Comparison of temperature effects on soil respiration and bacterial and fungal growth rates

Trichoderma harzianum AKH-5: A novel fungal isolate with antimicrobial efficacy for phytopathogen management and environmental remediation

Trichoderma harzianum isolate AKH-5 is recognized as a biological control agent, effective in managing harmful phytopathogens while promoting plant growth and enhancing resistance to various stresses. In this study, a total of 140 morphological different fungal isolates were isolated and in primary screening isolate AKH-5 exhibited significant antifungal activity in vitro. Trichoderma harzianum isolate AKH-5 proved to be effective and was characterized morphologically, physiologically and through 18S rRNA gene sequencing and identified as Trichoderma harzianum. GC-MS profiling of the ethyl acetate extract identified 22 distinct bioactive compounds, including phenylethyl alcohol, dibutyl phthalate, and N-carbobenzyloxy-L-tyrosyl-L-valine, which possess antibacterial, antifungal and antioxidant properties. Further, in antibacterial assessment, AKH-5 extract exhibited significant antibacterial activity on microbial pathogens in a dose-dependent manner. The lowest MIC value against Escherichia coli was 8 μg/mL, indicating strong antibacterial activity. MBC values (32, 64 μg/mL) were higher than MIC values, indicating the need for higher concentrations for bactericidal effects and significant antioxidant activity with an IC50 value of 90.78 μg/mL. The extract exhibited significant inhibition efficacy on Fusarium oxysporum, and Colletotrichum capsici, further moderate activity on Curvularia lunata, Alternaria alternata, and Rhizoctonia solani. The isolate AKH-5 showed good azo-dye degradation capacity and Triticum aestivum L. (wheat) seeds treated with dyes degraded with the isolate AKH-5 broth extract exhibited a germination rate of 98 %, compared to the untreated and control seeds which showed germination of 50 and 94 %, respectively. This study highlights the unexplored habitats as rich sources of diverse antifungal metabolite-producing fungi, which can be promising candidates for developing novel antifungal strains. Overall, the results demonstrate the beneficial role of AKH-5 in controlling phytopathogens and minimizing phytotoxicity through biodegradation of dyes for environmental remediation purposes.

Patterns and controlling factors of soil microbial necromass carbon in global ecosystems

Microbial necromass is a critical source of soil organic carbon (SOC) in terrestrial ecosystems, and the quantity and quality of microbial necromass carbon (MNC) can influence long-term soil carbon sequestration. However, few studies have explored the distribution of soil MNC and its contribution to SOC along the soil profiles across different ecosystems globally. Here, we collected a global dataset (2, 411 samples from 216 papers) of soil MNC at a depth of 0-100 cm depth from wetlands, farmlands, grasslands, and forests. Our findings indicated that the average MNC at 0-30 cm was 2.7 g kg-1 in wetlands, 7.1 g kg-1 in farmlands, 17.2 g kg-1 in grasslands, and 14.6 g kg-1 in forests. The MNC content in deep soils (30-100 cm) was 70 % lower (p < 0.05) than in topsoil (0-30 cm), whereas the contribution of the MNC to the SOC in deep soils (50 %) was higher than in topsoil in forests (32 %). On average, the fungal necromass carbon(FNC) content (7.5 g kg-1) was almost three times higher than the bacterial necromass carbon (BNC) content (2.8 g kg-1) in the topsoill. The mean annual temperature played an important role in affecting the MNC by altering soil total nitrogen, soil texture and microbial biomass. These findings are important for understanding SOC formation mechanisms and the crucial role of microbial necromass in global ecosystems.

Determinism and stochasticity drive microbial community assembly and microbial interactions in calcareous glacier forefields

Calcareous glacier forefields challenge prevailing ecological frameworks on microbial biodiversity and community assembly due to their unique bedrock. Early stages of soil development in these environments are notorious for their high turnover rates, demanding a high degree of replication for obtaining conclusive data. However, studies across different calcareous glaciers are still missing. Here, we robustly investigated both bacterial and fungal diversity, association networks, and assembly processes in four calcareous glacier forefields of the Alps, focusing on the earliest soil developmental stages (<25 years) early in the snow-free season. We found a diverse community of bacteria and fungi, potentially involved in P and N nutrient cycling. A core microbiome existing across all four locations suggests that certain microbes might be more successful colonizers of these ecosystems than others. Nearest taxon index revealed phylogenetically clustered microbial communities. These findings suggest that the distribution and colonization of some microbes were influenced by selective forces such as geography and climate during the early stages of soil development in calcareous glaciers. Interestingly, there were no common bacterial-fungal associations across the four locations, indicating that this habitat does not select for specific bacterial-fungal associations and that associations were driven by neutral processes. We discuss microbial communities and their interactions in these special calcareous glacier forefield habitats. Moreover, we present innovative approaches for studying microbial assembly that address both deterministic, intrinsic drivers, like specific microbial traits, and stochastic, extrinsic drivers, such as the opportunistic behavior of microbes.IMPORTANCEOur study is based on three fundamental and unique approaches: (i) we utilize the early stages of soil development in four glacier forefields across the Alpine range. This design implies high replicability in a natural setting, which is crucial for drawing general conclusions. (ii) Our study investigates glacier forefields with calcareous bedrock directly after snowmelt. These habitats and periods remain surprisingly underexplored. (iii) Our results underline the relevance of bacterial-fungal associations in microbial community assembly alongside dispersal, drift, and natural selection. Taken together, our study provides new insights into the development of complex microbial communities, their stabilization and predictability, including ecological implications.

Identification and fungicide sensitivity of Brunneomyces pennisetum, a new species causing wilt disease of Pennisetum purpureum × P. americanum in southern China

Pennisetum purpureum × P. americanum is an important forage in southwest China. In recent years, a considerable number of wilting plants have occurred in forage-growing regions located in Yunnan Province. The typical symptoms were that the surface of the wilted stems turned brown with a covering of white powder. Six isolates were identified as a new Brunneomyces species based on morphological characteristics and combined phylogenetic analysis of partial 28S nuc rDNA region (28S), internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1-α), and the RNA polymerase II second largest subunit (RPB2) sequence data. The Koch's postulates test confirmed Brunneomyces pennisetum, sp. nov. as a pathogen causing wilt disease in Pennisetum purpureum × P. americanum. The colony diameter of B. pennisetum, sp. nov. exhibited different sensitivity to the six fungicides. Carbendazol (50%) was demonstrated to be the most effective in slowing the growth rate of the pathogen. The pathogen exhibited a higher growth rate at pH 7.0 but could not grow when the pH was greater than 9. The pathogen growth peaked at 25 C, but it could not grow at 5, 10, and 35 C.

