Alison Buchan

University of Tennessee at Knoxville

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Mary Ann Moran

University of Georgia

Gary R. LeCleir

University of Tennessee at Knoxville

José M. González

Universidad de La Laguna

Matthew J. Tuttle

United States Air Force Research Laboratory

Steven W. Wilhelm

University of Tennessee at Knoxville

Ronald P. Kiene

University of South Alabama

Andrew Johnston

University of East Anglia

Maria Vila‐Costa

Institute of Environmental Assessment and Water Research

Barbara J. Campbell

Clemson University

Thomas G. Demas

Tennessee Temple University

Cooperative Institutions

University of Tennessee at Knoxville

Joint Genome Institute

Lawrence Berkeley National Laboratory

University of Georgia

University of Washington

J. Craig Venter Institute

University of California, Berkeley

Georgia Institute of Technology

University of Maryland, Baltimore

University of Wisconsin–Madison

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In situ activity of NAC11‐7 roseobacters in coastal waters off the Chesapeake Bay based on ftsZ expression

Environmental Microbiology (2011)

Daohong Yao Alison Buchan Marcelino T. Suzuki

Summary Determining in situ growth rates for specific bacterioplankton is of critical importance to understanding their contributions to energy and matter flow in the Ocean. Quantifying expression of genes central to cell division is a plausible approach for obtaining these measurements. In order to test this approach's assumptions, a quantitative PCR assay targeting the cell division gene ftsZ in the ubiquitous NAC11‐7 group of the Rhodobacterales order of marine bacteria was developed. ftsZ genes and their corresponding mRNAs were measured in diel in situ samples and in parallel on‐deck incubations. Strong correlations between ftsZ expression and gene abundance (R‐squared = 0.62) were observed in situ . Rapid changes in NAC11‐7 ftsZ gene copies suggested that different populations from different water types were sampled with a significant positive correlation between ftsZ expression and water temperature (R‐squared = 0.68, P < 0.001). An outlier to this trend occurred at a single time point (9:00), which was remarkably consistent with a concomitant peak in ftsZ expression in on‐deck incubations, suggesting the possibility of synchronous population growth.

FtsZ

Bacterioplankton

10.1111/j.1462-2920.2010.02408.x

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Citations (7)

Genetics and Molecular Features of Bacterial Dimethylsulfoniopropionate (DMSP) and Dimethyl Sulfide (DMS) Transformations

Springer eBooks (2019)

José M. González Andrew Johnston Maria Vila‐Costa Alison Buchan

Dimethylsulfoniopropionate

Dimethyl sulfide

Sulfur Cycle

Bacterioplankton

Osmolyte

10.1007/978-3-319-50418-6_26

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Citations (2)

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Nature Communications (2021)

Kristopher Kieft Zhichao Zhou R. Anderson Alison Buchan Barbara J. Campbell

Biogeochemical Cycle

Sulfur Metabolism

Sulfur Cycle

Biogeochemistry

Microbial Metabolism

10.1038/s41467-021-23698-5

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Citations (157)

Microbiomes and Planctomycete diversity in large-scale aquaria habitats

PLoS ONE (2022)

Claire E. Elbon Gary R. LeCleir Matthew J. Tuttle Sophie Jurgensen Thomas G. Demas

In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1–15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.

Anammox

Planctomycetes

Nitrogen Cycle

Candidatus

10.1371/journal.pone.0267881

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Citations (6)

Seasonal Enhancement of the Viral Shunt Catalyzes a Subsurface Oxygen Maximum in the Sargasso Sea

bioRxiv (Cold Spring Harbor Laboratory) (2025)

Naomi E. Gilbert Daniel Muratore Camelia Shopen Gochev Gary R. LeCleir Shelby M. Cagle

Subsurface oxygen maxima (SOMs) occur directly beneath the mixed layer of stratified water columns across oligotrophic open ocean basins. SOMs occur seasonally and are hypothesized to result from elevated microbial net primary productivity (NPP). Here, we set out to identify mechanistic drivers of the SOM near the Bermuda Atlantic Time Series (BATS) site in the Sargasso Sea in October 2019. Coupled time-series analysis of metatranscriptomics, flow cytometry, and family-specific cyanophage quantification revealed elevated Prochlorococcus abundances, cyanophage abundances, and cyanophage-specific transcriptional activity in the SOM. These findings spurred us to analyze historical oxygen saturation profiles at BATS - identifying a repeated, seasonal cycle in SOM emergence associated with elevated virus-like particles and Prochlorococcus numbers. Returning to the 2019 study site, we found that transcriptional markers for increased dissolved organic matter uptake by copiotrophic bacteria were enriched in the SOM, consistent with enhanced catabolic activity due to the viral shunt. In addition, Prochlorococcus exhibited enrichment in ammonium transport transcripts at the SOM, consistent with increased responsiveness to remineralization activity by heterotrophs. Altogether, these findings suggest that enhanced viral lysis leads to locally elevated nutrient recycling and oxygen production, further reinforcing hypotheses that viruses may play a critical role in the emergence of SOMs in the oligotrophic ocean.

Sargasso sea

10.1101/2025.01.23.634377

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Citations (0)

De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

PLoS ONE (2012)

Christopher A. Gulvik T. Chad Effler Steven W. Wilhelm Alison Buchan

Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI's BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.

Primer (cosmetics)

Amplicon

10.1371/journal.pone.0050362

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Citations (14)

Correction: Microbiomes and Planctomycete diversity in large-scale aquaria habitats

PLoS ONE (2024)

Claire E. Elbon Gary R. LeCleir Matthew J. Tuttle Sophie Jurgensen Thomas G. Demas

[This corrects the article DOI: 10.1371/journal.pone.0267881.].

10.1371/journal.pone.0307131

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Citations (0)

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

The ISME Journal (2013)

Nana Y. D. Ankrah Amanda L. May Jesse Lee Middleton Dan Jones Mary K. Hadden

Biogeochemistry

Microbial Metabolism

10.1038/ismej.2013.216

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Citations (142)

Bacterial Taxa That Limit Sulfur Flux from the Ocean

Science (2006)

Erinn C. Howard James R. Henriksen Alison Buchan Chris R. Reisch Helmut Bürgmann

Flux of dimethylsulfide (DMS) from ocean surface waters is the predominant natural source of sulfur to the atmosphere and influences climate by aerosol formation. Marine bacterioplankton regulate sulfur flux by converting the precursor dimethylsulfoniopropionate (DMSP) either to DMS or to sulfur compounds that are not climatically active. Through the discovery of a glycine cleavage T-family protein with DMSP methyltransferase activity, marine bacterioplankton in the Roseobacter and SAR11 taxa were identified as primary mediators of DMSP demethylation to methylmercaptopropionate. One-third of surface ocean bacteria harbor a DMSP demethylase homolog and thereby route a substantial fraction of global marine primary production away from DMS formation and into the marine microbial food web.

Dimethylsulfoniopropionate

Bacterioplankton

Sulfur Cycle

Roseobacter

Marine bacteriophage

10.1126/science.1130657

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Citations (332)

Genetics and Molecular Features of Bacterial Dimethylsulfoniopropionate (DMSP) and Dimethyl Sulfide (DMS) Transformations

Springer eBooks (2017)

José M. González Andrew Johnston Maria Vila‐Costa Alison Buchan

Dimethylsulfoniopropionate