Microbiology Commons^™

Maintaining And Axenizing Live Cyanobacterial Cultures For Bacterial Genome Sequencing, Yufei Wang, Louisa Acquah

SACAD: Scholarly Activities

Harmful cyanobacterial blooms are an

increasing concern in western Kansas, yet the

bloom-forming species in this region remain

poorly characterized. In this study, we

established and maintained axenic

cyanobacterial cultures to support future

genomic and ecological investigations. By

ensuring low contamination levels and stable

growth conditions, this work provides a

foundation for downstream analyses of bloom-

forming cyanobacteria. It contributes to a better

understanding of freshwater ecosystem health

in western Kansas.

Waters At Risk: Preventive Methods Against Cyanobacteria Blooms In Rhode Island, Ryan Boline

CAFE Symposium 2026

This project analyzes the rise of cyanobacteria blooms in Rhode Island freshwater systems and identifies a policy gap in the state’s largely reactive management approach. Drawing on state reports and interviews with environmental experts, it highlights nutrient runoff, climate change, and limited public education as key drivers of bloom severity. To address this gap, I developed a prevention-focused public education poster designed for integration into existing state alert and outreach systems.

Investigating The Influence Of Environmental Stressors To Exopolysaccharide Production In Soil Cyanobacteria: Genomic And Physiological Perspectives, Benjy Sedano-Herrera

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cyanobacteria are photosynthetic microbes with essential roles in Earth’s ecosystems. The secretion of long–chain polysaccharides, known as exopolysaccharides (EPS), is a key trait facilitating cyanobacterial adaptation to diverse ecosystems. Genomics studies have shown that aquatic cyanobacteria harbor multiple gene copies encoding EPS export proteins, likely conferring a selective advantage in lakes or oceans. In addition, physiological experiments showed that nutrient limitation in aquatic habitats influences EPS production, affecting cyanobacterial fitness. However, whether terrestrial cyanobacteria also harbor multiple EPS-related genes and how nutrient limitation impacts their EPS production is not well understood.In the first chapter of my thesis, we investigated the …

The Impact Of Maternal Age On The Expression Of Transgenerational Plasticity In Daphnia Pulicaria, Calvin Nguyen

2025 Spring Honors Capstone Projects - Archive

Transgenerational plasticity refers to heritable, non-genetic changes in phenotype that persist across multiple generations and can enhance offspring survivability in variable environments. In Daphnia, increasing maternal age has been associated with maladaptive plasticity. To investigate this relationship, six clones were collected from two Wisconsin lakes and acclimated to laboratory conditions through a common garden rearing process. For each clone, ten replicates were generated and evenly divided between young (clutches 2–4) and old (clutches 5–8) maternal age groups. Offspring were exposed to three dietary treatments for three experimental generations: one fed only green algae, one fed only cyanobacteria (a nutritionally …

Validation Of A Passive Sampler For Tracking Harmful Algal Toxins In Natural Waters, Hailee Eiker

Honors Theses

Algal blooms that produce toxins that are harmful to the health of people, animals, and the environment are known as harmful algal blooms (HABs). Recently, rising global temperatures, nutrient pollution, and an increase in the frequency of extreme hydrologic events have made HABs a bigger problem. This has all led to greater cultural eutrophication which is a major contributor to the spread of HABs. Cyanobacteria make up the bulk of HABs in freshwater systems, microcystins being among the cyanotoxins that are most frequently reported and studied. Taking grab samples of water is the current standard procedure for sampling cyanotoxins, however, …

Poor Water Quality As A Trigger Of Harmful Algal Blooms In Lake Manzala, Mohammed A. Hussein, Alaa Eldin Eissa, Reham M. Eltarabily, Mohamed F. Abdelghany, Mahmoud A. Elnakeeb, Eman M. Ismail, Reham H. Ragab, Amina A. Dessouki

Mansoura Veterinary Medical Journal

Objective: The current study aimed to assess the direct effects of poor water quality on the eruption of heavy harmful algal blooms and to assess the physicochemical properties of water in Lake Manzala, as well as the molecular identification of the retrieved green algae.

Procedures: Subsurface water samples were collected from three different sites in September 2023 for water quality assessment. Moreover, morphological and molecular identification of suspected harmful algae is the most reliable diagnostic tool for this eruption.

