Cave Decorating with Microbes: Geomicrobiology of Caves

Elements ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. 107-112 ◽  
Author(s):  
Daniel S. Jones ◽  
Diana E. Northup
Keyword(s):  
Metal Oxidation ◽  
Element Cycling ◽  
Direct Role ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Energy Inputs ◽  
Mineral Deposition ◽  
Limestone Bedrock ◽  
Inorganic Chemical ◽  
Slow Growing

Microorganisms are important for the formation and biogeochemistry of caves. Some caves are energy-rich systems with abundant organic or inorganic chemical energy inputs that support robust microbial ecosystems, but most are extremely oligotrophic settings with slow-growing microbial communities that rely on limited energy resources. Microorganisms are catalysts for element cycling in subterranean environments and act as agents of mineral precipitation and dissolution. Microbes can contribute to cave formation by producing acids and corroding limestone bedrock, and they can form secondary mineral deposits by catalyzing metal oxidation and inducing carbonate precipitation. We describe the energy sources for microbial life in caves, and we review three situations in which microorganisms may play a direct role in mineral deposition and bedrock corrosion.

scholarly journals Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems

2019 ◽  
Author(s):  
Julia M. McGonigle ◽  
Susan Q. Lang ◽  
William J. Brazelton
Keyword(s):  
Carbon Cycling ◽  
Hydrothermal Vents ◽  
Reducing Power ◽  
Single Species ◽  
Hydrogen Gas ◽  
Ambient Seawater ◽  
Lost City ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Lost City Hydrothermal Field

ABSTRACTThe Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by low-abundance Chloroflexi species. Additionally, we present evidence that metabolically diverse, formate-utilizing Sulfurovum species are living in the transition zone between the interior and exterior of the chimneys.IMPORTANCEPrimitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also extraterrestrial ecosystems that might support life. The microscopic life covering towering chimney structures at the Lost City has been well characterized, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.

Microstructure and mineral composition of Holocene stromatolites from Lagoa Vermelha, a hypersaline lagoon in Brazil: Insights into laminae genesis

2020 ◽  
Vol 90 (8) ◽  
pp. 887-905
Author(s):  
Carolina N. Keim ◽  
Hélisson Nascimento dos Santos ◽  
Carolina Souza Santiago ◽  
Simone Pennafirme ◽  
Reiner Neumann ◽  
...  
Keyword(s):  
Microbial Mats ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fine Grained ◽  
Left Behind ◽  
Microbial Ecosystems ◽  
Mineral Deposition ◽  
Magnesium Calcite ◽  
Hypersaline Lagoon ◽  
Janeiro State

ABSTRACT Stromatolites are domes, columns, or nearly flat crusts of laminated sedimentary rocks, usually consisting of Ca-Mg carbonates. Stromatolites result from lithification of microbial mats, which are benthic microbial ecosystems where microorganisms arrange themselves in layers according to their physiology. Despite a century of research, the hypothesis of stromatolite genesis by lithification of microbial mats remains controversial, and a convincing explanation for how stromatolites arise from microbial mats is still lacking. In this work, we analyze in detail a stromatolite from Lagoa Vermelha, a coastal hypersaline lagoon in Rio de Janeiro State, Brazil. The stromatolite presents a laminated core and thrombolitic regions at the periphery. Both thrombolitic and laminated facies consist of fine-grained authigenic minerals with minor contributions of bioclasts and quartz grains. X-ray diffraction shows aragonite, high-magnesium calcite (HMC) containing about 17% MgCO3, a very-high-Mg calcite (VHMC) containing 29–46% MgCO3, and small amounts of quartz and pyrite. Scanning electron microscopy of polished samples coupled to energy-dispersive X-ray analysis (EDS) showed that each lamina was composed of 1–4 distinct mineral phases embedded within each other, indicating sequential steps of precipitation of Ca-Mg carbonates under distinct biogeochemical conditions. The coexistence of different phases in a single lamina suggests that several processes contribute to mineral deposition as the incipient stromatolite laminae are left behind by microorganisms from the lower layers of the microbial mat when they grow and/or move upwards.

