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At least 163 records · Page 9

Comets, Asteroids, Meteorites, and the Origin of the Biosphere

During the past few decades, the delivery of water, organics, and prebiotic chemicals to the Biosphere of Earth during the Hadean (4.5-3.8 Ga) period of heavy bombardment by comets and asteroids has become more widely accepted. Comets are still largely regarded as frigid, pristine bodies of protosolar nebula material that are devoid of liquid water and therefore unsuitable for life. Complex organic compounds have been observed in comets and on the water-rich asteroid 1998 KY26 and near IR observations have indicated the presence of crystalline water ice and ammonia hydrate on the large Kuiper Belt object (50000) Quaoar that has resurfacing suggesting cryovolcanic outgassing. Spacecraft observations of the chemical compositions and characteristics of the nuclei of several comets (Halley, Borrelly, Wild 2, and Tempel 1) have shown that comets contain complex organic chemicals; that water is the predominant volatile; and that extremely high temperatures (approx. 350-400 K) can be reached on the surfae of the very black (albedo approx. 0.03) nuclei of comets when they approach the Sun. Impact craters and pinnacles observed on comet Wild 2 suggest a thick crust. Episodic outbursts and jets from the nuclei of several comets indicate that localized regimes of liquid water and water vapor can periodically exist beneath the comet crust. The Deep Impact mission found the temperature of the nucleus of comet Tempel 1 at 1.5 AU varied from a minimum of 280 plus or minus 8 K the 330K (57 C) on the sunlit side. In this paper it is argued that that pools and films of liquid water exist (within a wide range of temperatures) in cavities and voids just beneath the hot, black crust. The possibility of liquid water existing over a wide range of temperatures significantly enhances the possibility that comets might contain niches suitable for the growth of microbial communities and ecosystems. These regimes would be ideal for the growth of psychrophilic, mesophilic, and thermophilic photoautotrophs and chemolithotrophs such as the motile filamentous cyanobacteria (e.g., Calothrix, Oscillatoria, Phormidium, and Spirulina) that grow in geothermal springs and geysers of Earth at temperatures ranging fiom 320K to 345K and are also found growing in cold polar desert soils. The mineralized remains of morphotypes of all of these cyanobacteria have also been found in the Orgueil CI1 and the Murchison CN2 carbonaceous meteorites that may derive from cometary parent bodies. Observational results that support the hypothesis that liquid water can in active regions just beneath the surface of comets and that comets, carbonaceous meteorites, and asteroids may have played a significant role in the origin and evolution of the Biosphere and in the distribution of microbial life throughout the Solar System.

Hoover, Richard B.↗

Carbon acquisition ecological strategies to connect soil microbial biodiversity and carbon cycling

Soil carbon feedbacks to global change are uncertain, and the biological processes that govern soil organic matter decomposition are not resolved in current ecosystem models. Though it is recognized that microbial biodiversity influences decomposition rates, incorporating this relationship into ecosystem models is challenging because microbial communities are prohibitively diverse. It is likely necessary to distill microbial biodiversity by focusing on functional groups or ecological strategies. The ecological strategies that currently dominate the microbial ecology literature derive from macroecological theory, have clear weaknesses, and have had limited success when applied to predict soil carbon dynamics. Here, we present a new framework for soil microorganisms: Carbon Acquisition Ecological Strategies (CAES), and we outline a path toward incorporating microbial biodiversity into ecosystem models using this framework to enhance predictions of soil carbon feedbacks to global change. Because a microorganism's diet is central to its ecological niche and likely to covary with other ecologically significant traits, we posit that carbon acquisition may serve as a tractable foundation for developing ecological strategies. Further, we describe four candidate ecological strategies for soil microorganisms: 1° decomposers that assimilate complex plant polymers, 2° decomposers that assimilate microbial necromass, passive consumers that assimilate dissolved organic carbon, and predatory microbes that assimilate live microbial biomass. These strategies are directly linked to soil carbon pools currently represented in ecosystem models and may provide a foundation for greater integration of microbial community dynamics into ecosystem models.

59 BASIC BIOLOGICAL SCIENCES↗

Volatilized Ammonia Supports Subterranean Ecosystems with Unusual Nitrogen Isotopic Signatures

The Frasassi cave system hosts a robust subterranean ecosystem based on microbial lithoautotrophy. Curiously, acidic biofilms forming above degassing sulfidic cave streams, and the invertebrates that feed on them, are extremely depleted in nitrogen-15 (δ 15 N values less than −20‰). In this study, we tested the hypothesis that these low δ 15 N values result from the volatilization, trapping, and uptake of ammonia degassed from circumneutral streams. We found that dissolved ammonium in the streams had δ 15 N values near +3‰, whereas NH 3(g) in the cave atmosphere above streams exhibited δ 15 N values as low as −27‰, consistent with fractionation by NH 3 volatilization. Extremely acidic condensation droplets on cave walls efficiently trapped airborne NH 3 , accumulating up to 4 mM NH 4 + with δ 15 N values as low as −29‰, thereby confirming volatilized and trapped ammonia as the primary N source to cave wall biofilms and the extensive subsurface ecosystem they support. Airborne ammonia trapping represents a novel mechanism for biological N acquisition and provides abundant N for growth in an extreme subsurface environment that otherwise receives very limited nutrient input.

