Soil carbon cycling proxies: Understanding their critical role in predicting climate change feedbacks

Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments

Knowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (k_ref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and k_ref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and k_ref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.

Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient

Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.

Global patterns and abiotic drivers of ecosystem multifunctionality in dominant natural ecosystems

The potential patterns and processes of ecosystem multifunctionality (EMF) across global ecosystems are largely unknown, which limits our understanding of how ecosystems respond to drivers. Here we compile a global dataset that consists of 973 unique sites across the forest, grassland, and shrub ecosystems. We identify a critical global pattern of hump-shaped EMF relationship with mean annual precipitation at a threshold of ∼671 mm, where low and high precipitation patterns are discriminated. We find that climatic and soil factors jointly drive the EMF in low precipitation areas, and climatic factors dominate the EMF in high precipitation regions. However, when comparing across the three dominant ecosystems and precipitation regions, the key driver in EMF differs substantially. Specifically, climatic and soil factors dominate the EMF of low and high precipitation regions across forest ecosystems, respectively. Climatic drivers dominate the EMF under different precipitation conditions across grassland and shrub ecosystems. Overall, our findings highlight the importance of climatic and soil drivers on EMF, which should be considered in ecosystem stability models in response to global climate and land-use change scenarios.

Explicit spatial modeling at the pore scale unravels the interplay of soil organic carbon storage and structure dynamics

The structure of soil aggregates plays an important role for the turnover of particulate organic matter (POM) and vice versa. Analytical approaches usually do not disentangle the continuous re-organization of soil aggregates, caught between disintegration and assemblage. This led to a lack of understanding of the mechanistic relationship between aggregation and organic matter dynamics in soils. In this study, we took advantage of a process-based mechanistic model that describes the interaction between the dynamic (re-)arrangement of soil aggregates, based on dynamic image analysis data of wet-sieved aggregates, to analyze the turnover of POM, and simultaneous soil surface interactions in a spatially and temporally explicit way. Our novel modeling approach enabled us to unravel the temporal development of aggregate sizes, organic carbon (OC) turnover of POM, and surface coverage as affected by soil texture, POM input, and POM decomposition rate comparing a low and high clay soil (18% and 33% clay content). Our results reveal the importance of the dynamic re-arrangement of soil structure on POM-related turnover of OC in soils. Firstly, aggregation was largely determined by the POM input fostering aggregates through additional gluing joints outweighing soil texture at lower decomposition rate, whereas at higher decomposition rate, soil texture had a higher influence leading to larger aggregates in the high clay soil. Secondly, the POM storage increased with clay content, showing that surface interactions may delay the turnover of OC into CO₂ . Thirdly, we observed a structural priming effect in which the increased input of POM induced increased structural re-arrangement stimulating the mineralization of old POM. This work highlights that the dynamic re-arrangement of soil aggregates has important implications for OC turnover and is driven by underlying surface interactions where temporary gluing spots stabilize larger aggregates.

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 CO₂  × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO₂ 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 CO₂ concentration. 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.

Warming and elevated CO2 promote rapid incorporation and degradation of plant-derived organic matter in an ombrotrophic peatland

Rising temperatures have the potential to directly affect carbon cycling in peatlands by enhancing organic matter (OM) decomposition, contributing to the release of CO₂ and CH₄ to the atmosphere. In turn, increasing atmospheric CO₂ concentration may stimulate photosynthesis, potentially increasing plant litter inputs belowground and transferring carbon from the atmosphere into terrestrial ecosystems. Key questions remain about the magnitude and rate of these interacting and opposing environmental change drivers. Here, we assess the incorporation and degradation of plant- and microbe-derived OM in an ombrotrophic peatland after 4 years of whole-ecosystem warming (+0, +2.25, +4.5, +6.75 and +9°C) and two years of elevated CO₂  manipulation (500 ppm above ambient). We show that OM molecular composition was substantially altered in the aerobic acrotelm, highlighting the sensitivity of acrotelm carbon to rising temperatures and atmospheric CO₂ concentration. While warming accelerated OM decomposition under ambient CO₂ , new carbon incorporation into peat increased in warming × elevated CO₂ treatments for both plant- and microbe-derived OM. Using the isotopic signature of the applied CO₂ enrichment as a label for recently photosynthesized OM, our data demonstrate that new plant inputs have been rapidly incorporated into peat carbon. Our results suggest that under current hydrological conditions, rising temperatures and atmospheric CO₂  levels will likely offset each other in boreal peatlands.