Results: This study was conducted in the northern and northeastern regions of Lake Manzala. These regions receive large amounts of municipal, …

Ascertaining A Biochemical Approach To Chlorophyll D Biosynthesis In Acaryochloris Spp., Rashmi Shivni

Graduate Research Theses & Dissertations

Photosynthesis is one of the most abundant metabolic systems on Earth, and specifically, oxygenic photosynthesis primed the planet for complex, multicellular life. The hallmark of modern oxygenic photosynthesis is the photopigment chlorophyll a found in nearly all oxygenic phototrophs as their primary photopigment in their photosynthesis pathways. There are also many organisms that tap into a variety of chlorophylls to extend the energetic limits of photosynthesis, which are largely found as accessory pigments. One genus of cyanobacteria, Acaryochloris, has garnered attention for the ability to undergo photosynthesis by harnessing the far-red part of the visible light spectrum using chlorophyll d …

The Response Of Microcystis And The Microbiome To Exogenous Hydrogen Peroxide, Bryan A. Puma

Masters Theses, 2020-current

Microcystis spp. produce prolific annual blooms in freshwater systems worldwide. The success of these blooms depends heavily on the Microcystis spp. overcoming environmental factors such as oxidative stress caused by reactive oxygen species (ROS) like hydrogen peroxide. Most Microcystis genomes do not contain many genes for responding to oxidative stress, including those that encode the enzyme catalase. Other cyanobacteria such as Prochlorococcus that also lack hydrogen peroxide degrading enzymes have been shown to benefit from partnerships with heterotrophic bacteria. Microcystis spp. may also receive similar benefits from heterotrophic bacteria in the phycosphere. To test this hypothesis, we examined the …

Effects Of Cyanobacteria Harmful Algal Blooms On The Microbial Community Within Lake Okeechobee, Fl, Usa, Paisley S. Samuel

All HCAS Student Capstones, Theses, and Dissertations

The Lake Okeechobee (Lake O) watershed is a Floridian freshwater ecosystem that has been affected by the increased frequency and intensity of harmful cyanobacterial bloom (cyanoHAB) events occurring over recent decades. Lake O has several ecological and economic purposes such as providing habitats for various organisms and providing drinking water to urban communities surrounding the lake. Toxic cyanoHAB events are posing a threat to the ecosystem and economy of the lake due to the degradation of water quality. This study investigates how the microbial community structure within Lake O is affected by annual cyanobacterial harmful algal blooms over several years …

Damped Oscillating Phosphoryl Transfer Reaction In The Cyanobacterial Circadian Clock, Hye In Jang, Pyonghwa Kim, Yongick Kim

Chemistry Faculty Research

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without “damping,” or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC’s two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported …

Investigating The Impacts Of Ammonium Phosphate-Based Fire Retardants On Cyanobacteria (Anabaena) Growth, Gavin Sutter, Brenda Gonzalez Flores, Grace Laskey, Shane Jurak

Humboldt Journal of Microbiology

In recent years the effects of climate change have taken a devastating toll on ecosystems around the world. With high temperatures and extreme droughts, wildfires have become increasingly common. In order to combat these natural disasters wildland firefighters, drop millions of gallons of fire retardant on public lands and forests. These fire retardants consist of between 80%-100% ammonium phosphate which are incredibly effective as fire suppressants yet is more commonly known for its use in fertilizer. Ammonium phosphate fertilizers can lead to stream eutrophication and undesirable environmental impacts. Our research aims to address the effects of fire retardant on growth …

Allelopathic Effect Of Cereal Straw Extracts On Growth Of Raphidocelis Subcapitata And Microcystis Aeruginosa, Holly Wren

Graduate Theses and Dissertations

Harmful algal blooms are increasing in size, duration, and intensity around the globe. For several decades, cereal straws have been recognized as a viable algal control method, though the mechanisms by which cereal straws inhibit algae remain a topic of research. The objectives of this study were to evaluate the effectiveness of decomposing cereal straw extract, particularly rice (Oryza sativa) and barley (Hordeum vulgare) straw extract, to inhibit the green alga Raphidocelis subcapitata or cyanobacteria Microcystis aeruginosa in bioassays and to determine if the effectiveness of decomposing rice straw extract is altered by the presence of natural organic matter or …

Nitrogen Fixation Rates In Forested Mountain Streams: Are Sediment Microbes More Important Than Previously Thought?, Erica A. H. Bakker, Carmella Vizza, Clay Arango, Sarah S. Roley

Biology Faculty Scholarship

1. Biological nitrogen (N) fixation, the microbial conversion of N₂ gas to ammonia, makes N available to food webs. Low-N streams often have a high relative abundance of N-fixing taxa, suggesting that N fixation is an important N source in these systems. Despite this potential, stream N fixation has not been well-characterised, particularly compared to lakes and marine environments. One unknown is the relative contributions of various N-fixing organisms, particularly heterotrophic microbes.
2. In low-N streams in the Cascade Mountains (Washington, USA), three groups of N-fixers predominate: cyanobacteria (Nostoc paramelioides) colonies that house a midge symbiont (Cricotopus spp.), …

Assessing Environmental Factors That Influence Cyanobacterial Blooms In Skinn Lake, Kloe Atwood

