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Groundwater aquifers worldwide experience unsustainable depletion, compounded by population growth, economic development, and climate forcing. Managed aquifer recharge provides one tool to alleviate flood risk and replenish groundwater. However, concerns grow that intentional flooding of farmland for groundwater recharge, a practice known as Ag-MAR, may increase the leaching of pesticides and other chemicals into groundwater. This study employs a physically based unsaturated flow model to determine the fate and transport of residues of four pesticide in three vadose zone profiles characterized by differing fractions of sand (41 %, 61 %, and 84 %) in California's Central Valley. Here, we show that the complex heterogeneity of alternating coarse and fine-grain hydrogeologic units controls the transit times of pesticides and their adsorption and degradation rates. Unsaturated zones that contain a higher fraction of sand are more prone to support preferential flow, higher recharge rates (+8 %), and faster (42 %) water flow and pesticide transport, more flooding-induced pesticide leaching (about 22 %), as well as more salt leaching correlating with increased risks of groundwater contamination. Interestingly, considering preferential flow predicted higher degradation and retention rates despite shorter travel times, attributed to the trapping of pesticides in immobile zones where they degrade more effectively. The findings underscore the importance of considering soil texture and structure in Ag-MAR practices to minimize environmental risks while enhancing groundwater recharge. The study also highlights that selecting less mobile pesticides can reduce leaching risks in sandy areas.

Preplant soil disinfestation often relies on harmful soil fumigants; however, the efficacy of sustainable alternatives using biomass amendment fermentation is limited to tillage depths (0-15 cm). This soil column study evaluated whether increasing the irrigation frequency could promote anaerobic pest-suppressive conditions in deeper soils by leaching biocidal fermentation products (organic acids) from surface-applied amendments. Columns received either singular (standard) or weekly irrigation. Almond hulls, an agricultural byproduct, were either incorporated 0-15 cm into soil or applied as a surface mulch. Oxygen and organic acids were measured at 4-50 cm over 21 days, and the experiment was conducted in triplicate. Anaerobic conditions (3% O2) were achieved after 5 days, corresponding to acetic acid accumulation below amended layers: maximum concentrations ranged from 42 to 93 mM at 19-50 cm depths. Additional irrigation further increased concentrations in the deepest layer (50 cm) by almost 50%, demonstrating that water management can enable strategies for depth-dependent soil pest control. This may be particularly valuable for soil disinfestation ahead of the establishment of deep-rooted crops.

Context: The rice-wheat (RW) system, spanning 13.5 million hectares in South Asia, is crucial for food security and livelihoods. However, intensive conventional tillage-based practices have harmed soil and environmental health, decreased productivity trends and increased greenhouse gas emissions. Objective: This study aims to develop resilient, climate-smart cropping systems within the RW system, focusing on soil and crop productivity, economic viability, and reduced greenhouse gas (GHG) emissions. Methods: Over eight years, the study evaluated diverse parameters compared to farmer practices (FP) in seven scenarios (Sc), including one representing FP (Sc1) and six based on conservation agriculture (CA) principles. The study assessed system crop productivity, economic returns, soil quality (organic carbon; OC, nitrogen; N, phosphorus; P, potassium; K contents, bulk density; BD, soil aggregation, infiltration rates, microbial counts, and earthworm density), and GHG emissions. Results: CA-based scenarios (Sc2 to Sc7) showed improved soil quality, lower bulk density, enhanced soil aggregation, and increased infiltration rates compared to Sc1. In the 0–15 cm layer, surface soil organic carbon (OC) and C stock were 63.7 % and 49.6 % higher, respectively, in CA-based scenarios. Additionally, available N, P and K contents in the surface layer increased by 10.2 %, 28.6 %, and 21.8 % under CA-based scenarios. Adoption of CA in intensified maize-based scenarios (Sc4 and Sc5) led to the increased system and economic yields, higher soil quality index (SQI), reduced GHG emissions and increased C stock compared to Sc1. Implications: The study highlights that Conservation Agriculture (CA) practices and diversified crop rotations can address issues like falling crop productivity, reduced economic returns, soil degradation, and increasing environmental impacts in northwestern India's traditional rice-wheat system. However, widespread adoption requires government policies, including C credit payments and guaranteed markets with supportive pricing.

Soil microorganisms help transform plant inputs into mineral-associated soil organic carbon (SOC) – the largest and slowest-cycling pool of organic carbon on land. However, the microbial traits that influence this process are widely debated. While current theory and biogeochemical models have settled on carbon-use efficiency (CUE) and growth rate as positive predictors of mineral-associated SOC, empirical tests are sparse, with contradictory observations. Using 13C-labeling of an annual grass (Avena barbata) under two moisture regimes, we found that microbial traits associated with formation of 13C-mineral-associated SOC varied by soil habitat, as did active microbial taxa and SOC chemical composition. In the rhizosphere, bacterial-dominated communities with fast growth, high biomass, and high extracellular polymeric substance (EPS) production were positively associated with 13C-mineral-associated SOC. In contrast, the detritusphere held communities dominated by fungi and more filamentous bacteria, and with greater exoenzyme activity; there, 13C-mineral-associated SOC was associated with slower microbial growth and lower microbial biomass. CUE was a negative predictor of 13C-mineral-associated SOC in both habitats. Using 13C-quantitative stable isotope probing, we found that the majority of 13C assimilation in the rhizosphere and detritusphere at week 12 of the experiment was performed by very few bacterial and fungal taxa (3–5% of the total taxa that assimilated 13C). Several complementary chemical analyses (13C-NMR, FTICR-MS, and STXM-NEXAFS) suggested that SOC in the rhizosphere had a more oxidized chemical signature, while SOC in the detritusphere had a less oxidized, more lignin-like chemical signature. Our findings challenge current theory by demonstrating that microbial traits linked with mineral-associated SOC are not universal, but vary with soil habitat and moisture conditions, and are shaped by a small number of active taxa. Emerging SOC models that explicitly reflect these interactions may better predict SOC storage, since climate change causes shifts in soil moisture regimes and the ratio of living versus decaying roots.

Permafrost stability is significantly influenced by the thermal buffering effects of snow and active-layer peat soils. In the warm season, peat soils act as a barrier to downward heat transfer mainly due to their low thermal conductivity. In the cold season, the snowpack serves as a thermal insulator, retarding the release of heat from the soil to the atmosphere. Currently, many global land models overestimate permafrost soil temperature and active layer thickness (ALT), partially due to inaccurate representations of soil organic matter (SOM) density profiles and snow thermal insulation. In this study, we evaluated the impacts of SOM and snow schemes on ALT simulations at pan-Arctic permafrost sites using the Energy Exascale Earth System Model (E3SM) land model (ELM). We conducted simulations at the Circumpolar Active Layer Monitoring (CALM) sites across the pan-Arctic domain. We improved ELM-simulated site-level ALT using a knowledge-based hierarchical optimization procedure and examined the effects of precipitation-phase partitioning methods (PPMs), snow compaction schemes, and snow thermal conductivity schemes on simulated snow depth, soil temperature, ALT, and CO2 fluxes. Results showed that the optimized ELM significantly improved agreement with observed ALT (e.g. RMSE decreased from 0.83 m to 0.15 m). Our sensitivity analysis revealed that snow-related schemes significantly impact simulated snow thermal insulation levels, soil temperature, and ALT. For example, one of the commonly used snow thermal conductivity schemes (quadratic Sturm or SturmQua) generally produced warmer soil temperatures and larger ALT compared to the other two tested schemes. The SturmQua scheme also amplified the model’s sensitivity to PPMs and predicted deeper ALTs than the other two snow schemes under both current and future climates. The study highlights the importance of accurately representing snow-related processes and peat soils in land models to enhance permafrost dynamics simulations.

