Effect of microbial growth rate on temperature and metabolic water recorded in 18O/16O ratios of PO4 in DNA
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Fei Wang↗
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Growth rate as a link between microbial diversity and soil biogeochemistry
The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.
54 ENVIRONMENTAL SCIENCES↗
Drought Reduces Formation, but Enhances Persistence, of Mineral‐Associated Organic Matter in a Grassland Soil
Drought effects are pervasive in terrestrial ecosystems, yet there is limited understanding of how drought impacts the transformation of plant carbon (C) inputs to mineral-associated organic matter (MAOM)—the largest and slowest-cycling pool of soil organic carbon (SOC). In a 12-week 13 C-CO 2 greenhouse labeling experiment, we tracked the formation of MAOM derived from the two dominant sources of plant C input to the mineral soil—living root inputs ( 13 C-rhizodeposits) and decaying root inputs ( 13 C-root detritus)—under normal moisture and droughted conditions in a semiarid grassland soil. At the end of the 12-week period, we also measured the persistence of 13 C-MAOM formed from rhizodeposits versus root detritus via a subsequent persistence assay. Drought reduced the formation of MAOM derived from living roots by decreasing rhizodeposits, reducing microbial growth rates, and altering the composition of organic matter, lipids, and metabolites. Drought initially delayed the formation of MAOM derived from root detritus by slowing the early stages of root litter decomposition (week 4–8), but did not decrease total MAOM formation by the end of the 12-week period. Notably, drought enhanced the persistence of MAOM derived from root detritus, but did not influence the persistence of MAOM derived from rhizodeposits. Our results provide some of the first direct evidence that drought can reduce the formation of MAOM in a grassland soil, but may enhance its persistence, based on the source of plant input from which MAOM is derived.
13C- labeling↗
Microbial growth and physiology in space - A review
An overview of microbial behavior in closed environments is given with attention to data related to simulated microgravity and actual space flight. Microbes are described in terms of antibiotic sensitivity, subcellular structure, and physiology, and the combined effects are considered of weightlessness and cosmic radiation on human immunity to such microorganisms. Space flight results report such effects as increased phage induction, accelerated microbial growth rates, and the increased risk of disease communication and microbial exchange aboard confining spacecraft. Ultrastructural changes are also noted in the nuclei, cell membranes, and cytoplasmic streaming, and it appears that antibiotic sensitivity is reduced under both actual and simulated conditions of spaceflight.
Cioletti, Louis A.↗
Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model
Abstract Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
59 BASIC BIOLOGICAL SCIENCES↗
Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”
This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.
54 ENVIRONMENTAL SCIENCES↗
Microbiological challenges of space habitation
The effects of space flight on the growth and pathogenicity of microorganisms and on the human immune response are reviewed giving attention to the implications for spacecraft design. The major sources of microbes within space habitats on long-duration missions are listed including food, crewmembers, and payloads. Many of the microorganisms are shown to be airborne suggesting that effective air-filtration techniques are required for the designs of the Space Station and other vehicles. It is shown that microbial growth rates generally increase during space flight, and space flight is thought to attenuate the human immune response. Some beneficial roles for microbes are identified demonstrating the need for careful control, application, and monitoring of microorganisms in the long-duration spaceflight environment.
Pierson, D. L.↗
Shrub and sedge rhizosphere communities display distinct affinities toward exudates and soil organic matter degradation: a quantitative stable isotope probing analysis
Warming temperatures are accelerating permafrost thaw and changing tundra vegetation, where woody shrubs are displacing sedges. Shrubs, such as Betula nana, and sedges, such as Eriophorum vaginatum, exhibit distinct life strategies including unique root-associated, or rhizosphere microbial communities. As permafrost thaws it unlocks previously unavailable carbon and nutrient sources resulting in deeper roots and a translocation of rhizosphere communities. Because permafrost microbial communities contain lower diversity and biomass than rhizosphere communities, the coalescence of rhizosphere and permafrost microbial communities could alter soil organic matter (SOM) degradation rates and increase greenhouse gas emissions. To identify metabolic strategies across distinct rhizosphere and permafrost microbial communities we conducted an isotope tracing incubation experiment. We inoculated thawed permafrost with shrub and sedge rhizosphere communities while adding exudates or water daily and compared this to an uninoculated control. After 46 days, we spiked samples with 18O enriched water or 13C enriched exudates and measured isotope incorporation into microbial DNA with quantitative stable isotope probing (qSIP). Our results indicate that exudate additions had little effect on uninoculated permafrost communities but the addition of exudates and rhizosphere inoculants had a compounding effect on respiration rates. We found that soils inoculated with shrub rhizosphere communities contained a mixture of exudate and SOM degraders while soils inoculated with sedge rhizosphere communities contained mainly SOM degraders. Finally, we found that individual microbial taxa exhibited maximum growth rates under specific combinations of microbial inoculant communities and exudate addition treatments. Our results reveal that microbial niches are strongly influenced by substrate preferences and community context, and suggest that a reduction in sedges and an expansion of shrubs may provide a mechanism by which permafrost carbon losses are mitigated through corresponding shifts in microbial communities and their substrate preferences.
