Download or read book Bacterial Diversity and Function Within an Epigenic Cave System and Implications for Other Limestone Cave Systems written by Kathleen Merritt Brannen-Donnelly and published by . This book was released on 2015 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are approximately 48,000 known cave systems in the United States of America, with caves formed in carbonate karst terrains being the most common. Epigenic systems develop from the downward flow of meteoric water through carbonate bedrock and the solutional enlargement of interconnected subsurface conduits. Despite carbonate karst aquifers being globally extensive and important drinking water sources, microbial diversity and function are poorly understood compared to other Earth environments. After several decades of research, studies have shown that microorganisms in caves affect water quality, rates of carbonate dissolution and precipitation, and ecosystem nutrition through organic matter cycling. However, limited prior knowledge exists for the most common system, epigenic caves, regarding microbial taxonomic diversity, their metabolic capabilities, and how community function changes during and following environmental disturbances. To evaluate community development and succession, as well as potential roles in organic matter cycling, bacteria from the Cascade Cave System (CCS) in Kentucky were investigated. From geochemical and metagenomic data collected during a five-month colonization experiment, taxonomically distinct planktonic and sediment-attached bacterial communities formed along the epigenic cave stream. This represents one of the largest metagenomic studies done from any cave. Betaproteobacteria, Gammaproteobacteria, Alphaproteobacteria, and Opitutae were the most abundant groups. Planktonic bacteria pioneered sediment-attached communities, likely attributed to functional differences related to cell motility and attachment. Organic matter cycling affected exogenous heterotrophic community composition and function downstream because of diminished organic matter quality over time. This was reflected in significantly different abundances of genes encoding for carbohydrate and lignin degradation between habitats and depending on cave location. The ubiquity of environmental controls on bacteria functional diversity in karst is unknown because these environments have generally been left out of microbial biogeography research. In spatial meta-analyses of bacterial diversity data from global cave systems, the ubiquity of some bacteria in karst is evident. Despite evidence for undersampling and difficulties comparing sequencing technologies and strategies, some caves appear to have novel lineages while other caves have taxonomically similar communities despite being 1000s of kilometers apart. The implications are that microbes in karst (i.e., carbonate) caves around the world are functionally comparable.

Download or read book Microbial Life of Cave Systems written by Annette Summers Engel and published by Walter de Gruyter GmbH & Co KG. This book was released on 2015-10-16 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: The earth's subsurface contains abundant and active microbial biomass, living in water, occupying pore space, and colonizing mineral and rock surfaces. Caves are one type of subsurface habitat, being natural, solutionally- or collapse-enlarged openings in rock. Within the past 30 years, there has been an increase in the number of microbiology studies from cave environments to understand cave ecology, cave geology, and even the origins of life. By emphasizing the microbial life of caves, and the ecological processes and geological consequences attributed to microbes, this book provides the first authoritative and comprehensive account of the microbial life of caves for students, professionals, and general readers.

Download or read book Microbial Life of Cave Systems written by Annette Summers Engel and published by Walter de Gruyter GmbH & Co KG. This book was released on 2015-10-16 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The earth's subsurface contains abundant and active microbial biomass, living in water, occupying pore space, and colonizing mineral and rock surfaces. Caves are one type of subsurface habitat, being natural, solutionally- or collapse-enlarged openings in rock. Within the past 30 years, there has been an increase in the number of microbiology studies from cave environments to understand cave ecology, cave geology, and even the origins of life. By emphasizing the microbial life of caves, and the ecological processes and geological consequences attributed to microbes, this book provides the first authoritative and comprehensive account of the microbial life of caves for students, professionals, and general readers.

