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Biochar offers opportunities for improving soil carbon (C) sequestration and reducing CO2 emissions to the atmosphere. It has emerged as a strategy for mitigating climate change and improving the soil carbon cycle (SCC). While previous review studies have primarily investigated the effects of biochar on greenhouse gas (GHG) emissions, a considerable research gap remains regarding its impact on the SCC. The present study aims to bridge this gap by examining the main SCC components: total CO2 flux, total microbial respiration, and C sequestration. We conducted a global meta-analysis which included 75 studies and 250 observations. The results show an average 11% increase in soil total CO2 flux from biochar, but the confidence interval (CI) slightly touches the no-effect line (CI [0%, 23%]). Total microbial respiration remains unchanged after the application (10%, CI [− 2%, 23%]). In contrast, soil C sequestration benefits from biochar by 61% (CI [36%, 90%]). Our analysis identified key predictors affecting SCC components: experimental design, continent, biochar application rate, feedstock type, and pyrolysis temperature. Incubation experiments reveal benefits for all SCC components. The Middle East, Europe, and Asia exhibit potential for enhancing C sequestration with biochar. Higher application rates amplify C sequestration and total microbial respiration. Manure biochar enhances total microbial respiration, while woody biochar influences total CO2 flux. Furthermore, lower pyrolysis temperatures show promise for improving C sequestration and total microbial respiration. In conclusion, while biochar holds promise for C sequestration, its impact on total microbial respiration and total CO2 flux remains inconclusive. Highlights: Meta-analyses revealed the impact of biochar on three key elements (C sequestration, total CO2 flux, and total microbial respiration) of the soil carbon cycle. Biochar increases soil carbon sequestration significantly. The effect of biochar wasn't significant for total microbial respiration and total CO2 flux responses. [ABSTRACT FROM AUTHOR]

The paper presents the results of studies aimed at assessing the variability of respiratory activity of soil microbiota (rates of basal and substrate-induced respiration), as well as of the content of organic matter carbon and microbial biomass carbon in soils formed and functioning in natural (slightly damaged) biogeocenoses along altitudinal gradient from the foothills to the high mountain regions of the Central Caucasus (500–3500 m a.s.l., Elbrus variant of altitudinal zonality, Kabardino-Balkaria). It is shown that the mean values of the studied indicators in surface horizons (0–10 and 0–20 cm, depending on the soil type) significantly increase with the altitude from mountain chernozems to subalpine mountain-meadow soils and significantly decrease at the maximum altitude in the zone of alpine mountain-meadow soils. The studied indicators in different soil types within the same altitudinal zone also differ; this difference is statistically significant (t > 2.5; p < 0.02) for most of the indicators for the compared pairs of soil types. The data obtained indicate that the impact of the altitudinal gradient is significantly transformed by additional factors. The multi-regression analysis has been performed to identify the effect of the main factors of relief (elevation above sea level and slope aspect and steepness) and climate (19 bioclimatic characteristics) on the studied indicators. It shows that the mean cumulative contribution of all 22 factors to the variation of the studied indicators is 40% in mountain chernozems, 66% in mountain-meadow chernozem-like soils, 31% in mountain meadow-steppe subalpine soils, 67% in subalpine mountain-meadow soils, and 67% in alpine mountain-meadow soils. Thus, the effect of the considered factors may significantly differ both for soils located along the altitudinal gradient and for soils functioning within the same altitudinal zone. Relief and climate play an important, but not the only, role in the formation of properties of mountainous soils in the Central Caucasus. [ABSTRACT FROM AUTHOR]

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products. [ABSTRACT FROM AUTHOR]

Actuotaphonomic experiments demonstrate how microbial mats prevent or delay destructive processes. The rate at which carcasses are covered is a key to their preservation. Because of the growth rate of microbial mats depends on environmental conditions, a set of experiments have been carried out emulating the Barremian environmental conditions, analysed for temperatures at 14°C and 26°C (cooler and warmer seasons respectively) and atmospheric pCO2 (1000 ppm). For this purpose, the microbial mats were grown in mesocosms within an environmental chamber. Variations in primary production were quantified by measuring changes in dissolved O2 concentration in the water. Zebrafish carcasses were laid on the mats, and their coverage rates were calculated from the daily surface area covered by the mat. The results showed that the fish was covered twice as fast at 26°C, in coincidence with the highest values for the gross primary production and community respiration of the microbial mats. Therefore, for these Barremian conditions, the early stages of carcasses preservation would take place most effectively during the warmer seasons as decomposing activity would release nutrients that would enhance, together with temperature, the growth of mats. [ABSTRACT FROM AUTHOR]

The main challenge in treating aged soils highly contaminated with total petroleum hydrocarbons (TPH) is to enhance their bioavailability for microbial degradation. Hydrocarbons in soils undergo chemical changes that make them more resistant to biodegradation. This study investigates toluene's efficacy in enhancing the biodegradation of aged hydrocarbon-contaminated soil containing 292,000 mg TPH kg−1 dry soil. Toluene's effect was compared between solid phase (SOP) and slurry phase (SLP) treatments using a microbial consortium isolated from Cyperus laxus rhizosphere. TPH biodegradation and microbial respiration were measured, the latter to estimate the respiratory quotient (RQ, the ratio between moles of carbon dioxide released and moles of oxygen absorbed during respiration). Toluene significantly accelerated TPH biodegradation in both treatments, achieving ~ 30% higher removal than in a non-solvent control, possibly through improved bioavailability of aromatic compounds and other low molecular weight compounds. According to the RQ analysis, toluene enhanced microbial respiratory processes and hydrocarbon catabolism with higher hydrocarbon mineralization (RQ = ~ 0.5) in both SOP and SLP assays. Our results reveal toluene's potential to increase hydrocarbon availability and microbial degradation efficiency in aged contaminated soils; its use in various bioremediation techniques could be of broad applicability across diverse soil types and pollutants. [ABSTRACT FROM AUTHOR]

Bcakground: Soil respiration (Rs), as the second largest CO2 emissions of terrestrial ecosystems, is sensitive to disturbance and consequent environmental changes. Mowing is strategically implemented as an management approach and has the potential to influence carbon cycling in meadow steppes. However, it remains unclear how and why Rs and its heterotrophic (Rh) and autotrophic (Ra) components respond to consecutive mowing and associated ecological consequences. Here, we conducted a field mowing experiment in a meadow steppe in 2018 and monitored Rs, Rh, and Ra from 2019 to 2022. Results: We observed a significant reduction in Rs by 4.8% across four years, primarily attributed to a decrease in Rh. This decline in Rs intensified over time, indicating an accumulative effect of mowing. In addition, mowing induced an generally increasing Ra/Rs ratio over the experimental years with a simultaneous increase in the ratio of belowground to aboveground biomass (BGB/AGB). Furthermore, structural equation modeling results revealed that the decline in Rs was largely ascribed to reduced microbial biomass carbon (MBC) under mowing, while the increased Ra/Rs was primarily explained by the enhanced BGB/AGB. Partial regression analysis suggested that the biotic factor of microbial biomass dominated changes in soil respiration induced by mowing rather than abiotic soil temperature. Conclusions: Our findings showed that consecutive mowing decreased Rs and raised Ra/Rs in meadow steppe by decreasing plant biomass and altering the proportion of biomass allocation. This observed decline in Rs would help to reduce CO2 concentration in atmosphere as well as alleviate global warming. However, considering the concurrent lower microbial biomass, the potential positive impacts of mowing on climate and ecosystem function should be reevaluated in future grassland management practices. [ABSTRACT FROM AUTHOR]

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Estuaries are generally considered to be important sources of atmospheric CO2. However, the differences between estuaries, and inadequate observations of partial pressure of CO2 in estuarine water (pCO2water) hamper global estuarine CO2 budgeting. In this study, the longitudinal distribution of CO2 in the waters of Modaomen (MSE) and Lingdingyang (LSE), two sub-estuaries of the Pearl River Estuary (PRE), and its influencing mechanism are studied. The change in the distribution of pCO2water along the distance from the upstream estuary to the ocean between LSE and MSE was significantly different. pCO2water at the LSE ranges from 238 to 7267 µatm, whereas the MSE ranges from 406 to 3078 µatm. Stronger microbial respiration and relatively long water retention times were the main influences that led to higher pCO2water at LSE than at MSE. Seasonally, the increase of soil CO2 into the water in the upstream basin caused by precipitation is the potential influencing factor that the water pCO2water in the flood season is higher than in the dry season. PRE was a net source of atmospheric CO2 with an average annual water–air flux of 41.2 ± 33.3 mmol m−2 day−1. Our results suggest that the differences in longitudinal gradients of pCO2water between estuaries in the same region and the effects of different gas transport velocity models on CO2 emission estimates need to be considered in estuarine CO2 emission budgeting. [ABSTRACT FROM AUTHOR]

