiers in Marine Science, 3, 6.

The identities and biochemical properties of extracellular enzymes present in natural environments are poorly constrained. We used a series of competitive inhibition experiments with samples from a freshwater environment (the Tennessee River at Knoxville, TN, USA) and a marine environment (Bogue …

Steen, A. D., Vazin, J. P., et al. (2015). Substrate specificity of aquatic extracellular peptidases assessed by competitive inhibition assays using synthetic substrates. Aquatic Microbial Ecology, 76, 259–270.

Marine sediments host a large population of diverse, heterotrophic, uncultured microorganisms with unknown physiologies that control carbon flow through organic matter decomposition. Recently, single-cell genomics uncovered new key players in these processes, such as the miscellaneous crenarchaeotal …

Michalska, K., et al., & Steen, A. D. (2015). New aminopeptidase from "microbial dark matter" archaeon. FASEB Journal, 29(9), 4071–4079.

Extracellular enzymes produced by heterotrophic microbial communities are major drivers of carbon and nutrient cycling in terrestrial, freshwater, and marine environments. Although carbon and nutrient cycles are coupled on global scales, studies of extracellular enzymes associated with terrestrial, …

Arnosti, C., et al., & Steen, A. D. (2014). Extracellular enzymes in terrestrial, freshwater, and marine environments: Perspectives on system variability and common research needs. Biogeochemistry, 117, 5–21.

In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of …

Cardman, Z., et al., & Steen, A. D. (2014). Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard. Applied and Environmental Microbiology, 80(12), 3749–3756.

The identities and biochemical properties of extracellular enzymes present in natural environments are poorly constrained. We used a series of competitive inhibition experiments with samples from a freshwater environment (the Tennessee River at Knoxville, TN, USA) and a marine environment (Bogue …

Lloyd, K. G., et al., & Steen, A. D. (2013). Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor. Applied and Environmental Microbiology, 79(24), 7790–7799.

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International …

Murray, A. E., et al., & Steen, A. D. (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5, 987–994.

To describe a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and …

Lloyd, K. G., Steen, A. D., et al. (2018). Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes. mSystems, 3(5), e00055-18.