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At least 199 records · Page 11

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity

Background: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean type grassland administrated with 14 years of 7 g m –2 year –1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. Results: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. Conclusions: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation.

59 BASIC BIOLOGICAL SCIENCES↗

The influence of alfalfa-switchgrass intercropping on microbial community structure and function

The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N 2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. Here we analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N 2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.

59 BASIC BIOLOGICAL SCIENCES↗

Assimilation of SMAP and ASCAT Soil Moisture Retrievals into the JULES Land Surface Model Using the Local Ensemble Transform Kalman Filter

A land data assimilation system is developed to merge satellite soil moisture retrievals into the Joint U.K. Land Environment Simulator (JULES) land surface model (LSM) using the Local Ensemble Transform Kalman Filter (LETKF). The system assimilates microwave soil moisture retrievals from the Soil Moisture Active Passive (SMAP) radiometer and the Advanced Scatterometer (ASCAT) after bias correction based on cumulative distribution function fitting. The soil moisture assimilation estimates are evaluated with ground-based soil moisture measurements over the continental U.S. for five consecutive warm seasons (May–September of 2015–2019). The result shows that both SMAP and ASCAT retrievals improve the accuracy of soil moisture estimates. Especially, the SMAP single-sensor assimilation experiment shows the best performance with the increase of temporal anomaly correlation by ΔR ~ 0.05 for surface soil moisture and ΔR ~ 0.03 for root-zone soil moisture compared with the LSM simulation without satellite data assimilation. SMAP assimilation is more skillful than ASCAT assimilation primarily because of the greater skill of the assimilated SMAP retrievals compared to the ASCAT retrievals. The skill improvement also depends significantly on the region; the higher skill improvement in the western U.S. compared to the eastern U.S. is explained by the Kalman gain in the two experiments. Additionally, the regional skill differences in the single-sensor assimilation experiments are attributed to the number of assimilated observations. Finally, the soil moisture assimilation estimates provide more realistic land surface information than model-only simulations for the 2015 and the 2016 western U.S. droughts, suggesting the advantage of using satellite soil moisture retrievals in the current drought monitoring system.

SMAP↗

Potential application of satellite radar to monitor soil moisture

The microwave backscattering characteristics of soils as a function of moisture content are reviewed as a basis for the evaluation of the applicability of satellite radar to soil moisture determinations. Results of experiments showing the dependence of the complex dielectric constant, power reflection coefficient and backscattering coefficient of soil on its volumetric moisture content are presented. Results of a research program using the truck-mounted University of Kansas microwave active spectrometer to determine if, by the proper choice of sensor frequency, polarization and incidence, the sensor dynamic range in response to moisture variations may be greater than its response to other variations are considered in detail, and the optimum conditions of frequency (between 4 and 5 GHz), angular incidence (between 7 and 20 deg from nadir) and polarization (HH) obtained are indicated. An empirical model for the backscattering coefficient as a function of gravimetric moisture content derived on the basis of the experimental data is presented, and it is noted that available airborne and spaceborne data confirm the results of the ground-based sensors.

Ulaby, F. T.↗

Spectral properties /0.04 to 0.75 microns/ of soils exposed at the Viking 1 landing site

The bidirectional reflectance and photometric function (Hapke, 1981) was determined for seven patches of soil located near the Viking Lander 1 spacecraft. The soil photometric function has a prominent opposition effect in addition to a phase function that is strongly backscattering. The ratio of reflectances at a 1 deg phase angle to that at a 10 deg phase angle averages 1.25, 1.24, and 1.19 for blue, green, and red wavelengths respectively. The photometric function has a wavelength dependence, which causes color ratios to vary by up to 33% as a function of phase angle. Estimates of soil reflectance at a 5 deg phase angle averaged over the blue and green passbands of the Viking Lander cameras are 0.11 and 0.17, respectively, while estimates over the red channel range from 0.30 to 0.39. Brightness and color variations within the soil can be correlated with particle size, finer-grained soil being brighter and redder than coarser-grained soil. Lander soils, homogeneous in nature, are typical of brighter soils covering a large portion of the Martian surface.

Guinness, E. A.↗

Switchgrass ( Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function

Abstract Switchgrass ( Panicum virgatum L.) production for biofuel has the potential to produce reasonable yields on lands not suited for conventional agriculture. We assessed nine switchgrass cultivars representing lowland and upland ecotypes grown for 11 years at a site in the upper Midwest USA for belowground differences in soil carbon and nitrogen stocks, soil organic matter fractions, and standing root biomass to 1 m depth. We also compared potential nitrogen mineralization and carbon substrate use through community‐level physiological profiling in surface soils (0–10 cm depth). Average yields and standing root biomass differed among cultivars and between ecotypes, but we found no significant cultivar‐related impacts on soil carbon and nitrogen stocks, on the distribution of particulate and mineral‐associated soil organic matter fractions, nor on potential nitrogen mineralization or microbial community‐level physiological profiles. That these traits did not differ among cultivars suggests that soil carbon and nitrogen gains under switchgrass are likely to be robust with respect to cultivar differences, and to this point not much affected by breeding efforts.