Understanding connectivity between the soil and deeper bedrock groundwater is needed to accurately predict a watershed's response to perturbation, such as drought. Yet, the bedrock groundwater dynamics in mountainous environments are typically under-constrained and excluded from watershed hydrologic models. Here, we investigate the role of groundwater characterized with decadal and longer water ages on the hydrologic and mass-transport processes within a steep snow-dominated mountain hillslope in the Central Rocky Mountains (USA). We quantify subsurface and surface water mass-balance, groundwater flowpaths, and age distributions using the ParFlow-CLM integrated hydrologic and EcoSLIM particle tracking models, which are compared to hydrometric and environmental tracer observations. An ensemble of models with varied soil and hydrogeologic parameters reproduces observed groundwater levels and century-scale mean ages inferred from environmental tracers. The numerical models suggest soil water near the toe of the hillslope contains considerable (>60 % of the mass-flux) contributions from bedrock flowpaths characterized with water ages >10 years. Flowpath connectivity between the deeper bedrock and soil systems is present throughout the year, highlighting the potentially critical role of groundwater with old ages on processes such as evapotranspiration and streamflow generation. The coupled numerical model and groundwater age observations show the bedrock groundwater system influences the hillslope hydrodynamics and should be considered in mountain watershed conceptual and numerical models.

Understanding the mechanisms that control seasonal groundwater recharge at local and intermediate scales is critical for understanding contaminant transport. The recharge mechanism of seasonal precipitation and irrigation, companied with legacy wastewater in porewater in alluvial aquifer were complicated due to the seasonal variation of multiple recharge sources. In this study, a long-term wastewater leakage and irrigation region along the Tanghe Wastewater Reservoir (TWR) in the alluvial plain area of North China Plain to investigate the recharge mechanism from unsaturated zone to the upper shallow groundwater affected by multiple water sources. Water chemical ions and stable isotopes of water (2H and 18O) of 30 m deep sediment profiles and groundwater boreholes were used to trace the recharge processes. The porewater stable isotopes of the sediment profiles revealed vertical recharge rates ranging from 0.63 to 1.09 m/year for the layered unsaturated zone with silt and silty clay. Due to the matrix flow through unsaturated zone, the legacy wastewater in the unsaturated zone affected the variation of groundwater quality in long term. However, fast flow (i.e., preferential or lateral flow) occurred in sand layers of alluvial aquifers lead to significant precipitation contributions (44 to 61 %) to the upper shallow groundwater (USGW) recharge, resulting in the seasonal variation of stable isotopes and water chemical ions. Affected by the fast flow with seasonal variations and matrix flow with legacy wastewater in the unsaturated zone, the δ2H and δ18O relationship of the USGW showed two types of hysteresis loops in the dual isotope space: 1) groundwater in regions affected by the TWR wastewater leakage shows narrow loops and a nearly straight line with end-members of precipitation that recharged to groundwater by fast flow, and evaporated porewater plotting along the TWR evaporation line; and 2) groundwater in irrigated farmlands with low and high irrigation amounts and intense evaporation shows stronger hysteresis with loops overlapping with shallow porewater, suggesting the impact of legacy wastewater of the unsaturated zone on groundwater. The residual pollutants in soil and the type of fast flow determine the different seasonal variation of groundwater quality. Preferential flow in alluvial aquifer regions can increase the proportion of seasonal recharge from precipitation, resulting in the rapid introduction of contaminants from surface or shallow soils into the alluvial aquifer.

Background: Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations. Objectives: We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations. Results and conclusions: Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.

Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms such as Escherichia coli observed in higher frequency in young calves compared to older cattle. In this study, we characterized the genomes of enteric MDR E. coli from pre-weaned dairy calves with and without diarrhea and evaluated the influence of host-level factors on genomic composition. Whole genome sequence comparative analysis of E. coli (n = 43) revealed substantial genomic diversity that primarily clustered by sequence type and was minimally driven by calf diarrheal disease status (healthy, diarrheic, or recovered), antimicrobial exposure, and dietary zinc supplementation. Diverse AMR genes (ARGs)-including extended-spectrum beta-lactamase genes and quinolone resistance determinants-were identified (n = 40), with unique sets of ARGs co-occurring in gene clusters with large AMR plasmids IncA/C2 and IncFIB(AP001918). Zinc supplementation was not significantly associated with the selection of individual ARGs in E. coli, however analysis of ARG and metal resistance gene pairs identified positive associations between certain aminoglycoside, beta-lactam, sulfonamide, and trimethoprim ARGs with acid, tellurium and mercury resistance genes. Although E. coli in this study lacked the typical virulence factors of diarrheagenic strains, virulence genes overlapping with those in major pathotypes were identified. Among the 103 virulence genes detected, the highest abundance and diversity of genes corresponded to iron acquisition (siderophores and heme uptake). Our findings indicate that the host-level factors evaluated in this study were not key drivers of genomic variability, but that certain accessory genes in enteric MDR E. coli may be enriched. Collectively, this work provides insight into the genomic diversity and host-microbe interface of MDR E. coli from pre-weaned dairy calves.

Nitrate (NO−3 ), mainly leaching with soil porewater, is the primary nonpoint source pollutant of groundwater worldwide. Obtaining real-time information on nitrate levels in soils would allow for gaining a better understanding of the sources and transport dynamics of nitrate through the unsaturated zone. However, conventional nitrate detection techniques (e.g., soil sample analysis) necessitate costly, laboratory-grade equipment for analysis, along with human resources, resulting in a laborious and time-intensive procedure. These drawbacks raise the need to develop cost-effective and automated systems for in situ nitrate measurements in field conditions. This study presents the development of a low-cost, portable, automated system for field measurements of nitrate in soil porewater and open water bodies. The system is based on the spectrophotometric determination of nitrate using a single reagent. The system design and processing software are openly accessible, including a building guide, to allow duplicating or changing the system according to user-specific needs. Three field tests, conducted over 5 weeks, validated the system’s measurement capabilities within the range of 0–10 ppm NO−3 –N with a low RMSE of < 0.2 ppm NO−3 –N when comparing the results to standard laboratory nitrate analysis. Data derived from such a system allow for tracking of the temporal variation in soil nitrate, thus opening new possibilities for diverse soil and nutrient management studies.

IntroductionMetabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly 25% of the population and is the leading cause for liver-related mortality. Bariatric surgery is a well-known treatment for MASLD and obesity. Understanding the fundamental mechanisms by which bariatric surgery can alter MASLD can lead to new avenues of therapy and research. Previous studies have identified the microbiome's role in bariatric surgery and in inflammatory immune cell populations. The host innate immune system modulates hepatic inflammation and fibrosis, and thus the progression of MASLD. The precise role of immune cell types in the pathogenesis of MASLD remains an active area of investigation. The aim of this study was to understand the interplay between microbiota composition post-bariatric surgery and the immune system in MASLD.MethodsEighteen morbidly obese females undergoing sleeve gastrectomy were followed pre-and post-surgery. Stool from four patients, showing resolved MASLD post-surgery with sustained weight loss, was transplanted into antibiotic treated mice. Mice received pre-or post-surgery stool and were fed a standard or high-fat diet. Bodyweight, food intake, and physiological parameters were tracked weekly. Metabolic parameters were measured post-study termination.ResultsThe human study revealed that bariatric surgery led to significant weight loss (p > 0.05), decreased inflammatory markers, and improved glucose levels six months post-surgery. Patients with weight loss of 20% or more showed distinct changes in blood metabolites and gut microbiome composition, notably an increase in Bacteroides. The mouse model confirmed surgery-induced microbiome changes to be a major factor in the reduction of markers and attenuation of MASLD progression. Mice receiving post-surgery fecal transplants had significantly less weight gain and liver steatosis compared to pre-surgery recipients. There was also a significant decrease in inflammatory cytokines interferon gamma, interleukin 2, interleukin 15, and mig. This was accompanied by alterations in liver immunophenotype, including an increase in natural killer T cells and reduction of Kupfer cells in the post-surgery transplant group.DiscussionOur findings suggest surgery induced microbial changes significantly reduce inflammatory markers and fatty liver progression. The results indicate a potential causal link between the microbiome and the host immune system, possibly mediated through modulation of liver NKT and Kupffer cells.

Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.

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.

The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

Hydrogeophysical methods have been increasingly used to study subsurface soil–water dynamics, yet their application beyond the soil compartment or the quantitative link to soil hydraulic properties remains limited. To examine how these methods can inform model-based evapotranspiration (ET) calculation under varying soil water conditions, we conducted a pilot-scale field study at an experimental maize plot with manipulated irrigation treatments. Our goal was to develop a workflow for (1) acquiring and inverting field electrical resistivity tomography (ERT) data, (2) correlating ERT to soil hydraulic properties, (3) spatially characterizing soil water stress that feeds into ET modeling (the FAO-56 model), and (4) evaluating the performance of ERT-based ET computation. Our results showed that ERT was able to capture decimeter-scale soil water content (SWC) dynamics from root water uptake and irrigation manipulation and the contrast of soil water stress between deficiently and fully irrigated maize. We also demonstrated the flexibility of using ERT to spatially integrate soil water stress in the soil volume of interest, which could be adjusted based on different crops and plot layouts. The integration of the ERT datasets into ET modeling provided insights into the spatial heterogeneity of the subsurface that has been challenging for point-based sensing, which can further our understanding of the hydraulic dynamics in the soil-plant-atmosphere continuum.

In recent years, there has been a focus on improving geotechnical systems by implementing and constructing new deep foundation such as helical and expanded piles. This study examined the effects of parameters such as embedment depth, pile geometry, and axial loading direction on the load-displacement behaviour of these piles. To conduct the research, a database was compiled consisting of 80 axial loading test records for different piles. The embedment depth of the piles ranged from 2.4 to 36.8 m, and the diameter of helices or expanded parts ranged from 254 to 1500 mm. The ultimate load of the piles was determined using the 2.5% and 5% displacement ratio criteria and the Brinch-Hansen 80% method. Additionally, hyperbolic functions were fitted to the load-displacement curves, allowing for consistent estimation of the limit load and the initial tangent modulus. Analysis of the results from the database revealed that the dominant factors influencing the ultimate load, limit load, maximum measured load, initial stiffness, and load-displacement behaviour were the ratio of helices or expanded part diameter to shaft diameter, shaft and toe surface area, and load direction. Correlations derived from the database were validated using measurements from eight full-scale helical and expanded piles.

This manuscript presents a multiomics investigation into the metabolic and proteomic responses of wheat to molybdenum (Mo)- and copper (Cu)-based engineered nanomaterials (ENMs) exposure via root and leaf application methods. Wheat plants underwent a four-week growth period with a 16 h photoperiod (light intensity set at 150 μmol·m-2·s-1), at 22 °C and 60% humidity. Six distinct treatments were applied, including control conditions alongside exposure to Mo- and Cu-based ENMs through both root and leaf routes. The exposure dosage amounted to 6.25 mg of the respective element per plant. An additional treatment with a lower dose (0.6 mg Mo/plant) of Mo ENM exclusively through the root system was introduced upon the detection of phytotoxicity. Utilizing LC-MS/MS analysis, 82 metabolites across various classes and 24 proteins were assessed in different plant tissues (roots, stems, leaves) under diverse treatments. The investigation identified 58 responsive metabolites and 19 responsive proteins for Cu treatments, 71 responsive metabolites, and 24 responsive proteins for Mo treatments, mostly through leaf exposure for Cu and root exposure for Mo. Distinct tissue-specific preferences for metabolite accumulation were revealed, highlighting the prevalence of organic acids and fatty acids in stem or root tissues, while sugars and amino acids were abundant in leaves, mirroring their roles in energy storage and photosynthesis. Joint-pathway analysis was conducted and unveiled 23 perturbed pathways across treatments. Among these, Mo exposure via roots impacted all identified pathways, whereas exposure via leaf affected 15 pathways, underscoring the reliance on exposure route of metabolic and proteomic responses. The coordinated response observed in protein and metabolite concentrations, particularly in amino acids, highlighted a dynamic and interconnected proteomic-to-metabolic-to-proteomic relationship. Furthermore, the contrasting expression patterns observed in glutamate dehydrogenase (upregulation at 1.38 ≤ FC ≤ 1.63 with high Mo dose, and downregulation at 0.13 ≤ FC ≤ 0.54 with low Mo dose) and its consequential impact on glutamine expression (7.67 ≤ FC ≤ 39.60 with high Mo dose and 1.50 ≤ FC ≤ 1.95 with low Mo dose) following Mo root exposure highlighted dose-dependent regulatory trends influencing proteins and metabolites. These findings offer a multidimensional understanding of plant responses to ENMs exposure, guiding agricultural practices and environmental safety protocols while advancing knowledge on nanomaterial impacts on plant biology.