Download or read book Microbial Roles in Caves written by Valme Jurado and published by Frontiers Media SA. This book was released on 2024-07-17 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Caves are dark, underground hollow spaces with relatively constant temperature, high humidity, and limited nutrients. Many caves are associated with karst topography, which is formed by the dissolution of soluble bedrock, such as limestone, dolomite and gypsum, in areas where groundwaters are undersaturated with respect to the minerals in the host rock. Karst landforms spread widely, accounting for approximately 20% of the earth’s dry ice-free surface (Ford and Williams, 2007). As a typical feature of subsurface landscape, karst caves develop globally, with over 50,000 distributed in the United States (Barton and Jurado, 2007). China also has a large contiguous karst terrain, and the Yunnan–Guizhou plateau in the southwest developed most karst caves, among which the longest cave exceeds 138 km (Zhang and Zhu, 2012). Many caves are relatively shallow and form near the water table in karst terranes, although some caves develop by deep-seated hypogenic process at substantial depths and by process other than dissolution such as lava flows. Caves are oligotrophic ecosystems with less than 2 mg of total organic carbon per liter, yet host flourishing microbial groups (Figure 1A), with an average number of 106 microbial cells per gram of cave rock (Barton and Jurado, 2007). The study revealed a high diversity within Bacteria domain and Proteobacteria and Actinobacteria were abundant in oligotrophic cave samples of air, rock, sediment and water. Chloroflexi, Planctomycetes, Bacteroidetes, Firmicutes, Acidobacteria, Nitrospirae, Gemmatimonadetes, and Verrucomicrobia also accounted for large proportions of the total microbial community in caves (Wu et al., 2015; Zhu et al., 2019). In some organic cave samples such as biofilms in sulfur cave, bat guanos, spiders’ webs and earthworm castings, Mycobacterium was prevalently detected (Modra et al., 2017; Sarbu et al., 2018; Hubelova et al., 2021; Pavlik et al., 2021). Over 500 genera of fungi, such as Penicillium, Aspergillus and Mortierella have been reported in caves (Vanderwolf et al., 2013), and new fungal species were identified from cave air, rock, sediment and water samples (Zhang et al., 2017, 2021). These microbial communities contain novel diversity, and promote important biogeochemical processes. With no sunlight, microorganisms in cave environment cannot perform photosynthesis, and are intensively involved in the biogeochemical cycles of carbon, nitrogen, sulfur, and metals such as Fe and Mn to offset the lack of exogenous nutrients and energy.

Download or read book The Impact of Carbon Availability and Geochemical Variation on Habitability of Epigenic Cave Systems written by Michael E. Cyrier and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Caves are unique environments that can support ecosystems largely independent of photosynthetic primary production and are heavily influence by the geochemistry of the geologic units they are formed within. This study investigated five epigenic cave systems in the Black Hills of South Dakota—Rushmore Cave, Bethlehem Cave, Stagebarn Cave, Dahm Springs Cave, and Brooks Cave—with the goal of delimiting microbial habitability. Habitability, defined as the potential for life to thrive or survive, was determined by examining the physical, biological, and geochemical composition of waters and sediments within these five caves. Microbial (aerobic) respiration rates and DNA concentrations in cave sediments were used to define biological activity. Microbial respiration rates within sediments were found to strongly correlate with organic carbon content (p-value = 0.004) through Spearman Rho tests but did not significantly correlate with DNA concentration. The correlation between microbial respiration rate and organic carbon content can be attributed to heterotrophic activity. However, for chemoautotrophic bacteria in caves to gain energy though biomineralization of CaCO3 from inorganic carbon, cave waters should be supersaturated with respect to CaCO3. Every pool that was sampled in this study was supersaturated with respect to calcite and aragonite, increasing the potential habitability for chemoautotrophs. Trace metal data also provide important constraints on active metabolisms potentially in each cave, such as ions with a valency of +2 (i.e., Fe2+, Mn2+, Ba2+, and Sr2+) and the precipitation of metal-bound carbonate minerals siderite (FeCO3), rhodochrosite (MnCO3), witherite (BaCO3), and strontianite (SrCO3). Using non-metric multidimensional scaling, each cave was found to have distinct geochemistry despite occurring in the same geologic unit, the Pahasapa Formation. Some of the most important distinguishing parameters of the caves were sediment organic and inorganic carbon content, dissolved organic (TOC) and inorganic (TIC) carbon in pool water, air CO2 concentration, and various dissolved ion concentrations. Distance between caves did not play a major role in subsurface environmental variability. Surface sediment chemistry and microbial activity above each cave did not correlate with subsurface sediments within each cave. Tourism, however, was found to heavily impact the cave environment in Rushmore Cave through an increased CO2 concentration from visitor respiration, introduction of dissolved metals from pollutants (coins) in pools, and elevated NO3-. The results of this study provide important insights into the potential habitability of Black Hills caves by microorganisms. Additionally, these results provide context for future studies of microbial diversity within the region, and for exploring the limits to life in nutrient-limited ecosystems.

Download or read book Cave Microbiomes A Novel Resource for Drug Discovery written by Naowarat Cheeptham and published by Springer Science & Business Media. This book was released on 2012-10-06 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book details recent findings in the field of cave microbiology and builds on fast-paced efforts to exploit an unconventional and underexplored environment for new microorganisms which may provide an untapped source of drugs: microorganisms from caves.