Microbial acetate metabolism is an important part of marine carbon cycling. We present a comprehensive study to constrain microbial acetate metabolism and its regulation in surface seawater of the northwest Pacific Ocean. We found that acetate oxidation (rate constant k: 0.016–0.506 day−1) accounted for 77.6%–99.4% of the total microbial acetate uptake, suggesting that acetate was predominantly used as a microbial energy source. Acetate also served as a significant biomass carbon source, as reflected by the elevated contribution of acetate assimilation to bacterial carbon production. Acetate turnover was largely influenced by water mass mixing and nutrient conditions. Atmospheric deposition was a source of acetate in surface water and this process can also impact the microbial acetate uptake. Microbial utilization of acetate could account for up to 25.9% of the bacterial carbon demand, suggesting the significant role of acetate metabolism in microbial carbon cycling in the open ocean. Plain Language Summary: Acetate is a key metabolic intermediate during the mineralization of organic matter and microbial acetate metabolism plays a crucial role in marine carbon cycling. However, the microbial metabolism of acetate and its environmental controls in pelagic waters remain poorly understood. We investigated biogeochemical cycling of acetate in the Kuroshio‐Oyashio extension region of northwest Pacific Ocean. Acetate concentrations in surface waters were generally low and atmospheric deposition was a source of acetate in the upper ocean. Acetate was used preferentially as a microbial energy source and the proportion of acetate devoted to bacterial growth or respiration largely depended on local nutrient conditions. Rapid biological turnover of acetate contributed significantly to bacterial carbon demand, exceeding the contributions of other compounds such as methanol. These results constrain the atmospheric sources and microbial sinks of marine acetate and reveal the ecological significance of microbial acetate metabolism in the open ocean. Key Points: Microbial uptake rates of acetate ranged from 1.7 to 495 nmol L−1 day−1 in surface waters of the northwest Pacific OceanAcetate is used preferentially as a microbial energy source rather than as a biomass carbon sourceMicrobial acetate metabolism is influenced by water mass mixing and atmospheric deposition [ABSTRACT FROM AUTHOR]

High stability magnetic nanocomposites wrapped by carbon layers were efficiently synthesized using electrical arc powered by single arc unit. This is sufficient to ionize the nickel, and carbon electrodes immersed in distilled water through applying strong electric field between carbon rotatory cathode and nickel anode. Nickle decorated by carbon (Ni@C) nanocomposite was fully characterized by transmission electron microscope (TEM), X-ray Diffraction (XRD), Vibrating-sample magnetometer (VSM), UV/Visible Spectrophotometer (UV), Fourier-transform infrared spectroscopy (FTIR), Particle size analyzer (PZ), Zeta potential, and X-ray photoelectron spectroscopy (XPS). Ni particle was spherical with average size equals to 17 nm wrapped by carbon where its energy band gap values were 2.84 for C, and 3.36 eV for Ni. The estimated phase percentage of nickel was 64.8 % which is higher than the percentage of carbon layers that's donating the sample the observed high stability of zeta potential was found to be 26.4 mV. The saturation magnetization (M s) and coercivity (H c) examined were 10.624 emu/g and 80.648 G, respectively. The antibacterial effect of the synthesized nanocomposites was tested against standard ATCC (American Type Colony Collection) strains namely Pseudomonas aeruginosa 27853, Proteus mirabilis 35659, Proteus vurgalis 13315, Klebsiella pneumoniae 13883, and Staphylococcus epidermidis 12228. Proteus vurgalis 13315 was the most resistant strain which wasn't completely eradicated after 24 h incubation with the prepared nanoparticles. Further assessments through confocal microscope and reactive oxygen species (ROS) generation percentage were done to predict the possible antibacterial mechanism of the synthesized nanocomposite. Ultimately, the combined influence of nickel ions and carbon in the prepared Ni@C nanocomposite results in the suppression of bacterial respiration and the induction of oxidative stress, ultimately leading to bacterial cell death. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m3 ha−1 year−1, installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0–10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m3 ha−1 year−1 doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant. [ABSTRACT FROM AUTHOR]

Soil carbon (C) stability is an important consideration for management that aims to increase long-term C storage. The fraction of soil C allocated to physico-chemically protected mineral-associated organic matter (MAOM) is a common soil C stability benchmark. However, the reality of soil C persistence is more complex than MAOM content alone—particularly in ecosystems such as meadows with high rates of belowground C inputs that can stimulate MAOM decomposition. Here, we combined three metrics of soil C persistence to characterize soil C stability across a meadow restoration chronosequence averaging belowground C gains of 330 g C m−2 y−1 for ~20 y. The metrics were: (1) the fraction of soil C in MAOM and particulate organic matter (POM), (2) the susceptibility of soil C to decomposition under varying temperatures, and (3) the utilization of MAOM-C by microbes. Two metrics suggested soil C stability may increase following montane meadow restoration. As soil C concentration increased with restoration, C storage in MAOM, but not POM, increased (metric 1). The susceptibility of MAOM-C to decomposition (microbial respiration relative to MAOM-C) decreased with increasing soil C concentration across temperatures (metric 2). Stable isotope results could not definitively determine the source of carbon dioxide efflux (metric 3) but generate hypotheses for future research to address. We posit that C sequestered following montane meadow restoration could be stable, with implications for regional C storage objectives. Further, our data point toward complex mineral-associated C dynamics including the potential importance of plant inputs for MAOM formation in meadow soils. [ABSTRACT FROM AUTHOR]

Measuring ecosystem multifunctionality (EMF) could be a valuable method for assessing whether nature‐based solutions, such as introducing non‐native species to benefit ecosystem functioning, yield net positive outcomes. While EMF metrics may provide a coarse overview of the functioning of a system, such metrics can obscure the interactions among multiple simultaneously occurring ecosystem functions. This could limit the predictive value and overall efficacy of EMF metrics for the management of environmental change impacts on ecosystem functioning.We carried out a mesocosm experiment with dung beetle temporal species richness (diversity) treatments in a pasture ecosystem in Aotearoa New Zealand and quantified cascading biotic and abiotic effects of introduced dung beetles (Onthophagus binodis and Onitis alexis) on multiple ecosystem functions. We measured nine individual ecosystem functions affected by dung beetles, including dung removal, total soil carbon, nitrogen, phosphorus, soil microbial respiration, nitrate N, ammonium N, anaerobically mineralisable N and pasture biomass production.We first tested the effects of temporal dung beetle diversity on the nine individual ecosystem functions. We then tested how introduced dung beetle temporal diversity affects ecosystem multifunctionality by calculating EMF metrics using the averaging, threshold and the Hill numbers approaches. Finally, to investigate the underlying interactions among individual functions, we tested the direct and indirect effects of introduced dung beetles on the nine ecosystem functions using structural equation modelling (SEM).Only one out of the nine individual ecosystem functions was significantly affected by dung beetle introductions, whereas five of the six calculated EMF metrics increased significantly with temporal diversity of introduced dung beetles. However, when modelled within an SEM framework, dung beetle temporal diversity was found to directly affect dung removal, but with cascading effects on total N and anaerobically mineralisable N.Our results suggest that introducing and increasing dung beetle temporal diversity enhances the provisioning of multiple ecosystem functions, but that our ability to detect and explain changes in ecosystem multifunctionality is critically dependent on how EMF is quantified. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Plastic mulch is a commonly employed technique in agriculture to enhance crop production. Given the persistence of plastic residues in soil, bioplastics offer a potential alternative. Unfortunately, little is known about the medium-term consequences of both plastic and bioplastic mulches on soil properties. This study aimed to assess the medium-term consequences of plastic and bioplastic mulches and their replacement on soil properties. To this aim, the impact of conventional plastic (polyethylene, CP) and biodegradable plastic (BP) mulches on soil's abiotic (pH, water content, total and organic carbon and total nitrogen contents) and biotic (microbial biomass, microbial respiration, enzymatic activities and microarthropod communities) properties after 2 years of exposure (T1) and after 3 (T2) and 6 (T3) months of mulch replacement was investigated. Moreover, uncovered soils were assessed as a control. The results highlighted that the samples were more significantly impacted by exposure time to mulches than by the different kinds of mulches. The replacement of both mulches (T2 and T3) decreased the content of C and increased the microbial biomass and activities; moreover, the mulch replacement changed the microarthropod community composition with a decrease of Collembola and an increase of Oribatida and Gamasida, especially in soils covered by biodegradable plastic mulches. Further investigations are needed to better understand the long-term impact of mulches on soil biota in order to prove the potential ecological implications of transitioning to sustainable alternatives. [ABSTRACT FROM AUTHOR]

