Biofilm communities host complex biogeochemical processes and play a role in the formation of many carbonate rocks by influencing both carbonate precipitation and dissolution. In this study, the biogeochemistry of microbial mats from a hypersaline pond and biofilm from a coral reef are described using SEM, microelectrode profiling, Biolog, fatty acid methyl ester (FAME) and carbon nitrogen analysis. Results show that the microbial mats are distinctly layered, having an oxic upper portion and an H2S-rich lower portion. The most significant conclusions are that the mats have exceptionally high TOC values and display significant differences in microbial communities present, both between layers and between cores. Additionally, organic matter is abundant in microbial mat and biofilm samples, but evidence of precipitation is surprisingly lacking.

Microbial mats have played an important role in the carbon (C) and nutrient cycles since the Archean Eon and modern mats are important contributors to the biogeochemistry of intertidal wetlands. Microbial mats are flat assemblages of microbes that are currently found in many unvegetated habitats globally. Intertidal salt pans are a common habitat for microbial mats, however little is known about the distribution of microbial mats within the intertidal landscape. Understanding the spatial distribution of microbial mats is critical to developing quantitative estimates of the impacts of microbial mats on their ecosystems. We photographically measured the presence and density of microbial mats within 1 m2 quadrats across a landscape scale (~1000 Ha) on the Gulf Coast of Florida. The wide variety of metabolic processes that are found within microbial mats makes the net biogeochemical impacts of the microbial mats highly variable as well. To explore the biogeochemistry associated with microbial mats, we measured a suite of soil attributes under microbial mats and compared those measurements to nearby soils without microbial mats. We found that microbial mats are found on soils with biogeochemical attributes that are significantly different than soils without microbial mats. Soil organic matter, nitrate concentration, and soil temperature significantly increased in soils under microbial mats; pH was significantly lower in soils under microbial mats. Also notable was although the concentration of soil organic matter was higher, the bioavailability of that organic matter was significantly lower. Microbial mat presence is correlated with geomorphic variables such as proximal boundaries, as well as neighboring vegetation and other microbial mats.

Unusual Fe-rich mineral formations were collected from the Calvert Cliffs area of Maryland. Surficial features such as wire-like filaments and columnar “chimneys” indicated a potential biological origin for the samples. Reference samples were collected from an Fe-rich acid mine drainage site near Carbondale, IL to serve as a comparison. The Chesapeake Bay samples were subjected to X-ray diffraction analysis, Scanning Electron Microscope-Electron Dispersive Spectroscopy analysis and Next-Generation Sequencing microbial assay. Minor ferrihydrite in the surficial wires and extensive microcrystalline goethite throughout the rest of the samples indicates a relatively recent origin. The small particle size and unusual microscale morphologies of iron (oxy)hydroxides and the presence of birnessite suggest that microbial metabolism was involved in the formation of these Fe minerals. EDS data indicate a strong relationship between Fe and C, as well as between Fe and P, while a lack of inorganic phosphate and carbonate minerals also indicates biological input. Genetic analysis reveals distinct internal and external microbial communities and the most common taxon within the sample interior was a novel bacterial phylum, indicating the mineralization may be a product of previously undescribed metabolic pathways. The presence of SO4- reducing, nitrogen-reducing and Fe-oxidizing bacteria as described by NGS analysis lends support to a microbially-mediated origin. Microbially driven oxidation of Fe and minor Mn into metal hydroxides is the proposed formation mechanism.