Download or read book The Biology of Caves and Other Subterranean Habitats written by David C. Culver and published by Oxford University Press, USA. This book was released on 2009 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a concise but comprehensive introduction to cave ecology. The emphasis is on the organisms that dominate this unique environment, although conservation and management aspects are also considered. The book is intended for both graduate students and professionals and assumes no previous knowledge of cave biology. -;Caves and other subterranean habitats with their often strange (even bizarre) inhabitants have long been objects of fascination, curiosity, and debate. The question of how such organisms have evolved, and the relative roles of natural selection and genetic drift, has engaged subterranean biologists for decades. Indeed, these studies continue to inform the more general question of adaptation and evolution. However, interest in subterranean biology is not limited to questions of. evolutionary biology. Both the distribution and the apparent ancient age of many subterranean species continue to be of significant interest to biogeographers. Subterranean ecosystems generally exhibit little or no primary productivity and, as extreme ecosystems, provide general insights into ecosystem. function. Furthermore, the simplicity of subterranean communities relative to most surface-dwelling communities makes them useful model systems for the study of species interactions such as competition and predation, as well as more general principles of ecosystem function. The rarity of many cave species makes them of special interest in conservation biology. The Biology of Caves and other Subterranean Habitats offers a concise but comprehensive introduction to cave ecology. Whilst there is an emphasis on the organisms that dominate this unique environment, conservation and management aspects are also considered. The book includes a global range of examples and case studies from both caves and non-cave subterranean habitats; it also provides a clear explanation of specialized terms used by speleologists. This accessible text will appeal to. researchers new to the field and to the many professional ecologists and conservation practitioners requiring a concise but authoritative overview. Its engaging style will also make it suitable for senior undergraduate and graduate students taking courses in cave and subterranean biology. -

Download or read book Treatise on Geomorphology written by and published by Academic Press. This book was released on 2013-02-27 with total page 6392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The changing focus and approach of geomorphic research suggests that the time is opportune for a summary of the state of discipline. The number of peer-reviewed papers published in geomorphic journals has grown steadily for more than two decades and, more importantly, the diversity of authors with respect to geographic location and disciplinary background (geography, geology, ecology, civil engineering, computer science, geographic information science, and others) has expanded dramatically. As more good minds are drawn to geomorphology, and the breadth of the peer-reviewed literature grows, an effective summary of contemporary geomorphic knowledge becomes increasingly difficult. The fourteen volumes of this Treatise on Geomorphology will provide an important reference for users from undergraduate students looking for term paper topics, to graduate students starting a literature review for their thesis work, and professionals seeking a concise summary of a particular topic. Information on the historical development of diverse topics within geomorphology provides context for ongoing research; discussion of research strategies, equipment, and field methods, laboratory experiments, and numerical simulations reflect the multiple approaches to understanding Earth’s surfaces; and summaries of outstanding research questions highlight future challenges and suggest productive new avenues for research. Our future ability to adapt to geomorphic changes in the critical zone very much hinges upon how well landform scientists comprehend the dynamics of Earth’s diverse surfaces. This Treatise on Geomorphology provides a useful synthesis of the state of the discipline, as well as highlighting productive research directions, that Educators and students/researchers will find useful. Geomorphology has advanced greatly in the last 10 years to become a very interdisciplinary field. Undergraduate students looking for term paper topics, to graduate students starting a literature review for their thesis work, and professionals seeking a concise summary of a particular topic will find the answers they need in this broad reference work which has been designed and written to accommodate their diverse backgrounds and levels of understanding Editor-in-Chief, Prof. J. F. Shroder of the University of Nebraska at Omaha, is past president of the QG&G section of the Geological Society of America and present Trustee of the GSA Foundation, while being well respected in the geomorphology research community and having won numerous awards in the field. A host of noted international geomorphologists have contributed state-of-the-art chapters to the work. Readers can be guaranteed that every chapter in this extensive work has been critically reviewed for consistency and accuracy by the World expert Volume Editors and by the Editor-in-Chief himself No other reference work exists in the area of Geomorphology that offers the breadth and depth of information contained in this 14-volume masterpiece. From the foundations and history of geomorphology through to geomorphological innovations and computer modelling, and the past and future states of landform science, no "stone" has been left unturned!

Download or read book Cave Biology written by Aldemaro Romero Díaz and published by Cambridge University Press. This book was released on 2009-07-23 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: A critical examination of current knowledge and ideas on cave biology, with emphasis on evolution, ecology, and conservation.