Calcretes are indurated terrestrial carbonates that are widespread in arid and semi-arid settings and serve as important archives of present and past environments. Here, we use geochemical tools to explore the nature and origin of calcretes documented from tropical Niue Island in the Southwest Pacific. The study recognizes two types of calcretes that differ in their mineral assemblage, microfabrics, elemental chemistry, and carbon and oxygen isotopes. The calcretes common in the paleo-lagoon soils consist of 90% low-Mg calcite and ~10% highly weathered Mg-Al silicates. These pedogenic calcretes formed in the soil profiles within the vadose zone bear the following distinctions: (i) Fe/Al ratio of 0.75, identical to the ratio in soils (Fe/Al = 0.76 ± 0.5), substantiating the link between the calcretes and soils; (ii) presence of rhizoliths, root voids, micritic nodules, and clasts, which are consistent with a pedogenic calcrete fabric; and (iii) 13C and 18O depletions of −10.6‰ and −5.3‰, respectively, which are compatible with carbon sources from microbial and root respiration, as well as formation in oxygen isotope equilibrium with vadose waters. Unlike the pedogenic calcrete, a rare calcrete from the coastal terrace contains an exceptionally rare hydrotalcite [Mg6Al2(CO3)(OH)16(H2O)4] mineral (65%) coated by microbial films. We contend that the hydrotalcite-rich calcrete was deposited through interaction of dolomite with seawater, similar to the method of producing hydrotalcite in the laboratory. 13C and 18O enrichments of 0.8 to 1.7‰ and −1.0 to −1.6‰, respectively, are in agreement with (i) mixed carbon sources consisting of microbial CO2 degassing, seawater HCO3, and dolomite dissolution, and (ii) oxygen isotope equilibration with seawater-derived fluid. [ABSTRACT FROM AUTHOR]

The mineralogical composition of the parent material, together with plant species and soil microorganisms, constitutes the foundational components of an ecosystem's energy cycle. Afforestation in arid-semi arid regions plays a crucial role in preventing erosion and enhancing soil quality, offering significant economic and ecological benefits. This study evaluated the effects of afforestation and different parent materials on the physicochemical and microbiological properties of soils, including microbial basal respiration (MR), as well as how these changes in soil properties after 15 years influence plant growth. For this purpose, various soil physicochemical parameters, MR, soil microbial biomass carbon (Cmic), stoichiometry (microbial quotient = Cmic/Corg = qMic and metabolic quotient = MR/Cmic = qCO2), and tree growth metrics such as height and diameter were measured. The results indicated that when the physicochemical and microbiological properties of soils from different bedrock types, along with the average values of tree growth parameters, were analyzed, afforestation areas with limestone bedrock performed better than those with andesite bedrock. Notably, sensitive microbial properties, such as Cmic, MR, and qMic, were positively influenced by afforestation. The highest values of Cmic (323 μg C g−1) and MR (1.3 CO2–C g−1 h−1) were recorded in soils derived from limestone. In contrast, the highest qCO2 was observed in the control plots of soils with andesite parent material (7.14). Considering all the measured soil properties, the samples can be ranked in the following order: limestone sample (LS) > andesite sample (AS) > limestone control (LC) > andesite control (AC). Similarly, considering measured plant growth parameters were ranked as LS > AS. As a result, the higher plant growth capacity and carbon retention of limestone soil indicate that it has high microbial biomass and microbial activity. This study emphasizes the importance of selecting suitable parent material and understanding soil properties to optimize future afforestation efforts on bare lands. [ABSTRACT FROM AUTHOR]

Conservation management practices often produced positive but limited desirable outcomes in US Southeast sandy soils, likely due to their intrinsically low clay contents that constrain the soil’s capacity to preserve organic carbon (C) and nutrients. In the field, we tested the effectiveness of a novel approach, that is, clay soil amendment, to improve sandy soils. In October 2017, clay-rich soils (25% clay) were spread at 25 metric tons ha−1 and tilled onto a sandy soil (1.9% clay) in the field, which was further mixed by light tillage at 0- to 15-cm depth, followed by planting winter cover crop mixtures (cereal rye, crimson clover, and winter pea). The crop rotation was cotton and corn with cover crop mixtures planted in the winter fallow season. Soils (0–15 cm) were collected in August 2021 and subjected to physiobiochemical analyses. Clay amendment increased soil clay content to 3.4%, which improved nitrogen (N) availability by 51% but inhibited the activities of C (β-Dcellubiosidase [CB]; β-xylosidase [BX]; N-acetyl-β-glucosaminidase [NAG]) and N (leucine aminopeptidase [LAP]) cycling enzymes, resulting in up to 78% reduction in microbial respiration. A follow-up kinetic study on BG and LAP enzymes suggested that clay addition can have different impacts on enzymes with diverse biological origins through distinct mechanisms. Clay addition can potentially improve sandy soils by stabilizing the organic inputs in soils. However, more research is required to understand its long-term impacts making this approach practical. [ABSTRACT FROM AUTHOR]

Climate change presents an unprecedented global challenge, demanding collective action to both mitigate its effects and adapt to its consequences. Soil health and function are profoundly impacted by climate change, particularly evident in the sensitivity of soil microbial respiration to warming, known as Q10. Q10 measures the rate of microbial respiration's increase with a temperature rise of 10 degrees Celsius, playing a pivotal role in understanding soil carbon dynamics in response to climate change. Leveraging machine learning techniques, particularly explainable artificial intelligence (XAI), offers a promising avenue to analyze complex data and identify biomarkers crucial for developing innovative climate change mitigation strategies. This research aims to evaluate the extent to which chemical, physical, and microbiological soil characteristics are associated with high or low Q10 values, utilizing XAI approaches. The Extra Trees Classifier algorithm was employed, yielding an average accuracy of 0.923 ± 0.009 , an average AUCROC of 0.964 ± 0.004 , and an average AUCPRC of 0.963 ± 0.006 . Additionally, through XAI techniques, we elucidate the significant features contributing to the prediction of Q10 classes. The XAI analysis shows that the temperature sensitivity of soil respiration increases with microbiome variables but decreases with non-microbiome variables beyond a threshold. Our findings underscore the critical role of the soil microbiome in predicting soil Q10 dynamics, providing valuable insights for developing targeted climate change mitigation strategies. [ABSTRACT FROM AUTHOR]

The intratumor microbiome imbalance in pancreatic cancer promotes a tolerogenic immune response and triggers immunotherapy resistance. Here we show that Lactobacillus rhamnosus GG probiotics, outfitted with a gallium-polyphenol network (LGG@Ga-poly), bolster immunotherapy in pancreatic cancer by modulating microbiota-immune interactions. Upon oral administration, LGG@Ga-poly targets pancreatic tumors specifically, and selectively eradicates tumor-promoting Proteobacteria and microbiota-derived lipopolysaccharides through a gallium-facilitated disruption of bacterial iron respiration. This elimination of intratumor microbiota impedes the activation of tumoral Toll-like receptors, thus reducing immunosuppressive PD-L1 and interleukin-1β expression by tumor cells, diminishing immunotolerant myeloid populations, and improving the infiltration of cytotoxic T lymphocytes in tumors. Moreover, LGG@Ga-poly hampers pancreatic tumor growth in both preventive and therapeutic contexts, and amplifies the antitumor efficacy of immune checkpoint blockade in preclinical cancer models in female mice. Overall, we offer evidence that thoughtfully designed biomaterials targeting intratumor microbiota can efficaciously augment immunotherapy for the challenging pancreatic cancer. The intratumor microbiota in pancreatic cancer has been described as pro-tumorigenic. Here the authors modify the probiotic Lactobacillus rhamnosus GG with a gallium-polyphenol network and chitosan nanocoating, showing accumulation in pancreatic lesions and modulation of the intratumor microbiota, eliciting anti-tumor immune response in preclinical models. [ABSTRACT FROM AUTHOR]

