Microbiology for Earth Scientists

Microorganisms are the most abundant form of life on Earth and in recent decades it has become increasingly clear that their collective activities are one of the dominant forces shaping the Earth. This book provides earth scientists with an introduction to microbiology and a look at the ways microorganisms are important to their area of expertise. The first part of this book summarizes some basic information about microorganisms, including a discussion of their diversity, physical properties, and metabolisms. From there, the second and third portions of the book are organized around the two-way interactions between microorganisms and their environments. The second portion of the book considers the ways that environmental conditions help determine distributions of microbial activity, including chapters focused on thermodynamic, kinetic, and biological factors. The third and final portion of the book examines the impacts of microbes on their environments. These impacts are placed within the context of earth system science, with chapters focused on impacts to the lithosphere, atmosphere, and hydrosphere. In these chapters, emphasis is placed on microbial impacts to greenhouse gas levels and the quality of water resources, underscoring the relevance of microbiology to environmental concerns of keen interest in the earth science community and beyond. This book is specifically designed for earth science students and can provide a helpful free resource for students in Geomicrobiology courses. However, portions of the book can also have value for students and professionals from any field who are interested in environmental microbiology.https://newprairiepress.org/ebooks/1053/thumbnail.jp

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

Citation: Jin Q and Kirk MF (2016) Thermodynamic and Kinetic Response of Microbial Reactions to High CO2. Front. Microbiol. 7:1696. doi: 10.3389/fmicb.2016.01696Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses

Broad-scale evidence that pH influences the balance between microbial iron and sulfate reduction

Understanding basic controls on aquifer microbiology is essential to managing water resources and predicting impacts of future environmental change. Previous theoretical and laboratory studies indicate that pH can influence interactions between microorganisms that reduce ferric iron and sulfate. In this study, we test the environmental relevance of this relationship by examining broad-scale geochemical data from anoxic zones of aquifers. We isolated data from the U.S. Geological Survey National Water Information System for 19 principal aquifer systems. We then removed samples with chemical compositions inconsistent with iron- and sulfate-reducing environments and evaluated the relationships between pH and other geochemical parameters using Spearman's rho rank correlation tests. Overall, iron concentration and the iron-sulfide concentration ratio of groundwater share a statistically significant negative correlation with pH (P < 0.0001). These relationships indicate that the significance of iron reduction relative to sulfate reduction tends to increase with decreasing pH. Moreover, thermodynamic calculations show that, as the pH of groundwater decreases, iron reduction becomes increasingly favorable relative to sulfate reduction. Hence, the relative significance of each microbial reaction may vary in response to thermodynamic controls on microbial activity. Our findings demonstrate that trends in groundwater geochemistry across different regional aquifer systems are consistent with pH as a control on interactions between microbial iron and sulfate reduction. Environmental changes that perturb groundwater pH can affect water quality by altering the balance between these microbial reactions.Citation: Kirk, M. F., Jin, Q. and Haller, B. R. (2015), Broad-Scale Evidence That pH Influences the Balance Between Microbial Iron and Sulfate Reduction. Groundwater. doi:10.1111/gwat.1236

pH as a Primary Control in Environmental Microbiology: 2. Kinetic Perspective

In a companion paper, we examined the thermodynamic responses of microbial redox reactions to pH changes. Here we explore how these thermodynamic responses may affect the composition and function of microbial communities. We simulate butyrate syntrophic oxidation, sulfate reduction, and methanogenesis by microbial consortia at pH ranging from 7 to 5. The simulation accounts for the thermodynamics of microbial metabolisms and the interactions among microbes. The results show that thermodynamic responses to variation in pH can be strong enough to speed up or slow down microbial metabolisms. These kinetic changes then shape the outcome of microbial interactions, including the membership and activity of microbial consortia. Moreover, the kinetic changes modulate carbon fluxes and the efficiency of methane production. The simulation results support the hypothesis that environmental pH can shape the composition and metabolic function of microbial communities by changing the energy yields of redox reactions. They also add to the current theories of microbial ecology. Specifically, due to pH-induced thermodynamic responses, the principle of competitive exclusion fails for microbial processes with significant thermodynamic limitations, which allows the co-occurrence of competing respiration reactions in natural environments. Taken together, these results confirm that pH is a primary control in environmental microbiology. They also highlight the feasibility and potential of biogeochemical kinetic modeling in uncovering and illuminating mechanistic relationships between environmental parameters and microbial communities

Interplay between Microorganisms and Geochemistry in Geological Carbon Storage

Citation: Kirk, MF, Altman, SJ, Santillan, EFU, Bennett, PC (2016) Interplay between microorganisms and geochemistry in geological carbon storage. International Journal of Greenhouse Gas Control 47, 386-395.Researchers at the Center for Frontiers of Subsurface Energy Security (CFSES) have conducted laboratory and modeling studies to better understand the interplay between microorganisms and geochemistry for geological carbon storage (GCS). We provide evidence of microorganisms adapting to high pressure CO2 conditions and identify factors that may influence survival of cells to CO2 stress. Factors that influenced the ability of cells to survive exposure to high-pressure CO2 in our experiments include mineralogy, the permeability of cell walls and/or membranes, intracellular buffering capacity, and whether cells live planktonically or within biofilm. Column experiments show that, following exposure to acidic water, biomass can remain intact in porous media and continue to alter hydraulic conductivity. Our research also shows that geochemical changes triggered by CO2 injection can alter energy available to populations of subsurface anaerobes and that microbial feedbacks on this effect can influence carbon storage. Our research documents the impact of CO2 on microorganisms and in turn, how subsurface microorganisms can influence GCS. We conclude that microbial presence and activities can have important implications for carbon storage and that microorganisms should not be overlooked in further GCS research

An Integrated Content and Metadata based Retrieval System for Art

In this paper we describe aspects of the Artiste project to develop a distributed content and metadata based analysis, retrieval and navigation system for a number of major European Museums. In particular, after a brief overview of the complete system, we describe the design and evaluation of some of the image analysis algorithms developed to meet the specific requirements of the users from the museums. These include a method for retrievals based on sub images, retrievals based on very low quality images and retrieval using craquelure type

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA

Microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4-1.1 m) coalbeds with marginal thermal maturities (0.5-0.7% Ro) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na-Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L?1. Gas dryness values [C1/(C2 + C3)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183%. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.Citation: Kirk MF, Wilson BH, Marquart KA, Zeglin LH, Vinson DS and Flynn TM (2015) Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA. Front. Microbiol. 6:1287. doi: 10.3389/fmicb.2015.0128

Heteroatom substitution effects in spin crossover dinuclear complexes

We probe the effect of heteroatom substitution on the spin crossover (SCO) properties of dinuclear materials of the type [Fe2(NCX)4(R-trz)5]·S (X = S, Se; S = solvent; R-trz = (E)-N-(furan-2-ylmethylene)- 4H-1,2,4-triazol-4-amine (furtrz); (E)-N-(thiophen-2-ylmethylene)-4H-1,2,4-triazole-4-amine (thtrz)). For the furtrz family ([Fe2(NCX)4(furtrz)5]·furtrz·MeOH; X = S (furtrz-S) and X = Se (furtrz-Se)) gradual and incomplete one-step SCO transitions are observed (furtrz-S (T1/2 = 172 K) and furtrz-Se (T1/2 = 205 K)) and a structural evolution from [HS-HS] to [HS-LS] per dinuclear species. Contrasting this, within the thtrz family ([Fe2(NCX)4(thtrz)5]·4MeOH; X = S (thtrz-S) and X = Se (thtrz-Se)) more varied SCO transitions are observed, with thtrz-S being SCO-inactive (high spin) and thtrz-Se showing a rare complete two-step SCO transition (T1/2(1,2) = 170, 200 K) in which the FeII sites transition from [HS-HS] to [HS-LS] to [LS-LS] per dinuclear unit with no long range ordering of spin-states at the intermediate plateau. Detailed structure- function analyses have been conducted within this growing dinuclear family to rationalise these diverse spin-switching properties

Isolation of Isotrichophycin C and Trichophycins G–I from a Collection of Trichodesmium thiebautii

The trichophycin family of compounds are chlorinated polyketides first discovered from environmental collections of a bloom-forming Trichodesmium sp. cyanobacterium. In an effort to fully capture the chemical space of this group of metabolites, the utilization of MS/MS-based molecular networking of a Trichodesmium thiebautii extract revealed a metabolome replete with halogenated compounds. Subsequent MS-guided isolation resulted in the characterization of isotrichophycin C and trichophycins G–I (1–4). These new metabolites had intriguing structural variations from those trichophycins previously characterized, which allowed for a comparative study to examine structural features that are associated with toxicity to murine neuroblastoma cells. Additionally, we propose the absolute configuration of the previously characterized trichophycin A (5). Overall, the metabolome of the Trichodesmium bloom is hallmarked by an unprecedented amount of chlorinated molecules, many of which remain to be structurally characterized

The census of dense cores in the Serpens region from the Herschel Gould Belt Survey

Abstract The Herschel Gould Belt survey mapped the nearby (d &amp;lt; 500 pc) star-forming regions to understand better how the prestellar phase influences the star formation process. Here we report a complete census of dense cores in a ∼15 deg2 area of the Serpens star-forming region located between d ∼ 420 pc and 484 pc. The PACS and SPIRE cameras imaged this cloud from 70 μm to 500 μm. With the multi-wavelength source extraction algorithm getsources , we extract 833 sources, of which 709 are starless cores and 124 are candidate proto-stellar cores. We obtain temperatures and masses for all the sample, classifying the starless cores in 604 prestellar cores and 105 unbound cores. Our census of sources is $80\%$ complete for M &amp;gt; 0.8 M⊙ overall. We produce the core mass function (CMF) and compare it with the initial mass function (IMF). The prestellar CMF is consistent with log-normal trend up to ∼2 M⊙, after which it follows a power-law with slope of −2.05 ± 0.34. The tail of its CMF is steeper but still compatible with the IMF for the region we studied in this work. We also extract the filaments network of the Serpens region, finding that $81\%$ of prestellar cores lie on filamentary structures. The spatial association between cores and filamentary structure supports the paradigm, suggested by other Herschel observations, that prestellar cores mostly form on filaments. Serpens is confirmed to be a young, low-mass and active star-forming region