Schaefer, Sean R [Natural Resources and Earth Syst↗
Root Zone Respiration on Hydroponically Grown Wheat Plant Systems
Root respiration is a biological phenomenon that controls plant growth and physiological development during a plant's lifespan. This process is dependent on the availability of oxygen in the system where the plant is located. In hydroponic systems, where plants are submerged in a solution containing vital nutrients but no type of soil, the availability of oxygen arises from the dissolved oxygen concentration in the solution. This oxygen concentration is dependent on the , gas-liquid interface formed on the upper surface of the liquid, as given by Henry's Law, depending on pressure and temperature conditions. Respiration rates of the plants rise as biomass and root zone increase with age. The respiration rate of Apogee wheat plants (Triticum aestivum) was measured as a function of light intensity (catalytic for photosynthesis) and CO2 concentration to determine their effect on respiration rates. To determine their effects on respiration rate and plant growth microbial communities were introduced into the system, by Innoculum. Surfactants were introduced, simulating gray-water usage in space, as another factor to determine their effect on chemical oxygen demand of microbials and on respiration rates of the plants. It is expected to see small effects from changes in CO2 concentration or light levels, and to see root respiration decrease in an exponential manner with plant age and microbial activity.
Soler-Crespo, R. A.↗
Mass-Specific Power at the Organism and Biosphere Level
The concept of mass-specific power (MSP) quantitatively relates energy flux to the biomass that flux can sustain. We sought to assess the range and distribution of MSP as expressed at both the organism and biosphere level. The former serves to establish what is possible, and what predominates, in physiological terms; the latter reflects the expression of that physiological potential in an environmental context. To assess the potential range of MSP across a diversity of organisms and physiological states, we compiled a data set of more than 10,000 individual MSP measurements, encompassing more than 2900 unique species and spanning 22 orders of magnitude in body mass. Across the data set, MSP varies over six orders of magnitude, from 3 x 10-5 to 49 Watts per gram biomass carbon (W/gC), but the majority of measured values fall within a relatively narrow range of 0.018 ± 6.4-fold W/gC. It is well documented, and clearly expressed in the data set, that MSP exhibits a strong mass dependence within specific taxa (e.g., birds, mammals, and many others); however, MSP exhibits no mass dependence when considering the data set overall. To assess the expression of MSP in environmental context, we estimated energy utilization rates within eight distinct components of the global biosphere, and for the biosphere overall, and used recently published estimates of biomass within those components to compute MSP. We estimate MSP of 0.005 W/gC for the global biosphere as a whole. The close agreement with the organism-level all-species mean (within 4-fold) is noteworthy because the organism-level data set is dominated in statistical terms by animals, while the global biosphere is dominated in mass terms by trees and microorganisms. The various components of the microbe-dominated marine biosphere exhibit a systematic 5 order of magnitude decrease in MSP from the top of the water column (marine primary producers: 0.9 W/gC) to the depths of the sediment column (> 1m sediment biota: 3 x 10-6 W/gC). Biomass turnover rates, combined with the microbial capacity for both high specific growth rates and low maintenance rates, appear to underlie this large range in MSP, which is not expressed to the same extent in the terrestrial biosphere.
Tori M Hoehler↗
Terrestrial carbon dynamics in an era of increasing wildfire
In an increasingly flammable world, wildfire is altering the terrestrial carbon balance. However, the degree to which novel wildfire regimes disrupt biological function remains unclear. Here, we synthesize the current understanding of above and below ground processes that govern carbon loss and recovery across diverse ecosystems. In this study, we find that intensifying wildfire regimes are increasingly exceeding biological thresholds of resilience, causing ecosystems to convert to a lower carbon-carrying capacity. Growing evidence suggests that plants compensate for fire damage by allocating carbon below ground to access nutrients released by fire, while wildfire selects for microbial communities with rapid growth rates and the ability to metabolize pyrolyzed carbon. Determining controls on carbon dynamics following wildfire requires integration of experimental and modeling frameworks across scales and ecosystems. Fire severity is expected to increase as a result of warming. This will potentially amplify climate change due to its impact on the carbon cycle. This Review discusses ecosystem carbon loss and recovery following wildfire, and highlights where further work is needed to inform model predictions.
