Genomic and Physiologic Characterization of a Freshwater Photoarsenotroph, Cereibacter azotoformans str. ORIO, Isolated From Sediments Capable of Light-Dark Arsenic Redox Cycling

Photoarsenotrophy is an anoxygenic photosynthesis-dependent arsenite oxidation pathway encoded by the Arx gene cluster and is linked to light-dark cycling of arsenic in freshwater environments. This dissertation uses techniques from microbiology, molecular genetics, DNA sequencing, and analytical chemistry to characterize photoarsenotrophy in freshwater environments. The hypothesis is that photoarsenotrophy occurs in freshwater environments and is associated with light-dark cycling of arsenic, which may have a different effect on arsenic biogeochemical cycling when compared to Arx-type arsenotrophy. Light-dark arsenic redox cycling is defined herein as variations in arsenic species, arsenite and arsenate, that correlate to light or dark phases.Since the discovery of photoarsenotrophy in 2008, less than a dozen Arx-dependent arsenotrophs have been isolated, and light-dependent arsenite oxidation has only been detected in three genera (Ectothiorhodospira sp. strains MLW-1, PHS-1, BSL-9, Ect. shaposhnikovii strains DSM 243 and DSM 2001, Halorhodospira halophila SL-1, and now Cereibacter azotoformans str. ORIO). The other studied Arx-dependent arsenotrophs couple arsenite oxidation to anaerobic respiration (i.e., nitrate reduction) instead of anoxygenic photosynthesis (Alkalilimnicola ehrlichii str. MLHE-1, Azoarcus sp. CIB, Sterolibacteraceae strain M52, Desulfotomaculum strain TC-1, and Halomonas sp. ANAO440). In this thesis, I define the light requirement by referring to photosynthesis-dependent arsenite-oxidation as photoarsenotrophy, and photosynthesis-independent Arx-type arsenite-oxidation as Arx-type arsenotrophy. This difference in light requirement is important as it introduces the possibility that light-dark cycling of arsenic could occur in environments containing a photoarsenotroph and arsenate reducer, since Arx-type arsenotrophs are able to oxidize arsenite in the dark so long there is availability of a terminal electron acceptor.The first question investigated was: Does photoarsenotrophy occur in freshwater environments? This question was studied through the isolation and genetic characterization of a novel photoarsenotroph from freshwater sediments in Owens River, CA, USA. Our results show the photoarsenotrophs are present in freshwater environments and harbor the Arx genes required for photoarsenotrophy.The second question investigated was: Can arsenic be light-dark cycled in the environment? In other words, do concentrations of different arsenic forms correlate to the light phase or dark phase of a day? To answer this question, we performed anaerobic microcosm studies with sediment collected from Owens River. Arsenic speciation was measured over light-dark cycles and was followed by metagenome sequencing and analysis. The results provide evidence of light-dark cycling in freshwater sediments and the potential genes involved in the cycle. The third question investigated was: Can we develop a new model organism for studying photoarsenotrophy? We successfully determined that Cereibacter azotoformans str. ORIO is genetically malleable using traditional cloning techniques and can serve as a model for studying the biological mechanism underlying photoarsenotrophy. This was achieved by validating the role of the arxA gene in ORIO and characterizing the physiology surrounding arsenite oxidation.Taken together, these studies show photoarsenotrophy occurs in freshwater environments, ORIO can serve as a model organism for studying photoarsenotrophy, and evidence of light-dark arsenic redox cycling in freshwater sediments

Response of Vibrio cholerae to Low-Temperature Shifts: CspV Regulation of Type VI Secretion, Biofilm Formation, and Association with Zooplankton.