Simulating Net Ecosystem Productivity (NEP) in Mediterranean Pine Forests (Pinus brutia) During the 21st Century: The Effect of Leaf Area Index and Elevation

The Gross Primary Productivity (GPP) of Mediterranean forest is expected to change over the 21st century due to the warmer and drier conditions. In this study, we present a process-based forest carbon-flux model, where stand structure and soil heterotrophic respiration have been parameterized with long-term monitoring data in a Mediterranean Pinus brutia. Ten. forest. The developed model was validated using an independent annual tree-ring increment dataset from the 1980-2020 period (baseline climate) across a post-fire gradient (four plots) and an elevation gradient (five plots). Additionally, the model was forced with two downscaled climate change scenarios (RCP4.5 and RCP8.5) for the 2020-2100 period. Average GPP, Net Primary Productivity (NPP), ecosystem Respiration (Reco) and Net Ecosystem Productivity (NEP) were calculated for two future time periods (2051-2060 and 2091-2100) under the two climate change scenarios and compared along the two gradients. Under baseline climate conditions, our simulations suggest a temperature sensitivity of GPP and Reco, as expressed along the elevation gradient. However, the effect of stand structure (represented through the site-specific leaf area index (LAI)) was more prominent, both along the elevation gradient and the post-fire chronosequence. Under the two climate change scenarios, a reduced GPP and an increased Reco lead to reduced NEP compared to baseline climate conditions across all study plots.

Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments

Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.

Understanding the impacts of temperature and precipitation on antimicrobial resistance in wastewater: theory, modeling, observation, and limitations

Changing climate may contribute to increased antimicrobial resistance (AMR), particularly in wastewater which acts as a reservoir for resistant bacteria. Here, we determined how applying climate dependencies to our previously published model, rooted in theory, impacts computational simulations of AMR in wastewater. We found AMR levels were reduced at lower temperatures but increased with lower precipitation. The impact of precipitation on AMR was more pronounced at higher temperatures compared to lower temperatures. To validate our model, we investigated associations between total AMR gene abundance in wastewater from the Global Sewage Surveillance project and mean temperature and rainfall values extracted from European Centre for Medium-Range Weather Forcasts Reanalysis v5 (ERA5) reanalysis. We observed similar trends between the simulations and observations. Observations and simulations from our study can inform experiments to determine causal relationships as well as help identify other key drivers. We also discuss study challenges given the complex nature of AMR in the environment.

Sulfur-mediated transformation, export and mineral complexation of organic and inorganic C, N, P and Si in dryland soils

The transformation characteristics of mineral-associated soil components have profound impacts on their physical, biological, and chemical properties in drying-affected soils, whereas their mechanisms of sequestration and transformation remain elusive. To elucidate these phenomena, the solid-phase, water extracts (labile state, LS) and alkali-extracts (complexed state, CS) of four drying-affected soil types were examined. On average, the contents of soil organic carbon (SOC), soil total nitrogen (STN), and soil total hydrogen (STH) decreased in the order: forest > grassland > agriculture > desert. The extracted dissolved organic matter (DOM)LS, DOMCS and nutrients varied greatly among soil types, which indicated the occurrence of mineralization, sequestration, neoformation, and either export or emission. In particular, the relatively high levels of dissolved inorganic carbon (DIC)LS and relatively low levels of DICCS in agricultural soils could be ascribed to the impact of human activities, i.e., tilling and cultivation, on mineral-bound DIC, leading to its export in LS forms. The stable isotopes of δ13C-SOC and their significant relationships with DICLS and SO42‒LS+CS suggest the occurrence of carbon and sulfur sequestration through the uptake of CO2, DIC, or carbonyl sulfide (COS) following their generation from SOC or DOM mineralization. In forested and agricultural soils, the humic substances (HS) components in LS forms were subjected to a substantial degradation, whereas HSCS components remained mostly unaffected, implying their occurrence in organo-mineral protection. Overall, low soil total sulfur (STS) and sulfate (SO42‒)LS+CS contents were correlated with high amounts of soil components in both the solid and liquid phases, and vice versa. These findings suggest that microbial SO42‒ might operate in the dissolution and mineralization of HS-bound organo-minerals, which would potentially generate soil inorganic carbon (SIC) or DIC, leading to either their subsequent sequestration as carbonate minerals or their exports and emissions as DIC and CO2.

Climate and biological factors jointly shape microbial community structure in the Yarlung Zangbo River during the dry season

Microorganisms are crucial components of aquatic ecosystems, playing key roles in biogeochemical cycles. Understanding microbial diversity and community assembly mechanisms is essential for river management and sustainable utilization of freshwater resources. However, the role of inter-microbial taxonomic group relationships in shaping community structures within high-altitude river ecosystems is unclear. This study utilizes high-throughput sequencing and bioinformatics analysis to describe the spatial dynamics of fungal and bacterial communities in the Yarlung Zangbo River at a broad environmental scale and to elucidate their community assembly mechanisms. The results indicate a significant distance-decay pattern in the fungal (p < 0.001) and bacterial (p < 0.001) communities of the Yarlung Zangbo River, with substantial differences in microbial taxonomic composition, diversity, and community structure across different regions (fungi ANOSIM R = 0.20, bacteria ANOSIM R = 0.63). Homogeneous selection predominated the community assembly of fungi (average: 67.4 %) and bacteria (average: 74.5 %) in aquatic environments. As altitude decreases, the influence of deterministic processes on fungal communities increases, while their influence on bacterial communities decreases. At the basin scale, the community structures of fungi and bacteria are mainly influenced by the degree of functional or ecological niche differentiation of another taxonomic group, as well as the hydrothermal conditions of the basin that vary with longitude. This study enhances the understanding of fungal and bacterial biogeographic patterns and community assembly mechanisms in plateau rivers, providing new perspectives for microbial ecological research in these ecosystems.

The response of soil eukaryotic microbial communities to afforestation in mountainous area of the Loess Plateau, Northern China

Soil microorganisms are integral to nutrient cycling, ecosystem functioning, and soil restoration. However, the information on the response of soil eukaryotic microbial communities to land-use transformations, particularly for afforestation, remains underexplored in the mountainous region of northwest Shanxi on the Loess Plateau. The study based on high-throughput sequencing of 18S rRNA sequences, elucidated the impact of afforestation on soil eukaryotic microbial communities in this ecologically sensitive region. The findings indicated that afforestation significantly altered the composition of soil eukaryotic microbial communities. The dominant eukaryotic phyla were Streptophyta (16.8%-46.9%) and Ascomycota (20.5%-40.7%). At the genus level, Gymnoascus, Preussia, Mortierella, Chaetomium and Fusarium were biomarkers of soil eukaryotic microbes in farmland soil, while unidentified Streptophyta and Geopora were enriched in plantations soil. The result of non-metric multidimensional scaling (NMDS) analysis shows significant separation between eukaryotic microbial communities in farmland and plantation soils, which significantly correlated with soil temperature (T), nitrate nitrogen (NN) and available phosphorus (AP). These findings provided data support on regional ecological restoration assessments, highlighted the effect of soil physicochemical factors on the composition of soil eukaryotic microbial communities, and enhanced our understanding of the role of afforestation in modifying soil microbial ecosystems.

