Publications

Jump to the bottom of the page to see a full list of publications and Preprints. A complete list of papers and conference abstracts is also available in my Google Scholar profile.

Highlights

Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

The focus of this paper is a member of the Gammaproteobacteria found in marine sediments worldwide named Woeseiales (formerly JTB255). To understand the response to burial within this clade, we used a MAG-centric transcriptomic approach. We discovered that transcripts for a single gene increased by ~1000x upon burial within just the first few cm of sediment, while other gene transcripts decrease. This points to a potential dormancy response without canonical sporulation. Code for analysis and figures can be found on my Github.

J.Buongiorno, K. Sipes, K. Wasmund, A. Loy, K.G. Lloyd. . Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PloS ONE, 2020. 10.1371/journal.pone.0234839

Mineralized microbialites as archives of environmental evolution, Laguna Negra, Catamarca Province, Argentina

In this paper, we examined isotopic and elemental signatures in carbonate microbialites a.k.a microbially-mediated rocks. The concentric bands inside the rock preserve a time-series of lake evolution. Much like tree rings, these laminations allow reconstruction of lake history through interpretation of paired isotopes of carbon, sedimentary organic matter, and trace metal content. Code for analysis and figures can be found on my Github.

J. Buongiorno, F.J. Gomez, D.A. Fike, L.C. Kah. . Mineralized microbialites as archives of environmental evolution, Laguna Negra, Catamarca Province, Argentina. Geobiology, 2019. 10.1111/gbi.12327

Exploring Carbon Mineral Systems: Recent Advances in C Mineral Evolution, Mineral Ecology, and Network Analysis

Data science has a lot to offer to the geoscience community. This paper reviewes the latest developments in mineral ecology using cutting edge visualization techniques, network analysis, and affinity algorithms. When applied to large, public data repositories, these techniques can highlight the emergent properties underlying multidimensional datasets and help make better scientific predictions.

S.M Morrison, J. Buongiorno, R. T. Downs, A. Eleish, P. Fox, D. Giovannelli, J.T. Golden, D.R. Hummer, G. Hystad, L.H.Kellogg, O. Kreylos, S. Krivovichev, C. Liu, A. Merdith, A. Prabhu, J. Ralph, S. Runyon, S. Zahirovic, R.M. Hazen. . Exploring Carbon Mineral Systems: Recent Advances in C Mineral Evolution, Mineral Ecology, and Network Analysis. Frotiers in Earth Science, 2020. 10.3389/feart.2020.00208

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments

Iron and sulfur cycling in Van Keulenfjord, Svalbard, is mediated both by abiotic chemical reactions as well as microbial metabolisms and byproducts. In this paper, we examined microbial community composition by 16S rRNA gene analysis and sedimentary organic matter at high depth resolution of 1 cm down to ~20 cm at two sites. Ordination analysis and microbial networks suggests that as glaciers retreat, microbial communities will become less complex and sulfate reducers will potentially outcompete microorganisms that respire iron and manganese. Code for analysis and figures can be found on my Github.

J. Buongiorno, L.C. Herbert, L. M. Wehrmann, A. B. Michaud, K. Laufer, H. RØy, B.B. JØrgensen, A. Sznkiewicz, A. Faiia, K.M Yeager, K. Schindler, K.G. Lloyd. . Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments. Applied and Environmental Microbiology, 2019. 10.1128/AEM.00949-19

Interlaboratory Quantification of Bacteria and Archaea in Deeply Buried Sediments of the Baltic Sea (IODP Expedition 347)

For many years following the first discovery of microbes in deeply-buried marine sediments, failure to find Archaea seemed like good evidence that the deep subsurface biosphere is a bacterial world. However, we hypothesized that this finding was a result of a methodological artifact that biases results toward bacteria. In this paper, we test this hypthosis. We found that instead, failure to identify Archaea rests with very high limits of detection for microscopy and suggested qPCR as a better method for quantification of biomass.