Honors Projects

Global lakes are experiencing an increase in toxic algal blooms that can be damaging to the environment. These blooms are caused by cyanobacteria, specifically a species called Planktothrix. Skinn Lake, in Ohio, is a location of a cyanobacterial bloom that is mainly populated by Planktothrix rubescens. This lake was further examined to identify the major toxin-producing bacteria and identify environmental microbes surrounding the bloom. When the data was examined it was found that the microbiomes of the lake greatly differed between the winter (bloom) months and the summer (non-bloom) months. This difference can be viewed within the nutrient analysis from …

An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont

Graduate Student Theses, Dissertations, & Professional Papers

Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …

Characterization And Quantification Of Far Red Oxygen Production Rates In Acaryochloris Spp., Jose Manuel Orench-Benvenutti

Graduate Research Theses & Dissertations

Oxygenic photosynthesis is one of the primary metabolisms on Earth responsible for the evolution of complex life. Its advent around the Archean steadily increased Earth’s atmospheric oxygen from negligible amounts to biologically impressive quantities. Atmospheric oxygen is the sole result of billions of years of biological oxygenation and no abiotic process can account for its high presence in the Earth’s atmosphere. Understanding its origins and evolution can lead us to better understand Earth’s biological history and the possibility of analogues elsewhere. A research path that could lead to answers is comparing distinct incorporations of photopigments in various oxygenic phototrophs. In …

Monitoring Photosynthetic Activity Using In Vivo Chlorophyll A Fluorescence In Microalgae And Cyanobacteria Biofilms In The Nerja Cave (Malaga, Spain), Yolanda Del Rosal, Juan Muñoz-Fernández, Paula S.M. Celis-Plá, Mariona Hernández-Mariné, Félix Álvarez-Gómez, Salvador Merino, Félix L. Figueroa

International Journal of Speleology

The characterization of the most common photosynthetic biofilms in the Nerja Cave by the continuous monitoring of the in vivo chlorophyll a (Chl a) fluorescence and the incorporation of the irradiance as a new environmental variable related to previous studies in the cave, have allowed us to improve our knowledge about the photosynthetic pattern of the biofilms of the cave. Effective quantum yield (ΔF/F_m′) and relative electron transport rate (rETR) were determined during periods of the light, whereas the maximal quantum yield (F_v /F_m) was determined during dark periods. Increases in …

Investigation Into Bacterial Impairment Of Greene And Polk County Water Systems, John C. Kincaid

Graduate Theses/Dissertations

Bacterial impairment of water systems is a major issue facing mankind. Bacteria that are introduced into a system have the potential to cause harmful diseases to wildlife and humans. In Greene and Polk counties, many water systems have become bacterially impaired over the years. Despite this, little is known about the contamination of known harmful bacteria in this region. To address this issue, I investigated the presence of known human pathogens across water systems in these two counties, many of which have displayed high levels of E. coli and fecal indicator microorganisms over many years. I used a high-throughput sequencing …

A Stable-Isotope Probing Approach To Modeling Bidirectional Nutrient Exchange In The Microcystis Phycosphere, Malia Gardner

Masters Theses, 2020-current

Cyanobacterial harmful algal blooms (cHABs) plague freshwater systems worldwide and are projected to increase in intensity in the coming decades. cHABs damage aquatic ecosystems by blocking light penetration into the water column, creating hypoxic conditions, and releasing toxins. One of the most prolific cHAB formers is the cosmopolitan genus of cyanobacteria Microcystis. Global climate change and anthropogenic loading of nutrients such as nitrogen (N) and phosphorus (P) fuel Microcystis bloom formation. Increasing global temperatures favor Microcystis because of its high optimal growth temperature. N input is of particular importance for Microcystis because it is unable to fix atmospheric N, …

Ecophysiology Of Toxic Bloom-Forming Cyanobacteria And Their Symbionts, Dominique J. Lockwood

Masters Theses, 2020-current

Currently, there is a pernicious microbe in the genus Microcystis that is putting the world’s freshwater resources at risk. A member of the phylum Cyanobacteria, otherwise referred to as blue-green algae, Microcystis forms massive algal blooms in lakes and has the potential to produce a toxin, which does not only harm humans, but also pets, livestock, and aquatic life. As recently as 2016, in the city of Toledo, Ohio, nearly 1 million residents went without clean drinking water for an entire weekend due to one of these Microcystis blooms. However, Microcystis does not only bloom in Ohio. In fact, …

Evaluation Of Nickel Stress On Anabaena Cylindrica, Danielle L. Maragh

Seton Hall University Dissertations and Theses (ETDs)