Microbial communities play critical roles in biogeochemical cycles of aquatic and terrestrial ecosystems, but studies of soil microbial communities have been limited by the diversity and complexity found in most ecosystems. Here we report on work investigating the functional diversity of microbial mat and underlying soil communities in the McMurdo Dry Valleys of Antarctica across a gradient of phosphorus availability on glacial tills of distinct age and mineral composition in Taylor Valley, Antarctica. Microbial mat and soil DNA were extracted and sequenced on an Illumina NextSeq500 in a 150 bp paired end format. Raw sequences were uploaded to the MG-RAST server for processing and annotation. Community taxonomic and functional annotation were determined using the RefSeq and SEED Subsystem databases, respectively. The results revealed significant variation in microbial mat community taxonomic composition between the two tills, strongly associated with visual assessment of mat morphology, e.g., "black" and "orange" mats, and soil N:P ratios. The underlying soil microbial communities did not exhibit significant differences in diversity between the two tills, but community composition varied significantly across gradients of soil chemistry, particularly extractable-phosphate content even within tills. The relative abundance of biogeochemistry-relevant pathways determined from the SEED database varied amongst soil microbial communities between the two tills. For example, microbial mat communities exhibited significant variation in the relative abundance of key nitrogen and phosphorus metabolism associated genes strongly associated with the underlying soil N:P. These results suggest that spatial variation in geochemistry influences the distribution and activity of microbial mats, but that the microbial mats themselves also exert a significant homogenizing effect on the underlying soil communities and some of the key biogeochemical processes they facilitate. / Master of Science / Microbial communities play critical roles in the processes of aquatic and terrestrial ecosystems. Still, studies of soil microbial communities have been limited by the complex nature of the ecosystems we study. This study examined the diversity of microbial communities in the McMurdo Dry Valleys of Antarctica, specifically looking at how different levels of phosphorus availability in the soil affected microbial function. We used DNA sequencing and databases to determine the taxonomic and functional makeup of these communities. We found that while the microbial mat communities varied significantly based on soil chemistry and appearance, the underlying soil microbial communities did not. We also found evidence suggesting that the microbial mats played a role in regulating some of the key ecosystem processes in the soil. Overall, this study sheds light on how microbial communities are impacted by their environment and how they, in turn, impact their surroundings.

Primary productivity is a fundamental ecological process and an important measure of ecosystem response to environmental change. Currently, there is a considerable lapse in our understanding of primary productivity in hot and cold deserts, due to the difficulty of measuring production in cryptogam vegetation. However, remote sensing can provide long-term, spatially-extensive estimates of primary production and are particularly well suited to remote environments, such as in the McMurdo Dry Valleys (MDV) of Antarctica, where cyanobacterial communities are the main drivers of primary production. These microbial communities form multi-layered sheets (i.e., microbial mats) on top of desert pavement. The cryptic nature of these communities, their often patchy spatial distribution, and their ability to survive desiccation make assessments of productivity challenging. I used field-based surveys of microbial mat biomass and pigment chemistry in conjunction with analyses of multispectral satellite data to examine the distribution and activity of microbial mats. This is the first satellite-derived estimate of microbial mat biomass for Antarctic microbial mat communities. I show strong correlations between multispectral satellite data (i.e., NDVI) and ground based measurements of microbial mats, including ground cover, biomass, and pigment chemistry. Elemental (C, N) and isotopic composition (15N, 13C) of microbial mats show that they have significant effects on biogeochemical cycling in the soil and sediment of this region where they occur. Using these relationships, I developed a statistical model that estimates biomass (kg of C) in selected wetlands in the Lake Fryxell Basin, Antarctica. Overall, this research demonstrates the importance of terrestrial microbial mats on C and N cycling in the McMurdo Dry Valleys, Antarctica. / Master of Science / Primary productivity is an essential ecological process and a useful measure of how ecosystems respond to climate change. Primary production is more difficult to measure in polar desert ecosystems where there is little to no vascular vegetation. Polar regions are also ecosystems where we expect to see significant responses to a changing climate. Remote sensing and image analysis can provide estimates of primary production and are particularly useful in remote environments. For example, in the McMurdo Dry Valleys (MDV) of Antarctica, cyanobacterial communities are the main primary producers. These microbial communities form multi-layered sheets (i.e., microbial mats) on top of rocks and soil. These communities are cryptic, do not cover large areas of ground continuously, and are able to survive desiccation and freezing. All of these characteristics make assessments of productivity especially challenging. For my master’s research, I collected microbial mat samples in conjunction with the acquisition of a satellite image of my study area in the MDV, and I determined biological parameters (e.g., percent ground cover, organic matter, and chlorophyll-a content) through laboratory analyses using these samples. I used this satellite image to extract spectral data and perform a vegetation analysis using the normalized difference vegetation index (i.e., NDVI), which determines areas in the image that contain vegetation (i.e., microbial mats). By linking the spectral data to the biological parameters, I developed a statistical model that estimates biomass (i.e., carbon content) of my study areas. These are the first microbial mat biomass estimates using satellite imagery for this region of Antarctica. Additionally, I researched the importance of microbial mats on nitrogen cycling in Taylor Valley. Using elemental and isotopic analyses, I determined microbial mats have significant effects on the underlying soil and nutrient cycling. Overall, this research demonstrates the importance of terrestrial microbial mats on C and N fixation in Antarctic soil environments.