Phage therapy is a promising antibacterial strategy, especially given that drugresistant bacterial infections are escalating worldwide. Because phages are not active against all strains of a given species, phages being considered for therapeutic use would ideally be tested against bacterial isolates from individual patients prior to administration. Standardized, clinically validated phage susceptibility testing (PST) methods are needed for assessing in vitro phage activity. This study compared two high-throughput liquid-based PST assays. The first, using the Biolog Omnilog™, assessed changes in microbial respiration leading to color changes based on a tetrazolium dye. The second, Agilent BioTek Cytation 7, assessed changes in optical density. Both used 96-well microtiter plate formats. A total of 55 diverse phages with activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, or Enterococcus faecalis were studied against their respective susceptible bacterial hosts and non-susceptible controls, with susceptibility defined based on plaque assay. PST was performed by both assays in replicates, with results compared in terms of hold times (time through which bacterial growth is inhibited by phage compared to controls). Coefficients of variance and interclass correlation coefficients were used to assess inter- and intra-assay reproducibility. Based on a ≤50% coefficient of variance cutpoint, 87% of Biolog and 84% of Agilent assays were considered valid for susceptible bacteria, with 100% considered valid for non-susceptible bacteria by both systems. Using a 8 h hold time cutpoint, 100% of the results matched between the two assays. The interclass correlation coefficient showed 26% excellent agreement, 35% good agreement, and 17% moderate agreement between the two assays for susceptible isolates and 100% excellent agreement for non-susceptible isolates. Overall, the assays compared provided good/fair statistical reproducibility for the assessment of phage susceptibility. [ABSTRACT FROM AUTHOR]

The rise of antibiotic tolerance in bacteria harboring genetic elements conferring resistance to antibiotics poses an increasing threat to public health. However, the primary factors responsible for the emergence of antibiotic tolerance and the fundamental molecular mechanisms involved remain poorly comprehended. Here, we demonstrate that the commonly utilized food additive Benzaldehyde (BZH) possesses the capacity to induce a significant level of fluoroquinolone tolerance in vitro among resistant Escherichia coli. Our findings from animal models reveal that the pre-administration of BZH results in an ineffective eradication of bacteria through ciprofloxacin treatment, leading to similar survival rates and bacterial loads as observed in the control group. These results strongly indicate that BZH elicits in vivo tolerance. Mechanistic investigations reveal several key factors: BZH inhibits the formation of bacterial flagella and releases proton motive force (PMF), which aids in expelling antibiotics from within cells to reducing their accumulation inside. In addition, BZH suppresses bacterial respiration and inhibits the production of reactive oxygen species (ROS). Moreover, exogenous pyruvate successfully reverses BZH-induced tolerance and restores the effectiveness of antibiotics, highlighting how crucial the pyruvate cycle is in combating antibiotic tolerance. The present findings elucidate the underlying mechanisms of BZH-induced tolerance and highlight potential hazards associated with the utilization of BZH. [ABSTRACT FROM AUTHOR]

Variation in the condition of marine sediments provides selective preservation milieus, which act as a key determinant for the abundance and distribution of dinoflagellate resting cysts in natural sediments. Microbial degradation is an understudied biological factor of potential importance in the processes. However, gaps remain in our knowledge about the fundamental information of the bacterial consortia associated with dinoflagellate resting cysts both in laboratory cultures and in the field. Here we used Scrippsiella acuminata as a representative of cyst-producing dinoflagellates to delineate the diversity and composition of bacterial microbiomes co-existing with the laboratory-cultured resting cysts, and to explore possible impacts of low temperature, darkness, and anoxia (the mock conditions commonly observed in marine sediments) on the associated bacterial consortia. Bacterial microbiome with high diversity were revealed associated with S. acuminata at resting stage. The mock conditions could significantly shift bacterial community structure and exert notably inhibitory effects on growth-promoting bacteria. Resting cysts under conditions typically observed in marine sediments fostered bacterial microbiomes with more diverse trophic strategies, characteristic of prominently enriched anaerobic chemotrophic bacteria generating energy via respiration with several different terminal electron acceptors, which yielded more acidic milieu unfavorable for the preservation of calcareous resting cysts. Our findings suggest that there is complex and dynamic interaction between dinoflagellates resting cysts and the associated bacterial consortia in natural sediments. This intrinsic interaction may influence the maintenance and/or accumulation of dinoflagellate resting cysts with potential of germination and initiation blooms in the field. [ABSTRACT FROM AUTHOR]

Fungi are key decomposers of deadwood, but the impact of anthropogenic changes in nutrients and temperature on fungal community and its consequences for wood microbial respiration are not well understood. Here, we examined how nitrogen and phosphorus additions (field experiment) and warming (laboratory experiment) together influence fungal composition and microbial respiration from decomposing wood of angiosperms and gymnosperms in a subtropical forest. Nutrient additions significantly increased wood microbial respiration via fungal composition, but effects varied with nutrient types and taxonomic groups. Specifically, phosphorus addition significantly increased wood microbial respiration (65%) through decreased acid phosphatase activity and increased abundance of fast‐decaying fungi (e.g., white rot), while nitrogen addition marginally increased it (30%). Phosphorus addition caused a greater increase in microbial respiration in gymnosperms than in angiosperms (83.3% vs. 46.9%), which was associated with an increase in Basidiomycota:Ascomycota operational taxonomic unit abundance in gymnosperms but a decrease in angiosperms. The temperature dependencies of microbial respiration were remarkably constant across nutrient levels, consistent with metabolic scaling theory hypotheses. This is because there was no significant interaction between temperature and wood phosphorus availability or fungal composition, or the interaction among the three factors. Our results highlight the key role of tree identity in regulating nutrient response of wood microbial respiration through controlling fungal composition. Given that the range of angiosperm species may expand under climate warming and forest management, our data suggest that expansion will decrease nutrient effects on forest carbon cycling in forests previously dominated by gymnosperm species. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) residues (root and straw) are unique substrates for microbes in paddy soils. Microbial respiration (RH) of paddy soils is likely to be affected by substrate quality. However, no relevant study on the effects of changed rice residue chemistry by climate change on the temperature sensitivity (Q10) of the RH of soils amended with the residues is available. To fill this knowledge gap, we conducted an incubation experiment (at 15, 25, and 35 °C) with rice residues of which lignin, nonstructural carbohydrate (NSC), and carbon-to-nitrogen ratio (C/N) were modified by growing the rice plants under different CO2 and air temperature (Tair). Co-elevated CO2 and Tair decreased lignin and C/N but increased the NSC contents of the residues, leading to the greater RH in the soils amended with rice residues produced under co-elevated CO2 and Tair compared to other CO2 or Tair treatments. However, the Q10 values of the RH of soils amended with rice residues produced under different CO2 and Tair were marginally changed, probably due to other confounding factors such as soil enzyme activity and nutrient availability. Despite that, there was a negative relationship between NSC and Q10 for soils amended with straw of which C/N is lower than root, agreeing with the kinetic theory on "substrate quality–Q10 relationship". Our result suggests that residue chemistry may not affect the Q10 of soils with root residue, but for straw-amended soils, less-recalcitrant NSC rather than more-recalcitrant lignin of straw may be critical in determining the Q10 of the soils. [ABSTRACT FROM AUTHOR]

We study the bacterial respiration through the numerical solution of the Fairen–Velarde coupled nonlinear differential equations. The instantaneous concentrations of the oxygen and the nutrients are computed. The fixed point solution and the stable limit cycle are found in different parameter ranges as predicted by the linearized differential equations. In a specified range of parameters, it is observed that the system spends some time near the stable limit cycle and eventually reaches the stable fixed point. This metastability has been investigated systematically. Interestingly, it is observed that the system exhibits two distinctly different time scales in reaching the stable fixed points. The slow time scale of the metastable lifetime near the stable limit cycle and a fast time scale (after leaving the zone of limit cycle) in rushing towards the stable fixed point. The gross residence time, near the limit cycle (described by a slow time scale), can be reduced by varying the concentrations of nutrients. This idea can be used to control the harmful metastable lifespan of active bacteria. [ABSTRACT FROM AUTHOR]

