Genomic and Functional Investigations Into Seasonally-Impacted and Morphologically-Distinct Anoxygenic Photosynthetic Cyanobacterial Mats

Cyanobacteria are key members of modern photosynthetic microbial mats, by providing organic matter and nutrients to the ecosystem. With their innovation of oxygenic photosynthesis (OP) over 2 billion years ago and the wide distribution of microbial mats in the geologic record, cyanobacteria have shaped Earth’s redox history. Select modern cyanobacteria are also capable of anoxygenic photosynthesis using sulfide (AP), an older metabolism than OP and a less-understood biological mechanism that limited the rise of oxygen. This dissertation used molecular and ecological techniques to investigate modern anoxygenic cyanobacteria. In Chapter I, I outline the current understanding of AP cyanobacterial mats in modern and ancient ecosystems. In Chapter II, I described the genome of a cultured AP cyanobacterium, Geitlerinema sp. PCC9228. Genomic analysis of Geitlerinema revealed numerous adaptations to low-oxygen and sulfidic conditions, which were potentially prevalent for much of Earth’s history. I applied knowledge of cyanobacterial genetic adaptation to AP from Geitlerinema, to the microbial mats of Middle Island Sinkhole (MIS), a submerged sinkhole impacted by low-O2, sulfur-rich groundwater. In Chapter III, I characterized the impact of seasonally changing light conditions and geochemistry on the microbial community (16S rRNA genes and metagenomics) and its function (metaproteomics). The dominant AP cyanobacteria, Phormidium and Planktothrix, are abundant and active in summer when light is highest. In contrast, when light is lower in autumn, sulfide-oxidizing bacteria are more active. The shift in microbial community function has implications for oxygen and sulfur cycling in the mat. In Chapter IV, I applied metagenomics and metaproteomics to distinct mat morphotypes in MIS. I observed flat purple cyanobacterially-dominated mat (‘flat’), conical purple mat (‘fingers’), white-pigmented mat (‘white’), and a mottled purple/brown pigmented mat (‘giraffe’). The cyanobacterial community shifted from Phormidium and Planktothrix in fingers and some flat mat, to Pseudanabaena and Spirulina in giraffe and white mats. Sulfide-oxidizing bacteria and sulfate-reducing bacteria were widely observed in all mat types. The genomes and proteins suggest functional niche similarity with regard to sulfide and oxygen cycling between abundant cyanobacteria in different mats. Understanding the role of cyanobacteria in shaping the function and appearance of modern microbial mats informs the interpretation of the chemical environment, metabolisms, and biogeochemical impact of microbial mats through Earth history.PHDEarth and Environmental SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/151720/1/sgrim_1.pdfDescription of sgrim_1.pdf : Restricted to UM users only

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica ‘Solar Lake’), a Model Anoxygenic Photosynthetic Cyanobacterium

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth’s biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica ‘Solar Lake’, a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis. Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial anoxygenic photosynthesis and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating redox gradients and nitrogen availability that occur in benthic mats over a diel cycle. Such dynamic geochemical conditions likely also challenged Proterozoic cyanobacteria, modulating oxygen production. The genetic repertoire that underpins flexible oxygenic/anoxygenic photosynthesis in cyanobacteria provides a foundation to explore the regulation, evolutionary context, and biogeochemical implications of these co-occurring metabolisms in Earth history

Versatile Photophysiology of Compositionally Similar Cyanobacterial Mat Communities Inhabiting Submerged Sinkholes of Lake Huron

Recently discovered submerged sinkholes in Lake Huron are high-sulfur, lowoxygen extreme environments for microbial life. In order to understand the relationship between the physical environment, photophysiology and community composition, we measured the physical conditions, photophysiological indices, and genetic diversity at 3 microbial mat sites bathed in high conductivity groundwater under a natural light gradient during 2012 and 2013. A strong seasonal trend prevailed at all sites, characterized by decreased photosynthetic yield (Fv’/Fm’; 0.25 to 0.40) during the summer (April to August) and increased yield (0.70 to 0.75) during the winter (November to March). Chlorophyll a content varied seasonally in a similar manner to photo - synthetic yield. All sites were dominated by \u3e80% abundance of one cyanobacterial group, most closely related to Phormidium sp. Phycobilins (phycocyanin and phycoerythrin) were consistently higher in concentration than chlorophyll. Photosynthetic yield was statistically indistinguishable between sites, suggesting that these mat communities are able to acclimate across a wide range of photosynthetically active radiation (PAR). Interestingly, these cyanobacteria carried out oxygenic photosynthesis in the presence of in vitro H2S, further suggestive of their versatile photophysiologies under variable redox conditions. Collectively, our study provides insight into the adaptive capabilities of cyanobacteria by revealing how they photophysiologically respond to changes in light climate and redox conditions, and are thereby able to inhabit a wide range of physico-chemical environments. Such versatile physiologies may have enabled their ancestors to thrive across a range of habitats on early Earth

