Soil Bacteria Research Articles

Stress Response Proteins Are the Reliant Factors for Resilience in the Soil Bacterium Bacillus haynesii PSK.N4

Stress Response Proteins Are the Reliant Factors for Resilience in the Soil Bacterium Bacillus haynesii PSK.N4

Soil chemistry exerts a more significant influence on bacterial responses to nitrogen disturbances than root exudates

Abstract Atmospheric nitrogen (N) deposition is anticipated to stabilize or decline in numerous global regions. However, the residual effects of historical N enrichment on soil microbial communities—particularly their regulatory mechanisms—remain poorly understood. Our 18-year grassland experiment indicated that bacterial communities in bulk soil exhibited greater sensitivity to N addition compared to those in rhizosphere soil, suggesting host plants affect the response of soil bacteria to N enrichment. Following cessation of N addition, there was limited bacterial community recovery, especially in the rhizosphere soil of forb species. Although root exudates from plants underwent significant alterations under N enrichment, the sensitivity of bacterial communities was primarily governed by changes in soil properties and root traits. In contrast to host selection, environmental filtering factors, particularly soil pH and metal ions, mainly determined the resilience of overall community by differentially affecting bacterial groups with distinct life-history strategies. Oligotrophic bacteria were negatively impacted by reduced pH and elevated metal ion levels, leading a decline following N enrichment. Conversely, copiotrophic bacteria initially benefited from metal ions, exhibiting an increase followed by a decrease after the addition and subsequent cessation of N enrichment. These findings indicate that soil environmental filtration exerts a more substantial influence than host selection on bacterial communities in response to N disturbances, thereby enhancing our understanding of the mechanisms underlying plant-microbial interactions under ongoing global changes.

Soil microbiome dysbiosis and rhizosphere metabolic dysfunction drive continuous cropping obstacles of Codonopsis tangshen

Successive monocropping of Codonopsis tangshen causes continuous cropping obstacles, impairing growth, yield, and quality. To investigate the soil environmental and microbial changes caused by these obstacles, we collected both continuous cropping (C-crop) and non-continuous cropping (NC-crop) soil for analysis. We employed high-throughput sequencing, Biolog-ECO microplate, and metabolomics technology to evaluate microbial diversity, community structure, and carbon source utilization efficiency. Compared with NC-crop, C-crop decreased the yield and polysaccharide content of C. tangshen by 40.47 and 29.4%, respectively. Continuous cropping significantly altered soil physicochemical properties and metabolomes, driving distinct shifts in microbial community structure and impairing carbon utilization efficiency. Microbial carbon use efficiency was positively correlated with key soil bacteria and fungi. However, their abundance decreased significantly under continuous cropping, ultimately disrupting soil carbon cycling. Moreover, key bacterial (e.g., Flavobacterium, Lysobacter, Pseudomonas, Burkholderia) and fungal genera (e.g., Ophiosphaerella, Dactylonectria, Humicola) showed strong correlations with critical soil physicochemical properties, microbial carbohydrate metabolism, and rhizosphere metabolite profiles. The reduced abundance of these microbes disrupted soil nutrient balance and microbial activity, potentially contributing to C. tangshen continuous cropping obstacles. This study contributes to the understanding of the mechanisms underlying continuous cropping obstacles in C. tangshen and lays the foundation for developing strategies to alleviate these obstacles.

Microbial and phytochemical approaches to mosquito control: A review focusing on Lysinibacillus sphaericus and Sphagneticola trilobata