scholarly journals Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

2017 ◽  
Vol 114 (44) ◽  
pp. E9206-E9215 ◽  
Author(s):  
Elizabeth Trembath-Reichert ◽  
Yuki Morono ◽  
Akira Ijiri ◽  
Tatsuhiko Hoshino ◽  
Katherine S. Dawson ◽  
...  
Keyword(s):  
Stable Isotope Probing ◽  
Coal Bed ◽  
Rrna Gene ◽  
Deuterated Water ◽  
Diverse Range ◽  
Microbial Life ◽  
Ocean Drilling ◽  
Slow Growing ◽  
Deep Subseafloor

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of13C- or15N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

scholarly journals Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Julia M. McGonigle ◽  
Susan Q. Lang ◽  
William J. Brazelton
Keyword(s):  
Carbon Cycling ◽  
Hydrothermal Vents ◽  
Reducing Power ◽  
Single Species ◽  
Hydrogen Gas ◽  
Ambient Seawater ◽  
Lost City ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Lost City Hydrothermal Field

ABSTRACT The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by Chloroflexi populations. Additionally, we present evidence for metabolically diverse, formate-utilizing Sulfurovum populations and new genomic and phylogenetic insights into the unique Lost City Methanosarcinales. IMPORTANCE Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.

scholarly journals Molecular and Physiological Effects of Mycobacterial oxyR Inactivation

2006 ◽  
Vol 188 (7) ◽  
pp. 2674-2680 ◽  
Author(s):  
Eileen Pagán-Ramos ◽  
Sharon S. Master ◽  
Christopher L. Pritchett ◽  
Renate Reimschuessel ◽  
Michele Trucksis ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Isonicotinic Acid ◽  
Acid Hydrazide ◽  
High Sensitivity ◽  
Infection Model ◽  
Front Line ◽  
Gene Encoding ◽  
Direct Role ◽  
Increased Sensitivity ◽  
Slow Growing

ABSTRACT The majority of slow-growing mycobacteria have a functional oxyR, the central regulator of the bacterial oxidative stress response. In contrast, this gene has been inactivated during the evolution of Mycobacterium tuberculosis. Here we inactivated the oxyR gene in Mycobacterium marinum, an organism used to model M. tuberculosis pathogenesis. Inactivation of oxyR abrogated induction of ahpC, a gene encoding alkylhydroperoxide reductase, normally activated upon peroxide challenge. The absence of oxyR also resulted in increased sensitivity to the front-line antituberculosis drug isoniazid. Inactivation of oxyR in M. marinum did not affect either virulence in a fish infection model or survival in human macrophages. Our findings demonstrate, at the genetic and molecular levels, a direct role for OxyR in ahpC regulation in response to oxidative stress. Our study also indicates that oxyR is not critical for virulence in M. marinum. However, oxyR inactivation confers increased sensitivity to isonicotinic acid hydrazide, suggesting that the natural loss of oxyR in the tubercle bacillus contributes to the unusually high sensitivity of M. tuberculosis to isoniazid.

scholarly journals The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects

2021 ◽  
Vol 12 ◽  
Author(s):  
Hinako Takamiya ◽  
Mariko Kouduka ◽  
Yohey Suzuki
Keyword(s):  
Microbial Interactions ◽  
Radioactive Elements ◽  
Cell Level ◽  
High Iron Content ◽  
Microbial Life ◽  
Technological Advances ◽  
Energy Inputs ◽  
Microbial Proliferation ◽  
Rocky Habitats ◽  
Life On Earth

Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.

scholarly journals A rather dry subject; investigating the study of arid-associated microbial communities