Beach wrack is an important supplier of nutrients and organic matter to sandy beach ecosystems and underlying subterranean estuaries (STEs), producing metabolic hotspots in these otherwise organic carbon- and nutrient-poor environments. To assess the impact of beach wrack type (e.g., marine, terrestrial, plant, animal) and environmental settings (e.g., tidal inundation, precipitation, and solar irradiation) on nutrient and dissolved organic matter (DOM) release, a series of leaching experiments was conducted. Quantities of leached nutrients and dissolved organic carbon (DOC) were determined, and DOM molecular composition was investigated using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Millimolar—to molar amounts of DOC and dissolved nitrogen were released from the beach cast per kg dry weight, with type of wrack and leaching medium (fresh- vs. saltwater) exerting the biggest influences. Exemplary for animal cast, jellyfish leached up to two 100-fold more, mostly organic, nitrogen compared to all other beach wrack types. FT-ICR-MS data of solid-phase extracted DOM indicated that beach wrack releases compounds with putative mono- and oligosaccharide-, amino acid- and vitamin-type molecular formulae, which likely serve as valuable substrate for heterotrophic microorganisms. DOM from the brown seaweed Fucus sp. was more aromatic than seawater DOM and even beach wrack of terrestrial origin, probably from structural components and secondary metabolites such as phlorotannins. We conclude that DOM and nutrient release from beach wrack strongly depends on wrack type and leaching medium, may obscure molecular provenance proxies (e.g., terrestrial indices), and adds a nutritional boost to infiltrating sea- and rainwater which likely impact microbial respiration rates in the STE. [ABSTRACT FROM AUTHOR]

Soil microbial traits and functions play a central role in soil organic carbon (SOC) dynamics. However, at the macroscale (regional to global) it is still unresolved whether (i) specific environmental attributes (e.g., climate, geology, soil types) or (ii) microbial community composition drive key microbial traits and functions directly. To address this knowledge gap, we used 33 grassland topsoils (0–10 cm) from a geoclimatic gradient in Chile. First, we incubated the soils for 1 week in favorable standardized conditions and quantified a wide range of soil microbial traits and functions such as microbial biomass carbon (MBC), enzyme kinetics, microbial respiration, growth rates as well as carbon use efficiency (CUE). Second, we characterized climatic and physicochemical properties as well as bacterial and fungal community composition of the soils. We then applied regression analysis to investigate how strongly the measured microbial traits and functions were linked with the environmental setting versus microbial community composition. We show that environmental attributes (predominantly the amount of soil organic matter) determined patterns of MBC along the gradient, which in turn explained microbial respiration and growth rates. However, respiration and growth normalized for MBC (i.e., specific respiration and growth) were more linked to microbial community composition than environmental attributes. Notably, both specific respiration and growth followed distinct trends and were related to different parts of the microbial community, which in turn resulted in strong effects on microbial CUE. We conclude that even at the macroscale, CUE is the result of physiologically decoupled aspects of microbial metabolism, which in turn is partially determined by microbial community composition. The environmental setting and microbial community composition affect different microbial traits and functions, and therefore both factors need to be considered in the context of macroscale SOC dynamics. [ABSTRACT FROM AUTHOR]

Seed quality declines during storage depending on relative humidity, temperature, and oxygen concentration. Low-oxygen atmospheres significantly enhanced the germination and vigor of seeds during storage in laboratory-scale experiments. Low-oxygen atmospheres include self-modified atmospheres, where gas composition changes due to microbial respiration and oxidative processes, as well as modified atmospheres, where gas composition is initially altered from an external source without further adjustments. However, the potential of low-oxygen atmospheres to preserve the quality of maize (Zea mays) seeds in bags of 25–50 kg capacity, like those employed by seed companies and small-scale farmers, remains underexplored, hindering a broader adoption of this storage technology. Our study assessed the feasibility of applying low-oxygen atmospheres for seed storage on the pilot scale, i.e., hermetic containers of 25 kg capacity made of polyethylene and polyamide, under controlled conditions. We first evaluated the ability of the hermetic containers to maintain low oxygen levels over time. Then, we compared the germination and vigor of seeds stored in the hermetic containers under modified and self-modified atmospheres with those stored in traditional poly-paper bags under normal atmospheric conditions. The seeds had 14% moisture content (wet basis) and were stored at 25 °C and 10 °C. Maintaining low oxygen levels in polyethylene–polyamide bags was feasible. Moreover, at 25 °C, modified and self-modified atmospheres maintained higher germination values (95.8% and 94.4%, respectively) compared to traditional storage (68.3%), and both were as effective as refrigeration (97.6%). However, refrigeration was better for preserving seed vigor, with radicle emergence values of 85.2% in self-modified atmospheres and 78.9% in modified atmospheres, compared to 65.0% and 61.2%, respectively, at 25 °C. In conclusion, the advantages of modified atmospheres observed in laboratory-scale studies are achievable on a larger scale with a proper container design, advancing the prospects for the practical application of this technology for the seed industry and small farmers. [ABSTRACT FROM AUTHOR]

Abstract Bcakground Soil respiration (Rs), as the second largest CO2 emissions of terrestrial ecosystems, is sensitive to disturbance and consequent environmental changes. Mowing is strategically implemented as an management approach and has the potential to influence carbon cycling in meadow steppes. However, it remains unclear how and why Rs and its heterotrophic (Rh) and autotrophic (Ra) components respond to consecutive mowing and associated ecological consequences. Here, we conducted a field mowing experiment in a meadow steppe in 2018 and monitored Rs, Rh, and Ra from 2019 to 2022. Results We observed a significant reduction in Rs by 4.8% across four years, primarily attributed to a decrease in Rh. This decline in Rs intensified over time, indicating an accumulative effect of mowing. In addition, mowing induced an generally increasing Ra/Rs ratio over the experimental years with a simultaneous increase in the ratio of belowground to aboveground biomass (BGB/AGB). Furthermore, structural equation modeling results revealed that the decline in Rs was largely ascribed to reduced microbial biomass carbon (MBC) under mowing, while the increased Ra/Rs was primarily explained by the enhanced BGB/AGB. Partial regression analysis suggested that the biotic factor of microbial biomass dominated changes in soil respiration induced by mowing rather than abiotic soil temperature. Conclusions Our findings showed that consecutive mowing decreased Rs and raised Ra/Rs in meadow steppe by decreasing plant biomass and altering the proportion of biomass allocation. This observed decline in Rs would help to reduce CO2 concentration in atmosphere as well as alleviate global warming. However, considering the concurrent lower microbial biomass, the potential positive impacts of mowing on climate and ecosystem function should be reevaluated in future grassland management practices.

• Chlorella proteinosa was cultivated in an MPBR for secondary effluents treatment. • Highest TN removal rate of 23.8 mg/L/day was achieved at a lowest HRT of 8 hr. • Highest microalgae biomass productivity reached 20.2 mg/L/day at the HRT of 8 hr. • Bacterial nitrogen respiration was reduced by 95.5 % from an HRT of 24 hr to 8 hr. Further treatment of secondary effluents before their discharge into the receiving water bodies could alleviate water eutrophication. In this study, the Chlorella proteinosa was cultured in a membrane photobioreactor to further remove nitrogen from the secondary effluents. The effect of hydraulic retention time (HRT) on microalgae biomass yields and nutrient removal was studied. The results showed that soluble algal products concentration reduced in the suspension at low HRT, thereby alleviating microalgal growth inhibition. In addition, the lower HRT reduced the nitrogen limitation for Chlorella proteinosa 's growth through the phase-out of nitrogen-related functional bacteria. As a result, the productivity for Chlorella proteinosa increased from 6.12 mg/L/day at an HRT of 24 hr to 20.18 mg/L/day at an HRT of 8 hr. The highest removal rates of 19.7 mg/L/day, 23.8 mg/L/day, and 105.4 mg/L/day were achieved at an HRT of 8 hr for total nitrogen (TN), ammonia, and chemical oxygen demand (COD), respectively. However, in terms of removal rate, TN and COD were the largest when HRT is 24 hr, which were 74.5% and 82.6% respectively. The maximum removal rate of ammonia nitrogen was 99.2% when HRT was 8 hr. [Display omitted] [ABSTRACT FROM AUTHOR]

It remains unclear whether microbial carbon limitation exists in the rhizosphere, a microbial hotspot characterized by intensive labile carbon input. Here, we collected rhizosphere soils attached to absorptive and transport roots and bulk soils in three alpine coniferous forests and evaluated the limiting resources of microbes based on the responses of microbial growth (18O incorporation into DNA) and respiration to full-factorial amendments of carbon, nitrogen, and phosphorus. The results showed that adding carbon enhanced microbial growth and respiration rates in the rhizosphere soils by 1.2- and 10.3-fold, respectively, indicating the existence of carbon limitation for both anabolic and catabolic processes. In contrast, the promoting effects of nutrient addition were weak or manifested only after the alleviation of carbon limitation, suggesting that nutrients were co-limiting or secondarily limiting resources. Moreover, the category and extent of microbial resource limitations were comparable between the rhizosphere of absorptive and transport roots, and between the rhizosphere and bulk soils. Overall, our findings offer direct evidence for the presence of microbial carbon limitation in the rhizosphere. [ABSTRACT FROM AUTHOR]