Mosquito-borne diseases such as malaria, dengue, Zika virus, chikungunya, and yellow fever continue to pose significant threat for global public health. Traditional chemical pesticides, is somewhat effective to control mosquito populations, but has severe environmental concerns, such as damaging ecology, harmful for beneficial non-target animals, and an alarming increase in insecticide-resistant mosquito strains. Our review sheds light on microbiological and phytochemical approaches to mosquito control as effective and environmentally sustainable option. Lysinibacillus sphaericus. A gram-positive soil bacterium has great effectiveness as a biocontrol candidate because it generates specific larvicidal toxins such as the binary toxin complex (BinA and BinB) and mosquitocidal toxins (Mtx). These poisons selectively target mosquito larvae midgut cells and have no major impact on non-target species, making L. sphaericus a vital part in integrated vector management schemes. Phytochemical approaches disrupt crucial mosquito life cycle pathways using plant-derived bioactive chemicals. Sphagneticola trilobata, a widely distributed tropical plant, has demonstrated substantial potential in mosquito control as it contains a great range of bioactive compounds, including flavonoids, terpenoids, saponins, and phenolic acids. These substances have larvicidal, insecticidal, and repellant activities through an involvement with mosquito digestion, hormonal balance, and neural pathways. S. trilobata extracts are also a sustainable, biodegradable, and environmentally friendly alternative to synthetic insecticides. This analysis highlights L. sphaericus and S. trilobata's promise as eco-friendly and effective solutions to the expanding mosquito control difficulties by investigating their mechanisms of action, practical uses, and environmental advantages. J. Sylhet Agril. Univ. 11(2): 19-28, 2024

Root exudates of Withania somnifera prevent the risk of transmission of soil-dwelling Enterobacterales to nearby plants.

Soil-dwelling enteric pathogens are indicators of sewage or fecal matter contamination. When such organisms enter agricultural fields, they colonize crops and cause pre-harvest contamination of food products. Consumption of such contaminated products can lead to disease outbreaks. Thus, preventing pre-harvest contamination of food products by enteric bacteria dwelling in soil is essential. The Cooch Behar district of India receives > 3000mm rainfall annually causing an anaerobic condition in soil, creating an ambient condition for the survival of enteric bacteria. While screening for native Enterobacterales in this region, a serendipitous observation was made, wherein the rhizosphere of Withania somnifera plant had negligible number of enteric bacteria. Artificially inoculated native Citrobacter sp. was unable to colonize the roots of Withania. Water-soluble exudates had prolonged antimicrobial activity in vitro, proving that the antimicrobial molecule is secretory. Based on this observation, Withania plant was grown in pots with high numbers of enteric bacteria, and it was found that the colonization was significantly reduced. Moreover, the antimicrobial activity spread through the soil via irrigation water to the neighboring plants. Thus, it was concluded that growing Withania alongside susceptible plants, like Vigna radiata, can prevent the colonization of the rhizosphere, minimizing the risk of pre-harvest contamination of fresh produce. Additionally, it was found that the antimicrobial activity is not specific. However, the population of beneficial microbiota of soil was not affected much when Vigna and Withania were grown together. To the best of our knowledge, this is the first report on Withania, as a biocontrol plant, that reduced the chance of spreading enteric bacteria in soil.

A Natural Depsipeptide Antibiotic that Targets the E site of the Bacterial Ribosome.

A significant challenge in addressing the antibiotic resistance crisis is identifying new antimicrobial compounds. Although natural products produced by fungi and bacteria, particularly actinomycetes, have been the source of most antibiotics discovered over the past 80 years, they have fallen out of favor due to the frequent rediscovery of known drug scaffolds. The current perception is that antibiotic-producing actinomycetes have been over-mined and possess little novelty left to yield. Here, we demonstrate that by using improved fractionation approaches that enrich previously overlooked minor products, even well-studied strains of antibiotic-producing actinomycetes can provide new chemical scaffolds with unique modes of action. By fractionating a library of natural product extracts from soil bacteria, we show that Streptomyces rimosus, the source of the well-known antibiotic oxytetracycline, produces a previously overlooked cyclic depsipeptide antibiotic that we called manikomycin. Manikomycin can kill multi-drug-resistant Enterobacteriaceae and is not susceptible to resistance associated with clinically used antibiotics. Biochemical, genetic, and structural analyses reveal that manikomycin binds in the 'exit' or E site of the large subunit of the bacterial ribosome preventing the entry of the 3' end of the tRNA into the E site and effectively hindering the translocation step of protein synthesis in a sequence context-specific manner. Manikomycin is the first antibacterial agent to target the critical but underexplored E site in the large ribosomal subunit, highlighting its value as a lead for developing new antibiotics.