Primary productivity is a fundamental ecosystem process driven by vascular plants in most terrestrial ecosystems and by microbes in more extreme ecosystems. In dense associations, microbial organisms can form visually conspicuous layers on sediment, soil, and rock surfaces, called microbial mats and biological soil crusts (i.e., biocrusts). Both microbial mats and biocrusts consist of cyanobacteria, moss, diatoms, and green algae, and also support diverse heterotrophic taxa. These communities exist in harsh environments worldwide such as hypersaline environments, tundra ecosystems, and hot and cold deserts where they are foundational taxa, providing most of the primary production and nitrogen fixation, as well as promoting cohesion and stability to soil surfaces. In the McMurdo Dry Valleys of Antarctica, microbial mats are the main source of fixed carbon in lentic and lotic environments, but their contribution to soil carbon and nitrogen cycling has not been systematically examined. In my dissertation, I investigated the relationships between microbial mats and the soil environments in which they occur. Using a combination of field surveys, soil analyses, and remote sensing, my objectives were to examine the influence of microbial mats and biocrusts on underlying soils and model the main drivers of their distribution and abundance. In Chapter 2, I investigated the relationships between underlying soil chemistry and microbial mat distribution, composition, and function in the Taylor Valley, finding that microbial mats enrich underlying soils, contributing to soil organic carbon and nitrogen. In Chapter 3, I assessed the spectral detectability of patchy biocrusts using multispectral satellite imagery to examine the environments in which biocrusts occur, finding that spectral unmixing of satellite imagery can successfully detect the presence of biocrust and its association with seasonal snow patches. As a direct continuation, in Chapter 4, I created a habitat suitability model using machine learning algorithms to determine the distribution and abundance of biocrusts in the Lake Fryxell basin. I found that biocrusts contribute a significant amount of carbon to the surface soil in the Lake Fryxell basin, with biocrust presence primarily driven by snow frequency, moisture content, and salinity. This dissertation contributes to ongoing questions about the sources of energy fueling soil food webs and regional carbon balance in the Taylor Valley, and how we can use remote sensing techniques for researching these critical soil communities in the dynamic Antarctic landscape. / Doctor of Philosophy / Photosynthesis is the process where plants and other organisms use sunlight to transform carbon dioxide into chemical energy. This is crucial because it provides the energy and nutrients that support all other life forms. In this dissertation, I focused on colonial microorganisms, which are the main primary producers in extreme environments, like deserts. I used a combination of field surveys and satellite imaging to study these organisms in the McMurdo Dry Valleys, Antarctica, which is a harsh polar desert environment that lacks vascular plants. Microbes colonize the surface of soil and form mm-cm thick microbial mats and biological soil crusts (called biocrusts). These organisms are found within the glacial-melt streams that flow on and off for only a few weeks each year, and they also occur on the stream margins and other periodically wet areas like near snow patches. This dissertation investigates the ecological importance of microbial mats and biocrusts, the ability to measure where they are using satellite imagery, and how much organic material they contribute to the broader landscape. Field work in the McMurdo Dry Valleys and laboratory analyses were required for each of these chapters. In Chapter 2, I investigated the relationships between microbial mats and the soils below them, and I found that microbial mats increase the organic matter and nutrient content in the soils. In Chapter 3, I assessed whether satellite imagery could be used to study the presence of sparse biocrusts and examined the environments in which biocrusts occur. I discovered that satellite imagery can successfully detect the presence of biocrust and that biocrusts occurred near melting snow patches. Lastly, in Chapter 4, I created models to determine where biocrusts occur in the Lake Fryxell basin and why biocrusts occur in those areas. I found that biocrusts occur over a significant area of the Lake Fryxell basin, containing a lot of organic material, and that biocrusts thrive in wet areas near snow patches where the soils are less salty. This dissertation contributes to ongoing questions about the sources of nutrients fueling soil food webs and contributing to the amount of organic material in the McMurdo Dry Valleys, and how we can use satellite imagery for monitoring these important soil communities in the changing Antarctic landscape.