The two-term infiltration equation (Formula presented.) is commonly used to determine the sorptivity, (Formula presented.) (Formula presented.), and product, (Formula presented.) (Formula presented.), of the dimensionless multiple (Formula presented.) and saturated soil hydraulic conductivity (Formula presented.) (Formula presented.) from cumulative vertical infiltration measurements (Formula presented.) (L) at times (Formula presented.) (T). This reduced form of the quasi-analytical power series solution of Richardson's equation of Philip enjoys a solid physical underpinning but at the expense of a limited time validity. Using simulated infiltration data, Jaiswal et al. have shown this time validity to equal about 2.5 cm of cumulative infiltration. The goals of this work are twofold. First, we investigate the extent to which cumulative infiltration measurements larger than 2.5 cm bias the estimates of (Formula presented.) and (Formula presented.). Second, we investigate the impact of epistemic errors on the inferred time validities and parameters. Partial infiltration curves up to 2.5 cm of cumulative vertical infiltration improve substantially the agreement between actual and least squares estimates of (Formula presented.) and (Formula presented.). But this only holds if the data generating infiltration process follows Richardson's equation and experimental conditions satisfy assumptions of soil homogeneity and a uniform initial water content. Otherwise, autocorrelated cumulative infiltration residuals will bias the least squares estimates of (Formula presented.) and (Formula presented.). Our findings reiterate and reinvigorate earlier conclusions of Haverkamp et al. and show that epistemic errors deteriorate the physical significance of the coefficients of infiltration functions. As a result, the parameters of infiltration functions cannot simply be used in storm water and vadose zone flow models to forecast runoff and recharge at field and landscape scales unless these predictions are accompanied by realistic uncertainty bounds. We conclude that the time validity of Philip's two-term equation is an elusive theoretical quantity with arbitrary physical meaning.

Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp - 6.07 Mbp, and the bin completion ranges from 74.2-92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.

The herbicide oxyfluorfen [OXY; 2-chloro-1-(3-ethoxy-4-nitrophenoxy)-4-(trifluoromethyl)benzene] has recently surged in interest among rice farmers with the development of OXY-tolerant rice and its demonstrated effectiveness against problematic rice weeds in California. Not currently registered for use with rice, its fate in rice fields is poorly understood. Using a batch equilibrium method, we characterize the soil-water partitioning behavior of OXY under simulated California rice field conditions. Sorption data imply strong, primarily concentration-independent binding correlated with soil organic carbon (log[Koc] 4.79−5.19; N 0.87−1.08) across all soil, temperature, and salinity treatments. Temperature significantly enhanced binding affinity for sorption and desorption processes (P < 0.01). Bound OXY was poorly desorbed (9.3 to 27.0% desorption) from rice soils and exhibited significant sorption hysteresis (HI > 0) in all treatments. These results indicate that OXY will predominantly remain in soil and will be resistant to release into water in California rice fields.

Agricultural managed aquifer recharge (Ag-MAR) is a promising approach to replenish groundwater resources using flood water and cropland as spreading grounds. However, site selection, particularly the layering of sediment deposits in the subsurface, can greatly influence Ag-MAR efficacy as it controls water flow and solute transport in the vadose zone. In this study, we use the HYDRUS-1D software to simulate water flow and solute transport from the land surface to the groundwater table in three vadose zone profiles (LS, MS, HS) characterized by differing fractions of sand (44 %, 47 %, and 64 %). For each profile, the single- and dual-porosity models (i.e., considering or not nonequilibrium water flow and solute transport) were calibrated using observed surface ponding, soil water content, and KBr breakthrough data. Water flow and bromide transport in the profile with the lowest sand fraction (LS) were best captured using the model that considered both preferential flow and nonequilibrium bromide transport. Water flow and bromide transport in the profile with the highest sand fraction (HS) was best simulated with the model that considered preferential flow and equilibrium bromide transport. Uniform water flow and nonequilibrium bromide transport provided the best fit for the third profile (MS). The degree of preferential flow was highest in the profile with the largest sand fraction (HS), which also showed the largest flow velocities compared to the profiles with lower sand amounts (LS and MS). Preferential flow did not significantly impact the overall water balance (within 3 %), but caused a significant decrease in vadose zone travel times (bromide) by up to 38 %, relative to a single-porosity model fit. Recharge efficiency varied between 88 % and 90 %, while the average travel times from the soil surface to groundwater varied up to 119 % (from 3.6 to 7.9 days) between the three sites. This study demonstrates that similar recharge efficiency can be achieved at sites with differing soil texture profiles, but subsurface heterogeneity can substantially affect contaminant transport processes and their travel times.

Anthropogenic activities leading to erosion-induced topsoil loss still present a pertinent threat to maize (Zea mays L.) productivity across the U.S. Corn Belt region. Using soil amendments has been proven effective in reversing the effects caused by erosion-induced topsoil loss and restoring agronomic productivity and yields to pre-eroded conditions. The current study investigated the impact of simulated erosion and repeated amendment application on agronomic productivity and yields over five growing seasons for a 23-year-old experiment at two central Ohio sites (Waterman Farm: WF; Western Station: WS). Simulated erosion/deposition was employed in 1997 to create three incremental topsoil depths (TSD) (20 cm topsoil removed (TSD-0); 0 cm topsoil removed (TSD-1); 20 cm topsoil added (TSD-2). Three soil amendments (inorganic, synthetic N fertilizer (INO); organic, compost manure (MAN); no amendment (CON)) were investigated for their ability to restore productivity in these cropping systems. Greater TSD produced higher germination counts and crop stand and yielded greater canopy cover during the initial five weeks after germination. The MAN amended soils observed higher values for the productivity parameters during the 2016–2020 growing seasons. Grain and biomass yields were 34–51% and 5–12% lower, respectively, for the TSD-0 level and 4–10% and 3–6% greater, respectively, for the TSD-2 level when compared to the undisturbed, TSD-1 level. Relative biomass yield losses (% per cm topsoil depth lost) were 0.921 for the WF site and 0.254 for the WS site, corresponding to average biomass losses (Mg ha−1 cm−1 yr−1) of 0.083 and 0.026 for each site. Relative grain yield losses (% per cm topsoil depth lost) were 1.29 for the WF site and 0.514 for the WS site, equating to mean grain losses (Mg ha−1 cm−1 yr−1) of 0.083 and 0.026 for each site. The rehabilitative capacity of the soil amendments followed a trend of INO > MAN at the WF site and MAN > INO > CON at the WS site. The deleterious effects of erosion on grain and biomass yields were found to be reversed with the addition of the INO and MAN amendments at the WS site due to improvements in soil health and SOC pools. The MAN amended soils produced grain and biomass yields that were nearly 2.5% and 5.6% greater than the INO amended soil when compared to the reference treatment (TSD-1-CON). This study demonstrates that sustainable soil management practices coupled with annual soil amendment addition can mitigate the deleterious effects of erosion and rebound maize yields to pre-eroded conditions for soils experiencing severe topsoil loss.