Heavy metal contamination due to anthropogenic activities has steadily been on the rise over the past few decades. Cyanobacteria can thrive in water bodies that have been contaminated by heavy metal runoffs and are able to tolerate heavy metal stress even in relatively high concentrations. Cyanobacterial species can secrete toxins which can prove harmful to humans and life stock. Due to their high adaptation to heavy metal stress, understanding the potential mechanism behind their response may lead to solutions in curbing excessive cyanobacterial growth especially in water bodies that serves as sources of drinking water. Anabaena spp. is a genus …

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R_rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …

Potential Virus-Mediated Nitrogen Cycling In Oxygen-Depleted Oceanic Waters, M. Consuelo Gazitúa, Dean R. Vik, Simon Roux, Ann C. Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven J. Hallam, Osvaldo Ulloa, Matthew B. Sullivan

OES Faculty Publications

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ …

Comparison Of Three Analytical Techniques For General Characterisation Of Selected Algae And Cyanobacteria, Mohamed Iqbal Suhaina Nashath

Student Works (2020-2029)

Algae and cyanobacteria maintain the oxygenation of earth, and are utilised as biofuels, biofertilizers and nutrition feed. The characterisation of algae and cyanobacteria through conventional methods require technical expertise, laborious sample preparation, and moderately expensive instruments and reagents. Hence, in this study, selected bioanalytical techniques with minimal sample preparation were incorporated, to simplify the characterisation of algae and cyanobacteria. The objectives of this research were to study the phylogenetic relationship of the selected algae and cyanobacteria via the 23S plastid ribosomal ribonucleic acid (rRNA) and 18S rRNA biomarkers; to validate the presence of the microcystin synthetase (mcy) gene cluster encoding …

Effect Of Zinc On Microcystis Aeruginosa And Its Toxin Production, Jose L. Perez

Seton Hall University Dissertations and Theses (ETDs)

Cyanobacteria harmful algal blooms (CHABs) are globally increasing biomasses of detrimental cyanobacteria due to anthropogenic water phosphorous and nitrogen loading and climate change. CHABs often produce secondary metabolites, cyanotoxins, that cause harmful effects to organisms, most water systems, and socioeconomic infrastructures. Additionally, the presence of heavy metal pollutant runoff in CHAB affected environments may result in CHAB population changes – aggravating toxigenicity. Zinc metal resistance and stress response were studied in microcystin (MC) cyanotoxin-producing Microcystis aeruginosa UTEX LB 2385 (M. aeruginosa UTEX LB 2385) and non-MC producing Microcystis aeruginosa UTEX LB 2386 (M. aeruginosa UTEX LB 2386) cyanobacteria. Molecular analysis …

Biogeographic Patterns In Members Of Globally Distributed And Dominant Taxa Found In Port Microbial Communities., Ryan B Ghannam, Laura G. Schaerer, Timothy M. Butler, Stephen M Techtmann

Michigan Tech Publications, Part 1

We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility …

Detection, Identification, And Metagenomic Characterization Of Cyanobacteria In Barnegat Bay, New Jersey, Roksana M. Rahman

Seton Hall University Dissertations and Theses (ETDs)

Cyanobacterial harmful algal blooms (CHAB), caused by eutrophication, is known to threaten both wildlife and human health. Barnegat Bay, also home to Oyster Creek nuclear power plant, has experienced an elevated levels of nitrogen due to human activity such as recreational activity and urbanization. This has caused an increase of CHAB’s at a more frequent rate within Barnegat Bay. In order to detect possible CHAB causing cyanobacteria, water samples were collected from 12 different locations within Barnegat Bay. Each sample was filtered through a 30- and 0.4-mm polycarbonate filter sequentially. Chelex DNA extraction, polymerase chain reaction (PCR), and gel electrophoresis …

Cyanobacterial And Algal Abundance And Biomass In Cave Biofilms And Relation To Environmental And Biofilm Parameters, Slađana Popović, Nataša Nikolić, Jelena Jovanović, Dragana Predojević, Ivana Trbojević, Ljiljana Manić, Gordana Subakov Simić

International Journal of Speleology

Due to life in extreme environments, cyanobacteria and algae from cave biofilms that form at the entrances or deep inside the cave around artificial lights are of increasing interest to many scientists. It is well-known that many phototrophic microorganisms are first to colonize exposed substrata and produce the organic matter on which other biofilm constituents relly. Many studies dealing with phototrophic microorganisms from biofilms focus on the diversity and community composition of cyanobacteria and algae, while quantitative assessments are rarely implemented. Biofilm sampling was conducted in Degurić and Vernjikica Cave located in Western and Eastern Serbia, respectively. Ecological parameters (temperature, …

The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann

Electronic Theses and Dissertations

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-n^th generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO₂ and N₂), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …

Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher

Graduate Student Theses, Dissertations, & Professional Papers

Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …