I3 Symposium - TOPICS

Topics

1. Geomicrobiology – Understanding Processes that Shape a Planet
Pieter.T. Visscher, Center for Integrative Geosciences, University of Connecticut, Storrs, CT.

Although Geomicrobiology is an emerging field at the intersection of geosciences and biosciences, its prime focus involves interactions between microbes and the planet they inhabit on geological timescales. These interactions are processes, which have persisted for over 3.5 billion years, and therefore do not quite fill an “emerging role”, as the title of this symposium suggest. However, our understanding and appreciation of geomicrobiological processes as define here, is novel and continues to shed light on the critical role microbes play in planetary evolution. Microbial mats are the quintessential ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to the beginning of life on Earth, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-mm) scales. The activity of the mat communities has changed the geochemical conditions on micro- and macro-scales: On a sub-mm scale within the mat ecosystem, this has resulted in the formation of resilient biofilms, at the scale of Earth as a planet this has led to a major shift in redox conditions, the consequences of which are well-known.The interpretation of fossil microbial mats and their potential role in the alteration of the geochemical environment is challenging because of the poor preservation of these organic-rich mats. However, the preservation of microbial mats in the fossil record can be enhanced through lithification. Carbonate precipitation mediated by microbial processes is one of the most important mechanisms, which increases the conservation potential. Key components of the microbially-mediated mineralization process are the “alkalinity” engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and the organic matrix comprised of exopolymeric substances (EPS). In this presentation, a brief review of the different types of biologically-mediated mineralization will be followed by a detailed discussion of organomineralization sensu lato, focusing on the specific role of microbes and the EPS matrix in carbonate mineral formation. Examples of modern aquatic (freshwater, marine and hypersaline) microbialites will be discussed.

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2. The microbial role in herbivory: the case of the avian hoatzin
Maria Gloria Dominguez-Bello, Department of Biology, University of Puerto Rico, Rio Piedras

The hoatzin is unique among known avian species by virtue of its strict herbivory and the fermentative function of its crop. As such, it provides an interesting model to test the role of diet in shaping the structure of a gut microbial community. Therefore we characterized the crop microbiota in 6 adult hoatzins captured from the wild. Novelty in this ecosystem is great: a total of 1,235 bacterial 16S rRNA sequences were assigned to nine phyla grouped into 580 phylotypes, 94% of which were unclassified. UniFrac-based analysis indicate that the hoatzin crop microbiota is closer to the cow rumen than to the chicken gut but it does not contain common known cellulolytic bacterial lineages.

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3. Microbes are the Best Chemists in the World: Making a Living on Arsenic
Lily. Y Young, Department of Environmental Sciences, Cook College, at Rutgers, the State University of New Jersey, New Brunswick, NJ.

Bacteria catalyze a variety of chemical reactions in response to hazardous metals in their environment which can result in volatilization, precipitation or solubilization of the metal. They are the only life forms on earth that obtain energy for growth from oxidation or reduction of various metal species including iron, manganese mercury, arsenic and selenium. Arsenic is a toxic element found in groundwaters in different parts of the world (Bangladesh, Taiwan) including New Jersey. Human exposure is typically from contaminated drinking water and regulated levels in the U.S. recently have been reduced from 50 ppb to 10 ppb by the EPA. We demonstrate that a diversity of naturally occurring microbes in the environment are able to reduce As(V) in place of oxygen as a respiratory electron acceptor, and others are able to oxidize As(III) for energy for autotrophic carbon fixation. From our results we propose that a microbial arsenic cycle may be important to understanding the fate and transport of arsenic in environmental habitats. We also have evidence that these microbially mediated reactions can release arsenic from mineral formations and can serve as a mechanism for mobilization of arsenic into groundwater.

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4. Fungi in salterns and glaciers – a new world of eukaryotic extremophile
Nina Gunde – Cimerman, Department of Biology, University of Ljubljana, Ljubljana, Slovenia

Extreme environments have been over the last two decades thoroughly investigated for the presence of microorganisms. However, all these studies were almost entirely dedicated to Bacteria and Archaea, while fungi, one of the environmentally most successful eukaryotic lineages, remained mainly unknown. This lack of attention is surprising, since fungi are able to colonize food preserved with extreme concentrations of sugar, salt, acids, low water activity, etc. and can be thus expected also in natural extreme environments. Recent investigations have discovered a surprisingly rich diversity of extremophilic fungi in hypersaline waters of solar salterns. The initial studies have been conducted at the Adriatic salterns Sečovlje, situated at the Adriatic coast, on the border between Slovenia and Croatia. The salterns originate from the 13^th century and have remained since that time almost unchanged. Studies have been later extended to salterns on three continents and later also to the Arctic polar glaciers, which due to the freezing of water into ice, also represent extreme environments with little biologically available water. An overview of halophilic and halotolerant fungal diversity in hypersaline waters and polar ice will be presented. Many studies exist on the adaptations of prokaryotic microorganisms to life at high salt concentrations, while information on eukaryotic microbes were limited to mechanisms employed by the halophilic alga Dunaliella salina. Recently discovered halophilic fungi represent appropriate eukaryotic models for in depth studies of adaptation to extreme physicochemical conditions. Three model species will be compared. The ubiquitous halotolerant black yeast Aureobasidum pullulans, the halophilic black yeast Hortaea werneckii, as the dominant fungal inhabitant in the salterns, able to adapt to a wide range of NaCl concentrations and the most halophilic eukaryote known to date, the basidiomycetous fungus Wallemia ichtyophaga. The model organisms will be compared on the level of membranes, cell walls, osmolytes and ion regulation.

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5. Roles of decomposer fungi in wet tropical forests, and potential effects of climate change.
Lodge, D. Jean. Center for Forest Mycology Research, USDA-Forest Service, NRS, PO Box 1377, Luquillo PR 00773-1377.

Fungi are important in wet tropical forests in Puerto Rico as they are the primary agents in decomposition of leaf litter and wood on the forest floor. Decomposer fungi exhibit specialization in substratum type, and size, and some are restricted to high elevation. Furthermore, microfungi (mostly asexual states of ascomycetes) and many leaf-inhabiting species of Xylaria (Ascomycetes) show ‘preferences’ for particular leaf litter based on host family or genus (probably secondary plant compounds) and quality (i.e., nutrient and lignin content, leaf thickness). In a study using the particle filtration culturing method to obtain abundances actively growing mycelia, >60% of the microfungi were differentially abundant in one of the leaf species occurring together on the forest floor. The importance of such ‘preferences’ to rates of mass loss was investigated using irradiated litter of five species decomposed individually with vegetatively dominant fungi from the five leaf species (two fungal representatives per leaf species), in all possible fungus-substratum combinations. Matching the microfungi to their substrata increased rates of mass loss, whether matched by plant phylogenetic relatedness or by leaf quality, as compared to complete mismatches. However, a basidiomycete contaminant in some microcosms of one of the leaf species had a stronger effect on decomposition, and accelerated mass loss by 22% above that by microfungi. The effect of the basidiomycete was additive, and complemented the activity of microfungi. Field experiments with high versus low abundance of white-rot caused fungi showed a similar acceleration of mass loss by basidiomycetes. Litter mats formed by basidiomycete fungi were shown to be important in retaining leaf litter on steep slopes, thereby reducing losses from the ecosystem via erosion. Basidiomycete mats were most abundant at low elevation and on steep slopes. Global and regional climate changes may increase the frequency of hurricanes in the Caribbean. An experiment to determine effects of increased frequency of hurricanes showed that while canopy opening inhibited activity of lignin-degrading basidiomycetes in the litter layer, the thick layer of green hurricane debris protected the litter below from the drying effects of canopy opening, thus maintaining moisture and high rates of decomposition

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6. Searching for “prospects” in the environment: Unraveling activities with Applications in Microbial Biotechnology.
Carlos Ríos Velazquez, Department of Biology, University of Puerto Rico, Mayagüez, PR

The need of specific activities to solve biological problems requires the use of several approaches at different levels to search and unravel processes and microbial groups (prospects) which can also be used as study models. In order to begin such search, culture dependent and independent methods and several functional genomics and proteomics strategies have been developed. We will present what we have done, and the strategies we are currently using to isolate, and characterize microbes with potential application in Biotechnology. Also, educational strategies used to bring this knowledge to the K-12, and college student will be also presented.