The Grizzly, January 27, 1989

Constructium Ursini • Ad Hoc Hoists Honor • New GPA: 2.25 or Dive! • Letter: Green Shirt Makes Reed Red • Fair Not Just for Freshmen • Security Shacks in Reimert • Beverly Oehlert Named to Pottstown Board of Directors • Final Red and Gold Day • Hoopsters Stunning in Second • Lady Bears Go For Title • U.C. Hockey Bids Boyd Bon Voyage • A \u27bears Recover from Fla. • Dryfoos, Knauer Newest Dirs. • Bailey Bandies With Bush • Grim Gripes: Wismer Hard to Swallow • Quintet Jazzes Up First Forum • Greenstein to Performhttps://digitalcommons.ursinus.edu/grizzlynews/1226/thumbnail.jp

Oligotyping : differentiating between closely related microbial taxa using 16S rRNA gene data

© The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society.. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Methods in Ecology and Evolution 4 (2013): 1111–1119, doi:10.1111/2041-210X.12114.Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.This work was supported by the National Institutes of Health [1UH2DK083993 to M.L.S.] and the Alfred P. Sloan Foundation

The Grizzly, April 14, 1989

Middle States: What To Look For At U.C. • Sorority Songfest Continues • Letters: Lack of MACLAS Coverage Disturbing; I.D. Hassles; We Smell a Rat! • Middle States Closing Offers Suggestions • Canterbury Corner too Costly • Lacrosse Braces for Traditional Rivalry • Outmanned, But Still Best • Tennis Turns Tables • Ursinus Sweeps • Men\u27s Lax Gets Physical • Cinders Burnin\u27 Down the House • Guess Who\u27s Coming to Dinner? • Branker Wins Jazz Fellowship • MACLAS Meeting Absolute Success • Sternal: Functional Art at U.C. • Cyclists Rolling to Victories • Pilgrim Continues U.C. Evaluation • Admissions Reception • Grant to Give Biology a Boost • The Music Scenehttps://digitalcommons.ursinus.edu/grizzlynews/1235/thumbnail.jp

Ischaemic stroke, haemorrhage and mortality in elderly patients with chronic kidney disease newly started on anticoagulation for atrial fibrillation: a population-based study from UK primary care

Objective To assess the association between anticoagulation, ischaemic stroke, gastrointestinal and cerebral haemorrhage, and all cause mortality in older people with atrial fibrillation and chronic kidney disease. Design Propensity matched, population based, retrospective cohort analysis from January 2006 through December 2016. Setting The Royal College of General Practitioners Research and Surveillance Centre database population of almost 2.73 million patients from 110 general practices across England and Wales. Participants Patients aged 65 years and over with a new diagnosis of atrial fibrillation and estimated glomerular filtration rate (eGFR) of <50 mL/min/1.73m2, calculated using the chronic kidney disease epidemiology collaboration creatinine equation. Patients with a previous diagnosis of atrial fibrillation or receiving anticoagulation in the preceding 120 days were excluded, as were patients requiring dialysis and recipients of renal transplants. Intervention Receipt of an anticoagulant prescription within 60 days of atrial fibrillation diagnosis. Main outcome measures Ischaemic stroke, cerebral or gastrointestinal haemorrhage, and all cause mortality. Results 6977 patients with chronic kidney disease and newly diagnosed atrial fibrillation were identified, of whom 2434 were on anticoagulants within 60 days of diagnosis and 4543 were not. 2434 pairs were matched using propensity scores by exposure to anticoagulant or none and followed for a median of 506 days. The crude rates for ischaemic stroke and haemorrhage were 4.6 and 1.2 after taking anticoagulants and 1.5 and 0.4 in patients who were not taking anticoagulant per 100 person years, respectively. The hazard ratios for ischaemic stroke, haemorrhage, and all cause mortality for those on anticoagulants were 2.60 (95% confidence interval 2.00 to 3.38), 2.42 (1.44 to 4.05), and 0.82 (0.74 to 0.91) compared with those who received no anticoagulation. Conclusion Giving anticoagulants to older people with concomitant atrial fibrillation and chronic kidney disease was associated with an increased rate of ischaemic stroke and haemorrhage but a paradoxical lowered rate of all cause mortality. Careful consideration should be given before starting anticoagulants in older people with chronic kidney disease who develop atrial fibrillation. There remains an urgent need for adequately powered randomised trials in this population to explore these findings and to provide clarity on correct clinical management