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Peter Osborne ◽  
Lindsay J. Hall ◽  
Noga Kronfeld-Schor ◽  
David Thybert ◽  
Wilfried Haerty
Keyword(s):  
Microbial Communities ◽  
Land Surface ◽  
Animal Species ◽  
Arid Environment ◽  
Harsh Environments ◽  
Arid Environments ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Limited Food ◽  
Extremes Of Temperature

AbstractAlmost one third of Earth’s land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.

scholarly journals The lithic microbial ecosystems of Antarctica’s McMurdo Dry Valleys

2014 ◽  
Vol 26 (5) ◽  
pp. 459-477 ◽  
Author(s):  
Asunción De Los Ríos ◽  
Jacek Wierzchos ◽  
Carmen Ascaso
Keyword(s):  
Environmental Conditions ◽  
Extracellular Polymeric Substances ◽  
Heterotrophic Bacteria ◽  
Community Organization ◽  
Mcmurdo Dry Valleys ◽  
Microbial Consortia ◽  
Dry Valleys ◽  
Microbial Life ◽  
Environmental Controls ◽  
Microbial Ecosystems

AbstractWe review the lithic microbial ecosystems of the McMurdo Dry Valleys as the main form of terrestrial colonization in this region, and assess the role of environmental controls such as temperature, solar radiation, water availability, wind, nutrient availability, salinity and the physicochemical properties of the colonized rock. Epilithic communities, especially those dominated by lichens, are able to withstand extreme environmental conditions but subsurface endolithic microhabitats provide more tolerant conditions. Endolithic microbial communities can be grouped into two main classes: eukaryotic communities (dominated by lichenized fungi and algae) and prokaryotic communities (dominated by cyanobacteria). Heterotrophic bacteria and non-lichenized algae and fungi (mainly black fungi) are also components of these communities. These lithobiontic microorganisms generally have effective mechanisms against freezing temperatures and desiccation. Extracellular polymeric substances play an important role not only in protecting microbial cells but also in community organization and in mitigating microenvironmental conditions. Antarctic lithobiontic communities are comprised of microbial consortia within which multiple interactions between the different biological and abiotic components are essential for microbial survival, whilst fossils and biomarkers provide evidence of earlier successful microbial life in Antarctic deserts. Finally, the uniqueness of the present lithobiont assemblages suggests they are the outcome of geographical isolation during the evolution of the continent and not merely the descendants of a subset of globally distributed taxa that have adapted to the extreme environmental conditions.

Could Fe-metabolizing microbes weather sub-surface minerals in a semi-arid climate?

2020 ◽  
Author(s):  
Christopher Schwerdhelm
Keyword(s):  
Natural Resources ◽  
Critical Zone ◽  
Mineral Weathering ◽  
Environmental Research ◽  
Arid Environments ◽  
Element Cycling ◽  
Direct Role ◽  
Reducing Bacteria ◽  
Semi Arid