54 ENVIRONMENTAL SCIENCES↗
Enzyme activity in terrestrial soil in relation to exploration of the Martian surface
An exploration was made of enzyme activities in soil, including abundance, persistence and localization of these activities. An attempt was made to develop procedures for the detection and assaying of enzymes in soils suitable for presumptive tests for life in planetary soils. A suitable extraction procedure for soil enzymes was developed and measurements were made of activities in extracts in order to study how urease is complexed in soil organic matter. Mathematical models were developed, based on enzyme action and microbial growth in soil, for rates of oxidation of nitrogen as nitrogen compounds are moved downward in soil by water flow. These biogeochemical models should be applicable to any percolating system, with suitable modification for special features, such as oxygen concetrations, and types of hydrodynamic flow.
Ardakani, M. S.↗
Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture
The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.
59 BASIC BIOLOGICAL SCIENCES↗
Continuous propagation of microalgae. III.
Data are presented which give the specific photosynthetic rate and the specific utilization rates of urea and carbon dioxide as functions of specific growth rate for Chlorella. A mathematical model expresses a set of mass balance relations between biotic and environmental materials. Criteria of validity are used to test this model. Predictive procedures are complemented by a particular model of microbial growth. Methods are demonstrated for predicting substrate utilization rates, production rates of extracellular metabolites, growth limiting conditions, and photosynthetic quotients from propagator variables.
Hanson, D. T.↗
Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models
Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.
Tang, Jinyun [Lawrence Berkeley National Laborator↗
Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling
The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the number or growth rate of surviving cells. We are on our second prototype iteration, with demonstrated functions of microbial growth monitoring and dynamic exposure to UV-C radiation and temperature. We plan to add functionality for general chemical presence or absence by Nov. 2013. By making the project low-cost and open-source, we hope to encourage others to use it as a basis for future development of a common microbial environmental adaptation testbed.
Microbiology↗
CRADA Number NFE-24-10495 with Algaeo, LLC (CRADA Final Report)
This study investigated the potential for a synthetic consortium of mutualistic terrestrial microbes— comprising the fungi Laccaria bicolor and Serendipita indica alongside bacterial Pseudomonas strains—to influence the growth and productivity of the freshwater microalgae Chlorella vulgaris. The project aimed to determine if microbial complexes engineered to enhance terrestrial plant growth could provide similar growth-promoting benefits or pathogen resistance within an aquatic algal system. Using a quantitative experimental design, C. vulgaris was co-cultured with the microbial mix under controlled laboratory conditions, with growth rates, biomass density, and metabolic activity monitored over a standard cultivation period. The results demonstrated no significant symbiotic relationship or growth enhancement between these terrestrial microbes and the microalgae, as the C. vulgaris maintained independent growth trajectories unaffected by the fungal or bacterial inoculants. We conclude that the specialized mutualisms of these fungi and bacteria are likely niche-specific to vascular plants and do not readily translate to the phycosphere of C. vulgaris. These findings are valuable to synthetic biologists and bioenergy researchers, as they define the functional boundaries of inter-kingdom microbial engineering and underscore the necessity of selecting niche-compatible species when designing consortia for industrial algal cultivation.
60 APPLIED LIFE SCIENCES↗
Thermodynamic control on the decomposition of organic matter across different electron acceptors
The increasing availability of high-resolution characterization of natural organic matter (OM) data has shifted the paradigm of lumped descriptions of OM components and potential microbial activities. Our recent development of a substrate-explicit thermodynamic model uniquely enables incorporating complex OM pools to formulate biogeochemical reaction models based on their elemental compositions. While this previous work facilitates prediction of aerobic respiration of complex OM, it is equally imperative to consider the role of non-oxygenic electron acceptors in regulating OM turnover and the fate of carbon. In this study, we significantly expand our previous model by flexibly incorporating both detailed OM chemistry and electron acceptors other than oxygen. Here, our modeling analysis has revealed substantial variations in the energy status of OM molecules across different soils, which drive the co-occurrence of different electron-accepting processes. We demonstrated the effectiveness of the proposed model using a consistency check with experimental data. Through systematic evaluation of the impact of diverse chemical inputs (both electron donors and acceptors) on OM decomposition, the new model also revealed how key microbial growth parameters such as carbon use efficiency (CUE) and reaction rates vary across different electron-accepting processes. Our model provides a unified framework integrating thermodynamic and kinetic constraints on microbial metabolic activities. It complements traditional kinetic models, which are often designed solely to capture mass fluxes. We conclude that thermodynamic modeling emerges as a powerful tool for describing the mechanisms underlying the interplay between microbial growth and OM chemistry and cycling across different electron acceptors, enhancing our ability to project complex ecosystem behaviors in dynamic environments.
59 BASIC BIOLOGICAL SCIENCES↗