Download or read book Metabolic Potential and Diversity of the Microbial Communities in a Sulfidic Cave System written by Rebecca Mccauley Rench and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Probing of deep-sea sediments and terrestrial soils has made our lack of knowledge of microbial diversity, metabolism, and structure more evident. In order to further explore these microbial communities, we must investigate subsurface environments. Easily accessible and isolated from surface environments, caves host energy-limited (i.e. no light, anoxic, low organic carbon concentration) ecosystems and microbial communities that may provide insight to subsurface microbial communities. Cave microbial communities may be similar to microbes that would have thrived on Earth, prior to the rise in atmospheric oxygen. My dissertation addresses the taxonomic composition of novel cave microbial communities in Frasassi and the metabolic potential of cave microbes based on metagenomics and the geochemistry of their environment. Additional work completed at Magical Blue Hole, which is a low-light karst environment, is included in Appendix A. In Chapter 2, I discuss the taxonomic community composition of rope-like microbial communities from anoxic cave waters and the geochemistry of their environment. The population structure of microbial communities of unusual rope-like biofilms discovered in the stratified cave lakes of a sulfidic cave system were investigated using genetic markers. Additionally, bulk geochemistry for the cave lakes was measured and thermodynamic conditions affecting the energy availability of the biofilms was explored. Despite the aphotic, anoxic environment, the rope-like biofilms are diverse with high species richness dominated by Bacteria. The dominant species are Deltaproteobacteria, likely acting as sulfate-reducers, and Chloroflexi, which may be organotrophs. Geochemical analyses of bulk water revealed low levels of organic carbon and no detectable nitrate, suggesting sulfate to be the best available electron acceptor. Low levels of methane and hydrogen suggest these may be used as electron donors. The lack of abundant sources of organic carbon suggests these unique rope-like biofilms are dependent on chemolithoautotrophy. A comparison of the Bacterial community to Census of Deep Life (CoDL) amplicons from other sites, suggest these rope-like biofilms are unique as they create a separate group with the closest communities from the Guaymas basin methane seeps and sediment from the coastal regions of the Frisian Island Sylt. Their unique morphology and distinct community composition suggests these biofilms comprise a new type of subsurface microbial population.In Chapter 3, I describe the metabolic potential of one of the rope-like microbial communities (Lago Infinito) from Chapter 2 in detail using annotated bulk and binned metagenomic data. Most microbial populations are limited by the energy available in their surrounding ecosystem and can overcome environmental challenges, such as high salinity or low pH, with abundant energy supply. This would suggest that microbial populations would not survive in low energy environments, however, many such sites exist, such as Lago Infinito. Lago Infinito is a cave lake isolated from surface organic carbon, light, and oxygen in its bottom waters. A rope-like biofilm persists in this environment despite a lack of abundant energy and organic carbon sources. Geochemistry of the surrounding waters suggests very few lithotrophic thermodynamically favorable reactions for this microbial population to thrive on. The lack of organic carbon creates an environment that must rely on primary productivity and carbon fixation, but without an abundant energy source this is unlikely. A survey of carbon fixation genes in the Lago Infinito metagenome reveals an abundance of several autotrophic pathways and is consistent with isotopic data. The Lago Infinito rope-like biofilm is capable of carbon fixation utilizing the Wood-Ljungdahl pathway and/or Calvin Cycle and is using lithotrophic energy metabolisms to drive primary productivity. The Lago Infinito biofilm is an extremely diverse microbial community comprised of autotrophic sulfate-reducing microbes and other metabolically-diverse microorganisms.In Chapter 4, I explore the metabolic potential of Frasassi Beggiatoa spp. based on binned metagenomic sequences. Both marine and freshwater species of Beggiatoa oxidize reduced sulfur species using oxygen, yet the exact pathways for sulfur oxidation are unclear. Marine Beggiatoa spp. have also demonstrated the utilization of nitrate instead of oxygen, but the ability for freshwater Beggiatoa spp. to use nitrate as an electron acceptor is ambiguous. Previous studies of enzyme assays and genomics suggest a variety of enzymes may a play a role, including reverse-type dissimilatory sulfite reductase (rDSR) and heterodisulfide reductase (HDR). We analyzed four metagenomes and found eleven Beggiatoa-like binned genomes from three sample locations in the sulfidic, freshwater environment of the Frasassi caves. The presence of both periplasmic-type (NAP) and membrane-bound (NAR) nitrate reductase and other nitrogen reductase genes were ubiquitous throughout the binned genomes. Genes encoding rDSR and oxidases were also found in several binned genomes. Our analysis suggests the freshwater Beggiatoa spp. of the Frasassi caves are capable of nitrate reduction for energy conservation and supports other studies in which freshwater Beggiatoa strains utilized nitrate. Additionally, we found genes encoding RuBisCO, suggesting these freshwater Beggiatoa spp. are also capable of carbon fixation via the Calvin cycle, making them more similar to most marine Beggiatoa spp.In Appendix A, the variety of microbial populations from Magical Blue Hole, a karst sink hole filled will a mixture of freshwater and seawater rich in sulfide, are photographed and described. Most important of note is that despite light availability below detection limits, the photosynthetic clade of Prosthecochloris is a dominant feature in the biofilm at 33 meters (104 feet).

