Microbial carbon monoxide consumption in salt marsh sediments

We have examined sediments from a fringing salt marsh in Maine to further understand marine CO metabolism, about which relatively little is known. Intact cores from the marsh emitted CO during dark oxic incubations, but emission rates were significantly higher during anoxic incubations, which provided evidence for simultaneous production and aerobic consumption in surface sediments. CO emission rates were also elevated when cores were exposed to light, which indicated that photochemical reactions play a role in CO production. A kinetic analysis of marsh surface sediments yielded an apparent Km of about 82 ppm, which exceeded values reported for well-aerated soils that consume atmospheric CO (65nM). Surface (0-0.2 cm depth interval) sediment slurries incubated under oxic conditions rapidly consumed CO, and methyl fluoride did not inhibit uptake, which indicated that neither ammonia nor methane oxidizers contributed to the observed activity. In contrast, aerobic CO uptake was inhibited by additions of readily available organic substrates (pyruvate, glucose and glycine), but not by cellulose. CO was also consumed by surface and sub-surface sediment slurries incubated under anaerobic conditions, but rates were less than during aerobic incubations. Molybdate and nitrate or nitrite, but not 2-bromoethanesulfonic acid, partially inhibited anaerobic uptake. These results suggest that sulfidogens and acetogens, but not dissimilatory nitrate reducers or methanogens, actively consume CO. Sediment-free plant roots also oxidized CO aerobically; rates for Spartina patens and Limonium carolinianum roots were significantly higher than rates for Spartina alterniflora roots. Thus plants may also impact CO cycling in estuarine environments. © 2006 Federation of European Microbiological Societies

Urban microbiomes and urban agriculture: What are the connections and why should we care?

© Springer Science+Business Media Dordrecht 2016. A large percentage (~50 %) of the global human population lives in urban systems. The transition from largely rural to urban lifestyles began gradually, but has accelerated. Given the magnitude of anthropogenic changes in the Earth system as a whole and concerns about resource availability and continued population growth, questions about the sustainability of urban systems have become a focal point for a variety of research and civic efforts, including programs promoting urban agriculture as a means to provide local food sources and to better manage critical nutrients such as nitrogen and phosphorus. The last decade or so has also witnessed a remarkable transformation in our understanding of the centrality of microbes for virtually all aspects of human life and wellbeing. However, this transformation has not yet been incorporated into a fuller understanding of the biology and ecology of urban life. Research on microbial assemblages (or microbiomes) in the built environment, particularly building interiors, has provided compelling examples of the importance of microbes, but these results provide at most an incomplete picture of microbial distribution and activity in urban systems. For example, though very little is known about microbial interactions with urban agriculture, the success of urban agriculture and its potential to contribute to urban sustainability will depend in part of incorporating new knowledge about soil and plant microbiomes to optimize production and to minimize some of the adverse effects of agriculture in traditional settings (e.g., greenhouse gas emission, nitrogen and phosphorus eutrophication). To that end, this review defines and provides examples of the microbiome concept and the significance of microbiomes in urban systems; it also identifies large knowledge gaps and unanswered questions that must be addressed to develop a robust and predictive understanding of urban biology and ecology

Carbon Monoxide Based Ecological Interactions Between Legumes and Their Rhizobial Symbionts

Leguminous plants provide an important protein source for about one-third of the world\u27s population. Nitrogen-fixing nodules on the roots of these plants produce relative large amounts of carbon monoxide (CO). Although CO plays important and well-known roles in the chemistry of the troposphere and in cellular biology, the roles of CO in ecological interactions between legumes and their microbial symbionts are poorly known. Preliminary results suggest that use of CO by many legume symbionts (including strains of agriculturally important nitrogen-fixing bacteria) may promote their survival and viability in soils. Symbiont survival and viability in turn can affect plant performance and ultimately impact the role of legumes in a variety of ecosystems. To test this concept, we will use pairs of legume symbionts. One strain in each pair will be manipulated genetically to eliminate the capacity for CO utilization. We will monitor relative and absolute survival of each member of these pairs singly and in mixed populations with and without added CO. We also propose that bacterial CO oxidation controls in part net CO emission by nodules and overall plant performance. We will test this notion using pairs of legumes inoculated with CO-oxidizing symbionts or mutants that do not oxidize CO. Finally, we will use cultivation methods and our recently developed molecular tools to determine relationships between the distribution of CO-oxidizing rhizobia in soil and root and nodule CO production. We will focus on bulk soil, the rhizosphere and the rhizoplane in greenhouse and field studies. In order to expand the impact of our work, we will incorporate appropriate aspects of our research into modules that will be used in science education programs at a K-8 school in South Bristol, Maine

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities?