The investigation presented in this thesis examined the microbial and functional diversity of the meltwater ponds Fresh, Orange and Salt Ponds on the McMurdo Ice Shelf, near Bratina Island, Antarctica. These sites were chosen because of the ecological importance and absence of detailed characterisations of their diversity and function as part of Antarctica?s largest wetland. Particular focus was on cyanobacterial diversity, nitrogen fixation and secondary metabolite production. Using 16S rRNA gene and morphological analysis a large diversity of cyanobacteria (more than 22 phylotypes) was identified with high phylogenetic similarities (up to 99% sequence identity) to cyanobacteria from mats in other regions of Antarctica. In addition biogeographical distributions were identified including potentially endemic and cosmopolitan cyanobacteria. High salinities were also connected to the change and reduction of diversity. Lipid marker analyses were performed targeting hydrocarbons, ether-linked hydrocarbons, methylated fatty acid esters (FAME), wax esters, hopanols and sterols. Lipid biomarker profiles were similar to typical cyanobacteria dominated mats with major input from microorganisms including oxygenic and anoxygenic phototrophs, obligate aerobic and anaerobic heterotrophs that conduct the metabolic processes of fermentation, sulphate reduction, sulphate and iron-oxidation, methanogeneses. Signature lipids indicative of Chloroflexus and archaea, as well as branched aliphatic alkanes with quaternary substituted carbon atoms (BAQCs), were identified for the first time in Fresh, Orange and Salt Ponds. Based on nifH gene analysis, the nitrogen fixing diversity characterised in Orange Pond consisted of cyanobacterial Nostoc sp. as well as firmicutes, beta-, gamma- and delta-proteobacteria. Acetylene reduction assays and nifH gene RNA transcript diversity identified Nostoc sp. as a main contributor of nitrogenase activity in these ponds. Furthermore, analytical methods were used to identify the cyanobacterial secondary metabolites microcystins, although the genetic basis for this production and the toxin producer could not been identified. However non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) genes were identified which could be the genetic basis for novel bioactives. The use of a multi-disciplinary approach synthesis and subsequent results significantly increased our understanding of the diversity and function of microbial mat communities in the unique meltwater ponds of the McMurdo Ice shelf, Antarctica.

Biofilme sind eine der widerstandsfähigsten Formen mikrobiellen Lebens. Ihr frühzeitiges Auftreten in der Erdgeschichte konnte durch Stromatolithfunde bewiesen werden. Heutige Biofilme und mikrobielle Matten bieten somit eine Möglichkeit wichtige Einblicke und Erkenntnisse über das erste Leben auf unserem Planeten zu geben. In dieser Arbeit wurden die prokaryotischen Lebensgemeinschaften von verschiedenen Ökosystemen mittels metagenomischer und metatranskriptomischer Methoden analysiert. Mithilfe von „Next-Generation Sequencing“ wurden 16S rRNA Genanalysen, metatranskriptomische Analysen und funktionsbasierte Durchmusterungen von Fosmid-Metagenombanken durchgeführt. Die bakterielle Zusammensetzung und Diversität von kalzifizierenden Biofilmen und dem unterliegenden Kalktuff des Frischwasserbachs Westerhöfer Bach wurden analysiert. Es konnte gezeigt werden, dass der Biofilm hauptsächlich von filamentösen Cyanobacteria, aeroben Vertretern aus allen Klassen der Proteobacteria und Chloroflexi bevölkert wurde. Die bakterielle Diversität nahm flussabwärts zu, was auf Änderungen der physikochemischen Parameter zurückgeführt wird. Aufgrund geringerer UV-Einstrahlung waren im Kalktuff mehr Proteobacteria als Cyanobacteria vorhanden. Des Weiteren gab es deutliche Unterschiede zwischen den relativen Abundanzen der gesamten und aktiven proteobakteriellen Klassen im Biofilm. Die aktiven Funktionen der Biofilm-Mikrobiota einer Westerhöfer Bach Probe wurden mittels metatranskriptomischer Methoden genauer analysiert. Die meisten Transkripte der mikrobiellen Biofilmgemeinschaft umfassten Gene der Photosynthese, des Proteinmetabolismus, des Kohlenstoffmetabolismus und der Zellatmung. Um das metagenomische Potential des Westerhöfer Bach Biofilms zu erschließen, wurden vier „large-insert“ Metagenombanken konstruiert. Funktionsbasierende Durchmusterungsverfahren führten zur Identifikation von fünf bisher unbekannten Genen, die für proteolytische Enzyme kodieren und einem Gen-Cluster, welches für cellulolytische Enzyme kodiert. Bei dem zweiten untersuchten Habitat handelt es sich um eine mikrobielle Matte des hypersalinen Lake 21 auf Kiritimati. Die Mikrobialith-bildende Matte besteht aus neun klar abgegrenzten, unterschiedlich gefärbten Lagen, welche separat auf ihre bakterielle und archaelle Zusammensetzung analysiert wurden. Anhand der prokaryotischen Zusammensetzung und dem Sauerstoff- und Lichtgradienten ergab sich eine Einteilung der mikrobiellen Matte in drei Zonen. Im Allgemeinen erhöhte sich die prokaryotische Diversität mit Tiefe der Matte, wohingegen das Redoxpotential und der pH-Wert sanken. Passend zu den hydrochemischen Daten änderte sich die prokaryotische Zusammensetzung von der photisch-oxischen Zone, welche aus halophilen, oxygenen und anoxygenen Phototrophen und aeroben Heterotrophen bestand, zu Sulfat-reduzierenden Bakterien (SRB), Fermentierern und potentiell Sulfat-reduzierenden Archaeen in der Übergangszone. In der anoxischen Zone konnten hauptsächlich SRB, Fermentierer, Ammonium-oxidierende Archaea und geringe Mengen methanogene Archaeen detektiert werden. Von den kenianischen Natronseen Bogoria, Sonachi, Elementeita und Magadi wurde die prokaryotische Zusammensetzung und Diversität von Boden-, Sediment-, Wasser-, und mikrobiellen Mattenproben analysiert. Hier zeigte sich, dass Boden- sowie Sedimentproben hauptsächlich von Proteobacteria, Gemmatimonadetes, Firmicutes, Actinobacteria, Acidobacteria und Bacteroidetes bevölkert wurden, wohingegen in den Wasserproben Cyanobacteria vorherrschten. Die Archaeen wurden überwiegend von unterschiedlichen Vertretern der Halobacteria repräsentiert. In den humiden Proben wurden außerdem methanogene Archaeen und Thaumarchaeota nachgewiesen. Letztlich wurde in dieser Arbeit die bakterielle Zusammensetzung des Biofilms und des dazugehörigen Planktons von mikrobiellen Brennstoffzellen (MBZ) untersucht. Der erzeugte Datensatz demonstrierte, dass die aktive und gesamte bakterielle Lebensgemeinschaft in den einzelnen Replikaten minimal variierte. Generell zeigte sich, dass stromproduzierende MBZ eine niedrigere bakterielle Diversität aufwiesen als nicht stromproduzierende MBZ. Des Weiteren zeigte die Analyse, dass bisher unkultivierte Vertreter der Spezies Geobacter und Clostridium mit der Stromproduktion verbunden waren.