<p>Christopher Schwerdhelm<sup>1</sup>, Ferdinand Hampl<sup>2</sup>, Carolina Merino<sup>3,4</sup>, Francisco Matus<sup>4,5</sup>, Thomas Neumann<sup>2</sup>, Andreas Kappler<sup>1</sup>, Casey Bryce<sup>1</sup></p><p> </p><p><sup>1</sup> Geomicrobiology, Center for Applied Geoscience (ZAG), Eberhard-Karls-University Tuebingen, Sigwartstrasse 10, 72076 Tuebingen, Germany</p><p><sup>2</sup> Technische Universität Berlin, Institute of Applied Geosciences, Department of Applied Geochemistry, Office BH 9-3, Ernst-Reuter-Platz 1, 10587 Berlin, Germany</p><p><sup>3</sup> Center of Plant, Soil Interaction and Natural Resources Biotechnology Scientific and Technological Bioresource Nucleus (BIOREN), Temuco, Chile</p><p><sup>4</sup> Network for Extreme Environmental Research, Universidad de la Frontera, Temuco, Chile</p><p><sup>5</sup> Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Avenida Francisco Salazar, 01145 Temuco, Chile</p><p> </p><p>Mineral weathering shapes Earth’s surface by transforming bedrock to soil in the ‘critical zone’. Among these transformation processes, microbial weathering plays an important role, as it contributes to all stages of rock-soil transformation such as primary rock colonization, rock breakdown, saprolite formation, and element cycling. Fe-metabolizing microorganisms, i.e. Fe(II)-oxidizing and Fe(III)-reducing microorganisms, are key players in weathering as they can directly attack minerals via their metabolism. However, most direct evidence for the role of these microbes in critical zone processes comes from shallow and humid tropical soils and saprolite, or from transects across corestones. Much less is understood about the direct role of these microorganisms in critical zone processes in more arid climates.  </p><p>In this study we have obtained drill cores from the critical zone of a semi-arid region of the Chilean Coastal Cordillera (Santa Gracia Reserve). Despite receiving only 66 mm of rain per year, the weathering profile is very deep (>80 m). The rock material of the drill core is a Cretaceous quartz monzodiorite rich in hornblende, biotite and chlorite with ca. 1-2 wt.-% Fe(III) oxyhydroxides and very low TOC content. Using cultivation-based methods we found microaerophilic Fe(II)-oxidizing bacteria in zones of weathered saprolite (up to ca. 25 m depth) and at the weathering front (70-76 m), while Fe(III)-reducing bacteria, grown either with dihydrogen or organic carbon, were successfully enriched from samples across the whole 87 m profile. A robust contamination control confirmed that cultivated microbes were from the in-situ community and not related to drill fluid contamination.  </p><p>These findings suggest there is potential for Fe-metabolizing microbes to contribute to mineral-weathering processes even in deep weathering profiles in semi-arid environments. The occurrence of cultivatable Fe(II)-oxidizing bacteria is controlled by the presence of highly fractured zones functioning as fluid and oxygen transport pathways. It is notable that despite the fact that much of the silicate minerals contain Fe(II), Fe(III)-reducing bacteria are more common. The co-occurrence of Fe(II)-oxidizing and Fe(III)-reducing bacteria in some isolated parts of the profile could represent a self-sustaining cycle of iron redox reactions.</p>

Effects of Hypophysectomy on the Occurrence and Calcifiability of Matrix Vesicles in the Epiphyseal Growth Plate of Immature Rats

1980 ◽  
Vol 38 ◽  
pp. 578-579
Author(s):  
S. I. Coleman ◽  
W. J. Dougherty
Keyword(s):  
Growth Plate ◽  
Matrix Vesicles ◽  
Epiphyseal Growth Plate ◽  
Hard Tissue ◽  
Hormonal Factors ◽  
Post Surgery ◽  
Mineral Deposition ◽  
Thin Sectioning ◽  
Integral Role ◽  
Cellular Secretion

In the cellular secretion theory of mineral deposition, extracellular matrix vesicles are believed to play an integral role in hard tissue mineralization (1). Membrane limited matrix vesicles arise from the plasma membrane of epiphyseal chondrocytes and tooth odontoblasts by a budding process (2, 3). Nutritional and hormonal factors have been postulated to play essential roles in mineral deposition and apparently have a direct effect on matrix vesicles of calcifying cartilage as concluded by Anderson and Sajdera (4). Immature (75-85 gm) Long-Evans hooded rats were hypophysectomized by the parapharyngeal approach and maintained fourteen (14) days post-surgery. At this time, the animals were anesthetized and perfusion fixed in cacodylate buffered 2.5% glutaraldehyde. The proximal tibias were quickly dissected out and split sagittally. One half was used for light microscopy (LM) and the other for electron microscopy (EM). The halves used for EM were cut into blocks approximately 1×3 mm. The tissue blocks were prepared for ultra-thin sectioning and transmission EM. The tissue was oriented so as to section through the epiphyseal growth plate from the zone of proliferating cartilage on down through the hypertrophic zone and into the initial trabecular bone. Sections were studied stained (double heavy metal) and unstained.

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