Preliminary Evidence for the Role of Fungi, Specifically Chaetomium, in Gulf War Illness

INTRODUCTION

For veterans of the Persian Gulf War (1990-1991), dozens of possible causes for their illness have been proposed. We hypothesize that all may be correct. These may have weakened the immunity of the military personnel to fungal pathogens in the soil. These microbes, in turn, may have afflicted the veterans either directly by infection or indirectly by toxins.

MATERIALS AND METHODS

In 1990, the military (source confidential) provided the first author with soil samples from the Persian Gulf to determine if there were biothreats present. His team found that per gram of soil, there had few bacteria but many fungi. The National Centre for Human Mycotic Diseases (Edmonton) identified some of these fungi. They sent to the first author reference cultures of 12 pathogenic fungal species isolated from Canadian patients. Supernatant antigens of these fungi were used to assess if control and Gulf War Illness (GWI) patient sera had IgG antibodies against them.

RESULTS

Human sera were tested on pathogenic fungal supernatant antigens. Controls had low IgG titers against all 12 fungal sources. Gulf War Illness (GWI) patient sera had low IgG titers against 11 of the 12 fungal antigens. However, 12 of 28 GWI patient sera (43%, P ≤ .0002 compared to controls) had high IgG titers against one fungus, Chaetomium, supernatant antigen.

CONCLUSIONS

We suggest that the military personnel in the Persian Gulf War (1990-1991) may have had their immunity weakened from a variety of causes. The role of pathogenic fungi and/or their supernatant antigens or toxins as a contributing factor to GWI should be further investigated.

Bioleaching of lanthanum from nickel metal hydride dry battery using siderophores produced by Pseudomonas sp

There is still much to be learned about the properties of siderophores and their applications. This study was designed to characterize and optimize the production of the siderophore produced by a marine bacterium Pseudomonas sp. strain ASA235 and then evaluate their use in bioleaching of rare earth elements (REEs) from spent Nickel-metal hydride (NiMH) batteries. The results of both Tetrazolium and Arnow's tests indicated that the test organism produces a mixed-type siderophore of pyoverdine family, a result that was confirmed by FT-IR and MALDI-TOFF analyses. Optimization of pH, temperature, incubation period, and iron concentration for siderophore production led to a noticeable shift from 44.5% up to 91% siderophore unit when the test bacterium was incubated at 28 °C and pH 7 after 72 h in the absence of iron. The purified siderophore showed the ability to bleach about 14.8% of lanthanum from the anode of the NiMH battery along with other elements, although in lower amounts. This data put siderophores in distinct focus for further prospective studies intending the bioleaching of such precious elements. The scaling up of this process and optimization would make a big difference in such a green bioleaching strategy, allowing us to recover such precious elements in an environmentally friendly way.

Impacts of Weather Anomalies and Climate on Plant Disease

Predicting the effects of climate change on plant disease is critical for protecting ecosystems and food production. Here, we show how disease pressure responds to short-term weather, historical climate and weather anomalies by compiling a global database (4339 plant-disease populations) of disease prevalence in both agricultural and wild plant systems. We hypothesised that weather and climate would play a larger role in disease in wild versus agricultural plant populations, which the results supported. In wild systems, disease prevalence peaked when the temperature was 2.7°C warmer than the historical average for the same time of year. We also found evidence of a negative interactive effect between weather anomalies and climate in wild systems, consistent with the idea that climate maladaptation can be an important driver of disease outbreaks. Temperature and precipitation had relatively little explanatory power in agricultural systems, though we observed a significant positive effect of current temperature. These results indicate that disease pressure in wild plants is sensitive to nonlinear effects of weather, weather anomalies and their interaction with historical climate. In contrast, warmer temperatures drove risks for agricultural plant disease outbreaks within the temperature range examined regardless of historical climate, suggesting vulnerability to ongoing climate change.

Surface exposed and charged residues drive thermostability in fungi

Fungi, though mesophilic, include thermophilic and thermostable species, as well. The thermostability of proteins observed in these fungi is most likely to be attributed to several molecular factors, such as the presence of salt bridges and hydrogen bond interactions between side chains. These factors cannot be generalized for all fungi. Factors impacting thermostability can guide how fungal thermophilic proteins gain thermostability. We curated a dataset of proteins for 14 thermophilic fungi and their evolutionarily closer mesophiles. Additionally, the proteome of Chaetomium thermophilum and its evolutionarily related mesophile Chaetomium globosum was analyzed. Using eggNOG, we categorized the proteomes into clusters of orthologous groups (COGs). While the individual count of proteins is over-represented in mesophiles (for COGs S, G, L, and Q), there are certain features that are significantly enriched in thermophiles (such as charged residues, exposed residues, polar residues, etc.). Since fungi are known to be cellulolytic and chitinolytic by nature, we selected 37 existing carbohydrate-active enzymes (CAZyme) families in Eurotiales, Mucorales, and Sordariales. We looked at closely similar sequences and their modeled structures for further comparison. Comparing solvent accessibilities of thermophilic and mesophilic proteins, exposed and intermediate residues are observed higher in thermophiles whereas buried residues are observed higher in mesophiles. For specific five CAZYme families (GH7, GH11, GH18, GH45, and CBM1) we looked at position-specific substitutions between thermophiles and mesophiles. We also found that there are relatively more intramolecular interactions in thermophiles compared to mesophiles. Thus, we found factors such as surface exposed residues and charged residues that are highly likely to impart thermostability in fungi, and this study sets the stage for further studies in the area of fungal thermostability.

Prevalence and Antibiotic Susceptibility of Pathogenic Enterobacteria Strains from Three Biotopes in the City of Ouagadougou (Burkina Faso)

Purpose

The emergence of antibiotic resistance in pathogenic Enterobacteriaceae is a public health problem in tropical countries such as Burkina Faso. Antibiotic resistance could be identified using a variety of approaches. This study aimed to estimate the prevalence of pathogenic enterobacteria strains from three sources, as well as their antibiotic resistance profile to biotope and climatic season.

Material and Methods

The methodological approach consisted of identifying Enterobacteriaceae from human (urine, stool), animal (eggs, milk, fish), and environmental (soil, lettuce) samples, followed by assessing their antibiotic susceptibility. Samples were collected from February to December 2023. Bacterial species were isolated and phenotypically identified (morphologically, culturally, biochemically, and antigenically) using standard methods. The prevalence of bacterial susceptibility to ten antibiotics was determined using the agar disk diffusion method. The collected data were analyzed with IBM SPSS Statistics 25 software.

Results

A total of 615 Enterobacteriaceae isolates were collected, including 300, 168, and 147 samples from human, animal, and environmental sources respectively. Phenotypic characteristics allowed to partially identify 43 species, among these 29.76% belonged to Escherichia coli, 24.72% to Enterobacter cloacae, 13.82% to Klebsiella pneumoniae, 3.41% to Enterobacter sakazakii and 2.6% to Klebsiella oxytoca. Bacterial resistance rates were: aminopenicillins (54.8%), first-generation cephalosporins (35.3%), sulfonamides (33.3%), third-generation cephalosporins (30.7%), fourth-generation cephalosporins (22.5%), fluoroquinolones (21.8%), phenicols (16.8%), and carbapenems (16.2%). The distribution of antibiotic resistance was 45.3% from human sources, 19.3% from animal sources, and 13.8% from environmental sources.

Conclusion

The results indicate that resistant bacteria can come from any of the three biotopes, with human origin being the most frequent. The high prevalence of resistance to the antibiotics tested in isolated bacteria raises interest in investigating the genetic factors responsible.

Data-driven discovery of the interplay between genetic and environmental factors in bacterial growth

A complex interplay of genetic and environmental factors influences bacterial growth. Understanding these interactions is crucial for insights into complex living systems. This study employs a data-driven approach to uncover the principles governing bacterial growth changes due to genetic and environmental variation. A pilot survey is conducted across 115 Escherichia coli strains and 135 synthetic media comprising 45 chemicals, generating 13,944 growth profiles. Machine learning analyzes this dataset to predict the chemicals' priorities for bacterial growth. The primary gene-chemical networks are structured hierarchically, with glucose playing a pivotal role. Offset in bacterial growth changes is frequently observed across 1,445,840 combinations of strains and media, with its magnitude correlating to individual alterations in strains or media. This counterbalance in the gene-chemical interplay is supposed to be a general feature beneficial for bacterial population growth.

Antibiotic legacies shape the temperature response of soil microbial communities

Soil microbial communities are vulnerable to anthropogenic disturbances such as climate change and land management decisions, thus altering microbially-mediated ecosystem functions. Increasingly, multiple stressors are considered in investigations of ecological response to disturbances. Typically, these investigations involve concurrent stressors. Less studied is how historical stressors shape the response of microbial communities to contemporary stressors. Here we investigate how historical exposure to antibiotics drives soil microbial response to subsequent temperature change. Specifically, grassland plots were treated with 32-months of manure additions from cows either administered an antibiotic or control manure from cows not treated with an antibiotic. In-situ antibiotic exposure initially increased soil respiration however this effect diminished over time. Following the 32-month field portion, a subsequent incubation experiment showed that historical antibiotic exposure caused an acclimation-like response to increasing temperature (i.e., lower microbial biomass at higher temperatures; lower respiration and mass-specific respiration at intermediate temperatures). This response was likely driven by a differential response in the microbial community of antibiotic exposed soils, or due to indirect interactions between manure and soil microbial communities, or a combination of these factors. Microbial communities exposed to antibiotics tended to be dominated by slower-growing, oligotrophic taxa at higher temperatures. Therefore, historical exposure to one stressor is likely to influence the microbial community to subsequent stressors. To predict the response of soils to future stress, particularly increasing soil temperatures, historical context is necessary.

Improving fecal bacteria estimation using machine learning and explainable AI in four major rivers, South Korea

This study addresses the critical public health issue of fecal coliform contamination in the four major rivers in South Korea (Han, Nakdong, Geum, and Yeongsan rivers) by applying advanced machine learning (ML) algorithms combined with Explainable Artificial Intelligence to enhance both prediction accuracy and interpretability. Both traditional and machine learning models often face challenges in accurately estimating fecal coliform levels due to the complexity of environmental variables and data limitations. To address this limitation, we employed two tree-based models (i.e., random forest [RF] and extreme gradient boost [XGBoost]), and two neural network models (i.e., deep neural network and convolutional neural network [CNN]). we employed the use of Shapley Additive Explanations (SHAP) to facilitate a more comprehensive understanding of the influence exerted by each variable on the model's predictions. Based on a comprehensive dataset collected from the National Institute of Environmental Research covering 16 water quality parameters and meteorological data from 2014 to 2022, our study improved the accuracy of fecal coliform estimation using XGBoost and CNN models. The optimal result was obtained using XGBoost, which had a validation Nash-Sutcliffe efficiency of 0.597 in the Han River. In addition, this study provides insights into the significant factors influencing fecal coliform concentrations across different river environments using the SHAP model. The results indicated that the XGBoost model provided superior estimation accuracy and explanations for the contributions of variables. The SHAP results provided the precise contribution of each water quality variable that affected the fecal estimation results using the XGBoost model. The study facilitates an improved understanding of the relationship between water quality variables and fecal coliform contamination mechanisms in the four major rivers in South Korea.

Development of a Stringent Ex Vivo-Burned Porcine Skin Wound Model to Screen Topical Antimicrobial Agents

Background: Due to rising antibiotic-resistant microorganisms, there is a pressing need to screen approved drugs for repurposing and to develop new antibiotics for controlling infections. Current in vitro and ex vivo models have mostly been unsuccessful in establishing in vivo relevance. In this study, we developed a stringent ex vivo-burned porcine skin model with high in vivo relevance to screen topical antimicrobials. Methods: A 3 cm-diameter thermal injury was created on non-sterilized porcine skin using a pressure-monitored and temperature-controlled burn device. Commensals were determined pre- and post-burn. The burn wound was inoculated with a target pathogen, and efficacies of Silvadene, Flammacerium, Sulfamylon, and Mupirocin were determined. The in vivo relevance of this platform was evaluated by comparing the ex vivo treatment effects to available in vivo treatment outcomes (from our laboratory and published reports) against selective burn pathogens. Results: Approximately 1% of the commensals survived the skin burn, and these commensals in the burn wounds affected the treatment outcomes in the ex vivo screening platform. When tested against six pathogens, both Silvadene and Flammacerium treatment exhibited ~1-3 log reduction in viable counts. Sulfamylon and Mupirocin exhibited higher efficacy than both Silvadene and Flammacerium against Pseudomonas and Staphylococcus, respectively. The ex vivo treatment outcomes of Silvadene and Flammacerium against Pseudomonas were highly comparable to the outcomes of the in vivo (rats). Conclusions: The ex vivo model developed in our lab is a stringent and effective platform for antimicrobial activity screening. The outcome obtained from this ex vivo model is highly relevant to in vivo.

Surprising minimisation of CO2 emissions from a sandy loam soil over a rye growing period achieved by liming (CaCO3)

Agricultural liming improves acidic soils productivity and is considered a lever for mitigating nitrous oxide (N2O) emissions from soils. However, the benefit of liming in reducing soil greenhouse gas (GHG) emissions depends on the evolution of carbon from the calcium carbonate (CaCO3), and on the evolution of soil organic carbon (SOC) after CaCO3 application. The literature, based on limited field data, presents contrasting effects of liming on inorganic- and SOC-derived CO2 emissions, raising concerns that the reduction in N2O emissions could be offset by increased CO2 emissions. Therefore, this study aimed to monitor N2O and CO2 emissions following the application of lime materials to an acidic soil. In situ, we monitored the effect of two liming products (SC = synthetic CaCO3 and MC = marine CaCO3) on soil CO2 emissions and compared this with control plots, during the growing season of a winter rye, using the static chamber method. Soil pH, N2O emissions, mineral nitrogen concentrations, soil moisture and temperature were measured during the experiment, as were plant biomass and SOC (stock and composition) on the day of harvest. Lime addition increased soil pH from 5.7 to around 7.0, kernel yield from 320 to >400 g m-2 and resulted in a significant reduction in soil CO2 emissions by approximately 40 % for both liming materials while it slightly increased N2O emissions, that had nevertheless remained very low during the experiment. SOC at harvest was not significantly affected, while an increase in dissolved organic and inorganic carbon in the soil was observed. Further investigations is needed to clarify the mechanisms explaining these observations and to define conditions where liming application could act as a potential lever for carbon storage. Our results suggest that the IPCC principles, predicting increased CO2 emissions from lime-derived C, may need to be re-examined in the future.

Fungal community determines soil multifunctionality during vegetation restoration in metallic tailing reservoir

Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals.

Culturable yeast diversity in urban topsoil influenced by various anthropogenic impacts

In urban ecosystems, processes associated with anthropogenic influences almost always lead to changes in soil micromycete complexes. The taxonomic structure of soil micromycete complexes is an important informative parameter of soil bioindication in the ecological control of urban environments. Unicellular fungi, such as culturable yeasts, are a very suitable and promising object of microbiological research for monitoring urban topsoil. This review aims to give an overview of the yeast communities in urban topsoil in different areas of Moscow (heating main area, household waste storage and disposal area, highway area) and to discuss the changes in the taxonomic structure of culturable yeast complexes depending on the type and intensity of anthropogenic impact.

Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment

The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5-35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86-181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25-35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.

Drivers of virulence and antimicrobial resistance in Gram-negative bacteria in different settings: A genomic perspective

The human gut presents a complex ecosystem harboring trillions of microorganisms living in close association with each other and the host body. Any perturbation or imbalance of the normal gut microbiota may prove detrimental to human health. Enteric infections and treatment with antibiotics pose major threats to gut microbiota health. Recent genomics-driven research has provided insights into the transmission and evolutionary dynamics of major enteric pathogens such as Escherichia coli, Klebsiella pneumoniae, Vibrio cholerae, Helicobacter pylori and Salmonella spp. Studies entailing the identification of various dominant lineages of some of these organisms based on artificial intelligence and machine learning point to the possibility of a system for prediction of antimicrobial resistance (AMR) as some lineages have a higher propensity to acquire virulence and fitness advantages. This is pertinent in the light of emerging AMR being one of the immediate threats posed by pathogenic bacteria in the form of a multi-layered fitness manifesting as phenotypic drug resistance at the level of clinics and field settings. To develop a holistic or systems-level understanding of such devastating traits, present methodologies need to be advanced with the high throughput techniques integrating community and ecosystem/niche level data across different omics platforms. The next major challenge for public health epidemiologists is understanding the interactions and functioning of these pathogens at the community level, both in the gut and outside. This would provide new insights into the dimensions of enteric bacteria in different environments and niches and would have a plausible impact on infection control strategies in terms of tackling AMR. Hence, the aim of this review is to discuss virulence and AMR in Gram-negative pathogens, the spillover of AMR and methodological advancements aimed at addressing it through a unified One Health framework applicable to the farms, the environment, different clinical settings and the human gut.

Dissipation of pesticides and responses of bacterial, fungal and protistan communities in a multi-contaminated vineyard soil

The effect of pesticide residues on non-target microorganisms in multi-contaminated soils remains poorly understood. In this study, we examined the dissipation of commonly used pesticides in a multi-contaminated vineyard soil and its effect on bacterial, fungal, and protistan communities. We conducted laboratory soil microcosm experiments under varying temperature (20°C and 30°C) and water content (20 % and 40 %) conditions. Pesticide dissipation half-lives ranged from 27 to over 300 days, depending on the physicochemical properties of the pesticides and the soil conditions. In both autoclaved and non-autoclaved soil experiments, over 50 % of hydrophobic pesticides (dimethomorph > isoxaben > simazine = atrazine = carbendazim) dissipated within 200 days at 20°C and 30°C. However, the contribution of biodegradation to the overall dissipation of soluble pesticides (rac-metalaxyl > isoproturon = pyrimethanil > S-metolachlor) increased to over 75 % at 30°C and 40 % water content. This suggests that soluble pesticides became more bioavailable, with degradation activity increasing with higher temperature and soil water content. In contrast, the primary process contributing to the dissipation of hydrophobic pesticides was sequestration to soil. High-throughput amplicon sequencing analysis indicated that water content, temperature, and pesticides had domain-specific effects on the diversity and taxonomic composition of bacterial, fungal, and protistan communities. Soil physicochemical properties had a more significant effect than pesticides on the various microbial domains in the vineyard soil. However, pesticide exposure emerged as a secondary factor explaining the variations in microbial communities, with a more substantial effect on protists compared to bacterial and fungal communities. Overall, our results highlight the variability in the dissipation kinetics and processes of pesticides in a multi-contaminated vineyard soil, as well as their effects on bacterial, fungal, and protistan communities.

Synergistic effects of warming and humic substances on driving arsenic reduction and methanogenesis in flooded paddy soil

Microbially-driven arsenic reduction and methane emissions in anaerobic soils are regulated by widespread humic substances (HS), while how this effect responds to climate change remains unknown. We investigated potential synergistic effects of HS in response to temperature changes in arsenic-contaminated paddy soils treated with humic acid (HA) and fulvic acid (FA) at temperatures ranging from 15 to 45 °C. Our results reveal a significant increase in arsenic reduction (5.6 times) and methane emissions (178 times) driven by HS, which can be exponentially stimulated at 45 °C. Acting as a electron shuttle, HS determines microbial arsenic reduction, further stimulated by warming. The top three sensitive genera are Geobacter, Anaeromyxobacter, and Gaiella which are responsible for enhanced arsenic reduction, as well as for the reduction of iron and HS with their functional genes; arrA and Geobacter spp. The top three sensitive methanogens are Methanosarsina, Methanocella, and Methanoculleus. Our study suggests notable synergistic effects between HS and warming in stimulating arsenic reduction and methanogenesis in paddy soils. Overall, the findings of this work highlight the high sensitivity of HS-mediated microbial arsenic transformation and methanogenesis in response to warming, which add potential value in predicting the biogeochemical cycling of arsenic and methane in soil under the context of climate change.

Soil microbial identity explains home-field advantage for litter decomposition

Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Breathing Clean Air: Navigating Indoor Air Purification Techniques and Finding the Ideal Solution

The prevalence of airborne pathogens in indoor environments presents significant health risks due to prolonged human occupancy. This review addresses diverse air purification systems to combat airborne pathogens and the factors influencing their efficacy. Indoor aerosols, including bioaerosols, harbor biological contaminants from respiratory emissions, highlighting the need for efficient air disinfection strategies. The COVID-19 pandemic has emphasized the dangers of airborne transmission, highlighting the importance of comprehending how pathogens spread indoors. Various pathogens, from viruses like SARS-CoV-2 to bacteria like Mycobacterium (My) tuberculosis, exploit unique respiratory microenvironments for transmission, necessitating targeted air purification solutions. Air disinfection methods encompass strategies to reduce aerosol concentration and inactivate viable bioaerosols. Techniques like ultraviolet germicidal irradiation (UVGI), photocatalytic oxidation (PCO), filters, and unipolar ion emission are explored for their specific roles in mitigating airborne pathogens. This review examines air purification systems, detailing their operational principles, advantages, and limitations. Moreover, it elucidates key factors influencing system performance. In conclusion, this review aims to provide practical knowledge to professionals involved in indoor air quality management, enabling informed decisions for deploying efficient air purification strategies to safeguard public health in indoor environments.

Investigating the influence of sulphur amendment and temperature on microbial activity in bioremediation of diesel-contaminated soil

This study investigated the effectiveness of incorporating sulphur (S) with nitrogen (N) and phosphorus (P) for enhancing microbial activity in diesel-contaminated soil during ex-situ bioremediation. While N and P amendments are commonly used to stimulate indigenous microorganisms, the potential benefits of adding S have received less attention. The study found that historically contaminated soil with a moderate concentration of total petroleum hydrocarbons (TPH; 1270 mg/kg) did not have nutrient limitation, and incubation temperature was found to be more critical for enhancing microbial activity. However, soil spiked with an additional 5000 mg/kg of diesel showed increased activity following NP and NPS amendment. Interestingly, NPS amendment at 10 °C resulted in higher microbial activity than at 20 °C, indicating the potential for a tailored nutrient amendment approach to optimize bioremediation in cold conditions. Overall, this study suggests that incorporating S with N and P can enhance microbial activity in diesel-contaminated soil during ex-situ bioremediation. Furthermore, the study highlights the importance of considering incubation temperature in designing a nutrient amendment approach for bioremediation, especially in cold conditions. These findings can guide the design and implementation of future effective bioremediation strategies for petroleum hydrocarbon-contaminated soil.

Microbial assisted multifaceted amelioration processes of heavy-metal remediation: a clean perspective toward sustainable and greener future

Rapidly increasing heavy metal waste has adversely affected the environment and the Earth's health. The lack of appropriate remediation technologies has worsened the issue globally, especially in developing countries. Heavy-metals contaminants have severely impacted the environment and led to devastating conditions owing to their abundance and reactivity. As they are nondegradable, the potential risk increases even at a low concentration. However, heavy-metal remediation has increased with the up-gradation of technologies and integration of new approaches. Also, of all the treatment methodologies, microbial-assisted multifaceted approach for ameliorating heavy metals is a promising strategy for propagating the idea of a green and sustainable environment with minimal waste aggregation. Microbial remediation combined with different biotechniques could aid in unraveling new methods for eradicating heavy metals. Thus, the present review focuses on various microbial remediation approaches and their affecting factors, enabling recapitulation of the interplay between heavy-metals ions and microorganisms. Additionally, heavy-metals remediation mechanisms adapted by microorganisms, the role of genetically modified (GM) microorganisms, life cycle assessment (LCA), techno-economic assessment (TEA) limitations, and prospects of microbial-assisted amelioration of heavy-metals have been elaborated in the current review with focus toward "sustainable and greener future."

Evaluation of the efficacy of cinnamon oil on Aspergillus flavus and Fusarium proliferatum growth and mycotoxin production on paddy and polished rice: Towards a mitigation strategy

In the present investigation, the effect of cinnamon oil (CO) (10, 30, 50 and 70 %) on the growth rate (mm/day) and aflatoxin B1 (AFB1) and fumonisin B1 (FB1) production of Aspergillus flavus (AF01) and Fusarium proliferatum (FP01) isolates, respectively was determined at optimum water activities (0.95 and 0.99 aw) and temperatures (25, 30 and 35 °C) on paddy and polished rice grains. The results showed that the growth rate, AFB1 and FB1 production of all the fungal isolates decreased with an increase in CO concentrations on both matrices. AF01 and FP01 failed to grow under all conditions on paddy at 50 % of CO concentration whereas both fungi were completely inhibited (No Growth-NG) at 70 % of CO on polished rice. Regarding mycotoxin production, 30 % of CO concentrations could inhibit AFB1 and FB1 production in both matrices (No Detection-ND). In this study, the production of mycotoxins was significantly influenced by cinnamon oil compared to the growth of both fungi. These results indicated the promising potential of CO in improving the quality of rice preservation in post-harvest; however, further investigations should be evaluated on the effects on the qualitative characteristics of grains. Especially, the prospective application of CO in rice storage in industry scales to mitigate mycotoxin contamination need also to be further researched. Moreover, collaboration between researchers, agricultural experts, and food industry should be set up to achieve effective and sustainable strategies for preserving rice.

A Thermotolerant Yeast Cyberlindnera rhodanensis DK Isolated from Laphet-so Capable of Extracellular Thermostable β-Glucosidase Production

This study aims to utilize the microbial resources found within Laphet-so, a traditional fermented tea in Myanmar. A total of 18 isolates of thermotolerant yeasts were obtained from eight samples of Laphet-so collected from southern Shan state, Myanmar. All isolates demonstrated the tannin tolerance, and six isolates were resistant to 5% (w/v) tannin concentration. All 18 isolates were capable of carboxy-methyl cellulose (CMC) degrading, but only the isolate DK showed ethanol production at 45 °C noticed by gas formation. This ethanol producing yeast was identified to be Cyberlindnera rhodanensis based on the sequence analysis of the D1/D2 domain on rRNA gene. C. rhodanensis DK produced 1.70 ± 0.01 U of thermostable extracellular β-glucosidase when cultured at 37 °C for 24 h using 0.5% (w/v) CMC as a carbon source. The best two carbon sources for extracellular β-glucosidase production were found to be either xylose or xylan, with β-glucosidase activity of 3.07-3.08 U/mL when the yeast was cultivated in the yeast malt extract (YM) broth containing either 1% (w/v) xylose or xylan as a sole carbon source at 37 °C for 48 h. The optimal medium compositions for enzyme production predicted by Plackett-Burman design and central composite design (CCD) was composed of yeast extract 5.83 g/L, peptone 10.81 g/L and xylose 20.20 g/L, resulting in a production of 7.96 U/mL, while the medium composed (g/L) of yeast extract 5.79, peptone 13.68 and xylan 20.16 gave 9.45 ± 0.03 U/mL for 48 h cultivation at 37 °C. Crude β-glucosidase exhibited a remarkable stability of 100%, 88% and 75% stable for 3 h at 35, 45 and 55 °C, respectively.

Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature

Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.

Total Soil CO2 Efflux from Drained Terric Histosols

Histosols cover about 8-10% of Lithuania's territory and most of this area is covered with nutrient-rich organic soils (Terric Histosols). Greenhouse gas (GHG) emissions from drained Histosols contribute more than 25% of emissions from the Land Use, Land Use Change and Forestry (LULUCF) sector. In this study, as the first step of examining the carbon dioxide (CO2) fluxes in these soils, total soil CO2 efflux and several environmental parameters (temperature of air and topsoil, soil chemical composition, soil moisture, and water table level) were measured in drained Terric Histosols under three native forest stands and perennial grasslands in the growing seasons of 2020 and 2021. The drained nutrient-rich organic soils differed in terms of concentrations of soil organic carbon and total nitrogen, as well as soil organic carbon and total nitrogen ratio. The highest rate of total soil CO2 efflux was found in the summer months. Overall, the rate was statistically significant and strongly correlated only with soil and air temperature. A trend emerged that total soil CO2 efflux was 30% higher in perennial grassland than in forested land. Additional work is still needed to estimate the net CO2 balance of these soils.

Characterization of microbial populations in two distinct dairy manure management systems: seasonal effect and implications for pollutant gases emissions

Following an increase in the demand for dairy products, higher quantities of manure are consequently produced, with the subsequent pollutant gas emission charge associated with its management. The 2 mostly used housing systems in the northeast of Spain, cubicles (CUB) and compost-bedded pack (CBP), entail different manure management techniques; thus, our main objective was to describe the microbiota present in the manure of both systems during 2 distinct climatic situations (winter, mean temperature of 6.2 °C; and summer, mean temperature of 36.4 °C). The secondary aim was to correlate these microbiological profiles with literature findings on the emission of certain well-known pollutant gases from manure. CBP showed to have higher alpha biodiversity as well as presenting a remarkable clustering by season but showed lower network complexity than CUB. Firmicutes/Bacteroidetes ratio was found superior in CUB, which also presented a significantly higher abundance of methanogenic genera belonging to Euryarchaeota phylum, such as Methanobrevibacter, Methanosaeta or Methanosarcina. On the other hand, CBP manure presented a significant presence of Corynebacterium, Pseudomonas, or Truepera, among other genera, which activity has been linked to nitrogen (N) transformation pathways in manure. The season also had a relevant role to play in the fluctuation of these populations within each housing system under study. These results show how microbial populations change when manure is differently managed, and how these variations can be related to the synthesis of certain pollutant gases in housing systems.

Development of a robust daily soil temperature estimation in semi-arid continental climate using meteorological predictors based on computational intelligent paradigms

Changes in soil temperature (ST) play an important role in the main mechanisms within the soil, including biological and chemical activities. For instance, they affect the microbial community composition, the speed at which soil organic matter breaks down and becomes minerals. Moreover, the growth and physiological activity of plants are directly influenced by the ST. Additionally, ST indirectly affects plant growth by influencing the accessibility of nutrients in the soil. Therefore, designing an efficient tool for ST estimating at different depths is useful for soil studies by considering meteorological parameters as input parameters, maximal air temperature, minimal air temperature, maximal air relative humidity, minimal air relative humidity, precipitation, and wind speed. This investigation employed various statistical metrics to evaluate the efficacy of the implemented models. These metrics encompassed the correlation coefficient (r), root mean square error (RMSE), Nash-Sutcliffe (NS) efficiency, and mean absolute error (MAE). Hence, this study presented several artificial intelligence-based models, MLPANN, SVR, RFR, and GPR for building robust predictive tools for daily scale ST estimation at 05, 10, 20, 30, 50, and 100cm soil depths. The suggested models are evaluated at two meteorological stations (i.e., Sulaimani and Dukan) located in Kurdistan region, Iraq. Based on assessment of outcomes of this study, the suggested models exhibited exceptional predictive capabilities and comparison of the results showed that among the proposed frameworks, GPR yielded the best results for 05, 10, 20, and 100cm soil depths, with RMSE values of 1.814°C, 1.652°C, 1.773°C, and 2.891°C, respectively. Also, for 50cm soil depth, MLPANN performed the best with an RMSE of 2.289°C at Sulaimani station using the RMSE during the validation phase. Furthermore, GPR produced the most superior outcomes for 10cm, 30cm, and 50cm soil depths, with RMSE values of 1.753°C, 2.270°C, and 2.631°C, respectively. In addition, for 05cm soil depth, SVR achieved the highest level of performance with an RMSE of 1.950°C at Dukan station. The results obtained in this research confirmed that the suggested models have the potential to be effectively used as daily predictive tools at different stations and various depths.

Genetic adaptations in the population history of Arabidopsis thaliana

A population encounters a variety of environmental stresses, so the full source of its resilience can only be captured by collecting all the signatures of adaptation to the selection of the local environment in its population history. Based on the multiomic data of Arabidopsis thaliana, we constructed a database of phenotypic adaptations (p-adaptations) and gene expression (e-adaptations) adaptations in the population. Through the enrichment analysis of the identified adaptations, we inferred a likely scenario of adaptation that is consistent with the biological evidence from experimental work. We analyzed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes and identified 650 p-adaptations and 3,925 e-adaptations [false discovery rate (FDR) = 0.05]. The population underwent large-scale p-adaptations and e-adaptations along 4 lineages. Extremely cold winters and short summers prolonged seed dormancy and expanded the root system architecture. Low temperatures prolonged the growing season, and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected alleles for lower heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The p-adaptations are directly interpretable, while the coadapted gene expressions reflect the physiological requirements for the adaptation. The integration of this information characterizes when and where the population has experienced environmental stress and how the population responded at the molecular level.

Land use alters bacterial growth dynamics in soil

Microbial growth and mortality are major determinants of soil carbon cycling. We measured in situ growth dynamics of individual bacterial taxa in cropped and successional soils in response to a resource pulse. We hypothesized that land use imposes selection pressures on growth characteristics. We estimated growth and death for 453 and 73 taxa, respectively. The average generation time was 5.04 ± 6.28 (SD; range 0.7-63.5) days. Lag times were shorter in cultivated than successional soils and resource amendment decreased lag times. Taxa exhibiting the greatest growth response also exhibited the greatest mortality, indicative of boom-and-bust dynamics. We observed a bimodal growth rate distribution, representing fast- and slow-growing clusters. Both clusters grew more rapidly in successional soils, which had more organic matter, than cultivated soils. Resource amendment increased the growth rate of the slower growing but not the faster-growing cluster via a mixture of increased growth rates and species turnover, indicating that competitive dynamics constrain growth rates in situ. These two clusters show that copiotrophic bacteria in soils may be subdivided into different life history groups and that these subgroups respond independently to land use and resource availability.

Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil

In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.

Microbiology and Biochemistry of Pesticides Biodegradation

Pesticides are chemicals used in agriculture, forestry, and, to some extent, public health. As effective as they can be, due to the limited biodegradability and toxicity of some of them, they can also have negative environmental and health impacts. Pesticide biodegradation is important because it can help mitigate the negative effects of pesticides. Many types of microorganisms, including bacteria, fungi, and algae, can degrade pesticides; microorganisms are able to bioremediate pesticides using diverse metabolic pathways where enzymatic degradation plays a crucial role in achieving chemical transformation of the pesticides. The growing concern about the environmental and health impacts of pesticides is pushing the industry of these products to develop more sustainable alternatives, such as high biodegradable chemicals. The degradative properties of microorganisms could be fully exploited using the advances in genetic engineering and biotechnology, paving the way for more effective bioremediation strategies, new technologies, and novel applications. The purpose of the current review is to discuss the microorganisms that have demonstrated their capacity to degrade pesticides and those categorized by the World Health Organization as important for the impact they may have on human health. A comprehensive list of microorganisms is presented, and some metabolic pathways and enzymes for pesticide degradation and the genetics behind this process are discussed. Due to the high number of microorganisms known to be capable of degrading pesticides and the low number of metabolic pathways that are fully described for this purpose, more research must be conducted in this field, and more enzymes and genes are yet to be discovered with the possibility of finding more efficient metabolic pathways for pesticide biodegradation.

Spatiotemporal Variations of Soil Reactive Nitrogen Oxide Fluxes across the Anthropogenic Landscape

Volatile reactive nitrogen oxides (NOy) are significant atmospheric pollutants, including NOx (nitric oxide [NO] + nitrogen dioxide [NO2]) and NOz (nitrous acid [HONO] + nitric acid [HNO3] + nitrogen trioxide [NO3] + ...). NOy species are products of nitrogen (N) cycle processes, particularly nitrification and denitrification. Biogenic sources, including soil, account for over 50% of natural NOy emissions to the atmosphere, yet emissions from soils are generally not included in atmospheric models as a result of a lack of mechanistic data. This work is a unique investigation of NOy fluxes on a landscape scale, taking a comprehensive set of land-use types, human influence, and seasonality into account to determine large-scale heterogeneity to provide a basis for future modeling and hypothesis generation. By coupling 16S rRNA amplicon sequencing and quantitative polymerase chain reaction, we have linked significant differences in functional potential and activity of nitrifying and denitrifying soil microbes to NOy emissions from soils. Further, we have identified soils subject to increased N deposition that are less microbially active despite increased available N, potentially as a result of poor soil health from anthropogenic pollution. Structural equation modeling suggests human influence on soils to be a more significant effector of soil NOy emissions than land-use type.

Origin of fungal hybrids with pathogenic potential from warm seawater environments

Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.

The need to increase antimicrobial resistance surveillance among forcibly displaced persons (FDPs)

Antimicrobial resistance (AMR) poses a significant threat to human health as 4.95 million deaths were associated with bacterial AMR in 2019 and is projected to reach 10 million by 2050. To mitigate AMR, surveillance is an essential tool for determining the burden of AMR and providing the necessary information for its control. However, the global AMR surveillance is inadequate and particularly limited among forcibly displaced persons (FDPs) despite having higher risks of harboring these pathogens. Predisposing factors among this group include poor living conditions, limited access to treatment and diagnostic tests, and inadequate trained health professionals in refugee camps. Strengthening AMR surveillance among FDPs would address the identified gaps and facilitate formulation and implementation of evidence-based policies on AMR control and prevention response. This article provides information on the growing population of FDPs, factors contributing to the AMR burden and AMR surveillance gaps in FDPs and highlighted recommendations for control.

Emerging Antimicrobial Resistance

The burden of emerging antimicrobial resistance (AMR) in the United States is significant and even greater worldwide. Mitigation efforts have decreased the incidence and deaths from antimicrobial-resistant organisms in the United States. Yet more than 2.8 million antimicrobial-resistant infections occur every year and more than 35,000 patients die as a result. Infection prevention and control, data tracking, antimicrobial stewardship, vaccines, therapeutics, diagnostics, and sanitation are all required to decrease AMR threats. In 2019, in the second version of the Centers for Disease Control and Prevention (CDC) report on antibiotic-resistant threats, the agency categorized AMR threats as urgent, serious, concerning, or to be watched. This review will discuss the following aspects of each bacterium in the CDC report: estimated numbers of cases and deaths, identify the better known and impactful mechanisms of resistance, diagnostic testing and its limitations, and current and possible future therapies. This review also presents anatomical pathology case examples that highlight the altered morphology of antibiotic partially treated bacteria in tissues.

Recent advances in enhancing the production of long chain omega-3 fatty acids in microalgae

Omega-3 fatty acids have gained attention due to numerous health benefits. Eicosapentaenoic (EPA) and docosahexaenoic acid (DHA) are long chain omega-3 fatty acids produced from precursor ALA (α-linolenic acid) in humans but their rate of biosynthesis is low, therefore, these must be present in diet or should be taken as supplements. The commercial sources of omega-3 fatty acids are limited to vegetable oils and marine sources. The rising concern about vegan source, fish aquaculture conservation and heavy metal contamination in fish has led to the search for their alternative source. Microalgae have gained importance due to the production of high-value EPA and DHA and can thus serve as a sustainable and promising source of long chain omega-3 fatty acids. Although the bottleneck lies in the optimization for enhanced production that involves strategies viz. strain selection, optimization of cultivation conditions, media, metabolic and genetic engineering approaches; while co-cultivation, use of nanoparticles and strategic blending have emerged as innovative approaches that have made microalgae as potential candidates for EPA and DHA production. This review highlights the possible strategies for the enhancement of EPA and DHA production in microalgae. This will pave the way for their large-scale production for human health benefits.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Microbial responses to soil cooling might explain increases in microbial biomass in winter

In temperate, boreal and arctic soil systems, microbial biomass often increases during winter and decreases again in spring. This build-up and release of microbial carbon could potentially lead to a stabilization of soil carbon during winter times. Whether this increase is caused by changes in microbial physiology, in community composition, or by changed substrate allocation within microbes or communities is unclear. In a laboratory incubation study, we looked into microbial respiration and growth, as well as microbial glucose uptake and carbon resource partitioning in response to cooling. Soils taken from a temperate beech forest and temperate cropland system in October 2020, were cooled down from field temperature of 11 °C to 1 °C. We determined microbial growth using 18O-incorporation into DNA after the first two days of cooling and after an acclimation phase of 9 days; in addition, we traced 13C-labelled glucose into microbial biomass, CO2 respired from the soil, and into microbial phospholipid fatty acids (PLFAs). Our results show that the studied soil microbial communities responded strongly to soil cooling. The 18O data showed that growth and cell division were reduced when soils were cooled from 11 to 1 °C. Total respiration was also reduced but glucose uptake and glucose-derived respiration were unchanged. We found that microbes increased the investment of glucose-derived carbon in unsaturated phospholipid fatty acids at colder temperatures. Since unsaturated fatty acids retain fluidity at lower temperatures compared to saturated fatty acids, this could be interpreted as a precaution to reduced temperatures. Together with the maintained glucose uptake and reduced cell division, our findings show an immediate response of soil microorganisms to soil cooling, potentially to prepare for freezing events. The discrepancy between C uptake and cell division could explain previously observed high microbial biomass carbon in temperate soils in winter.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-023-01050-x.