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Bowman, JS, Amaral-Zettler L, Rich J, Luria C, Ducklow H.  2017.  Bacterial community segmentation facilitates the prediction of ecosystem function along the western Antarctic Peninsula. ISME J. 11:1460–1471.: Nature Publishing Group   10.1038/ismej.2016.204   Website
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Bowman, JS, Sachs JP.  2008.  Chemical and physical properties of some saline lakes in Alberta and Saskatchewan. Saline systems. 4:3.   10.1186/1746-1448-4-3   AbstractWebsite

The Northern Great Plains of Canada are home to numerous permanent and ephemeral athalassohaline lakes. These lakes display a wide range of ion compositions, salinities, stratification patterns, and ecosystems. Many of these lakes are ecologically and economically significant to the Great Plains Region. A survey of the physical characteristics and chemistry of 19 lakes was carried out to assess their suitability for testing new tools for determining past salinity from the sediment record.

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Stüeken, EE, Anderson RE, Bowman JS, Brazelton WJ, Colangelo-Lillis J, a Goldman D, Som SM, Baross JA.  2013.  Did life originate from a global chemical reactor? Geobiology. 11:101–26.   10.1111/gbi.12025   AbstractWebsite

Many decades of experimental and theoretical research on the origin of life have yielded important discoveries regarding the chemical and physical conditions under which organic compounds can be synthesized and polymerized. However, such conditions often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose a new approach that considers the origin of life within the global context of the Hadean Earth. We review previous ideas and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life. We conclude that no single environmental setting can offer enough chemical and physical diversity for life to originate. Instead, any plausible model for the origin of life must acknowledge the geological complexity and diversity of the Hadean Earth. Future research may therefore benefit from identifying further linkages between organic precursors, minerals, and fluids in various environmental contexts.

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Barber, DG, Ehn JK, Pucko M, Rysgaard S, Deming JW, Bowman JS, Papakyriakou T, Galley RJ, Søggard DH.  2014.  Frost flowers on young Arctic sea ice: The climatic, chemical, and microbial significance of an emerging ice type. Journal of Geophysical Research: Atmospheres. 119:11593–11612.   10.1002/2014JD021736.Received   Abstract

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Bowman, JS, Berthiaume CT, Armbrust EV, Deming JW.  2014.  The genetic potential for key biogeochemical processes in Arctic frost flowers and young sea ice revealed by metagenomic analysis. FEMS microbiology ecology. 89:376–387.   10.1111/1574-6941.12331   AbstractWebsite

Newly formed sea ice is a vast and biogeochemically active environment. Recently we reported an unusual microbial community dominated by members of the Rhizobiales in frost flowers at the surface of Arctic young sea ice based on the presence of 16S gene sequences related to these strains. Here we use metagenomic analysis of two samples, from a field of frost flowers and the underlying young sea ice, to explore the metabolic potential of this surface ice community. The analysis links genes for key biogeochemical processes to the Rhizobiales, including dimethylsulfide uptake, betaine glycine turnover, and halocarbon production. Nodulation and nitrogen fixation genes characteristic of terrestrial root-nodulating Rhizobiales were generally lacking from these metagenomes. Non-Rhizobiales clades at the ice surface had genes that would enable additional biogeochemical processes, including mercury reduction and dimethylsulfoniopropionate catabolism. Although the ultimate source of the observed microbial community is not known, considerations of the possible role of aeolian deposition or transport with particles entrained during ice formation favor a suspended particle source for this microbial community. This article is protected by copyright. All rights reserved.

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Bowman, JS.  2018.  Identification of microbial dark matter in Antarctic environments. Frontiers in Microbiology. 9   10.3389/fmicb.2018.03165   AbstractWebsite

Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI's Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumine platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.