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

The strategic use of ruminant grazing in perennial cropland is steadily increasing throughout Mediterranean perennial agroecosystems. Integrated sheep-vineyard (ISV) management, where small ruminant livestock graze on understory vegetation, is viewed by some practitioners as a feasible transition opportunity to facilitate less petrochemically intensive vineyard understory management. However, our knowledge of soil carbon dynamics associated with grazing in perennial integrated crop-livestock (ICL) agroecosystems is notably limited, especially within Mediterranean climate contexts. Here, we use a series of on-farm paired surveys to assess soil ecosystem habitat and resource conditions related to SOC flux and storage in vineyards utilizing sheep-integration (ISV) and conventional understory management techniques (CONV). Our results show that long-term grazing increased the quantity of active, labile, and soluble carbon (C) within ISV soils, with much higher quantities of microbial biomass carbon (MBC). Vineyard soils with sheep grazing also showed increases in phospholipid fatty acid (PLFA) biomarkers, particularly amongst core functional groups related to decomposition. Soil microbial communities under ISV had higher C mineralization rates as well as higher carbon use-efficiency, as indicated by less CO2-C respired relative to the size of the MBC pool. Whereas inorganic soil nitrogen (N) and phosphorous (P) were also higher under ISV, microbial communities showed distinct metabolic investment strategies related to nutrient acquisition, with lower P-cycling enzyme activity and higher N-cycling enzyme activity. Additionally, ISV resulted in an increase in subsoil SOC storage, including higher quantities of physicochemical stabilization in the mineral-associated organic carbon (MAOC) pool of the deepest measured subsoil layer (30–45 cm). We observed no differences in soil structure indicators between treatments nor differences in the carbon fractions associated with four distinct aggregate size categories. We propose a framework to explain observed shifts in SOC dynamics of perennial ICL systems that include i) deposition of C and nutrient inputs with higher lability and solubility; ii) ruminant-induced decoupling of C from N and P, resulting in increased nutrient bioavailability; and iii) altered soil microbial metabolic strategies with more efficient biomass accumulation. These findings show strong potential of strategically applied ICL grazing to enhance soil functioning and increase SOC storage in Mediterranean perennial agroecosystems.

Persian walnut is a drought-sensitive species with considerable genetic variation in the photosynthesis and water use efficiency of its populations, which is largely unexplored. Here, we aimed to elucidate changes in the efficiency of photosynthesis and water content using a diverse panel of 60 walnut families which were submitted to a progressive drought for 24 days, followed by two weeks of re-watering. Severe water-withholding reduced leaf relative water content (RWC) by 20%, net photosynthetic rate (Pn) by 50%, stomatal conductance (gs) by 60%, intercellular CO2 concentration (Ci) by 30%, and transpiration rate (Tr) by 50%, but improved water use efficiency (WUE) by 25%. Severe water-withholding also inhibited photosystem II functionality as indicated by reduced quantum yield of intersystem electron transport (φEo) and transfer of electrons per reaction center (ET0/RC), also enhanced accumulation of QA (VJ) resulted in the reduction of the photosynthetic performance (PIABS) and maximal quantum yield of PSII (FV/FM); while elevated quantum yield of energy dissipation (φDo), energy fluxes for absorption (ABS/RC) and dissipated energy flux (DI0/RC) in walnut families. Cluster analysis classified families into three main groups (tolerant, moderately tolerant, and sensitive), with the tolerant group from dry climates exhibiting lesser alterations in assessed parameters than the other groups. Multivariate analysis of phenotypic data demonstrated that RWC and biophysical parameters related to the chlorophyll fluorescence such as FV/FM, φEo, φDo, PIABS, ABS/RC, ET0/RC, and DI0/RC represent fast, robust and non-destructive biomarkers for walnut performance under drought stress. Finally, phenotype-environment association analysis showed significant correlation of some photosynthetic traits with geoclimatic factors, suggesting a key role of climate and geography in the adaptation of walnut to its habitat conditions.

Organo-mineral and organo-metal associations play an important role in the retention and accumulation of soil organic carbon (SOC). Recent studies have demonstrated a positive correlation between calcium (Ca) and SOC content in a range of soil types. However, most of these studies have focused on soils that contain calcium carbonate (pH > 6). To assess the importance of Ca-SOC associations in lower pH soils, we investigated their physical and chemical interaction in the grassland soils of Point Reyes National Seashore (CA, USA) at a range of spatial scales. Multivariate analyses of our bulk soil characterisation dataset showed a strong correlation between exchangeable Ca (CaExch; 5-8.3 c.molc kg-1) and SOC (0.6-4%) content. Additionally, linear combination fitting (LCF) of bulk Ca K-edge X-ray absorption near-edge structure (XANES) spectra revealed that Ca was predominantly associated with organic carbon across all samples. Scanning transmission X-ray microscopy near-edge X-ray absorption fine structure spectroscopy (STXM C/Ca NEXAFS) showed that Ca had a strong spatial correlation with C at the microscale. The STXM C NEXAFS K-edge spectra indicated that SOC had a higher abundance of aromatic/olefinic and phenolic C functional groups when associated with Ca, relative to C associated with Fe. In regions of high Ca-C association, the STXM C NEXAFS spectra were similar to the spectrum from lignin, with moderate changes in peak intensities and positions that are consistent with oxidative C transformation. Through this association, Ca thus seems to be preferentially associated with plant-like organic matter that has undergone some oxidative transformation, at depth in acidic grassland soils of California. Our study highlights the importance of Ca-SOC complexation in acidic grassland soils and provides a conceptual model of its contribution to SOC preservation, a research area that has previously been unexplored.Supplementary informationThe online version contains supplementary material available at 10.1007/s10533-023-01059-2.

Permafrost-affected ecosystems are subject to warming and thawing, which can increase the availability of subsurface nitrogen (N) with consequences in otherwise N-limited tundra and alpine vegetation. Here, we quantify the extent of warming and permafrost thawing and the corresponding effects on nitrogen availability and plant growth based on a 20-year survey across 14 sites on the Tibetan Plateau. The survey showed that most sites have been subject to warming and thawing and that the upper permafrost zone across all sites was rich in inorganic N, mainly as ammonium. We further explore the efficiency of plants to utilize 15N-labelled inorganic N over five years following 15N addition at the permafrost table far below the main root zone. The 15N experiment showed that deep-rooted plant species were able to utilize the labelled N. A SEM model suggests that changes in vegetation can be explained by both active layer warming and permafrost thawing and the associated changes in inorganic nitrogen availability. Our results highlight a feedback mechanism of climate warming, in which released plant-available N may favour deep-rooted plants. This can explain important changes in plant composition and growth across the sites on the Tibetan Plateau.