Differences in substrate use linked to divergent carbon flow during litter decomposition

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles

Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C₆₀) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C₆₀ on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO₂ fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C₆₀. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.

Soil carbon loss with warming: New evidence from carbon-degrading enzymes

Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long-term predictions of climate C-feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta-analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long-term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short-term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long-term climate-C feedbacks.

Microbial dynamics and soil physicochemical properties explain large-scale variations in soil organic carbon

First-order organic matter decomposition models are used within most Earth System Models (ESMs) to project future global carbon cycling; these models have been criticized for not accurately representing mechanisms of soil organic carbon (SOC) stabilization and SOC response to climate change. New soil biogeochemical models have been developed, but their evaluation is limited to observations from laboratory incubations or few field experiments. Given the global scope of ESMs, a comprehensive evaluation of such models is essential using in situ observations of a wide range of SOC stocks over large spatial scales before their introduction to ESMs. In this study, we collected a set of in situ observations of SOC, litterfall and soil properties from 206 sites covering different forest and soil types in Europe and China. These data were used to calibrate the model MIMICS (The MIcrobial-MIneral Carbon Stabilization model), which we compared to the widely used first-order model CENTURY. We show that, compared to CENTURY, MIMICS more accurately estimates forest SOC concentrations and the sensitivities of SOC to variation in soil temperature, clay content and litter input. The ratios of microbial biomass to total SOC predicted by MIMICS agree well with independent observations from globally distributed forest sites. By testing different hypotheses regarding (using alternative process representations) the physicochemical constraints on SOC deprotection and microbial turnover in MIMICS, the errors of simulated SOC concentrations across sites were further decreased. We show that MIMICS can resolve the dominant mechanisms of SOC decomposition and stabilization and that it can be a reliable tool for predictions of terrestrial SOC dynamics under future climate change. It also allows us to evaluate at large scale the rapidly evolving understanding of SOC formation and stabilization based on laboratory and limited filed observation.

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest

The spatial and temporal linkages between turnover of soil microbial communities and their associated functions remain largely unexplored in terrestrial ecosystems. Yet defining these relationships and how they vary across ecosystems and microbial lineages is key to incorporating microbial communities into ecological forecasts and ecosystem models. To define linkages between turnover of soil bacterial and fungal communities and their function we sampled fungal and bacterial composition, abundance, and enzyme activities across a 3-ha area of wet tropical primary forest over 2 yr. We show that fungal and bacterial communities both exhibited temporal turnover, but turnover of both groups was much lower than in temperate ecosystems. Turnover over time was driven by gain and loss of microbial taxa and not changes in abundance of individual species present in multiple samples. Only fungi varied over space with idiosyncratic variation that did not increase linearly with distance among sampling locations. Only phosphorus-acquiring enzyme activities were linked to shifts in septate, decomposer fungal abundance; no enzymes were affected by composition or diversity of fungi or bacteria. Although temporal and spatial variation in composition was appreciable, because turnover of microbial communities did not alter the functional repertoire of decomposing enzymes, functional redundancy among taxa may be high in this ecosystem. Slow temporal turnover of tropical soil microbial communities and large functional redundancy suggests that shifts in abundance of particular functional groups may capture ecosystem function more accurately than composition in these heterogeneous ecosystems.

Legacy of a Pleistocene bacterial community: Patterns in community dynamics through changing ecosystems

Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.

Resource Legacies of Organic and Conventional Management Differentiate Soil Microbial Carbon Use

Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with ¹³C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.