Abstract\nNOVELTY STATEMENTThe objective of this study was to determine the efficiency of the microbial rhizosphere (Canavalia ensiformis) in the phytoremediation of sulfentrazone using quantification methods (CO2 evolution, microbial biomass carbon, and metabolic quotient) and identification of bacteria (PCR-DGGE technique). The experiment was conducted in a completely randomized design, in a 2x4 factorial scheme, with four replications. The treatments were composed of rhizospheric soil (cultivated with C. ensiformis) and non-rhizosphere soil (uncultivated soil); and four levels of contamination by sulfentrazone (0, 200, 400, and 800 g ha−1 a.i.). The microbiota associated with the rhizosphere of C. ensiformis efficiently reduced sulfentrazone residues in the soil, with better performance at the dose of 200 g ha−1 a.i. Using the PCR-DGGE technique allowed the distinction of two profiles of bacteria in the rhizospheric activity of C. ensiformis. The second bacterial profile formed was more efficient in decontaminating soil contaminated with sulfentrazone residue. The microbiota associated with the rhizosphere of C. ensiformis has an efficient profile in decontaminating soils with residues equivalent to 200 g ha−1 a.i. the herbicide sulfentrazone.Phytoremediation of soils contaminated with herbicide residues is a viable technique for decontamination of the environment.Canavalia ensiformis has an efficient profile in the decontamination of soils with residue equivalent to 200 g ha−1 a.i. of the herbicide sulfentrazone.The PCR technique and microbial respiration used to analyze the diversity and estimate the bacterial population of a soil are viable tools to evaluate the phytoremediation potential of the microbiota associated with plant species. [ABSTRACT FROM AUTHOR]

Little is known about oxygen utilization during infection by bacterial respiratory pathogens. The classical Bordetella species, including B. pertussis, the causal agent of human whooping cough, and B. bronchiseptica, which infects nearly all mammals, are obligate aerobes that use only oxygen as the terminal electron acceptor for electron transport-coupled oxidative phosphorylation. B. bronchiseptica, which occupies many niches, has eight distinct cytochrome oxidase-encoding loci, while B. pertussis, which evolved from a B. bronchiseptica-like ancestor but now survives exclusively in and between human respiratory tracts, has only three functional cytochrome oxidase-encoding loci: cydAB1, ctaCDFGE1, and cyoABCD1. To test the hypothesis that the three cytochrome oxidases encoded within the B. pertussis genome represent the minimum number and class of cytochrome oxidase required for respiratory infection, we compared B. bronchiseptica strains lacking one or more of the eight possible cytochrome oxidases in vitro and in vivo. No individual cytochrome oxidase was required for growth in ambient air, and all three of the cytochrome oxidases conserved in B. pertussis were sufficient for growth in ambient air and low oxygen. Using a high-dose, large-volume persistence model and a low-dose, small-volume establishment of infection model, we found that B. bronchiseptica producing only the three B. pertussis-conserved cytochrome oxidases was indistinguishable from the wild-type strain for infection. We also determined that CyoABCD1 is sufficient to cause the same level of bacterial burden in mice as the wild-type strain and is thus the primary cytochrome oxidase required for murine infection, and that CydAB1 and CtaCDFGE1 fulfill auxiliary roles or are important for aspects of infection we have not assessed, such as transmission. Our results shed light on the environment at the surface of the ciliated epithelium, respiration requirements for bacteria that colonize the respiratory tract, and the evolution of virulence in bacterial pathogens. Author summary: Cytochrome oxidases, critical components for aerobic respiration, have been shown to be vital for pathogenesis and tissue tropism in several bacterial species. However, the majority of the research has focused on facultative anaerobes and infections of microoxic to anaerobic host environments, like the gut. We sought to understand the role of cytochrome oxidases during respiratory infection by Bordetella bronchiseptica, an obligate aerobe, performing the first analysis of cytochrome oxidases in an extracellular respiratory pathogen that we know of. By comparing B. bronchiseptica to the closely related B. pertussis, a strictly human-specific pathogen and the causative agent of whooping cough, we found three cytochrome oxidases that are important for growth and survival within the mammalian respiratory tract. We also found that a bo3-type cytochrome oxidase, predicted to have a low affinity for oxygen and therefore best suited to ambient air levels of oxygen, was sufficient for both the establishment of infection and persistence in the respiratory tract in mice. Our findings reveal the importance of low affinity cytochrome oxidases in respiratory pathogens, and emphasize the need to study the physiology of diverse classes of pathogens. [ABSTRACT FROM AUTHOR]

Climate influences near-surface biogeochemical processes and thereby determines the partitioning of carbon dioxide (CO2) in shale, and yet the controls on carbon (C) weathering fluxes remain poorly constrained. Using a dataset that characterizes biogeochemical responses to climate forcing in shale regolith, we implement a numerical model that describes the effects of water infiltration events, gas exchange, and temperature fluctuations on soil respiration and mineral weathering at a seasonal timescale. Our modeling approach allows us to quantitatively disentangle the controls of transient climate forcing and biogeochemical mechanisms on C partitioning. We find that ~3% of soil CO2 (1.02 mol C/m²/y) is exported to the subsurface during large infiltration events. Here, net atmospheric CO2 drawdown primarily occurs during spring snowmelt, governs the aqueous C exports (61%), and exceeds the CO2 flux generated by pyrite and petrogenic organic matter oxidation (~0.2 mol C/m²/y). We show that shale CO2 consumption results from the temporal coupling between soil microbial respiration and carbonate weathering. This coupling is driven by the impacts of hydrologic fluctuations on fresh organic matter availability and CO2 transport to the weathering front. Diffusion-limited transport of gases under transient hydrological conditions exerts an important control on CO2(g) egress patterns and thus must be considered when inferring soil CO2 drawdown from the gas phase composition. Our findings emphasize the importance of seasonal climate forcing in shaping the net contribution of shale weathering to terrestrial C fluxes and suggest that warmer conditions could reduce the potential for shale weathering to act as a CO2 sink. [ABSTRACT FROM AUTHOR]

This work provides insights into the effect of fire on soil processes in Mediterranean-type ecosystems in Cyprus. Soil samples from mountainous sites that were subjected to a summer wildfire and adjacent control samples were collected. Incubations were used to estimate basal respiration and isolate soil CO2 release of heterotrophic microorganisms from autotrophic root respiration and heterotrophic respiration from litter decomposition. Physicochemical property changes, bacteria community changes using DNA extraction and 16S rRNA gene analysis, and the effects of ash and fresh litter addition were studied to reveal the microbial composition and the post-fire soil function. Laboratory incubation showed that burned soils constantly showed higher microbial respiration rates compared with control unburned areas, even six months after a fire. Adding ash to unburned samples increased microbial respiration, suggesting that increased nutrient availability positively corelates with the increased release of CO2 from fire-affected soil. Elevated temperatures due to the wildfire exerted significant effects on the composition of soil bacterial microbiota. Nevertheless, the wildfire did not affect the alpha-diversity of soil bacteria. New communities of microorganisms are still able to decompose fresh plant material after a fire, but at a slower rate than natural pre-fire populations. [ABSTRACT FROM AUTHOR]

Rhizodeposition fuels carbon (C) and nutrient cycling in soil. However, changes in the dynamics of microbial growth on rhizodeposits with increasing distance from the root is not well studied. This study investigates microbial growth on individual organic components of rhizodeposits and maize root‐derived exudates and mucilage from agricultural soil. By creating a gradient of substrate concentrations, we simulated reduced microbial access to rhizosphere C with increasing distance to the root surface. We identified distinct C‐thresholds for the activation of microbial growth, and these were significantly higher for rhizodeposits than singular, simple sugars. In addition, testing for stoichiometric constraints of microbial growth by supplementing nitrogen (N) and phosphorus (P) showed accelerated and increased microbial growth by activating a larger proportion of the microbial biomass. Early and late season exudates triggered significantly different microbial growth responses. The mineralization of early‐season exudates was induced at a high C‐threshold. In contrast, the mineralization of late‐season exudates showed 'sugar‐like' properties, with a low C‐threshold, high substrate affinity, and a reduced maximum respiration rate of microorganisms growing on the added substrate. Mucilage exhibited the highest C‐threshold for the activation of microbial growth, although with a short lag‐period and with an efficient mucilage degradation comparable to that of sugars. By determining kinetic parameters and turnover times for different root‐derived substrates, our data enable the upscaling of micro‐scale processes to the whole root system, allowing more accurate predictions of how rhizodeposition drives microbial C and nutrient dynamics in the soil. [ABSTRACT FROM AUTHOR]