Buongiorno J., Turner S. Webster G., Asai M., Shumaker A. K., Roy T., Weightman A, Schippers, Lloyd K. G.. . Interlaboratory Quantification of Bacteria and Archaea in Deeply Buried Sediments of the Baltic Sea (IODP Expedition 347). FEMS Microbiology Ecology, 2017. 10.1093/femsec/fix007

Methanogens in the Antarctic Dry Valley Permafrost

Methanogens generate the powerful greenhouse gas, methane. A large question with climate change is how thawing permafrost will affect the trajectory of methane dynamics – will thawing lead to a positive feedback loop where more warming means more methane which means more warming? In this paper, we interrogated a methanogenic genome from Antarctica, the first ever recontructed from Antarctic permafrost. We found several different methane-generating pathways. Protein modeling highlights protein adaptations that allow this microbe to endure the harsh permafrost environment.

J. Buongiorno, J.T. Bird, K.G. Lloyd, T. Vishnivetskaya. . Methanogens in the Antarctic Dry Valley Permafrost. FEMS Microbiology Ecology, 2018. https://doi.org/10.1093/femsec/fiy109

 

Full List

J.Buongiorno, K. Sipes, K. Wasmund, A. Loy, K.G. Lloyd. . Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PloS ONE, 2020. 10.1371/journal.pone.0234839

J. Buongiorno, F.J. Gomez, D.A. Fike, L.C. Kah. . Mineralized microbialites as archives of environmental evolution, Laguna Negra, Catamarca Province, Argentina. Geobiology, 2019. 10.1111/gbi.12327

S.M Morrison, J. Buongiorno, R. T. Downs, A. Eleish, P. Fox, D. Giovannelli, J.T. Golden, D.R. Hummer, G. Hystad, L.H.Kellogg, O. Kreylos, S. Krivovichev, C. Liu, A. Merdith, A. Prabhu, J. Ralph, S. Runyon, S. Zahirovic, R.M. Hazen. . Exploring Carbon Mineral Systems: Recent Advances in C Mineral Evolution, Mineral Ecology, and Network Analysis. Frotiers in Earth Science, 2020. 10.3389/feart.2020.00208

Lloyd, K.G., Bird, J.T., Buongiorno, J., Deas, E., Kevorkian, R., Noordhoek, T., Rosalsky, J., Roy, T.. . Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments.. Applied and Environmental Microbiology, 2020. 10.1128/AEM.00877-20

J. Buongiorno, L.C. Herbert, L. M. Wehrmann, A. B. Michaud, K. Laufer, H. RØy, B.B. JØrgensen, A. Sznkiewicz, A. Faiia, K.M Yeager, K. Schindler, K.G. Lloyd. . Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments. Applied and Environmental Microbiology, 2019. 10.1128/AEM.00949-19

Buongiorno J., Turner S. Webster G., Asai M., Shumaker A. K., Roy T., Weightman A, Schippers, Lloyd K. G.. . Interlaboratory Quantification of Bacteria and Archaea in Deeply Buried Sediments of the Baltic Sea (IODP Expedition 347). FEMS Microbiology Ecology, 2017. 10.1093/femsec/fix007

J. Buongiorno, J.T. Bird, K.G. Lloyd, T. Vishnivetskaya. . Methanogens in the Antarctic Dry Valley Permafrost. FEMS Microbiology Ecology, 2018. https://doi.org/10.1093/femsec/fiy109

Preprints

Fullerton KM, Schrenk M, Yucel M, Manini E, Basili M, Rogers T, Fattorini D, di Carlo M, RegoliF, Nakagawa M, Smedile F, Vetriani C, Miller H, Morrison S, Buongiorno J, Jessen, G, Martinez M, de Moor JM, Barry PH, Giovannelli D, Lloyd K. 2019. Plate tectonics drive deep biosphere microbial community composition. EarthArxiv, doi 10.31223/osf.io/gyr7n

Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. 2020. Woeseiales transcriptional response in Arctic fjord surface sediment. bioRxiv, doi 10.1101/2020.06.04.134015

Lloyd, K, Bird, JT, Buongiorno J, Deas, E, Kevorkian R, Noordhoek T, Rosalsky J, Roy T. 2020. Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments. bioRxiv, doi 10.1101/2020.03.24.005512

Flieder M, Buongiorno J, Herbold C, Hausmann B, Rattei T, Lloyd K, Loy A, Wasmund K. 2020. Novel taxa of Acidobacteriota involved in seafloor sulfur cycling. bioRxiv, doi 10.1101/2020.10.01.322446