Agriculture↗

The role of soil chemical properties and microbial communities on Dendrocalamus brandisii bamboo shoot quality, Yunnan Province, China

Objective To explore the effects of soil nutrients and microbial communities on the quality of Dendrocalamus brandisii shoots in different regions, providing a scientific basis for their development and utilization. Methods Using seven different geographic sources of D. brandisii from Yunnan Province as research subjects, this study employs chemical analysis and high-throughput sequencing to reveal the relationship between soil nutrients, microbial functional groups, and the nutritional quality of bamboo shoots. Results The results indicate that there are significant differences in soil nutrient content among the regions ( p < 0.05), with bamboo shoots from Baoshan Changning (CN) exhibiting the best overall nutritional quality. The key factors influencing bacterial community changes include pH, available phosphorus (AP), and available potassium (AK). In contrast, the main factors affecting fungal community changes are pH, soil organic matter (SOM), available potassium (AK), and total nitrogen (TN). This version maintains clarity and logical flow, making it easier for readers to understand the different factors influencing bacterial and fungal community changes. The diversity indices of soil microbial communities among different sources of Dendrocalamus brandisii show significant differences ( p < 0.05). The dominant groups in the seven regions include Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Ascomycota, and Basidiomycota. The soil microbial community in Baoshan Changning (CN) shows significant structural differences compared to the other six regions, with the highest relative abundances of Chloroflexi and Acidobacteriota. In contrast, the highest relative abundance of Proteobacteria is found in Honghe Shiping (SP), while Actinobacteriota has the highest relative abundance in Yuxi Xinping (XP). RDA analysis indicates that soil nutrients (SOM, pH, AP, TN) affect the water content, soluble sugar, and crude fat of bamboo shoots. Additionally, the bacterial communities including Actinobacteriota, Chloroflexi, Patescibacteria, GAL15, and Cyanobacteria influence the water content, soluble sugar, ash content, protein, and lignin of bamboo shoots. Discussion In the fungal community, Basidiomycota, Kickxellomycota, Mucoromycota, unclassified-k-Fungi, and Glomeromycota affect the water content and tannin levels in bamboo shoots. In summary, soil nutrients and soil microorganisms are interconnected and work together to influence the quality of bamboo shoots.

Chen, Qian↗

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple spatiotemporal scales, from which macrosystem patterns in SOM emerge. Theory on SOM turnover recognizes the resulting spatial and temporal conditionality in the effect sizes of controls that play out across macrosystems, and couples them through evolutionary and community assembly processes. For example, climate history shapes plant functional traits, which in turn interact with contemporary climate to influence SOM dynamics. Selection and assembly also shape the functional traits of soil decomposer communities, but it is less clear how in turn these traits influence temporal macrosystem patterns in SOM turnover. Here, we review evidence that establishes the expectation that selection and assembly should generate decomposer communities across macrosystems that have distinct functional effects on SOM dynamics. Representation of this knowledge in soil biogeochemical models affects the magnitude and direction of projected SOM responses under global change. Yet there is high uncertainty and low confidence in these projections. To address these issues, we make the case that a coordinated set of empirical practices are required which necessitate (1) greater use of statistical approaches in biogeochemistry that are suited to causative inference; (2) long-term, macrosystem-scale, observational and experimental networks to reveal conditionality in effect sizes, and embedded correlation, in controls on SOM turnover; and (3) use of multiple measurement grains to capture local- and macroscale variation in controls and outcomes, to avoid obscuring causative understanding through data aggregation. Here, when employed together, along with process-based models to synthesize knowledge and guide further empirical work, we believe these practices will rapidly advance understanding of microbial controls on SOM and improve carbon cycle projections that guide policies on climate adaptation and mitigation.

59 BASIC BIOLOGICAL SCIENCES↗

Prediction and measurement of soil bidirectional reflectance

The present model for soil bidirectional reflectance distribution functions in the visible and reflective IR ranges is based on a representation of soil surfaces by a collection of opaque spheres atop a Lambertian horizontal surface. The model is not sensitive to increases in the sphere area index beyond a value of 0.4. Observed soil reflectance factor data for a tilled field are noted to be consistent with those predicted by the model's expression of soil reflectance as a function of the horizontal area obscured by a sphere, the amount of surface in shadow, and relative brightness of a sphere, and the fraction of diffuse illumination.

Irons, James R.↗

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗

Joint retrieval of soil moisture and permafrost active layer thickness using L-band InSAR and P-band PolSAR

Seasonal subsidence measured by repeat-pass interferometric synthetic aperture radar (InSAR) can be used to infer the active layer thickness (ALT) in permafrost regions. The differential volume of soil water undergoing the phase change over the thaw season is one of the factors impacting the seasonal subsidence and is a function of both soil moisture profile and thaw depth. Without the information about soil moisture, this InSAR approach can have large biases in the ALT estimates when soil moisture profile is below saturation. Soil moisture and ALT can also be estimated from polarimetric synthetic aperture radar (PolSAR) backscatter observations but the sensing depth of the PolSAR approach is limited when deep ALT is present. In this paper, we integrated these two approaches and applied a joint retrieval method to estimate the soil moisture profiles and ALT from the L-band InSAR and P-band PolSAR data acquired over the Arctic-boreal region during the 2017 Arctic-Boreal Vulnerability Experiment (ABoVE) airborne campaign.

Schaefer, Kevin M.↗

Steady state, exposure age, and growth of agglutinates in lunar soils

Mineralogical evolution of lunar soils as a function of agglutinate content can be described with the help of a two-component model. Steady-state condition of exposed lunar soils can be achieved only by the balance of comminution, agglutination, and replenishment processes. Rate of replenishment depends on the meteoroid flux and the nature of the substrate which varies both in space and time. Rates of agglutination and comminution depend not only on the micrometeoritic flux but also on the chemical and modal composition of an exposed soil. It is concluded from modeling the above that steady-state condition of lunar soils is independent of its maturity or exposure age. Agglutinate content of a lunar soil can be used to estimate the relative exposure age of the soil only if the soil is in a non-steady-state condition.

Basu, A.↗

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types.

59 BASIC BIOLOGICAL SCIENCES↗

Pore2Chip: All-in-one python tool for soil microstructure analysis and micromodel design

The Pore2Chip Python package is designed to create 2D micromodels using extracted data from 3D X-ray computed tomography (XCT) images. This package helps analyze soil structure and function, allowing for the investigation of hydro-biogeochemical processes that impact mineral extraction and reactivity, oxygen concentrations, and nutrient availability in disturbed or managed soils. Key metrics encompass pore size distributions, pore throat size distributions, and connectivity (pore coordination numbers). The final output is a 2D scalable SVG design representing a core or aggregate. Designs can be fabricated with methods such as laser etching, 3D printing, and photolithography.

lab-on-chip↗

Corrinoids as model nutrients to probe microbial interactions in a soil ecosystem

Earth’s soils are habitats for microbial communities that drive biogeochemical cycling, plant growth, and carbon storage and persistence. The thousands of microbial species living in soil form an intricate web of interactions involving the exchange of molecules produced by different microbes. Understanding in detail how these molecular exchanges occur and how they shape microbial communities may lead to new methods to improve soil health, bioremediation efforts, and better understanding of biogeochemical processes. The overall goal of this research is to gain a deeper knowledge of the microbial interactions that drive soil community structure. However, the high functional and genomic diversity in soil microbiomes has posed a challenge for current microbiology methods to achieve this goal. This research leverages a model group of key metabolites related to cobalamin (vitamin B 12 ), known as corrinoids, to investigate microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗

Inclusion of a cold hardening scheme to represent frost tolerance is essential to model realistic plant hydraulics in the Arctic–boreal zone in CLM5.0-FATES-Hydro

As temperatures decrease in autumn, vegetation of temperate and boreal ecosystems increases its tolerance to freezing. This process, known as hardening, results in a set of physiological changes at the molecular level that initiate modifications of cell membrane composition and the synthesis of anti-freeze proteins. Together with the freezing of extracellular water, anti-freeze proteins reduce plant water potentials and xylem conductivity. To represent the responses of vegetation to climate change, land surface schemes increasingly employ “hydrodynamic” models that represent the explicit fluxes of water from soil and through plants. The functioning of such schemes under frozen soil conditions, however, is poorly understood. Nonetheless, hydraulic processes are of major importance in the dynamics of these systems, which can suffer from, e.g., winter “frost drought” events. In this study, we implement a scheme that represents hardening into CLM5.0-FATES-Hydro. FATES-Hydro is a plant hydrodynamics module in FATES, a cohort model of vegetation physiology, growth, and dynamics hosted in CLM5.0. We find that, in frozen systems, it is necessary to introduce reductions in plant water loss associated with hardening to prevent winter desiccation. This work makes it possible to use CLM5.0-FATES-Hydro to model realistic impacts from frost droughts on vegetation growth and photosynthesis, leading to more reliable projections of how northern ecosystems respond to climate change.

58 GEOSCIENCES↗

Spatial variability of soil hydraulics and remotely sensed soil parameters

The development of methods to correctly interpret remotely sensed information about soil moisture and soil temperature requires an understanding of water and energy flow in soil, because the signals originate from the surface, or from a shallow surface layer, but reflect processes in the entire profile. One formidable difficulty in this application of soil physics is the spatial heterogeneity of natural soils. Earlier work has suggested that the heterogeneity of soil hydraulic properties may be described by the frequency distribution of a single scale factor. The sensitivity of hydraulic and energetic processes to the variation of this scale factor is explored with a suitable numerical model. It is believed that such an analysis can help in deciding how accurately and extensively basic physical properties of field soils need to be known in order to interpret thermal or radar waveband signals. It appears that the saturated hydraulic conductivity needs to be known only to its order of magnitude, and that the required accuracy of the soil water retention function is about 0.02 volume fraction. Furthermore, the results may be helpful in deciding how the total scene or view field, as perceived through a sensor, is composed from the actual mosaic of transient soil properties, such as surface temperature or surface soil moisture. However, the latter proposition presupposes a random distribution of permanent properties, a condition that may not be met in many instances, and no solution of the problem is apparent.

Lascano, R. J.↗