© 2014, The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg. Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems

Stability of trifluoromethane in forest soils and methanotrophic cultures

Trifluoromethane (TFM) has been reported as an endproduct of trifluoroacetate degradation under oxic conditions. Although other halomethanes, such as chloroform, methyl bromide, and methyl fluoride, inhibit methane oxidation or are degraded by methanotrophs, the fate of TFM is unknown. TFM had no affect on atmospheric methane consumption when added to forest soils at either 10 ppm or 10,000 ppm. No degradation of TFM was observed at either concentration for incubations of 6 days. Cultures of Methylobacter albus BG8 and Methylosinus trichosporium OB3b grown with and without added copper were also used to assay TFM degradation at 10-10000 ppm levels. TFM did not inhibit methane oxidation under any growth conditions, including those inducing expression of soluble methane monooxygenase, nor was it degraded at measurable rates. In contrast, parallel assays showed that both methyl fluoride and chloroform inhibited methane oxidation in M. trichosporium OB3b. Our results suggest that TFM may be relatively inert with respect to methanotrophic degradation. Although TFM has a negligible ozone depletion potential, it absorbs infrared radiation and has a relatively long atmospheric residence time. Thus, accumulation of TFM in the atmosphere as a consequence of the decomposition of hydrochlorofluorocarbons may have significant unpredicted climate impacts

U.S.-Korea Cooperative Research: Carbon Monoxide as a Substrate for Microbial Maintenance

Bacteria play an important role in the global budget of carbon monoxide (CO). Largely unknown bacterial populations in soils and the water column of aquatic systems oxidize hundreds of teragrams per year, or about 10%-20% of the estimated annual flux to the atmosphere. In spite of their biogeochemical significance, relatively little is known about the identity of CO-oxidizing populations active in situ, their phylogenic and physiological diversity or the importance of CO as substrate for their basic metabolic needs. of CO oxidizers. It is clear that CO at high concentrations (\u3e 1000 ppm) can serve as a sole source of cell carbon and energy for laboratory-grown cultures, but ambient CO concentrations seldom reach or exceed a few ppm. Bacteria readily use such concentrations, but are they sufficient to contribute significantly to cellular metabolic needs? This award supports Professor Gary M. King and one of his graduate students at the University of Maine to collaborate in research on this question with Dr. Y. M. Kim and his research group from Yonsei University in Korea. They will evaluate the significance of low, ecologically realistic CO concentrations for growth and survival of two common soil isolates, Mycobacterium smegmatis and Bradyrhizobium japonicum. This collaborative project will include both molecular and physiological analyses of the ability of CO at low concentrations to promote the survival and viability of CO oxidizers under conditions relevant to their natural dynamics in soils. Dr. Kim has extensive experience with the molecular biology, physiology and growth of CO-oxidizing bacteria, including mycobacteria, and characterization of the genetics and biochemistry of CO dehydrogenase, while Dr. King has extensive experience in studying the ecophysiology and biogeochemistry of microbial trace gas utilization, analytical techniques and instrumentation for near-ambient CO analyses, and expertise in the design of microcosms and gas flow systems for research. Broader significance Results of the study will significantly improve our understanding of the ecophysiology of microbial CO metabolism, particularly at real-world levels. This information is an important factor in predicting potential responses to long-term, regional-scale disturbances in climate, land use and eutrophication of aquatic systems. The work will involve exchanges of both U.S. and Korean graduate students, who will benefit from learning new research techniques and from the cultural experience. The international research experience is likely to expand the future research opportunities of the US students in Dr. King\u27s group. The exchange of techniques and methods in this research partnership will enhance the capabilities of both labs to address topical issues in the ecophysiology of microbial groups that affect atmospheric composition

The Dynamics and Significance of Carbon Monoxide Exchanges Between Wetlands and the Atmosphere

Carbon monoxide (CO) plays a major role in atmospheric chemistry. Through a series of reactions, CO can contribute to the formation of tropospheric ozone, which poses a serious health concern on a regional scale. While anthropogenic sources of CO are reasonably well understood, relatively little is known about natural CO sources and sinks. Wetlands have been discounted as CO sources on the basis of sediment CO concentrations. However, plant leaves and stems produce significant amounts of CO when illuminated by the sun. Because of their large amounts of plant biomass, wetlands are likely strong net CO sources. Our work will determine the extent and controls of CO emission from wetlands, and contrast the behavior of CO with that of methane, another important atmospheric trace gas for which wetlands are a primary global source. Our work will also examine links between CO production and increased ultraviolet (UV) irradiation due to stratospheric ozone depletion

LExEn: Role of Atmospheric Trace Gases in Microbial Colonization and Succession on Recent Lava Flows