The investigation presented in this thesis examined the microbial and functional diversity of the meltwater ponds Fresh, Orange and Salt Ponds on the McMurdo Ice Shelf, near Bratina Island, Antarctica. These sites were chosen because of the ecological importance and absence of detailed characterisations of their diversity and function as part of Antarctica?s largest wetland. Particular focus was on cyanobacterial diversity, nitrogen fixation and secondary metabolite production. Using 16S rRNA gene and morphological analysis a large diversity of cyanobacteria (more than 22 phylotypes) was identified with high phylogenetic similarities (up to 99% sequence identity) to cyanobacteria from mats in other regions of Antarctica. In addition biogeographical distributions were identified including potentially endemic and cosmopolitan cyanobacteria. High salinities were also connected to the change and reduction of diversity. Lipid marker analyses were performed targeting hydrocarbons, ether-linked hydrocarbons, methylated fatty acid esters (FAME), wax esters, hopanols and sterols. Lipid biomarker profiles were similar to typical cyanobacteria dominated mats with major input from microorganisms including oxygenic and anoxygenic phototrophs, obligate aerobic and anaerobic heterotrophs that conduct the metabolic processes of fermentation, sulphate reduction, sulphate and iron-oxidation, methanogeneses. Signature lipids indicative of Chloroflexus and archaea, as well as branched aliphatic alkanes with quaternary substituted carbon atoms (BAQCs), were identified for the first time in Fresh, Orange and Salt Ponds. Based on nifH gene analysis, the nitrogen fixing diversity characterised in Orange Pond consisted of cyanobacterial Nostoc sp. as well as firmicutes, beta-, gamma- and delta-proteobacteria. Acetylene reduction assays and nifH gene RNA transcript diversity identified Nostoc sp. as a main contributor of nitrogenase activity in these ponds. Furthermore, analytical methods were used to identify the cyanobacterial secondary metabolites microcystins, although the genetic basis for this production and the toxin producer could not been identified. However non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) genes were identified which could be the genetic basis for novel bioactives. The use of a multi-disciplinary approach synthesis and subsequent results significantly increased our understanding of the diversity and function of microbial mat communities in the unique meltwater ponds of the McMurdo Ice shelf, Antarctica.

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