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 14900-14905, doi:10.1073/pnas.1507380112.During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable in the hydrocarbon-rich, 1100m deep, plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep-waters during the discharge. In contrast, oil addition lacking dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. Dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. Extrapolating this comprehensive data set to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates.This research was supported by a grant from BP/the Gulf of Mexico Research Initiative to support the "Ecosystem Impacts of Oil and Gas Inputs to the Gulf (ECOGIG)” consortium. PMM also acknowledges funding from the National Science Foundation (OCE-1057683)

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis

Abstract Background Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway colonization by bacteria and fungi, and these infections cause irreversible lung damage. Fungi are detected more frequently in CF sputum samples upon initiation of antimicrobial therapy, and several studies have implicated the detection of fungi in sputum with worse outcomes. Thus, a more complete understanding of fungi in CF is required. Results We characterized the fungi and bacteria in expectorated sputa from six CF subjects. Samples were collected upon admission for systemic antibacterial therapy and upon the completion of treatment and analyzed using a pyrosequencing-based analysis of fungal internal transcribed spacer 1 (ITS1) and bacterial 16S rDNA sequences. A mixture of Candida species and Malassezia dominated the mycobiome in all samples (74%–99% of fungal reads). There was not a striking trend correlating fungal and bacterial richness, and richness showed a decline after antibiotic therapy particularly for the bacteria. The fungal communities within a sputum sample resembled other samples from that subject despite the aggressive antibacterial therapy. Quantitative PCR analysis of fungal 18S rDNA sequences to assess fungal burden showed variation in fungal density in sputum before and after antibacterial therapy but no consistent directional trend. Analysis of Candida ITS1 sequences amplified from sputum or pure culture-derived genomic DNA from individual Candida species found little (<0.5%) or no variation in ITS1 sequences within or between strains, thereby validating this locus for the purpose of Candida species identification. We also report the enhancement of the publically available Visualization and Analysis of Microbial Population Structures (VAMPS) tool for the analysis of fungal communities in clinical samples. Conclusions Fungi are present in CF respiratory sputum. In CF, the use of intravenous antibiotic therapy often does not profoundly impact bacterial community structure, and we observed a similar stability in fungal species composition. Further studies are required to predict the effects of antibacterials on fungal burden in CF and fungal community stability in non-CF populations.http://deepblue.lib.umich.edu/bitstream/2027.42/134558/1/40168_2014_Article_67.pd

Characterization and Quantification of the Fungal Microbiome in Serial Samples from Individuals with Cystic Fibrosis

Background: Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway colonization by bacteria and fungi, and these infections cause irreversible lung damage. Fungi are detected more frequently in CF sputum samples upon initiation of antimicrobial therapy, and several studies have implicated the detection of fungi in sputum with worse outcomes. Thus, a more complete understanding of fungi in CF is required. Results: We characterized the fungi and bacteria in expectorated sputa from six CF subjects. Samples were collected upon admission for systemic antibacterial therapy and upon the completion of treatment and analyzed using a pyrosequencing-based analysis of fungal internal transcribed spacer 1 (ITS1) and bacterial 16S rDNA sequences. A mixture of Candida species and Malassezia dominated the mycobiome in all samples (74% – 99% of fungal reads). There was not a striking trend correlating fungal and bacterial richness, and richness showed a decline after antibiotic therapy particularly for the bacteria. The fungal communities within a sputum sample resembled other samples from that subject despite the aggressive antibacterial therapy. Quantitative PCR analysis of fungal 18S rDNA sequences to assess fungal burden showed variation in fungal density in sputum before and after antibacterial therapy but no consistent directional trend. Analysis of Candida ITS1 sequences amplified from sputum or pure culture-derived genomic DNA from individual Candida species found little (\u3c0.5%) or no variation in ITS1 sequences within or between strains, thereby validating this locus for the purpose of Candida species identification. We also report the enhancement of the publically available Visualization and Analysis of Microbial Population Structures (VAMPS) tool for the analysis of fungal communities in clinical samples. Conclusions: Fungi are present in CF respiratory sputum. In CF, the use of intravenous antibiotic therapy often does not profoundly impact bacterial community structure, and we observed a similar stability in fungal species composition. Further studies are required to predict the effects of antibacterials on fungal burden in CF and fungalcommunity stability in non-CF populations