Water‐logged peatlands store tremendous amounts of soil carbon (C) globally, accumulating C over millennia. As peatlands become disturbed by human activity, these long‐term C stores are getting destabilized and ultimately released as greenhouse gases that may exacerbate climate change. Oxidation of the dissolved organic carbon (DOC) mobilized from disturbed soils to streams and canals may be one avenue for the transfer of previously stored, millennia‐aged C to the atmosphere. However, it remains unknown whether aged peat‐derived DOC undergoes oxidation to carbon dioxide (CO2) following disturbance. Here, we use a new approach to measure the radiocarbon content of CO2 produced from the oxidation of DOC in canals overlying peatland soils that have undergone widespread disturbance in Indonesia. This work shows for the first time that aged DOC mobilized from drained and burned peatland soils is susceptible to oxidation by both microbial respiration and photomineralization over aquatic travel times for DOC. The bulk radiocarbon age of CO2 produced during canal oxidation ranged from modern to ~1300 years before present. These ages for CO2 were most strongly influenced by canal water depth, which was proportional to the water table level where DOC is mobilized from disturbed soils to canals. Canal microbes preferentially respired older or younger organic C pools to CO2, and this may have been facilitated by the use of a small particulate organic C pool over the dissolved pool. Given that high densities of canals are generally associated with lower water tables and higher fire risk, our findings suggest that peatland areas with high canal density may be a hotspot for the loss of aged C on the landscape. Taken together, the results of this study show how and why aquatic processing of organic C on the landscape can enhance the transfer of long‐term peat C stores to the atmosphere following disturbance. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) are a type of bacteria that convert carbohydrates into lactate through fermentation metabolism. While LAB mainly acquire energy through this anaerobic process, they also have oxygen-consuming systems, one of which is flavoprotein oxidase and the other is exogenous heme- or heme- and quinone-dependent respiratory metabolism. Over the past two decades, research has contributed to the understanding of the roles of these oxidase machineries, confirming their suspected roles and uncovering novel functions. This review presents the roles of these oxidase machineries, which are anticipated to be critical for the future applications of LAB in industry and comprehending the virulence of pathogenic streptococci. [ABSTRACT FROM AUTHOR]

Microbial respiration is a critical component of the marine carbon cycle, determining the proportion of fixed carbon that is subject to remineralization as opposed to being available for export to the ocean depths. Despite its importance, methodological constraints have led to an inadequate understanding of this process, especially in low-activity oligotrophic and mesopelagic regions. Here, we quantify respiration rates as low as 0.2 µmol O2 L-1 d-1 in contrasting ocean productivity provinces using oxygen optode sensors to identify size-fractionated respiration trends. In the low productivity region of the North Pacific Ocean at Station Papa, surface whole water microbial respiration was relatively stable at 1.2 µmol O2 L-1 d-1. Below the surface, there was a decoupling between respiration and bacterial production that coincided with increased phytodetritus and small phytoplankton. Size-fractionated analysis revealed that cells <5 µm were responsible for the majority of the respiration in the Pacific, both at the surface and below the mixed layer. At the North Atlantic Porcupine Abyssal Plain, surface whole water microbial respiration was higher (1.7 µmol O2 L-1 d-1) than in the Pacific and decreased by 3-fold below the euphotic zone. The Atlantic size-fraction contributions to total respiration shifted on the order of days during the evolution of a phytoplankton bloom with regular storm disturbances. The high-resolution optode method used in the Atlantic captured these significant shifts and is consistent with coinciding stain-based respiration methods and historical site estimates. This study highlights the dynamic nature of respiration across vertical, temporal, and size-fractionated factors, emphasizing the need for sensitive, high-throughput techniques to better understand ocean ecosystem metabolism. [ABSTRACT FROM AUTHOR]

Molybdate inhibits sulfate respiration in sulfate-reducing bacteria (SRB). It is used as an inhibitor to indirectly evaluate the role of SRB in mercury methylation in the environment. Here, the SRB Pseudodesulfovibrio hydrargyri BerOc1 was used to assess the effect of molybdate on cell growth and mercury methylation under various metabolic conditions. Geobacter sulfurreducens PCA was used as the non-SRB counterpart strain with the ability to methylate mercury. While PCA growth and methylation are not affected by molybdate, 1 mM of molybdate inhibits BerOc1 growth under sulfate respiration (50% inhibition) but also under fumarate respiration (complete inhibition). Even more surprising, mercury methylation of BerOc1 is totally inhibited at 0.1 mM of molybdate when grown under sulfate or fumarate respiration with pyruvate as the electron donor. As molybdate is expected to reduce cellular ATP level, the lower Hg methylation observed with pyruvate could be the consequence of lower energy production. Although molybdate alters the expression of hgcA (mercury methylation marker) and sat (involved in sulfate reduction and molybdate sensitivity) in a metabolism-dependent manner, no relationship with mercury methylation rates could be found. Our results show, for the first time, a specific mercury methylation inhibition by molybdate in SRB. [ABSTRACT FROM AUTHOR]

The capacity of forests to sequester carbon in both above‐ and belowground compartments is a crucial tool to mitigate rising atmospheric carbon concentrations. Belowground carbon storage in forests is strongly linked to soil microbial communities that are the key drivers of soil heterotrophic respiration, organic matter decomposition and thus nutrient cycling. However, the relationships between tree diversity and soil microbial properties such as biomass and respiration remain unclear with inconsistent findings among studies. It is unknown so far how the spatial configuration and soil depth affect the relationship between tree richness and microbial properties. Here, we studied the spatial distribution of soil microbial properties in the context of a tree diversity experiment by measuring soil microbial biomass and respiration in subtropical forests (BEF‐China experiment). We sampled soil cores at two depths at five locations along a spatial transect between the trees in mono‐ and hetero‐specific tree pairs of the native deciduous species Liquidambar formosana and Sapindus saponaria. Our analyses showed decreasing soil microbial biomass and respiration with increasing soil depth and distance from the tree in mono‐specific tree pairs. We calculated belowground overyielding of soil microbial biomass and respiration – which is higher microbial biomass or respiration than expected from the monocultures – and analysed the distribution patterns along the transect. We found no general overyielding across all sampling positions and depths. Yet, we encountered a spatial pattern of microbial overyielding with a significant microbial overyielding close to L. formosana trees and microbial underyielding close to S. saponaria trees. We found similar spatial patterns across microbial properties and depths that only differed in the strength of their effects. Our results highlight the importance of small‐scale variations of tree–tree interaction effects on soil microbial communities and functions and are calling for better integration of within‐plot variability to understand biodiversity–ecosystem functioning relationships. [ABSTRACT FROM AUTHOR]

Invasive Spartina alterniflora has significant impacts on sediment carbon pool and turnover in the tidal wetlands of estuaries and coasts. Yet, how this exotic S. alterniflora affects sediment organic carbon mineralization dynamics remains poorly understood. In this study, sediment geochemical properties, organic carbon fractions, and mineralization dynamics were examined in a native Cyperus malaccensis habitat and three invasive S. alterniflora habitats (6-, 10-, and 14-year-old) in summer and winter. We found that invasive S. alterniflora generally increased sediment total organic carbon and their labile fraction contents. The organic carbon mineralization rates and cumulative carbon mineralization amounts were significantly influenced by invasive S. alterniflora, and their values increased with this exotic plant invasion chronosequences. The mineralization rates and cumulative mineralization amounts were also characterized by higher values in surface sediment (0 - 10 cm depth) compared to subsurface sediment (10 - 20 cm depth) and by seasonal variations with higher values in summer than in winter. The sediment organic carbon labile fractions, rather than total organic carbon, were the most important factor affecting carbon mineralization dynamics. The cumulative carbon mineralization amounts exhibited an excellent fit to the first-order kinetic equation (R2 = 0.93). The changes in modeled kinetic parameters (potential carbon mineralization amounts (C0) and carbon mineralization rate constant (k)) among these four habitats were similar to carbon mineralization rates, implying invasive S. alterniflora promoted the availabilities of organic compounds for microbial respiration metabolism. Overall, our findings highlighted the importance of S. alterniflora invasion in accelerating organic carbon decomposition and carbon dioxide release potential, although it also increases carbon accumulation. [ABSTRACT FROM AUTHOR]