In this work, the feasibility of using electrochemical remediation for treating municipal solid waste is explored. The viability of electrokinetic remediation is investigated prospectively to identify the electrochemical technology that can be applied to soil remediation using scientometrics, bibliometrics, and infometrics techniques. The study relies on Population, Intervention, Comparison, Outcomes, Context analysis to determine the research question, and Bibliometrix software helps build a theoretical background to search for solutions to soil contamination problems. Because electrokinetic remediation employs a significant amount of electrical energy, it is usually discarded as an applicable technique. However, this work emphasizes the studies where the technique works even in low-power situations. Thus, it can be said that this method serves as a backup for municipal soil waste landfill (MSWL) remediation in cases where none exists.

Bambara groundnuts (Vigna subterranea (L.) Verdc) provide essential proteins for African farmers, but the yield is largely affected by Alectra vogelii infestation, particularly on nutrient-depleted soils. Laboratory and field investigations were conducted to assess the influence of phosphorus rates and Bambara groundnut genotypes on Alectra vogelii infestation. In the laboratory, a 4 × 26 factorial experiment, varying phosphorus rates (0, 20, 30 and 40 kg ha−1) across 26 genotypes, revealed a significant (p

This study aimed to use a GIS-based approach in producing soil fertility maps and utilize the spatial data on achieving site-specific management of major nutrients in Morogoro, Tanzania. Soil samples were collected in six mapping units and analyzed for chemical properties such as pH, cation exchange capacity and electrical conductivity. ArcGIS 10.8 was used to produce nutrient variability maps of organic carbon, available P, total nitrogen and exchangeable K, Ca and Mg using the Inverse Distance Weight (IDW) interpolation method. The soil pH values ranged from 5.5 to 7.2. OC varied between 1.2 and 4.9 g kg−1, TN ranged from low to medium (1.0 to 5.0 g kg−1) whereas Av. P varied between l3.3 and 14.3 mg kg−1. Exchangeable K, Ca and Mg had ranges (in cmol kg−1) of between 0.1 to 0.8 (low to medium), 3.8 to 15.6 (low to high) and 0.3 to 0.5 (low), cmol kg−1. The recommended amounts were 74, 44, 36, 35 and 12 kg ha−1 for N, P2O5, K2O, MgO and CaO, respectively. Conducting soil analysis is key for monitoring the amount of nutrients that are available in the soil at time and space, to achieve site-specific nutrient management.

This research aims to investigate the effects of vermicompost on the growth of wheat plants (Triticum aestivum L.), soil enzyme activities, and nutrient uptake, while also monitoring plant development through thermal imaging. The study was conducted on wheat seeds sown in soil enriched with various rates of vermicompost (Control: 0, T1: 2, T2: 4, T3: 6, and T4: 8 Mg ha−1) and continued under greenhouse conditions for 120 days. The results showed that increasing doses of vermicompost application significantly increased the activities of soil enzymes such as β-glucosidase, urease, and catalase, and promoted the dry weight development of the wheat plant (P 0.05). However, a significant increase in the concentration of micronutrients such as iron (Fe), zinc (Zn), copper (Cu), and manganese (Mn) was observed in the plants (P

AbstractSoil erosion is the most challenging and major environmental problems in the Upper Meki Sub catchment. Therefore, this work aims to determine the relative influences of erosion governing factors and to estimate the annual soil loss in the sub catchment area using RUSLE model. The model variables including rainfall erosivity (R), soil erodibility (K), topography (LS), cover and management (C), and support practices (P) were implemented into the GIS environment and a layer of each of these factors was prepared. The estimated value of R, K, LS, C, and P for the sub catchment area ranges from 512 to 604 MJ mm ha-1 h-1 yr-1, 0.137 to 0.169 tons/ha, 0 to 59, 0.001 to 0.4 and 0.10 – 1.00 respectively. The raster values of all these factors were multiplied by using GIS calculator. Based on the results from GIS raster calculation and RUSLE model, the total annual potential soil loss from the sub catchment area is about 2,756,540 tons per year with a mean estimated soil loss rate of 28.12 + 34.77 t/ha/yr and the total actual annual soil loss is 492929 tons with an estimated erosion rate of 37.05 + 46.7 t/ha/yr. Rainfall is identified as the most sensitive factor of soil erosion in the sub catchment area. Our estimation of soil erosion provides notional basses that the area needs immediate action to sustain the soil. Nevertheless, further research on severity analysis and area prioritization, and sediment loss estimation in this watershed is highly recommended to develop practical way of conserving practices.

Corn is one of most important agricultural products in China. Understanding impacts of regional climate change, as well as agricultural management practices, on corn yields is critical for maintaining stable corn production. Using the DayCent model and observed climatic data in Sichuan province (a humid and hot environment) and Hebei province (a cold and dry environment) in China, corn yields in 1948-2010 were simulated. The spatial variations of simulated corn yields and the relationship between regional climate variability and warming with corn yields in these two environments were analyzed. The results demonstrated that: (1) corn yields in Zhangjiakou of Hebei and most regions of Sichuan decreased significantly after 2000 compared to other regions; (2) relative humidity and precipitation exhibit a significant negative correlation with observed crop yields in the growing season in Hebei province; (3) air temperature from 23.33 °C to 29 °C constitutes the ideal range influencing the increase of corn yields in Sichuan; (4) the planting of the large amount of silage maize in Sichuan compensated the negative impact of the rising air temperature on corn yields; (5) sensitivity tests for different fertilization levels and OMAD suggest that an increasing fertilization level significantly affects corn yields in Hebei province, a cold and dry environment, while a decreasing fertilization level has a significant negative effect in Sichuan province, a hot and humid environment. The overarching goal of these analyses is to provide the theoretical basic for maintaining stable corn production under regional climate warming and different agricultural management practices.

Early-stage pedogenic processes and formation rates on completely obliterated volcanic landscapes, such as the super explosive 1815 Mount Tambora eruption, have not previously been robustly explored. The objectives of this study were to determine (i) the mineralogical composition of the sand fraction, selected physical and chemical soil properties and potential nutrient reserves after 200 years of pedogenesis, and (ii) chemical weathering indices, rate of soil formation, and rates of C and N accretion. Soil formation was examined for five soil profiles on stable plain/foot slope positions representing the diversity of soils in these landscape positions, which are important for agricultural production. Results showed that the soil mineralogical composition of the sand fraction was dominated by easily weatherable minerals (e.g., labradorite and augite volcanic glass) indicating high potential nutrient reserves (e.g., Ca2+, Mg2+, K+, P) as confirmed by X-ray fluorescence (XRF) analyses. Allophanic material formation was minimal ( B horizons (45.4 ± 2.4) > C horizons (43.8 ± 4.2) ≈ tephra/lava (43.1), indicating accumulation of Al oxides and depletion of base cations in the upper horizons. Similarly, the base depletion index (BDI) showed a trend of A horizons (1.13 ± 0.18) < B horizons (1.25 ± 0.09) < C horizons (1.34 ± 0.20) ≈ tephra/lava (1.35), indicating depletion of base cations (Ca2+, Mg2+, K+, Na+) from the soil surface to C horizons. Based on solum depths (A + B horizons) and 200 years of post-eruption soil development, the solum formation rate ranged from 1.2 to 5.3 mm yr−1. Appreciable stocks of SOC (2.3–12.8 kg C m−2) and SON (0.21–0.77 kg m−2) accumulated over the 200 year period. Eruption materials from the Mt. Tambora eruption with a precisely known timescale contributed new pedological insights documenting rapid soil formation rates from pyroclastic materials leading to a rapid recovery of soil functions to support agricultural production.

