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Item Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream(2019-10) Dieser, Markus; Smith, Heidi J.; Ramaraj, Thiruvarangan; Foreman, Christine M.As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.Item When a habitat freezes solid: Microorganisms over-winter within the ice column of a coastal Antarctic lake(2011-03) Foreman, Christine M.; Dieser, Markus; Greenwood, Mark C.; Cory, R. M.; Laybourn-Parry, Johanna; Lisle, John T.; Jaros, C.; Miller, P. L.; Chin, Yu-Ping; McKnight, Diane M.A major impediment to understanding the biology of microorganisms inhabiting Antarctic environments is the logistical constraint of conducting field work primarily during the summer season. However, organisms that persist throughout the year encounter severe environmental changes between seasons. In an attempt to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the biological and chemical processes that occurred during winter freezeup. The ice contained bacteria and virus-like particles, while flagellated algae and ciliates over-wintered in the form of inactive cysts and spores. Both bacteria and algae were metabolically active in the ice core melt water. Bacterial production ranged from 1.8 to 37.9 μg C L−1 day−1. Upon encountering favorable growth conditions in the melt water, primary production ranged from 51 to 931 μg C L−1 day−1. Because of the strong H2S odor and the presence of closely related anaerobic organisms assigned to Pony Lake bacterial 16S rRNA gene clones, we hypothesize that the microbial assemblage was strongly affected by oxygen gradients, which ultimately restricted the majority of phylotypes to distinct strata within the ice column. This study provides evidence that the microbial community over-winters in the ice column of Pony Lake and returns to a highly active metabolic state when spring melt is initiated.Item Comparative analysis of morphological, mineralogical and spectral properties of cryoconite in Jakobshavn Isbræ, Greenland, and Canada Glacier, Antarctica(2013-07) Tedesco, Marco; Foreman, Christine M.; Anton, J.; Steiner, N.; Schwartzman, T.We report the results of a comparative analysis focusing on grain size, mineralogical composition and spectral reflectance values (400–2500 nm) of cryoconite samples collected from Jakobshavn Isbræ, West Greenland, and Canada Glacier, McMurdo Dry Valleys, Antarctica. The samples from the Greenland site were composed of small particles clumped into larger rounded agglomerates, while those from the site in Antarctica contained fragments of different sizes and shapes. Mineralogical analysis indicates that the samples from Jakobshavn Isbræ contained a higher percentage of quartz and albite, whereas those from Canada Glacier contained a higher percentage of amphibole, augite and biotite. Spectral measurements confirmed the primary role of organic material in reducing the reflectance over the measured spectrum. The reflectance of the samples from the Antarctic site remained low after the removal of organic matter because of the higher concentration of minerals with low reflectance. The reflectance of dried cryoconite samples in the visible region was relatively low (e.g., between ~ 0.1 and ~ 0.4) favouring increased absorbed solar radiation. Despite high reflectance values in the shortwave infrared region, the effect of the presence of cryoconite is negligible at infrared wavelengths where ice reflectance is low.Item Microbial growth under humic-free conditions in a supraglacial stream system on the Cotton Glacier, Antarctica(2013-07) Foreman, Christine M.; Cory, R. M.; Morris, Cindy E.; SanClements, M. D.; Smith, Heidi J.; Lisle, John T.; Miller, P. L.; Chin, Yu-Ping; McKnight, Diane M.During the austral summers of 2004 and 2009, we sampled a supraglacial stream on the Cotton Glacier, Antarctica. The stream dissolved organic matter (DOM) was low (44–48 µ M C) and lacked detectable humic fluorescence signatures. Analysis of the excitation emissions matrices (EEMs) indicated that amino-acid fluorophores dominated, consistent with DOM of microbial origin, with little humic-like fluorescence. In most aquatic ecosystems, humic DOM attenuates harmful UV radiation and its absence may represent an additional stressor influencing the microbial community. Nonetheless, the stream contained an active microbial assemblage with bacterial cell abundances from 2.94 x 104 to 4.97 x 105 cells ml-1, and bacterial production ranging from 58.8 to 293.2 ng C l-1 d-1. Chlorophyll-a concentrations ranged from 0.3 to 0.53 µ g 1-1 indicating that algal phototrophs were the probable source of the DOM. Microbial isolates produced a rainbow of pigment colors, suggesting adaptation to stress, and were similar to those from other cryogenic systems (Proteobacteria and Bacteroidetes lineages). Supraglacial streams provide an example of contemporary microbial processes on the glacier surface and a natural laboratory for studying microbial adaptation to the absence of humics.Item Physicochemical and biological dynamics in a coastal Antarctic lake as it transitions from frozen to open water(2013-03) Dieser, Markus; Foreman, Christine M.; Jaros, C.; Lisle, John T.; Greenwood, Mark C.; Laybourn-Parry, Johanna; Miller, P. L.; Chin, Yu-Ping; McKnight, Diane M.Pony Lake, at Cape Royds, Antarctica, is a shallow, eutrophic, coastal lake that freezes solid in the winter. Changes in Pony Lake's physicochemical parameters and microbial community were studied during the transition from ice to open water. Due to rising water temperatures, the progressive melt of the ice column and the gradual mixing of basal brines into the remaining water column, Pony Lake evolved physically and chemically over the course of the summer, thereby affecting the microbial community composition. Temperature, pH, conductivity, nutrients and major ion concentrations reached their maximum