Cis,cis-muconic acid production from lignin related molecules byAcinetobacter baylyi ADP1

BackgroundCis,cis-muconic acid (ccMA), an important platform chemical, can be produced from lignin related molecules (LRM) via a specific two-branch catabolic route known as the β-ketoadipate pathway, which is present in certain soil bacteria. This pathway enables high production yields because ccMA is a native intermediate in one of its branches. However, commonly obtained LRM, such as p-coumaric and ferulic acid, are typically metabolized through the branch that lacks the ccMA intermediate. To redirect these LRM toward ccMA production, the two branches must be functionally integrated. This is usually achieved by introducing a non-native enzymatic activity, specifically protocatechuate decarboxylase (PCADC), which catalyzes the conversion of protocatechuate to catechol. Nevertheless, this conversion often represents the rate-limiting step in the production process.ResultsHere, we established a growth-coupled selection system for screening PCADCs using the soil bacterium Acinetobacter baylyi ADP1 as the host. In this system, cell growth depends on the in vivo performance of PCADC, thereby enabling the selection of the optimal candidate for further ccMA production. In total, five PCADC candidates were screened. AGDC1, a gallic acid decarboxylase from the yeast Blastobotrys adeninivorans, was selected for production studies. In fed-batch cultivations, the engineered strain expressing AGDC1 achieved an 83% molar yield of ccMA from ferulate and p-coumarate, that were found in lignin hydrolysate derived from straw.ConclusionIn this study, we established a growth-based selection system for PCADCs. The outcome of the selection system was further validated in production cultivations using an engineered A. baylyi ADP1 strain. This study not only confirms the feasibility of AGDC1 in ccMA production in bacterial systems but also provides a practical screening system for future improvements.

Effects of Fire on Soil Bacterial Communities and Nitrogen Cycling Functions in Greater Khingan Mountains Larch Forests

Investigating the effects of fire disturbance on soil microbial diversity and nitrogen cycling is crucial for understanding the mechanisms underlying soil nitrogen cycling. This study examined the fire burn site of the Larix gmelinii forest in the Greater Khingan Mountains, Inner Mongolia, to analyze the impact of varying fire intensities on soil nitrogen, microbial communities, and the abundance of nitrogen cycle-related functional genes after three years. The results indicated the following findings: (1) Soil bulk density increased significantly following severe fires (7.06%~10.84%, p < 0.05), whereas soil water content decreased with increasing fire intensity (6.62%~19.42%, p < 0.05). The soil total nitrogen and ammonium nitrogen levels declined after heavy fires but increased after mild fires; (2) Mild fire burning significantly increased soil bacterial diversity, while heavy fire had a lesser effect. Dominant bacterial groups included Xanthobacteraceae, norank_o_norank_c_AD3, and norank_o_Elsterales. Norank_o_norank_c_AD3 abundance decreased with burn intensity (7.90% unburned, 3.02% mild fire, 2.70% heavy fire). Conversely, norank_o_Elsterales increased with burning (1.23% unburned, 5.66% mild fire, 5.48% heavy fire); (3) The abundance of nitrogen-fixing nifH functional genes decreased with increasing fire intensity, whereas nitrification functional genes amoA-AOA and amoA-AOB exhibited the opposite trend. Light-intensity fires increased the abundance of denitrification functional genes nirK, nirS, and nosZ, while heavy fires reduced their abundance; (4) The correlation analysis demonstrated a strong association between soil bacteria and denitrification functional genes nifH and amoA-AOA, with soil total nitrogen being a key factor influencing the nitrogen cycle-related functional genes. The primary bacterial groups involved in soil nitrogen cycling were Proteobacteria, Actinobacteria, and Chloroflexi. These findings play a critical role in promoting vegetation regeneration and rapid ecosystem restoration in fire-affected areas.

Stress-induced proteins enhance thermal endurance in soil bacterium Priestia aryabhattai strain PSK.N2.