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	Topics 1. Geomicrobiology – Understanding Processes that Shape a Planet Pieter.T. Visscher, Center for Integrative Geosciences, University of Connecticut, Storrs, CT. Although Geomicrobiology is an emerging field at the intersection of geosciences and biosciences, its prime focus involves interactions between microbes and the planet they inhabit on geological timescales. These interactions are processes, which have persisted for over 3.5 billion years, and therefore do not quite fill an “emerging role”, as the title of this symposium suggest. However, our understanding and appreciation of geomicrobiological processes as define here, is novel and continues to shed light on the critical role microbes play in planetary evolution. Microbial mats are the quintessential ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to the beginning of life on Earth, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-mm) scales. The activity of the mat communities has changed the geochemical conditions on micro- and macro-scales: On a sub-mm scale within the mat ecosystem, this has resulted in the formation of resilient biofilms, at the scale of Earth as a planet this has led to a major shift in redox conditions, the consequences of which are well-known.The interpretation of fossil microbial mats and their potential role in the alteration of the geochemical environment is challenging because of the poor preservation of these organic-rich mats. However, the preservation of microbial mats in the fossil record can be enhanced through lithification. Carbonate precipitation mediated by microbial processes is one of the most important mechanisms, which increases the conservation potential. Key components of the microbially-mediated mineralization process are the “alkalinity” engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and the organic matrix comprised of exopolymeric substances (EPS). In this presentation, a brief review of the different types of biologically-mediated mineralization will be followed by a detailed discussion of organomineralization sensu lato, focusing on the specific role of microbes and the EPS matrix in carbonate mineral formation. Examples of modern aquatic (freshwater, marine and hypersaline) microbialites will be discussed. Up 2. The microbial role in herbivory: the case of the avian hoatzin Maria Gloria Dominguez-Bello, Department of Biology, University of Puerto Rico, Rio Piedras The hoatzin is unique among known avian species by virtue of its strict herbivory and the fermentative function of its crop. As such, it provides an interesting model to test the role of diet in shaping the structure of a gut microbial community. Therefore we characterized the crop microbiota in 6 adult hoatzins captured from the wild. Novelty in this ecosystem is great: a total of 1,235 bacterial 16S rRNA sequences were assigned to nine phyla grouped into 580 phylotypes, 94% of which were unclassified. UniFrac-based analysis indicate that the hoatzin crop microbiota is closer to the cow rumen than to the chicken gut but it does not contain common known cellulolytic bacterial lineages. Up 3. Microbes are the Best Chemists in the World: Making a Living on Arsenic Lily. Y Young, Department of Environmental Sciences, Cook College, at Rutgers, the State University of New Jersey, New Brunswick, NJ. Bacteria catalyze a variety of chemical reactions in response to hazardous metals in their environment which can result in volatilization, precipitation or solubilization of the metal. They are the only life forms on earth that obtain energy for growth from oxidation or reduction of various metal species including iron, manganese mercury, arsenic and selenium. Arsenic is a toxic element found in groundwaters in different parts of the world (Bangladesh, Taiwan) including New Jersey. Human exposure is typically from contaminated drinking water and regulated levels in the U.S. recently have been reduced from 50 ppb to 10 ppb by the EPA. We demonstrate that a diversity of naturally occurring microbes in the environment are able to reduce As(V) in place of oxygen as a respiratory electron acceptor, and others are able to oxidize As(III) for energy for autotrophic carbon fixation. From our results we propose that a microbial arsenic cycle may be important to understanding the fate and transport of arsenic in environmental habitats. We also have evidence that these microbially mediated reactions can release arsenic from mineral formations and can serve as a mechanism for mobilization of arsenic into groundwater. Up 4. Fungi in salterns and glaciers – a new world of eukaryotic extremophile Nina Gunde – Cimerman, Department of Biology, University of Ljubljana, Ljubljana, Slovenia Extreme environments have been over the last two decades thoroughly investigated for the presence of microorganisms. However, all these studies were almost entirely dedicated to Bacteria and Archaea, while fungi, one of the environmentally most successful eukaryotic lineages, remained mainly unknown. This lack of attention is surprising, since fungi are able to colonize food preserved with extreme concentrations of sugar, salt, acids, low water activity, etc. and can be thus expected also in natural extreme environments. Recent investigations have discovered a surprisingly rich diversity of extremophilic fungi in hypersaline waters of solar salterns. The initial studies have been conducted at the Adriatic salterns Sečovlje, situated at the Adriatic coast, on the border between Slovenia and Croatia. The salterns originate from the 13^th century and have remained since that time almost unchanged. Studies have been later extended to salterns on three continents and later also to the Arctic polar glaciers, which due to the freezing of water into ice, also represent extreme environments with little biologically available water. An overview of halophilic and halotolerant fungal diversity in hypersaline waters and polar ice will be presented. Many studies exist on the adaptations of prokaryotic microorganisms to life at high salt concentrations, while information on eukaryotic microbes were limited to mechanisms employed by the halophilic alga Dunaliella salina. Recently discovered halophilic fungi represent appropriate eukaryotic models for in depth studies of adaptation to extreme physicochemical conditions. Three model species will be compared. The ubiquitous halotolerant black yeast Aureobasidum pullulans, the halophilic black yeast Hortaea werneckii, as the dominant fungal inhabitant in the salterns, able to adapt to a wide range of NaCl concentrations and the most halophilic eukaryote known to date, the basidiomycetous fungus Wallemia ichtyophaga. The model organisms will be compared on the level of membranes, cell walls, osmolytes and ion regulation. Up 5. Roles of decomposer fungi in wet tropical forests, and potential effects of climate change. Lodge, D. Jean. Center for Forest Mycology Research, USDA-Forest Service, NRS, PO Box 1377, Luquillo PR 00773-1377. Fungi are important in wet tropical forests in Puerto Rico as they are the primary agents in decomposition of leaf litter and wood on the forest floor. Decomposer fungi exhibit specialization in substratum type, and size, and some are restricted to high elevation. Furthermore, microfungi (mostly asexual states of ascomycetes) and many leaf-inhabiting species of Xylaria (Ascomycetes) show ‘preferences’ for particular leaf litter based on host family or genus (probably secondary plant compounds) and quality (i.e., nutrient and lignin content, leaf thickness). In a study using the particle filtration culturing method to obtain abundances actively growing mycelia, >60% of the microfungi were differentially abundant in one of the leaf species occurring together on the forest floor. The importance of such ‘preferences’ to rates of mass loss was investigated using irradiated litter of five species decomposed individually with vegetatively dominant fungi from the five leaf species (two fungal representatives per leaf species), in all possible fungus-substratum combinations. Matching the microfungi to their substrata increased rates of mass loss, whether matched by plant phylogenetic relatedness or by leaf quality, as compared to complete mismatches. However, a basidiomycete contaminant in some microcosms of one of the leaf species had a stronger effect on decomposition, and accelerated mass loss by 22% above that by microfungi. The effect of the basidiomycete was additive, and complemented the activity of microfungi. Field experiments with high versus low abundance of white-rot caused fungi showed a similar acceleration of mass loss by basidiomycetes. Litter mats formed by basidiomycete fungi were shown to be important in retaining leaf litter on steep slopes, thereby reducing losses from the ecosystem via erosion. Basidiomycete mats were most abundant at low elevation and on steep slopes. Global and regional climate changes may increase the frequency of hurricanes in the Caribbean. An experiment to determine effects of increased frequency of hurricanes showed that while canopy opening inhibited activity of lignin-degrading basidiomycetes in the litter layer, the thick layer of green hurricane debris protected the litter below from the drying effects of canopy opening, thus maintaining moisture and high rates of decomposition Up 6. Searching for “prospects” in the environment: Unraveling activities with Applications in Microbial Biotechnology. Carlos Ríos Velazquez, Department of Biology, University of Puerto Rico, Mayagüez, PR The need of specific activities to solve biological problems requires the use of several approaches at different levels to search and unravel processes and microbial groups (prospects) which can also be used as study models. In order to begin such search, culture dependent and independent methods and several functional genomics and proteomics strategies have been developed. We will present what we have done, and the strategies we are currently using to isolate, and characterize microbes with potential application in Biotechnology. Also, educational strategies used to bring this knowledge to the K-12, and college student will be also presented. Up Previous