Download or read book Cave Ecology written by Oana Teodora Moldovan and published by Springer. This book was released on 2019-01-05 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cave organisms are the ‘monsters’ of the underground world and studying them invariably raises interesting questions about the ways evolution has equipped them to survive in permanent darkness and low-energy environments. Undertaking ecological studies in caves and other subterranean habitats is not only challenging because they are difficult to access, but also because the domain is so different from what we know from the surface, with no plants at the base of food chains and with a nearly constant microclimate year-round. The research presented here answers key questions such as how a constant environment can produce the enormous biodiversity seen below ground, what adaptations and peculiarities allow subterranean organisms to thrive, and how they are affected by the constraints of their environment. This book is divided into six main parts, which address: the habitats of cave animals; their complex diversity; the environmental factors that support that diversity; individual case studies of cave ecosystems; and of the conservation challenges they face; all of which culminate in proposals for future research directions. Given its breadth of coverage, it offers an essential reference guide for graduate students and established researchers alike.

Download or read book Relation of Bacteria in Limestone Aquifers to Septic Systems in Berkeley County West Virginia written by M. V. Mathes and published by . This book was released on 2000 with total page 20 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book DNA Isolation and Bacteria Diversity Analysis from Cave Soils in Blowing Spring Cave Lauderdale County Alabama written by Samual K. Barron and published by . This book was released on 2009 with total page 70 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Hypogene Karst Regions and Caves of the World written by Alexander Klimchouk and published by Springer. This book was released on 2017-08-17 with total page 903 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book illustrates the diversity of hypogene speleogenetic processes and void-conduit patterns depending on variations of the geological environments by presenting regional and cave-specific case studies. The cases include both well-known and newly recognized hypogene karst regions and caves of the world. They all focus on geological, hydrogeological, geodynamical and evolutionary contexts of hypogene speleogenesis. The last decade has witnessed the boost in recognition of the possibility, global occurrence, and practical importance of hypogene karstification (speleogenesis), i.e. the development of solutional porosity and permeability by upwelling flow, independent of recharge from the overlying or immediately adjacent surface. Hypogene karst has been identified and documented in many regions where it was previously overlooked or misinterpreted. The book enriches the basis for generalization and categorization of hypogene karst and thus improves our ability to adequately model hypogene karstification and predict related porosity and permeability. It is a book which benefits every researcher, student, and practitioner dealing with karst.

Download or read book Geomicrobiology Molecular and Environmental Perspective written by Alexander Loy and published by Springer Science & Business Media. This book was released on 2010-07-23 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interaction of microorganisms with geological activities results in processes influencing development of the Earth’s geo- and biospheres. In assessing these microbial functions, scientists have explored short- and longterm geological changes attributed to microorganisms and developed new approaches to evaluate the physiology of microbes including microbial interaction with the geological environment. As the field of geomicrobiology developed, it has become highly interdisciplinary and this book provides a review of the recent developments in a cross section of topics including origin of life, microbial-mineral interactions and microbial processes functioning in marine as well as terrestrial environments. A major component of this book addresses molecular techniques to evaluate microbial evolution and assess relationships of microbes in complex, natural c- munities. Recent developments in so-called ‘omics’ technologies, including (meta) genomics and (meta)proteomics, and isotope labeling methods allow new insights into the function of microbial community members and their possible geological impact. While this book summarizes current knowledge in various areas, it also reveals unresolved questions that require future investigations. Information in these chapters enhances our fundamental knowledge of geomicrobiology that contributes to the exploitation of microbial functions in mineral and environmental biotechn- ogy applications. It is our hope that this book will stimulate interest in the general field of geomicrobiology and encourage others to explore microbial processes as applied to the Earth.

Download or read book The Development of Limestone Cave Systems in the Dimensions of Length and Depth written by Derek C. Ford and published by . This book was released on 1978 with total page 16 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Encyclopedia of Caves and Karst Science written by John Gunn and published by Routledge. This book was released on 2004-08-02 with total page 1971 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Encyclopedia of Caves and Karst Science contains 350 alphabetically arranged entries. The topics include cave and karst geoscience, cave archaeology and human use of caves, art in caves, hydrology and groundwater, cave and karst history, and conservation and management. The Encyclopedia is extensively illustrated with photographs, maps, diagrams, and tables, and has thematic content lists and a comprehensive index to facilitate searching and browsing.