The applicability of ionic liquids has grown exponentially over the last few decades. This growth is due to the easy modification of these compounds formed by ions, through the proper choice of both moieties, and the possibility of introducing functional groups into their cations and anions. However, studies of their toxicity and effects on the environment remain scarce. This study analyses firstly the response to adding different concentrations of choline dihydrogen phosphate to the germination of seeds of eight plant species. It also examines the microbial population and the respiration of two soils with contrasting organic matter contents. Seeds were incubated in a Petri dish in a Phytotron with a photoperiod of 16 h under light at 24 °C and 8 h in darkness at 16 °C. The activity of microbial populations of untreated and treated soils was analysed by isothermal microcalorimetry at 25 °C. Basal soil respiration kinetics were measured at optimal moisture (80% of field water retention capacity) and temperature (25 °C) over 10 days. The results indicate that this compound has diverse effects on the different endpoints. Nevertheless, this compound can be classified as non-toxic considering its effects on seeds and on soil, at least in the medium- to long-term. [ABSTRACT FROM AUTHOR]

Microbial necromass is increasingly recognized as an important fast‐cycling component of the long‐term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250–500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal–bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass‐infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co‐cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition. [ABSTRACT FROM AUTHOR]

Soil health is crucial to reaching high yields, and growing cover crops can help improve soil conditions. The goal of this study is to determine the effects of cover crops on soil health using potential respiration, potential nitrogen mineralization, and aggregates stability as indicators of soil health. The study has been conducted since 2019 at the University of Kentucky Spindletop Farm, Lexington, KY, and involves three landscape positions receiving a treatment with cereal rye, cereal rye– crimson clover mixture, and fallow soil. This study emphasized that cover crops can enhance potential respiration and microbial activity over landscape positions, with rye being more beneficial than the mixture treatment. However, cover crops were also beneficial for aggregate stability but not for potential nitrogen mineralization. [ABSTRACT FROM AUTHOR]

A recently emerging cell death pathway, known as copper‐induced cell death, has demonstrated significant potential for treating infections. Existing research suggests that cells utilizing aerobic respiration, as opposed to those reliant on glycolysis, exhibit greater sensitivity to copper‐induced death. Herein, a MnO2‐loaded copper metal–organic frameworks platform is developed denoted as MCM, to enhance bacterial cuproptosis‐like death via the remodeling of bacterial respiratory metabolism. The reversal of hypoxic microenvironments induced a cascade of responses, encompassing the reactivation of suppressed immune responses and the promotion of osteogenesis and angiogenesis. Initially, MCM catalyzed O2 production, alleviating hypoxia within the biofilm and inducing a transition in bacterial respiration mode from glycolysis to aerobic respiration. Subsequently, the sensitized bacteria, characterized by enhanced tricarboxylic acid cycle activity, underwent cuproptosis‐like death owing to increased copper concentrations and aggregated intracellular dihydrolipoamide S‐acetyltransferase (DLAT). The disruption of hypoxia also stimulated suppressed dendritic cells and macrophages, thereby strengthening their antimicrobial activity through chemotaxis and phagocytosis. Moreover, the nutritional effects of copper elements, coupled with hypoxia alleviation, synergistically facilitated the regeneration of bones and blood vessels. Overall, reshaping the infection microenvironment to enhance cuproptosis‐like cell death presents a promising avenue for eradicating biofilms. [ABSTRACT FROM AUTHOR]

Increased temperatures in Arctic tundra ecosystems are leading to higher microbial respiration rates of soil organic matter, resulting in the release of carbon dioxide and methane. To understand the effects of this microbial activity, it is important to better characterize the diverse microbial communities in Arctic soil. Our goal is to refine our understanding of the phylogenetic diversity of Terriglobia, a common but elusive group within the Acidobacteriota phylum. This will help us link this diversity to variations in carbon and nitrogen usage patterns. We used long‐read Oxford Nanopore MinION sequences in combination with metagenomic short‐read sequences to assemble complete Acidobacteriota genomes. This allowed us to build multi‐locus phylogenies and annotate pangenome markers to distinguish Acidobacteriota strains from several tundra soil isolates. We identified a phylogenetic cluster containing four new species previously associated with Edaphobacter lichenicola. We conclude that this cluster represents a new genus, which we have named Tunturibacter. We describe four new species: Tunturibacter lichenicola comb. nov., Tunturibacter empetritectus sp. nov., Tunturibacter gelidoferens sp. nov., and Tunturibacter psychrotolerans sp. nov. By uncovering new species and strains within the Terriglobia and improving the accuracy of their phylogenetic placements, we hope to enhance our understanding of this complex phylum and shed light on the mechanisms that shape microbial communities in polar soils. [ABSTRACT FROM AUTHOR]

The soil health concept has evolved over the past several decades, recognizing that the response of dynamic soil properties to management is dependent on site‐specific factors. The Soil Health Assessment Protocol and Evaluation (SHAPE) tool provides scores and benchmark values by forming soil peer groups based on site‐specific, climate‐edaphic characteristics. Data for model development were compiled from the Cornell Soil Health Laboratory and the Kellogg Soil Survey Laboratory databases. The SHAPEv1.0 interpretation curves produce scores between 0% and 100% for measured laboratory values that reflect the quantile within a population conditional cumulative distribution function along with measures of uncertainty. The original SHAPE tool was developed for soil organic carbon and has been expanded to include two wet aggregate stability methods, permanganate oxidizable organic carbon, autoclaved citrate extractable protein, and 4‐day microbial respiration. In addition, SHAPE provides site‐specific benchmark values at user‐defined percentiles within a given soil peer group. The difference between the actual measured value and the selected benchmark value represents the soil health opportunity gap. Case studies in Missouri and Texas show that the SHAPE scoring curves are sensitive to land‐use and management practices across multiple soil types and provide a regionally relevant interpretation of key soil health indicators. Core Ideas: Climate and edaphic factors are relevant to soil health data interpretation.Soil health assessment protocol and evaluation (SHAPE) provides site‐specific soil health scores and benchmarks.SHAPE accounts for inherent factors affecting soil health indicators.SHAPE scoring curves are sensitive to land management practices.SHAPE is a useful tool for landowner soil health assessments and interpretations. [ABSTRACT FROM AUTHOR]

Human activity is increasing salt concentrations in freshwaters worldwide, but effects of freshwater salinity gradients on biogeochemical cycling are less understood than in saline, brackish, or marine environments. Using controlled microcosm experiments, we characterized (1) short-term (one to five days) biogeochemical responses and (2) water column metabolism along a freshwater salinity gradient of multiple salt types. After one day, microcosms were oxic (4.48–7.40 mg O2 L−1) but became hypoxic (1.20–3.31 mg L−1) by day five. After one day in oxic conditions, microbial respiration in magnesium-, sodium-, and sea salt-based salinity treatments showed a subsidy-stress response, with respiration increasing by over 100% as salinity increased from 30 to 350–800 µS cm−1. Conversely, respiration consistently increased along a calcium-based salinity gradient, peaking at 1500 µS cm−1. By day five, an inverse subsidy-stress response was observed with elevated respiration at upper or lower ends of the gradient except for the magnesium treatment, which had the lowest respiration at the highest salinity. Calcium- and magnesium-based salinity treatments also caused considerable changes in phosphorus concentrations and C:P and N:P. In a separate experiment, microbial respiration and water column primary production also displayed subsidy-stress responses, but imbalances in effect sizes caused consistently declining net community production with increasing salinity. Collectively, our results establish that short-term exposure to different salt ion concentrations can enhance freshwater biogeochemical cycling at relatively low concentrations and alter resource stoichiometry. Furthermore, the nature of effects of freshwater salinization may also change with oxygen availability. [ABSTRACT FROM AUTHOR]

As the general population's diet has shifted to reflect current weight-loss trends, there has been an increase in zero-calorie artificial sweetener usage. Sucralose (C12H19Cl3O8), commonly known as Splenda® in the USA, is a primary example of these sweeteners. In recent years, sucralose has been identified as an environmental contaminant that cannot easily be broken down via bacterial decomposition. This study focuses on the impact of sucralose presence on microbial communities in brackish and freshwater systems. Microbial respiration and fluorescence were measured as indicators of microbial activity in sucralose-dosed samples taken from both freshwater and estuarine marsh environments. Results showed a significant difference between microbial concentration and respiration when dosed with varying levels of sucralose. Diatom respiration implied a negative correlation of community abundance with sucralose concentration. The freshwater cyanobacterial respiration increased in the presence of sucralose, implying a positive correlation of community abundance with sucralose concentration. This was in direct contrast to its brackish water counterpart. However, further investigation is necessary to confirm any potential utility of these communities in the breakdown of sucralose in the marsh environment. [ABSTRACT FROM AUTHOR]