Webb, SJ, Rabsattt T, Erazo N, Bowman JS.  2019.  Impacts of Zostera eelgrasses on microbial community structure in San Diego coastal waters. Elementa-Science of the Anthropocene. 7   10.1525/elementa.350   AbstractWebsite

Marine eelgrasses are influential to their surrounding environments through their many ecosystem services, ranging from the provisioning of food and shelter for marine life to serving as a natural defense against pollution and pathogenic bacteria. In the marine waters of San Diego, CA, USA, eelgrass beds comprised of Zostera spp. are an integral part of the coastal ecosystem. To evaluate the impact of eelgrass on bacterial and archaeal community structure we collected water samples in San Diego Bay and sequenced the 16S rRNA gene from paired eelgrass-present and eelgrass-absent sites. To test the hypothesis that microbial community structure is influenced by the presence of eelgrass we applied mixed effects models to these data and to bacterial abundance data derived by flow cytometry. This approach allowed us to identify specific microbial taxa that were differentially present at eelgrass-present and eelgrass-absent sites. Principal coordinate analysis organized the samples by location (inner vs. outer bay) along the first axis, where the first two axes accounted for a 90.8% of the variance in microbial community structure among the samples. Differentially present bacterial taxa included members of the order Rickettsiales, family Flavobacteriaceae, genus Tenacibaculum and members of the order Pseudomonadales. These findings constitute a unique look into the microbial composition of San Diego Bay and examine how eelgrasses contribute to marine ecosystem health, e.g., by supporting specific microbial communities and by filtering and trapping potentially harmful bacteria to the benefit of marine organisms.

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Miller, LA, Fripiat F, Else BGT, Bowman JS, Brown KA, Collins ER, Ewert M, Fransson A, Gosselin M.  2015.  Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations. Elementa. 3:1–53.   10.12952/journal.elementa.000038   Abstract

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Bowman, JS, Vick-Majors TJ, Morgan-Kiss RM, Takacs-Vesbach C, Ducklow HW, PRISCU JC.  2016.  Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem. BioScience. 66:830–847. Abstract

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Bowman, JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, Sicheritz-Ponten T.  2012.  Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J. 6:11–20.   10.1038/ismej.2011.76   Abstract

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Collins, JR, Fredricks HF, Bowman JS, Ward CP, Moreno C, Longnecker K, Marchetti A, Hansel CM, Ducklow HW, Van Mooy BAS.  2018.  The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters. Geochimica Et Cosmochimica Acta. 232:244-264.   10.1016/j.gca.2018.04.030   AbstractWebsite

The seasonal depletion of stratospheric ozone over the Southern Hemisphere allows abnormally high doses of ultraviolet radiation (UVR) to reach surface waters of the West Antarctic Peninsula (WAP) in the austral spring, creating a natural laboratory for the study of lipid photooxidation in the shallow mixed layer of the marginal ice zone. The photooxidation of lipids under such conditions has been identified as a significant source of stress to microorganisms and short-chain fatty acids altered by photochemical processes have been found in both marine aerosols and sinking marine particle material. However, the biogeochemical impact of lipid photooxidation has not been quantitatively compared at ecosystem scale to the many other biological and abiotic processes that can transform particulate organic matter in the surface ocean. We combined results from field experiments with diverse environmental data, including high-resolution, accurate-mass HPLC-ESI-MS analysis of lipid extracts and in situ measurements of ultraviolet irradiance, to address several unresolved questions about lipid photooxidation in the marine environment. In our experiments, we used liposomes-nonliving, cell-like aggregations of lipids-to examine the photolability of various moieties of the intact polar diacylglycerol (IP-DAG) phosphatidylcholine (PC), a structural component of membranes in a broad range of microorganisms. We observed significant rates of photooxidation only when the molecule contained the polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA). As the DHA-containing lipid was oxidized, we observed the steady ingrowth of a diversity of oxylipins and oxidized IP-DAG; our results suggest both the intact IP-DAG the degradation products were amenable to heterotrophic assimilation. To complement our experiments, we used an enhanced version of a new lipidomics discovery software package to identify the lipids in water column samples and in several diatom isolates. The galactolipid digalactosyldiacylglycerol (DGDG), the sulfolipid sulfoquinovosyldiacylglycerol (SQDG) and the phospholipids PC and phosphatidylglycerol (PG) accounted for the majority of IP-DAG in the water column particulate (>= 0.2 mm) size fraction; between 3.4 and 5.3% of the IP-DAG contained fatty acids that were both highly polyunsaturated (i.e., each containing >= 5 double bonds). Using a broadband apparent quantum yield (AQY) that accounted for direct and Type I (i.e., radical- mediated) photooxidation of PUFA-containing IP-DAG, we estimated that 0.7 + 0.2 mmol IP- DAG m(-2) d(-1) (0.5 +/- 0.1 mg C m(-2) d(-1)) were oxidized by photochemical processes in the mixed layer. This rate represented 4.4% (range, 3-21%) of the mean bacterial production rate measured in the same waters immediately following the retreat of the sea ice. Because our liposome experiments were not designed to account for oxidation by Type II photosensitized processes that often dominate in marine phytodetritus, our rate estimates may represent a sizeable underestimate of the true rate of lipid photooxidation in the water column. While production of such diverse oxidized lipids and oxylipins has been previously observed in terrestrial plants and mammals in response to biological stressors such as disease, we show here that a similar suite of molecules can be produced via an abiotic process in the environment and that the effect can be commensurate in magnitude with other ecosystem-scale biogeochemical processes. (C) 2018 Elsevier Ltd. All rights reserved.