Nitrogen↗

Changes in microbial community and network structure precede shrub degradation in a desert ecosystem

Large-scale restoration is intended to promote ecological recovery. Improvements in plant and microbial conditions, however, may slow or even reverse in late succession. To better understand long-term restoration outcomes and underlying drivers of successional pathways, we tracked plant, bacterial and fungal, and soil conditions across a 40-year shrub plantation that was intended to stabilize desertified land in northern China. Here, we found that planted Haloxylon ammodendron shrubs developed and then subsequently became degraded after 30–40 years. Bacterial abundance and α-diversity were much higher than those of fungi, but no significant differences in composition and structure were found in different plantation ages. In contrast, the dominant taxa of fungal communities shifted from symbiotroph and saprotroph species towards pathotroph species with increased soil nutrients in the plantation chronosequence after two decades. The changes in fungal dominant species led to a transition in microbial network structure and function, with an increase in negative linkages among taxa that began in the middle stages of succession. Changes in fungal community structure had direct and indirect negative effects on shrub leaf physiology, root activity, and biomass. Our results highlight the preceding role of a breakdown in soil microbial community composition and network structure on the degradation of shrub performance in long-term desert succession. Our study emphasizes the importance of understanding soil-microbial-plant linkages on restoration outcomes, and mechanisms that can slow or reverse the recovery of ecosystems.

Bacterial and fungal community composition↗

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO 2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO 2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO 2 concentration. In conclusion, our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

Developing Model Benchtop Systems for Microbial Experimental Evolution

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Developing↗

Microbial Ecology of Permafrost Soils: Populations, Processes, and Perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

54 ENVIRONMENTAL SCIENCES↗

Resilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradient

Wildfires can represent a major disturbance to ecosystems, including soil microbial communities belowground. Furthermore, fire regimes are changing in many parts of the world, altering and often increasing fire severity, frequency, and size. The boreal forest and taiga plains ecoregions of northern Canada are characterized by naturally-occurring stand-replacing wildfires on a 40–350 year basis. We previously studied the effects of wildfire on soil microbial communities one year post-fire across 40 sites, spanning a range of burn severity. Here, we return to the same sites five years post-fire to test a series of hypotheses about the effects of fire on bacterial community composition. We ask questions on two themes: which factors control bacterial community composition during post-fire recovery, and how does the importance of different fire-responsive traits change during post-fire recovery? We find the following: Five years post-fire, vegetation community, moisture regime, pH, total carbon, texture, and burned/unburned all remained significant predictors of bacterial community composition with similar predictive value (R 2 ). Bacterial communities became more similar to unburned sites five years post-fire, across the range of severity, suggesting resilience, while general structure of co-occurrence networks remained similar one and five years post-fire. Fast growth potential, as estimated using predicted 16S rRNA copy numbers, was no longer significantly correlated with burn severity five years post-fire, indicating the importance of this trait for structuring bacterial community composition may be limited to relatively short timescales. Many taxa that were enriched in burned sites one year post-fire remained enriched five years post-fire, although the degree to which they were enriched generally decreased. Specific taxa of interest from the genera Massilia, Blastococcus, and Arthrobacter all remained significantly enriched, suggesting that they may have traits that allow them to continue to flourish in the post-fire environment, such as tolerance to increased pH or ability to degrade pyrogenic organic matter. This hypothesis-based work expands our understanding of the post-fire recovery of soil bacterial communities and raises new hypotheses to test in future studies.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗

Perennial grass bioenergy cropping systems: Impacts on soil fauna and implications for soil carbon accrual

ABSTRACT Perennial grass energy crop production is necessary for the successful and sustainable expansion of bioenergy in North America. Numerous environmental advantages are associated with perennial grass cropping systems, including their potential to promote soil carbon accrual. Despite growing research interest in the abiotic and biotic factors driving soil carbon cycling within perennial grass cropping systems, soil fauna remain a critical yet largely unexplored component of these ecosystems. By regulating microbial activity and organic matter decomposition dynamics, soil fauna influence soil carbon stability with potentially significant implications for soil carbon accrual. We begin by reviewing the diverse, predominantly indirect effects of soil fauna on soil carbon dynamics in the context of perennial grass cropping systems. Since the impacts of perennial grass energy crop production on soil fauna will mediate their potential contributions to soil carbon accrual, we then discuss how perennial grass energy crop traits, diversity, and management influence soil fauna community structure and activity. We assert that continued research into the interactions of soil fauna, microbes, and organic matter will be important for advancing our understanding of soil carbon dynamics in perennial grass cropping systems. Furthermore, explicit consideration of soil faunal effects on soil carbon can improve our ability to predict changes in soil carbon following perennial grass cropping system establishment. We conclude by addressing the major knowledge gaps that should be prioritized to better understand and model the complex connections between perennial grass bioenergy systems, soil fauna, and carbon accrual.

sustainability↗

Metatranscriptomes of California grassland soil microbial communities in response to rewetting

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought—providing a time series of short-term transcriptional response during rewetting.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

Abstract Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.