The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.

Acid tropical soils may become more productive when treated with agricultural lime, but optimal lime rates have yet to be determined in many tropical regions. In these regions, lime rates can be estimated with lime requirement models based on widely available soil data. We reviewed seven of these models and introduced a new model (LiTAS). We evaluated the models' ability to predict the amount of lime needed to reach a target change in soil chemical properties with data from four soil incubation studies covering 31 soil types. Two foundational models, one targeting acidity saturation and the other targeting base saturation, were more accurate than the five models that were derived from them, while the LiTAS model was the most accurate. The models were used to estimate lime requirements for 303 African soil samples. We found large differences in the estimated lime rates depending on the target soil chemical property of the model. Therefore, an important first step in formulating liming recommendations is to clearly identify the soil property of interest and the target value that needs to be reached. While the LiTAS model can be useful for strategic research, more information on acidity-related problems other than aluminum toxicity is needed to comprehensively assess the benefits of liming.

Dynamic energy budget (DEB) theory has been applied to model a wide range of organisms, including microbes. In the standard DEB model, biomass is partitioned into reserve and structural compartments, where reserve biomass is mobilized in a pseudolinear manner (while the reserve biomass density, defined as the ratio between reserve and structural biomass, decays linearly) to drive maintenance and the growth of structural biomass (and extracellular enzyme production if it is considered). However, the linear dynamics of the reserve biomass density makes the standard DEB model incapable of explaining the slowdown of microbial growth at high reserve density that is caused by macromolecular crowding effect which reduces biochemical reaction rates (a typical situation occurs when microbes are experiencing severe moisture stress) and is inconsistent with the observation that intracellular enzymatic reactions generally follow non-linear kinetics. By partitioning biomass into reserve, kinetic, and structural compartments, we show here that the Equilibrium Chemistry Approximation (ECA) kinetics can be used to represent enzymatically catalyzed reserve biomass mobilization that can then drive the kinetic and structural biomass synthesis. This revised DEB model better represents the tradeoff in ribosome allocation for structural growth and internal enzyme production, is structurally compatible with metabolic models of cell individuals, and includes the standard DEB model and the popular compromise model as special cases for representing population growth. We then applied the revised DEB model to interpret components of bacterial respiration, their dependence on substrate availability, and emergent microbial carbon use efficiency dynamics for an exponentially growing population. We found that the revised DEB model enables a better understanding of bacterial substrates use (carbon in our examples) than that can be derived from a few other models in the literature. In particular, the revised DEB model explains why carbon use efficiency may first increase, then plateau, and finally decrease with growth rate (and substrate uptake rate), as a function of proteomics. Additionally, the revised DEB model explains why the kinetic biomass compartment needs to be divided to reasonably incorporate proteomic control of microbial growth.

Wetlands host ∼20% of terrestrial organic carbon and serve as a major sink for atmospheric carbon. Anoxic soils and sediments accrue soil organic carbon (SOC) partly by hampering the activity of extracellular oxidative enzymes that break down phenolic polymers. Upon aeration, fungal-driven oxidative enzymatic depolymerization and microbial respiration of released monomers ensue. Redox-active metals can simultaneously catalyze abiotic nonspecific oxidation of SOC, notable examples including Mn(III) or Fe(II) through Fenton-like, hydrogen peroxide-catalyzed oxidative radical production. However, the extent of reactive metal contributions to biotic and abiotic SOC degradation is not understood in the context of natural environments with diverse redox chemistry. We tested the relative contributions of fungi, Mn(III) and Fe(II) to phenolic substrate (L-DOPA) oxidation in floodplain soils representing a range of transient redox conditions driven by permanent vs. periodic flooding. Phenol oxidative potential was highest in permanently flooded soils with fewer fungal taxa known for observed (per)oxidase activity and instead correlated with HCl-extractable Fe(II), Fe(total) and Fe(II)/Fe(total), suggesting a specific role of Fe(II). Fe(II) additions enhanced phenol oxidative potential in sterilized and non-sterilized soils in the presence of hydrogen peroxide, indicating abiotic Fe-mediated radical chemistry could significantly enhance wetland SOC oxidative depolymerization throughout redox-active floodplain soils. Fungal community composition did not correlate to phenol oxidative potential overall and only more oxic soils adjacent to the river with diverse fungal communities showed declining oxidative potential after sterilization. Mn(III) addition did not significantly enhance phenol oxidative potential across all soils, although it appeared to drive fungal-mediated oxidative potential in the most aerated floodplain soils. Understanding how metals mediate SOC depolymerization as abiotic oxidants or microbially-harnessed enzyme cofactors and substrates in soils under variable hydrologic controls will improve our ability to represent depolymerization in terrestrial carbon models in wetland and other frequently saturated soils.

Agricultural managed aquifer recharge (Ag-MAR, on-farm recharge), where farmland is flooded with excess surface water to intentionally recharge groundwater, has received increasing attention by policy makers and researchers in recent years. However, there remain concerns about the potential for Ag-MAR to exacerbate nitrate (NO3-) contamination of groundwater, and additional risks, such as greenhouse gas emissions and crop tolerance to prolonged flooding. Here, we conducted a large-scale, replicated winter groundwater recharge experiment to quantify the effect of Ag-MAR on soil N biogeochemical transformations, potential NO3- leaching to groundwater, soil physico-chemical conditions, and crop yield. The field experiment was conducted in two grapevine vineyards in the Central Valley of California, which were each flooded for 2 weeks and 4 weeks, respectively, with 1.31 and 1.32 m3 m-2 of water. Hydrologic, geochemical, and microbial results indicate that NO3- leaching from the first 1 m of the vadose zone was the dominant N loss pathway during flooding. Based on pore water sample and N2O emission data, denitrification played a lesser role in decreasing NO3- in the root zone but prolonged anoxic conditions resulted in a significant 29 % yield decrease in the 4-week flooded vineyard. The results from this research, combined with data from previous studies, are summarized in a new conceptual model for integrated water-N dynamics under Ag-MAR. The proposed model can be used to determine best Ag-MAR management practices.

IntroductionBoth spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback.MethodsThe purpose of our study was to determine the SARS-CoV-2 entry mechanism using the mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors.ResultsMv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. TMPRSS2 inhibitors had minimal impact, which can be explained by the apparent lack of activity of this enzyme in the mink and its localization within the cell, not on the cell surface.DiscussionDyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.