UNLABELLED: The ability to sense and adapt to temperature fluctuation is critical to the aquatic survival, transmission, and infectivity of Vibrio cholerae, the causative agent of the disease cholera. Little information is available on the physiological changes that occur when V. cholerae experiences temperature shifts. The genome-wide transcriptional profile of V. cholerae upon a shift in human body temperature (37°C) to lower temperatures, 15°C and 25°C, which mimic those found in the aquatic environment, was determined. Differentially expressed genes included those involved in the cold shock response, biofilm formation, type VI secretion, and virulence. Analysis of a mutant lacking the cold shock gene cspV, which was upregulated >50-fold upon a low-temperature shift, revealed that it regulates genes involved in biofilm formation and type VI secretion. CspV controls biofilm formation through modulation of the second messenger cyclic diguanylate and regulates type VI-mediated interspecies killing in a temperature-dependent manner. Furthermore, a strain lacking cspV had significant defects for attachment and type VI-mediated killing on the surface of the aquatic crustacean Daphnia magna Collectively, these studies reveal that cspV is a major regulator of the temperature downshift response and plays an important role in controlling cellular processes crucial to the infectious cycle of V. cholerae IMPORTANCE: Little is known about how human pathogens respond and adapt to ever-changing parameters of natural habitats outside the human host and how environmental adaptation alters dissemination. Vibrio cholerae, the causative agent of the severe diarrheal disease cholera, experiences fluctuations in temperature in its natural aquatic habitats and during the infection process. Furthermore, temperature is a critical environmental signal governing the occurrence of V. cholerae and cholera outbreaks. In this study, we showed that V. cholerae reprograms its transcriptome in response to fluctuations in temperature, which results in changes to biofilm formation and type VI secretion system activation. These processes in turn impact environmental survival and the virulence potential of this pathogen

Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental variables such as nitrate and phosphate and temperature appear to influence some low abundant bacterial groups as well. Our results suggest that phytoplankton-associated bacterial communities are strongly affected not just by phytoplankton bloom in general, but also by the type of algal species that dominates in the natural bloom

Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental variables such as nitrate and phosphate and temperature appear to influence some low abundant bacterial groups as well. Our results suggest that phytoplankton-associated bacterial communities are strongly affected not just by phytoplankton bloom in general, but also by the type of algal species that dominates in the natural bloom

Size-fractionated distributions of suspended particle concentration and major phase composition from the U.S. GEOTRACES Eastern Pacific Zonal Transect (GP16)

Marine particles play key roles in the cycling of most elements in the ocean. Here we present full water column sections of size-fractionated (1–51 μm; > 51 μm) concentrations of suspended particulate matter (SPM) and major particle phase composition, including particulate organic matter (POM), calcium carbonate (CaCO3), opal, lithogenic particles, and iron and manganese (oxyhydr)oxides, as well as the Redfield (C:N:P) stoichiometry of particles, from the U.S. GEOTRACES GP16 Eastern Pacific Zonal Transect (EPZT). The GP16 cruise sampled the oxygen deficient waters of the productive eastern upwelling Peru margin westward to Tahiti through the East Pacific Rise (EPR) hydrothermal plume around 12°S in October–December 2013. In this region of relatively low mineral dust deposition, the sum of POM and CaCO3 concentrations accounted for > 80% of small size fraction (SSF) SPM for most of the section. Some exceptions to this include the southern EPR hydrothermal plume, where iron oxyhydroxides accounted for almost 60% of SSF SPM, and the coastal upwelling zone, where opal and lithogenic particles accounted for ~ 50% of SSF SPM. We discuss possible mechanisms to explain a large sediment resuspension feature on the deep Peru continental slope. Large size fraction (LSF) particles generally had relatively higher contributions of opal and lower contributions of POM compared to SSF particles, reflecting an unusually high size partitioning of opal to the LSF. Distributions of CaCO3 and other phases were more strongly controlled by particle dynamics than by dissolution. Our particle phase data are consistent with a conceptual model where particle production, aggregation, and disaggregation processes dominate in the euphotic, 100–300 m, and 300–500 m depth zones, respectively. Our direct measurements of particle composition showed 1) euphotic zone C vs P relationships (SSF: 48 ± 13; LSF: 65 ± 14) that were significantly lower than canonical Redfield values (~ 106), but that were consistent with previously published large scale inverse and box model estimates of exported C:P for this region, and 2) PIC:POC ratios (LSF: 0.088) that were remarkably similar to estimated rain ratios from a biogeochemical-transport box model of alkalinity and nitrate in the low latitude Pacific

Starlikeness of Libera transformation (II) (Applications of Complex Function Theory to Differential Equations)

The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González

The GEOTRACES Intermediate Data Product 2017

Unidad de excelencia María de Maeztu MdM-2015-0552The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González