Effects of initial microbial biomass abundance on respiration during pine litter decomposition
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59 BASIC BIOLOGICAL SCIENCES↗
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Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community
Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.
Active microbial community↗
Seasonal Controls on Microbial Depolymerization and Oxidation of Organic Matter in Floodplain Soils
Floodplain soils are vast reservoirs of organic carbon often attributed to anaerobic conditions that impose metabolic constraints on organic matter degradation. What remains elusive is how such metabolic constraints respond to dynamic flooding and drainage cycles characteristic of floodplain soils. Here, in this work, we show that microbial depolymerization and respiration of organic compounds, two rate-limiting steps in decomposition, vary spatially and temporally with seasonal flooding of mountainous floodplain soils (Gothic, Colorado, USA). Combining metabolomics and -proteomics, we found a lower abundance of oxidative enzymes during flooding coincided with the accumulation of aromatic, high-molecular weight compounds, particularly in surface soils. In subsurface soils, we found that a lower oxidation state of carbon coincided with a greater abundance of chemically reduced, energetically less favorable low-molecular weight metabolites, irrespective of flooding condition. Our results suggest that seasonal flooding temporarily constrains oxidative depolymerization of larger, potentially plant-derived compounds in surface soils; in contrast, energetic constraints on microbial respiration persist in more reducing subsurface soils regardless of flooding. Our work underscores that the potential vulnerability of these distinct anaerobic carbon storage mechanisms to changing flooding dynamics should be considered, particularly as climate change shifts both the frequency and extent of flooding in floodplains globally.
54 ENVIRONMENTAL SCIENCES↗
Heterotrophic respiration by soil microbes in a changing climate
Soil microbes strongly influence the soil organic carbon (SOC) pool, which globally stores ~2,000 PgC. Specifically, the balance between microbial heterotrophic respiration (R H ), which degrades SOC, and plant–microbe interactions that stabilize SOC determines whether terrestrial ecosystems are a net source or sink of CO 2 to the atmosphere. Here, in this Review, we evaluate how climate change alters these competing processes. R H is approximately half of total soil respiration, at ~50 PgC yr −1 , with 70% occurring in topsoils. Warming accelerates microbial metabolism, with a 10 °C temperature increase estimated to raise R H by ~50%, an effect that is particularly strong in Arctic soils. Warming also reduces soil moisture, further modulating R H , which responds nonlinearly to soil moisture, being limited by saturation and desiccation and meeting a maximum at intermediate levels. Consequently, R H is highly sensitive to future precipitation changes and drought. However, soil management strategies could enhance SOC stocks and persistence under climate change. Bacterial and fungal inoculants can promote SOC production and stabilization, while deep-rooting plants increase SOC inputs to deeper layers that experience lower R H . Agricultural practices and biochar amendments can also enhance SOC and reduce R H . Expanding field trials across regions, climates and soil types would improve empirical understanding of these responses and support better representation of R H in predictive models, enabling more accurate assessments of climate impacts on SOC storage.
Jansson, Janet K. [Pacific Northwest National Labo↗
Carbon availability, soil pH, and microbial allocation to nitrogen acquisition shape grassland heterotrophic respiration in response to a decade of nitrogen addition
Previous work has found that anthropogenic inputs of nitrogen (N) and phosphorus (P) impact heterotrophic respiration during soil organic matter decomposition in grasslands, a critical pathway through which carbon (C) is lost from soil to the atmosphere. While N addition typically reduces heterotrophic respiration, why the strength and direction of this N effect varies among sites is unclear. Here, to address this, we conducted a 339-day laboratory incubation to measure heterotrophic respiration from nine grasslands across North America that have received 10 years of factorial N and P fertilization. N addition reduced cumulative respiration most at sites with low pH, low microbial allocation towards N acquisition, and high soil C concentration and availability. However, N addition had neutral rather than positive effects on heterotrophic respiration in sites with high pH and decomposer allocation towards N acquisition. Across sites, a decade of N addition reduced heterotrophic respiration by ∼24 %, driven by reductions in microbial biomass. Heterotrophic respiration was less sensitive to P addition, despite its increasing microbial biomass. However, simultaneous N and P addition did ameliorate negative N effects. These results show that previously observed variation in the response of heterotrophic respiration to N addition can be explained by soil C availability and pH status, widely measured factors which can be used to predict how grassland C fluxes may change under continuing nutrient deposition.
N addition↗
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.↗
Generalizing Microbial Parameters in Soil Biogeochemical Models: Insights From a Multi‐Site Incubation Experiment
Abstract Incorporating microbial processes into soil biogeochemical models has received growing interest. However, determining the parameters that govern microbially driven biogeochemical processes typically requires case‐specific model calibration in various soil and ecosystem types. Here each case refers to an independent and individual experimental unit subjected to repeated measurements. Using the Microbial‐ENzyme Decomposition model, this study aimed to test whether a common set of microbially‐relevant parameters (i.e., generalized parameters) could be obtained across multiple cases based on a two‐year incubation experiment in which soil samples of four distinct soil series (i.e., Coland, Kesswick, Westmoreland, and Etowah) collected from forest and grassland were subjected to cellulose or no cellulose amendment. Results showed that a common set of parameters controlling microbial growth and maintenance as well as extracellular enzyme production and turnover could be generalized at the soil series level but not land cover type. This indicates that microbial model developments need to prioritize soil series type over plant functional types when implemented across various sites. This study also suggests that, in addition to heterotrophic respiration and microbial biomass data, extracellular enzyme data sets are needed to achieve reliable microbial‐relevant parameters for large‐scale soil model projections.
58 GEOSCIENCES↗
Sequential Abiotic-Biotic Processes Drive Organic Carbon Transformation in Peat Bogs
Peatlands, which store one-third of the terrestrial carbon (C), are subject to large disturbances under a changing climate. It is crucial to understand how microbial and physiochemical factors affect the vulnerability of these large C stores to predict climate induced greenhouse gas fluxes. Here, we used a combination of mass spectrometry and spectroscopy techniques, to understand sequential biotic and abiotic degradation pathways of Sphagnum fallax leachate in an anaerobic incubation experiment, in the presence and absence of microorganisms. Removal of microorganisms was carried out by passing aqueous samples through 0.2 µm filters. In this work, our results revealed that Sphagnum fallax leachate degradation by abiotic reactions is a significant contributor to CO 2 production. Further, abiotic factors, such as low pH, are responsible for partial dissolved organic carbon (DOC) degradation that produces bioavailable compounds that shift microbial metabolic pathways and stimulate respiration in peat bogs. Acid-catalyzed hydrolysis of Sphagnum-produced glycosides can provide the microbial communities with glucose and stimulate microbial respiration of DOC to CO 2 . These results, while unique to peatlands, demonstrate the importance and underscore the complexity of sequential abiotic and biotic processes on C cycling in peat bogs. It is therefore crucial to incorporate abiotic degradation and sequential below-ground biotic and abiotic interactions into climate models for a better prediction of the influence of climate change on DOC stability in peatlands. These findings might not be representative of other ecosystems with different environmental conditions including mineral-rich peatlands and plant matter in surface peat horizons that comprise discrete microbial populations, and DOC composition.
54 ENVIRONMENTAL SCIENCES↗
Electron transport across the cell envelope via multiheme c -type cytochromes in Geobacter sulfurreducens
Extracellular electron transfer (EET) enables certain microorganisms to respire using soluble and insoluble extracellular electron acceptors by transporting electrons across the cell envelope. Among these, G. sulfurreducens serves as a model organism for understanding direct EET pathways, where multiheme c-type cytochromes mediate electron transport from intracellular redox carriers to extracellular acceptors such as Fe(III) oxides and electrodes. This review focuses on heme-dependent electron transfer in Geobacter sulfurreducens, detailing the roles of inner membrane cytochromes, periplasmic carriers, outer membrane conduits, and recently characterized extracellular nanowires formed by polymerized multiheme c-type cytochromes, including OmcS, OmcE, and OmcZ. We examine the state of understanding of their physiological function, their structural features, expression patterns, and essentiality under various respiratory conditions. These insights advance our understanding of microbial anaerobic respiration and have implications for biogeochemical cycling, bioenergy generation, and bioremediation. The molecular architecture, assembly mechanisms, and secretion pathways of multiheme c-type cytochrome nanowires remain active areas of investigation, offering promising directions for future research and biotechnological innovation in engineered microbial systems.
Chemistry↗
Warming effects on grassland soil microbial communities are amplified in cool months
Abstract Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.
54 ENVIRONMENTAL 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↗
Linear two-pool models are insufficient to infer soil organic matter decomposition temperature sensitivity from incubations
Abstract Terrestrial carbon (C)-climate feedbacks depend strongly on how soil organic matter (SOM) decomposition responds to temperature. This dependency is often represented in land models by the parameter Q 10 , which quantifies the relative increase of microbial soil respiration per 10 °C temperature increase. Many studies have conducted paired laboratory soil incubations and inferred “active” and “slow” pool Q 10 values by fitting linear two-pool models to measured respiration time series. Using a recently published incubation study (Qin et al. in Sci Adv 5(7):eaau1218, 2019) as an example, here we first show that the very high parametric equifinality of the linear two-pool models may render such incubation-based Q 10 estimates unreliable. In particular, we show that, accompanied by the uncertain initial active pool size, the slow pool Q 10 can span a very wide range, including values as high as 100, although all parameter combinations are producing almost equally good model fit with respect to the observations. This result is robust whether or not interactions between the active and slow pools are considered (typically these interactions are not considered when interpreting incubation data, but are part of the predictive soil carbon models). This very large parametric equifinality in the context of interpreting incubation data is consistent with the poor temporal extrapolation capability of linear multi-pool models identified in recent studies. Next, using a microbe-explicit SOM model (RESOM), we show that the inferred two pools and their associated parameters (e.g., Q 10 ) could be artificial constructs and are therefore unreliable concepts for integration into predictive models. We finally discuss uncertainties in applying linear two-pool (or more generally multiple-pool) models to estimate SOM decomposition parameters such as temperature sensitivities from laboratory incubations. We also propose new observations and model structures that could enable better process understanding and more robust predictive capabilities of soil carbon dynamics.
54 ENVIRONMENTAL SCIENCES↗
Low-intensity frequent fires in coniferous forests transform soil organic matter in ways that may offset ecosystem carbon losses
The impact of shifting disturbance regimes on soil carbon (C) storage is a key uncertainty in global change research. Wildfires in coniferous forests are becoming more frequent in many regions, potentially causing large C emissions. Repeated low-intensity prescribed fires can mitigate wildfire severity, but repeated combustion may decrease soil C unless compensatory responses stabilize soil organic matter. Here, we tested how 30 years of decadal prescribed burning affected C and nitrogen (N) in plants, detritus, and soils in coniferous forests in the Sierra Nevada mountains, USA. Tree basal area and litter stocks were resilient to fire, but fire reduced forest floor C by 77% (-36.4 Mg C/ha). In mineral soils, fire reduced C that was free from minerals by 41% (-4.4 Mg C/ha) but not C associated with minerals, and only in depths ≤ 5 cm. Fire also transformed the properties of remaining mineral soil organic matter by increasing the proportion of C in a pyrogenic form (from 3.2% to 7.5%) and associated with minerals (from 46% to 58%), suggesting the remaining soil C is more resistant to decomposition. Laboratory assays illustrated that fire reduced microbial CO2 respiration rates by 55% and the activity of eight extracellular enzymes that degrade cellulosic and aromatic compounds by 40–66%. Lower decomposition was correlated with lower inorganic N (-49%), especially ammonium, suggesting N availability is coupled with decomposition. The relative increase in forms of soil organic matter that are resistant to decay or stabilized onto mineral surfaces, and the associated decline in decomposition suggest that low-intensity fires may promote mineral soil C storage in pools with long mean residence times in coniferous forests.
54 ENVIRONMENTAL SCIENCES↗
Southeastern U.S.A. Continental Shelf Respiratory Rates Revisited
Respiratory rates on the U. S. southeastern continental shelf have been estimated several times by different investigators, most recently by Jiang et al. (Biogeochemistry 98:101-113, 2010) who report lower mean rates thanwere found in earlier work and attribute the differences to analytical error in all methods used in earlier studies. The differences are, instead, attributable to the differences in the geographical scope of the studies. The lower estimates of regional organic carbon flux of Jiang et al. (Biogeochemistry 98:101-113, 2010) are a consequence of their extrapolation of data from a small portion of the shelf to the entire South Atlantic Bight. This comment examines the methodologies used as well as the variability of respiratory rates in this region over space and time.
Microbial respiration↗
Worswick Hot Springs: A Radioactive Hydrothermal Field Site
We report on a systematic characterization of the radiation environment and water temperatures of Worswick Hot Springs, which is in support of companion biochemical and microbial investigations of iron respiration in the ‘extreme’ microbial systems found at the field site. We have discovered localized areas of elevated radioactivity that are approximately four to five times greater than background radiation. Additionally, we have observed that both the radiation environment and the temperature of the spring waters vary over time. Because localized “hot spots” of elevated radiation and biofilms are easily accessible, various biological studies of radiation resistance and biosignature formation are possible, making this field site relevant for analog field studies that consider microbiology, geochemistry, and ionizing radiation. In addition to Worswick being a natural radiation biology laboratory that may also be relevant for space biology applications, we assert that these unusual environmental conditions may inform us about locations on Mars that are also enriched in radioactive elements and their potential for hosting biosignatures.
Jon C. Rask↗
Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications
Abstract Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
59 BASIC BIOLOGICAL SCIENCES↗
Coupled Biotic-Abiotic Processes Control Biogeochemical Cycling of Dissolved Organic Matter in the Columbia River Hyporheic Zone
A critical component of assessing the impacts of climate change on watershed ecosystems involves understanding the role that dissolved organic matter (DOM) plays in driving whole ecosystem metabolism. The hyporheic zone—a biogeochemical control point where ground water and river water mix—is characterized by high DOM turnover and microbial activity and is responsible for a large fraction of lotic respiration. Yet, the dynamic nature of this ecotone provides a challenging but important environment to parse out different DOM influences on watershed function and net carbon and nutrient fluxes. We used high-resolution Fourier-transform ion cyclotron resonance mass spectrometry to provide a detailed molecular characterization of DOM and its transformation pathways in the Columbia river watershed. Samples were collected from ground water (adjacent unconfined aquifer underlying the Hanford 300 Area), Columbia river water, and its hyporheic zone. The hyporheic zone was sampled at five locations to capture spatial heterogeneity within the hyporheic zone. Our results revealed that abiotic transformation pathways (e.g., carboxylation), potentially driven by abiotic factors such as sunlight, in both the ground water and river water are likely influencing DOM availability to the hyporheic zone, which could then be coupled with biotic processes for enhanced microbial activity. The ground water profile revealed high rates of N and S transformations via abiotic reactions. The river profile showed enhanced abiotic photodegradation of lignin-like molecules that subsequently entered the hyporheic zone as low molecular weight, more degraded compounds. While the compounds in river water were in part bio-unavailable, some were further shown to increase rates of microbial respiration. Together, river water and ground water enhance microbial activity within the hyporheic zone, regardless of river stage, as shown by elevated putative amino-acid transformations and the abundance of amino-sugar and protein-like compounds. This enhanced microbial activity is further dependent on the composition of ground water and river water inputs. Our results further suggest that abiotic controls on DOM should be incorporated into predictive modeling for understanding watershed dynamics, especially as climate variability and land use could affect light exposure and changes to ground water essential elements, both shown to impact the Columbia river hyporheic zone.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Representing Soil Microbial Dynamics and Organo‐Mineral Interactions in the E3SM Land Model (ELM‐ReSOM)
Explicit representation of soil microbial processes and interactions with biotic and abiotic processes in Earth System Models (ESMs) remains limited, despite their importance in biogeochemical cycles. To address this gap, which hinders prediction of global biogeochemial cycling and responses to atmospheric conditions, we integrated a microbe- and mineral-surface-explicit model, the Reaction-network-based model of soil organic matter and Microbes (ReSOM), into the Energy Exascale ESM (E3SM) land model (ELM). Here, we describe ELM-ReSOM and show a case study at a conifer forest in California. ELM-ReSOM accurately simulated surface CO 2 fluxes and SOM stocks, demonstrating improved representations of microbial and mineral interactions compared to the default ELM. We examined ELM-ReSOM sensitivity to microbial traits, enzyme properties, and organo-mineral interactions. Microbial traits such as the maximum mortality rate, transporter-density scaling factor, and maximum monomer assimilation rate were strong controllers of heterotrophic respiration, while these microbial traits and enzyme-related properties collectively influenced SOM stocks. Mineral surfaces primarily affected SOM stocks by adsorbing enzymes, thereby limiting depolymerization. Synergies among processes led to stronger impacts of parameters when evaluated together versus separately (i.e., most parameters had greater indirect than direct effects). For example, due to interactions of microbial necromass with mineral surface adsorption, the indirect effect of the maximum microbial mortality rate was 33% larger than its direct effect on SOM stock. Thus, microbial and enzyme dynamics and their interactions with mineral surfaces play critical roles in SOM cycling. Tackling the challenges of microbe-explicit models will advance understanding and modeling of SOM dynamics.
Tao, Jing [Lawrence Berkeley National Laboratory (↗