in January. Pony Lake was colonized by bacteria, viruses, phytoflagellates, ciliates, and a small number of rotifers. Primary and bacterial production were highest in mid-December (2.66 mg C 1-1 d-1 and 30.5 µg C 1-1 d-1, respectively). A 16S rRNA gene analysis of the bacterioplankton revealed 34 unique sequences dominated by members of the ß- and y-proteobacteria lineages. Cluster analyses on denaturing gradient gel electrophoresis (DGGE) banding patterns and community structure indicated a shift in the dominant members of the microbial community during the transition from winter ice, to early, and late summer lakewater. Our data demonstrate that temporal changes in physicochemical parameters during the summer months determine community dynamics and mediate changes in microbial species composition.Item Characterization of IHSS Pony Lake fulvic acid dissolved organic matter by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and fluorescence spectroscopy(2013-12) D'Andrilli, Juliana; Foreman, Christine M.; Marshall, Alan G.; McKnight, Diane M.We present the extensive characterization of Antarctic Pony Lake (PL) dissolved organic matter (DOM), an International Humic Substance Society (IHSS) fulvic acid (FA) reference standard, using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) and excitation–emission matrix fluorescence spectroscopy (EEMS). PLFA is the first reference standard available through IHSS derived solely from a microbial source. A number of factors differentiate PLFA from other IHSS standards, including source material, geographic location, sunlight exposure, freeze–thaw conditions, and other in situ environmental influences. ESI FT-ICR MS and EEMS were used to compare the PLFA microbial DOM compositional signature with the IHSS Suwannee River (SR) FA, a standard frequently studied for environmental DOM analysis. Although CcHhOoNnSs(n = 0, 1, or 2 and s = 0 or 1) constituents were present in both IHSS samples, PLFA contained more N and S molecular species, whereas SRFA was dominated by CcHhOo compounds. Proteinaceous character was detected with both methods, in greater abundance for PLFA, which we attributed to its microbial source material and labile, potentially more reactive nature than SRFA. Characterization from both analytical techniques resulted in complementary data that reinforce the importance of PLFA as an IHSS reference standard that should be utilized for other microbiological environmental DOM comparisons.Item Draft genome sequence and description of Janthinobacterium sp. strain CG3, a psychrotolerant antarctic Supraglacial stream bacterium(2013-11) Smith, Heidi J.; Akiyama, Tatsuya; Foreman, Christine M.; Franklin, Michael J.; Woyke, Tanja; Teshima, H; Davenport, K.; Daligault, H.; Erkkila, T.; Goodwin, L. A.; Gu, W.; Xu, Yan; Chain, P. S.Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight into the mechanisms necessary for bacteria to survive in UV-stressed icy environments.Item Characterization of fulvic acid fractions of dissolved organic matter during ice-out in a hyper-eutrophic, coastal pond in Antarctica(2013-10) Cawley, K. M.; McKnight, Diane M.; Penney, P. M.; Cory, R. M.; Fimmen, R. L.; Guerard, J.; Dieser, Markus; Jaros, C.; Chin, Yu-Ping; Foreman, Christine M.Dissolved humic material (HDOM) is ubiquitous to all natural waters and its source material influences its chemical structure, reactivity, and bioavailability. While terrestrially derived HDOM reference materials distributed by the International Humic Substances Society (IHSS) have been readily available to engineering and scientific communities, a microbially derived reference HDOM was not, despite the well-characterized differences in the chemistry and reactivity of HDOM derived from terrestrial versus microbial sources. To address this gap, we collected a microbial reference fulvic acid from Pony Lake (PLFA) for distribution through the IHSS. Pony Lake is a saline coastal pond on Ross Island, Antarctica, where the landscape is devoid of terrestrial plants. Sample collection occurred over a 17-day period in the summer season at Pony Lake. During this time, the dissolved organic carbon (DOC) concentrations increased nearly two-fold, and the fulvic acid fraction (collected using the XAD-8 method) accounted for 14.6% of the DOC. During the re-concentration and desalting procedures we isolated two other chemically distinct fulvic acid fractions: (1) PLFA-2, which was high in carbohydrates and (2) PLFA-CER, which was high in nitrogen. The chemical characteristics (elemental analysis, optical characterization with UV–vis and fluorescence spectroscopy, and 13C NMR spectroscopy) of the three fulvic acid fractions helped to explain their behavior during isolation.Item Draft genome sequence of a metabolically diverse Antarctic supraglacial stream organism, Polaromonas sp. strain CG9_12, determined using pacific biosciences single-molecule real-time sequencing technology(2014-12) Smith, Heidi J.; Foreman, Christine M.; Ramaraj, ThiruvaranganPolaromonas species are found in a diversity of environments and are particularly common in icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic, Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria phylum. Here, we present the draft genome sequence of Polaromonas sp. strain CG9_12, isolated from an Antarctic supraglacial stream.Item Genome sequence of Janthinobacterium sp. CG23_2, a violacein-producing isolate from an Antarctic supraglacial stream.(2016-01) Smith, Heidi J.; Foreman, Christine M.; Akiyama, Tatsuya; Franklin, Michael J.; Devitt, N. P.; Ramaraj, ThiruvaranganHere, we present the draft genome sequence for the violacein-producing Janthinobacterium sp. CG23_2 isolated from an Antarctic supraglacial stream. The genome is ~7.85 Mb, with a G+C content of 63.5%. The genome includes 7,247 candidate protein coding genes, which may provide insight into UV tolerance mechanisms.