Soong, Jennifer L.↗

Depth and microtopography influence microbial biogeochemical processes in a forested peatland

Background and aims: Peat-accumulating wetlands have undulating surfaces of raised areas (hummocks) and depressions (hollows). Hummock-hollow microtopography in relation to the water table influences the distribution of plant species, root density, and microbial community composition, which could in turn alter carbon (C) and nitrogen (N) cycling within peatlands. We used paired hummock and hollow cores from a boreal, forested peatland to assess how microtopography influences peatland microbial function and, in turn, ecosystem C and N cycling. Methods: The peat was analyzed for microbial biomass and potential enzyme activity in 10 cm depth increments relative to the water table, resulting in two increments for hollows and three for hummocks, which has a raised increment above the water table. Results: Across hummocks and hollows, microbial C and N and fungal biomass generally decreased with depth from the peat surface. In contrast, potential enzyme activity often increased with depth, but this varied within enzyme functional groups according to topography, depth, or both. The potential enzyme activity of C-N degrading peptidases, for example, differed across the five topography × depth increments with the lowest rate in the aerated hummocks. Hummocks compose approximately 66% of the land area at our study site and would therefore underestimate C turnover by an average of 25% if solely used to extrapolate patterns across a forested bog. Conclusion: In conclusion, our results suggest that asynchrony in C and N cycling across the undulating surface of forested peatlands impacts our ability to accurately predict biogeochemical cycling across this important ecosystem.

54 ENVIRONMENTAL SCIENCES↗

Compound-specific Isotope Analysis of Cyanobacterial Pure cultures and Microbial Mats: Effects of Photorespiration?

Microbial mats are considered modern homologs of Precambrian stromatolites. The carbon isotopic compositions of organic matter and biomarker lipids provide clues to the depositional environments of ancient mat ecosystems. As the source of primary carbon fixation for over two billion years, an understanding of cyanobacterial lipid biosynthesis, associated isotopic discriminations, and the influence of physiological factors on growth and isotope expression is essential to help us compare modern microbial ecosystems to their ancient counterparts. Here, we report on the effects of photorespiration (PR) on the isotopic composition of cyanobacteria and biomarker lipids, and on potential PR effects associated with the composition of various microbial mats. The high light, high O2 and limiting CO2 conditions often present at the surface of microbial mats are known to support PR in cyanobacteria. The oxygenase function of ribulose bisphosphate carboxylase/oxygenase can result in photoexcretion of glycolate and subsequent degration by heterotrophic bacteria. We have found evidence which supports an isotopic depletion (increased apparent E) scaled to O2 level associated with growth of Phormidium luridum at low CO2 concentrations (less than 0.04%). Similar to previous studies, isotopic differences between biomass and lipid biomarkers, and between lipid classes were positively correlated with overall fractionation, and should provide a means of estimating the influence of PR on overall isotopic composition of microbial mats. Several examples of microbial mats growing in the hydrothermal waters of Yellowstone National Park and the hypersaline marine evaporation ponds at Guerrero Negro, Baja Sur Mexico will be compared with a view to PR as a possible explanation of the relatively heavy C-isotope composition of hypersaline mats.

Jahnke, L. L.↗

Microbial Functional Responses Explain Alpine Soil Carbon Fluxes under Future Climate Scenarios

Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six in situ warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO 2 and CH 4 fluxes across all sites significantly (r > 0.70, P < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities.

54 ENVIRONMENTAL SCIENCES↗

Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms

Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.

Ecosystem engineering↗

Microbial dormancy and its impacts on northern temperate and boreal terrestrial ecosystem carbon budget

A large amount of soil carbon in northern temperate and boreal regions could be emitted as greenhouse gases in a warming future. However, lacking detailed microbial processes such as microbial dormancy in current biogeochemistry models might have biased the quantification of the regional carbon dynamics. Here the effect of microbial dormancy was incorporated into a biogeochemistry model to improve the quantification for the last century and this century. Compared with the previous model without considering the microbial dormancy, the new model estimated the regional soils stored 75.9 Pg more C in the terrestrial ecosystems during the last century and will store 50.4 and 125.2 Pg more C under the RCP8.5 and RCP2.6 scenarios, respectively, in this century. This study highlights the importance of the representation of microbial dormancy in earth system models to adequately quantify the carbon dynamics in the northern temperate and boreal natural terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Mason, Cayla N. (ORCID:0000000345983824)↗