Drs. Gary M. King of the University of Maine and Klaus Nusslein of the University of Massachusetts-Amherst have been awarded a grant from the NSF Life in Extreme Environment (LExEn) program to determine the role of atmospheric trace gases in microbial colonization and succession on recent lava flows. Volcanic activity has played an important role in the development of terrestrial ecosystems for much of Earth\u27s history, and continues to shape terrestrial environments at present. Deposition of lava and tephra result in surfaces that over time support complex, highly productive biological communities. However, young or recently extruded lavas represent extreme environments that contain few of the major nutrients necessary for sustaining life. Neither organic matter nor a fixed form of nitrogen (e.g., ammonium or nitrate) are readily available within or on the matrix of young lava. Thus, early colonization of lava by microbes requires a source of exogenous nutrients. Recent observations of young Hawaiian lava indicate that the atmosphere provides a significant source of carbon and energy for early microbial colonization. In particular, trace gases such as hydrogen and carbon monoxide (and possibly methane) serve as substrates that fuel the metabolism of functionally diverse microbes. Among these microbes are bacteria that use atmospheric nitrogen as a source of cellular nitrogen, and species that form important symbioses with plants. The nature of trace gas utilization by microbes colonizing young lavas will be the primary focus of this LExEn research effort. A variety of field and laboratory studies in the vicinity of the Kilauea volcano will document relationships among lava age (emphasizing chronosequences from 0-300 yr), microbial biomass, trace gas utilization (hydrogen, carbon monoxide and methane) and precipitation regimes (e.g., moist versus dry). Extractions of genomic DNA from lava will be used to determine the diversity of microbial communities across age and climate gradients, and the diversity of specific functional groups within these communities. Finally, the research will include efforts to enrich, isolate and characterize novel trace-gas utilizing microbes from young lava and to determine the significance of such isolates in situ. The research is expected to yield new insights about the survival and dynamics of microbes in extreme environments relevant for understanding both contemporary and ancient terrestrial systems as well as systems that might exist on other planets

TECO: Carbon Monoxide Consumption by Forest and Agroecosystem Soils

Carbon monoxide is a more dynamic component of the atmosphere than methane, occurring at a lower concentration but substantially higher flux. CO and hydroxyl radical interact rapidly, affecting a number of atmospheric parameters: the oxidative state of the troposphere; the fate and residence times of methane, non-methane organics and inorganics; tropospheric ozone; and the extent of thermal forcing. Soils consume atmospheric CO, accounting for 10-25% of the global carbon budget, depending on the source estimate. Some of the controls of soil CO uptake and production have been described generally, but much remains unknown. Details of CO uptake in agroecosystems are particularly sketchy, in spite of the fact that they occupy about 10% of terrestrial surface area, and have a disproportionate impact on a number of important trace gases. Limited field results have suggested that CO uptake in agroecosystems may be equivalent to or greater than uptake in undisturbed systems. Stimulation of CO consumption in agroecosystems could partially ameliorate the inhibition of methane uptake that accompanies agriculture by enhancing the availability of tropospheric OH. Since CO uptake is as much as 10-fold greater than methane uptake on a global basis, small changes in soil CO dynamics (positive or negative) can have a significant impact on the fate of methane. This study will determine specifically the extent to which agricultural practices affect atmospheric CO consumption by soils. Agricultural soils will be compared with similar non-agricultural soils across a gradient of texture using sites in Maine and Georgia. This study will focus on gas exchange, water regimes, temperature, and various agricultural disturbances (fertilization, pesticide use, tilling, no-till), as controls of CO fluxes. The extent to which several microbial groups of CO oxidizers vary as a function of land use will also be determined. The results of this study will establish both rates and the major controls of soil CO dyn amics, as well as the sensitivity of CO uptake to climate change and other anthropogenic perturbations

Effects of added manganic and ferric oxides on sulfate reduction and sulfide oxidation in intertidal sediments

Freshly precipitated iron or manganese oxides were added to surface sediments from a salt marsh and from the intertidal region of Lowes Cove, Maine. In the presence of added manganese, sulfate was formed under anoxic conditions, suggesting a manganese dependent sulfide oxidation. Sulfate formation was not observed with iron additions. Sulfate reduction was substantially but not completely inhibited by either metal oxide, even though both were added at levels well in excess though both were added at levels well in excess of natural concentrations. Manganese-catalysed sulfide oxidation was further documented using a combination of radiolabel, metal oxide, and inhibitor additions, Results from this study suggested that losses of radiolabelled sulfide could result in underestimates of gross sulfate reduction rates in the presence of significant manganic oxide concentrations. In addition, manganic oxides may facilitate the anaerobic regeneration of sulfate from sulfides. © 1990