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Bowman, JS, Kavanaugh MT, Doney SC, Ducklow HW.  2018.  Recurrent seascape units identify key ecological processes along the western Antarctic Peninsula. Global Change Biology. 24:3065-3078.   10.1111/gcb.14161   AbstractWebsite

The western Antarctic Peninsula (WAP) is a bellwether of global climate change and natural laboratory for identifying interactions between climate and ecosystems. The Palmer Long-Term Ecological Research (LTER) project has collected data on key ecological and environmental processes along the WAP since 1993. To better understand how key ecological parameters are changing across space and time, we developed a novel seascape classification approach based on insitu temperature, salinity, chlorophyll a, nitrate+nitrite, phosphate, and silicate. We anticipate that this approach will be broadly applicable to other geographical areas. Through the application of self-organizing maps (SOMs), we identified eight recurrent seascape units (SUs) in these data. These SUs have strong fidelity to known regional water masses but with an additional layer of biogeochemical detail, allowing us to identify multiple distinct nutrient profiles in several water masses. To identify the temporal and spatial distribution of these SUs, we mapped them across the Palmer LTER sampling grid via objective mapping of the original parameters. Analysis of the abundance and distribution of SUs since 1993 suggests two year types characterized by the partitioning of chlorophyll a into SUs with different spatial characteristics. By developing generalized linear models for correlated, time-lagged external drivers, we conclude that early spring sea ice conditions exert a strong influence on the distribution of chlorophyll a and nutrients along the WAP, but not necessarily the total chlorophyll a inventory. Because the distribution and density of phytoplankton biomass can have an impact on biomass transfer to the upper trophic levels, these results highlight anticipated links between the WAP marine ecosystem and climate.

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Bowman, JS, Deming JW.  2016.  Wind-driven distribution of bacteria in coastal Antarctica: Evidence from the Ross Sea region. Polar Biology. 40(1):25-35.: Springer Berlin Heidelberg   10.1007/s00300-016-1921-2   AbstractWebsite

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{
Domagal-Goldman, SD, Wright KE, Adamala K, {Arina de la Rubia} L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud M-E, Paulino-Lima IG, Singer K, Walter-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, {Imari Walker} S, Wong T.  2016.  {The Astrobiology Primer v2.0}. Astrobiology. 16:561–653.   10.1089/ast.2015.1460   AbstractWebsite

Astrobiology is the science that seeks to understand the story of life in our universe. Astrobiology includes investigation of the conditions that are necessary for life to emerge and flourish, the origin of life, the ways that life has evolved and adapted to the wide range of environmental conditions here on Earth, the search for life beyond Earth, the habitability of extraterrestrial environments, and consideration of the future of life here on Earth and elsewhere. It therefore requires knowledge of physics, chemistry, biology, and many more specialized scientific areas including astronomy, geology, planetary science, microbiology, atmospheric science, and oceanography.