A subset of microorganisms that perform respiration can endogenously utilize insoluble electron donors, such as Fe(II) or a cathode, in a process called extracellular electron transfer (EET). However, it is unknown whether similar endogenous EET can be performed by primarily fermentative species like lactic acid bacteria. We report for the first time electron uptake from a cathode by Lactiplantibacillus plantarum, a primarily fermentative bacteria found in the gut of mammals and in fermented foods. L. plantarum consumed electrons from a cathode and coupled this oxidation to the reduction of both an endogenous organic (pyruvate) and an exogenous inorganic electron acceptor (nitrate). This electron uptake from a cathode reroutes glucose fermentation toward lactate degradation and provides cells with a higher viability upon sugar exhaustion. Moreover, the associated genes and cofactors indicate that this activity is mechanistically different from that one employed by lactic acid bacteria to reduce an anode and to perform respiration. Our results expand our knowledge of the diversity of electroactive species and of the metabolic and bioenergetic strategies used by lactic acid bacteria.

Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

The objective of this study was to investigate the effects of dietary supplementation of Bacillus (B.) amyloliquefaciens on growth performance, diarrhea, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with F18 enterotoxigenic Escherichia coli (ETEC). A total of 50 weaned pigs (7.41 ± 1.35 kg BW) were individually housed and randomly allotted to one of the following five treatments: sham control (CON-), sham B. amyloliquefaciens (BAM-), challenged control (CON+), challenged B. amyloliquefaciens (BAM+), and challenged carbadox (AGP+). The experiment lasted 28 days, with 7 days of adaptation and 21 days after the first ETEC inoculation. ETEC challenge reduced (P < 0.05) average daily gain (ADG) of pigs. Compared with CON+, AGP+ enhanced (P < 0.05) ADG, while B. amyloliquefaciens supplementation tended (P < 0.10) to increase ADG in pigs from days 0 to 21 post-inoculation (PI). The ETEC challenge increased (P < 0.05) white blood cell (WBC) count on days 7 and 21 PI, while BAM+ pigs tended (P < 0.10) to have low WBC on day 7 PI and had lower (P < 0.05) WBC on day 21 PI compared with CON+. In comparison to AGP+ fecal microbiota, BAM+ had a lower (P < 0.05) relative abundance of Lachnospiraceae on day 0 and Clostridiaceae on day 21 PI, but a higher (P < 0.05) relative abundance of Enterobacyeriaceae on day 0. In ileal digesta, the Shannon index was higher (P < 0.05) in BAM+ than in AGP+. Bray-Curtis PCoA displayed a difference in bacterial community composition in ileal digesta collected from sham pigs vs. ETEC-infected pigs on day 21 PI. Pigs in BAM+ had a greater (P < 0.05) relative abundance of Firmicutes, but a lower (P < 0.05) relative abundance of Actinomycetota and Bacteroidota in ileal digesta than pigs in AGP+. Ileal digesta from AGP+ had a greater (P < 0.05) abundance of Clostridium sensu stricto 1 but lower (P < 0.05) Bifidobacterium than pigs in BAM+. In conclusion, supplementation of B. amyloliquefaciens tended to increase ADG and had limited effects on the diarrhea of ETEC-infected pigs. However, pigs fed with B. amyloliquefaciens exhibit milder systemic inflammation than controls. B. amyloliquefaciens differently modified the intestinal microbiota of weaned pigs compared with carbadox.

The COVID-19 pandemic caused by SARS-CoV-2 sparked intensive research into the development of effective vaccines, 50 of which have been approved thus far, including the novel mRNA-based vaccines developed by Pfizer and Moderna. Although limiting the severity of the disease, the mRNA-based vaccines presented drawbacks, such as the cold chain requirement. Moreover, antibody levels generated by these vaccines decline significantly after 6 months. These vaccines deliver mRNA encoding the full-length spike (S) glycoprotein of SARS-CoV-2, but must be updated as new strains and variants of concern emerge, creating a demand for adjusted formulations and booster campaigns. To overcome these challenges, we have developed COVID-19 vaccine candidates based on the highly conserved SARS CoV-2, 809-826 B-cell peptide epitope (denoted 826) conjugated to cowpea mosaic virus (CPMV) nanoparticles and bacteriophage Qβ virus-like particles, both platforms have exceptional thermal stability and facilitate epitope delivery with inbuilt adjuvant activity. We evaluated two administration methods: subcutaneous injection and an implantable polymeric scaffold. Mice received a prime-boost regimen of 100 μg per dose (2 weeks apart) or a single dose of 200 μg administered as a liquid formulation, or a polymer implant. Antibody titers were evaluated longitudinally over 50 weeks. The vaccine candidates generally elicited an early Th2-biased immune response, which stimulates the production of SARS-CoV-2 neutralizing antibodies, followed by a switch to a Th1-biased response for most formulations. Exceptionally, vaccine candidate 826-CPMV (administered as prime-boost, soluble injection) elicited a balanced Th1/Th2 immune response, which is necessary to prevent pulmonary immunopathology associated with Th2 bias extremes. While the Qβ-based vaccine elicited overall higher antibody titers, the CPMV-induced antibodies had higher avidity. Regardless of the administration route and formulation, our vaccine candidates maintained high antibody titers for more than 50 weeks, confirming a potent and durable immune response against SARS-CoV-2 even after a single dose.

Understanding how plant pathogenic fungi adapt to their hosts is of critical importance to securing optimal crop productivity. In response to pathogenic attack, plants produce reactive oxygen species (ROS) as part of a multipronged defense response. Pathogens, in turn, have evolved ROS scavenging mechanisms to undermine host defense. Thioredoxins (Trx) are highly conserved oxidoreductase enzymes with a dithiol-disulfide active site, and function as antioxidants to protect cells against free radicals, such as ROS. However, the roles of thioredoxins in Verticillium dahliae, an important vascular pathogen, are not clear. Through proteomics analyses, we identified a putative thioredoxin (VdTrx1) lacking a signal peptide. VdTrx1 was present in the exoproteome of V. dahliae cultured in the presence of host tissues, a finding that suggested that it plays a role in host-pathogen interactions. We constructed a VdTrx1 deletion mutant ΔVdTrx1 that exhibited significantly higher sensitivity to ROS stress, H2O2, and tert-butyl hydroperoxide (t-BOOH). In vivo assays by live-cell imaging and in vitro assays by western blotting revealed that while VdTrx1 lacking the signal peptide can be localized within V. dahliae cells, VdTrx1 can also be secreted unconventionally depending on VdVps36, a member of the ESCRT-II protein complex. The ΔVdTrx1 strain was unable to scavenge host-generated extracellular ROS fully during host invasion. Deletion of VdTrx1 resulted in higher intracellular ROS levels of V. dahliae mycelium, displayed impaired conidial production, and showed significantly reduced virulence on Gossypium hirsutum, and model plants, Arabidopsis thaliana and Nicotiana benthamiana. Thus, we conclude that VdTrx1 acts as a virulence factor in V. dahliae.

The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis.