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This study aims to investigate the biosurfactant production capabilities of bacterial strains isolated from oil-contaminated soil samples. Employing a comprehensive methodological approach, we collected soil samples from thirty different fuel pumps and conducted an extensive screening of bacterial isolates using various tests such as hemolytic activity, emulsification index, blue agar plate method, and drop collapsing test. The results revealed significant biosurfactant production among certain isolates, specifically highlighting the effectiveness of two particular strains. This paper presents a detailed analysis of these strains, including their optimal growth conditions in terms of pH, temperature, carbon, and nitrogen sources. Our findings indicate a notable potential of these bacterial strains in biosurfactant production, with implications for environmental bioremediation, particularly in oil pollution contexts. The study also sheds light on the limitations encountered and underscores the originality of the research in exploring biosurfactant production in a novel context. This study contributes to the field by offering insights into the effective utilization of microbial strains for biosurfactant synthesis, which is crucial for sustainable and eco-friendly bioremediation practices. [ABSTRACT FROM AUTHOR]

Introduction: Myxococcus sp. PT13 is a wild strain with multiple predatory properties that prey on multiple model microorganisms preserved in the laboratory. However, the lysis spectrum of PT13 on typical soil bacteria and its driving effect on soil microecosystems are still unclear. Methods: In this study, the lawn predation method was used to determine the predation diameter of 62 typical soil bacteria by myxobacteria PT13 and analyze their lysis spectra. Results and Discussion: The results showed that PT13 had a predation diameter greater than 15mm against typical soil microorganisms such as Aeromonas, Bacillus, Brevibacterium, Fictibacillus, Glutamicibacter, Herbaspirillum, and Leifsonia and had an outstanding lysis effect but a significant preference (p < 0.05). Absolute highthroughput sequencing results showed that PT13 predation drove the microcosmic system composed of 16 bacterial genera, with a significant decrease in the Shannon index by 11.8% (CK= 2.04, D = 1.80) and a significant increase in the Simpson index by 45.0% (CK= 0.20, D = 0.29). The results of principal coordinate analysis (PCoA) showed that myxobacterial addition significantly disturbed the microcosmic microbial community structure (ANOSIM, p < 0.05). LEfSe analysis showed that the relative and absolute abundances (copy numbers) of Bacillus, Pedobacter, Staphylococcus, Streptomyces and Fictibacillus decreased significantly very likely due to myxobacterial predation (p < 0.05). However, the predatory effect of PT13 also increased the relative or absolute abundances of some species, such as Sphingobacterium, Paenarthrobacter, Microbacterium, and Leifsonia. It can be concluded that PT13 has a broad-spectrum lysis spectrum but poor cleavage ability for Streptomyces, and the interaction between complex microorganisms limits the predation effect of PT13 on some prey bacteria. This in turn allows some prey to coexist with myxobacteria. This paper will lay a theoretical foundation for the regulation of soil microecology dominated by myxobacteria. [ABSTRACT FROM AUTHOR]

Dissolved organic matter (DOM) as critical redox active soil carbon plays a crucial role in shuttling electrons between bacteria and solid electron acceptors, such as iron oxides. However, research on DOM as an electron shuttle has traditionally focused on its impact on typical iron-reducing bacteria, namely strong exoelectrogens, like Geobacter. Besides these strong exoelectrogens, there is a significant presence of weak exoelectrogens in the soil, but studies examining how DOM affects their survival and competitiveness are lacking. This study focused on exploring the influence of DOM on weak exoelectrogens like Bacillus in the soil. By utilizing soil-bioelectrochemical systems (s-BESs) to enrich soil electroactive microorganisms, it investigated the relationship between the abundance of strong and weak exoelectrogens under conditions rich in DOM and conditions lacking DOM. The results showed that in the rich DOM treatment, the abundance of Geobacter was relatively lower (12 ± 0.5% vs. 41 ± 3%), and there was a significant negative correlation between the abundance changes of 18 weak exoelectrogens and Geobacter. This suggests that DOM caused a decrease in the population of strong exoelectrogens (e.g., Geobacter) while simultaneously promoting the growth of weak exoelectrogens (e.g., Bacillus and Sedimentibacter). Based on this, we propose that DOM, acting as an electron shuttle, creates favorable ecological niches for the thriving and propagation of weak exoelectrogens, enhancing their competitiveness within the microbial community. This new understanding provides deeper insights into the significance of DOM electron shuttling in soil microbial ecology, and raises the question: is the role of weak exoelectrogens in soil iron cycling underestimated due to the existence of DOM? Highlights: s-BESs reveal the critical role of DOM in altering the electroactive microbial community. DOM boosts the abundance of weak exoelectrogens such as Bacillus and Sedimentibacter in soil biofilms. The abundance changes between strong and weak exoelectrogens show a negative correlation. This underscores the often-overlooked significance of weak exoelectrogens in soil. [ABSTRACT FROM AUTHOR]

As plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum , collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution. [ABSTRACT FROM AUTHOR]

This document is an editorial published in Frontiers in Microbiology titled "Exploring microbial mat communities in extreme environments." The editorial discusses the biodiversity and ecological significance of microbial mats, which are communities of microorganisms that capture and recycle nutrients and energy. The authors highlight the importance of studying microbial mats in extreme environments, such as Antarctica and hot springs, to understand diversity, evolutionary processes, and the adaptability of life to extreme conditions. The editorial also provides a summary of eight articles published in the same research topic, which further explore the diversity and interactions of microbial mats in extreme environments. Overall, the editorial emphasizes the need for continued research to fully understand the complexities of microbial mat communities in extreme habitats. [Extracted from the article]

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology. [ABSTRACT FROM AUTHOR]

Replacing harmful chemical pesticides with compost extracts is steadily gaining attention, offering an effective way for plant growth enhancement and disease management. Food waste has been a major issue globally due to its negative effects on the environment and human health. The methane and other harmful organisms released from the untreated waste have been identified as causes of this issue. Soil bacteria impart a very important role in biogeochemical cycles. The interactions between plants and bacteria in the rhizosphere are some of the factors that determine the health and fertility of the soil. Free-living soil bacteria are known to promote plant growth through colonizing the plant root. PGPR (Plant Growth Promoting Rhizobacteria) inoculants in compost are being commercialized as they help in the improvement of crop growth yield and provide safeguard and resistance to crops from disease. Our focus is to understand the mechanism of this natural, wet waste recycling process and implementation of a sustainable operative adaptation with microbial association to ameliorate the waste recycling system. [ABSTRACT FROM AUTHOR]

Simple Summary: Model tests under laboratory conditions are very common in soil ecology and microbiology, but few of them are related to flooding, and comparison of the results of such an experiment with natural conditions is unprecedented. The present study investigated the basic parameters determining the biological activity of soil subjected to flooding under laboratory and natural conditions. The results obtained show that soil inundation under both natural and laboratory conditions significantly affects soil fertility and processes. The changes are more pronounced in the laboratory experiment than in the field conditions. Nevertheless, model studies are needed in environmental ecology and microbiology to predict changes under different stress factors, but their scale and pathway must be carefully planned. Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned. [ABSTRACT FROM AUTHOR]

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The possibilities of regulating soil microbial communities via various agricultural practices and the application of microbial preparations are considered. The total biomass, diversity and activity of microorganisms, as well as the intensity of certain processes, such as nitrogen transformation, can be regulated by agricultural practices. The complicated non-selective effect of these techniques on the microbial community, as well as the high variability of their effects, remains as the challenge. The effectiveness of microbial preparations is determined by the survival rate of introduced microorganisms in the soil, the variety of soil and climatic conditions, and the competition with native soil microorganisms. More rigorous testing of the effectiveness of microbial preparations and biofertilizers by analogy with medical preparations is needed. Integration of agrobiotechnologies with modern concepts of microbial ecology based on molecular-biological methods for studying soil microbial communities is required to develop effective microbial preparations. [ABSTRACT FROM AUTHOR]

Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON's newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced by neonMicrobe can be linked to NEON's other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporating neonMicrobe into reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and the neonMicrobe R package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors. [ABSTRACT FROM AUTHOR]

Immobilisation of fertiliser nitrogen (N) by soil microorganisms can reduce N availability to crops, decreasing growth and yield. To date, few studies have focussed on the effect of different plant species on immobilisation of fertiliser N. Canola (Brassica napus) is known to influence the soil microbiome and increase mineral N in soil for future crops compared with cereals. We tested the hypothesis that canola can reduce immobilisation of fertiliser N by influencing the composition of the rhizosphere microbiome. To investigate this, we conducted a glasshouse soil column experiment comparing N fertiliser uptake between canola and wheat (Triticum aestivium) and partitioning of fertiliser N between plants and microorganisms. Plants were grown in soil to which high C:N ratio wheat residues and 15N-labelled urea fertiliser were applied. There was no difference between wheat and canola in fertiliser N uptake despite differences in fungal community composition and the carbon metabolising enzyme alpha-glucosidase in the rhizosphere. Canola obtained more soil-derived N than wheat. There was no significant difference in the rhizosphere bacterial communities present between wheat and canola and unplanted controls. Our results highlight the capacity of canola to increase mineralisation of soil N compared with wheat although the study could not describe the microbial community which facilitated this increase. [ABSTRACT FROM AUTHOR]