Soil microbial communities play vital roles in ecological stability and offer significant potential for biotechnological innovations. These microorganisms frequently encounter abiotic stressors such as heat, which can activate protective mechanisms including the overexpression of heat shock proteins (HSPs). In this study, a resilient soil bacterium, Priestia aryabhattai strain PSK.N2, was isolated from the Western Ghats of India and identified through a polyphasic approach. Growth parameters were optimized before subjecting the strain to heat stress, both alone and in the presence of sub-lethal concentrations of antibiotics that target distinct cellular processes; DNA replication, RNA transcription, protein synthesis, and cell wall biosynthesis. Comparative protein profiling (via SDS-PAGE), protein aggregation assays, and survival assessments (single spot dilution and CFU enumeration) revealed that heat-stressed cells showed enhanced thermal tolerance compared to those grown under optimal conditions. This increased endurance was associated with the transient overexpression of ~ 17-90kDa stress-related proteins. In contrast, cells treated with transcription and translation-inhibiting antibiotics (rifampicin and chloramphenicol) showed diminished tolerance, likely due to impaired synthesis of stress-response proteins. These findings suggest that pre-exposure to stress enhances cellular preparedness through selective protein induction, offering insights for developing stress-resilient microbial strains for applications in bioprocessing, environmental remediation, and microbial therapeutics.

Study on the effects of winter irrigation during seasonal freezing–thawing period on soil microbial ecological properties

The seasonal freeze-thaw period is a critical time for restoring soil fertility. Winter irrigation during this period alters soil moisture in agricultural fields, which in turn affects the soil’s temperature, nutrients, and microbial factors within the soil micro-environment. Soil microorganisms play a crucial role in soil nitrogen fixation. Investigating the changes in soil microbial communities during the seasonal freeze-thaw period under winter irrigation conditions can help further understand the regulatory mechanisms of winter irrigation on the soil microenvironment. The experimental micro-areas were selected at the Key Laboratory of Modern Water-Saving Irrigation of Xinjiang Production &Construction Group. Based on soil moisture conditions, winter irrigation quotas of 0, 45, 90, and 135 mm were established. Soil samples were collected according to the seasonal freeze-thaw process in the experimental area, and measurements were taken for soil moisture, temperature, salinity, nutrients, as well as the quantity and diversity indices of soil bacteria and fungi. Using single-factor correlation and principal component analysis, the interactions between soil microbial indicators and their influencing factors under winter irrigation conditions were examined. Under winter irrigation conditions, during the seasonal freeze-thaw period, pH significantly affects the richness of soil bacterial populations and the quantity of bacteria (P < 0.05). Soil organic matter significantly influences the diversity of fungal populations (P < 0.05). The combined effects of soil moisture content, temperature, and pH significantly impact the quantity of soil microorganisms (P < 0.05), with soil moisture content being the determining factor. There is a significant correlation between the diversity and richness of soil microbial communities (P < 0.05). The results indicate that winter irrigation during the seasonal freeze-thaw period not only alters the composition and metabolic capacity of microbial communities but also affects the interrelationships among microbial diversity indices, thereby impacting microbial stability. Furthermore, a winter irrigation quota of 45 mm during the seasonal freeze-thaw period has multiple positive effects on the soil micro-environment, effectively promoting plant growth, improving soil health, and supporting the development of sustainable agriculture.

Artificial Endosymbiosis of Pedobacter sp. DDGJ Boosts the Growth Potential, Stress Resistance and Productivity of Morchella Mushrooms

ABSTRACTTrue morels are precious edible and medicinal mushrooms. The sustainable development of morel cultivation necessitates urgent breeding programmes to develop improved varieties or strains. Some soil bacteria, including Pedobacter spp., are recognised as morel's beneficial microbes. In this paper, the potential beneficial bacterium Pedobacter sp. DDGJ with minor chitinolytic activity was isolated and confirmed for improving morel's mycelial growth and identified using a combination of morphological characteristics, 16 S rRNA gene sequencing, and comparative genomics. Then, it was introduced into the hyphal cells of three cultivated Morchella strains (M. sextelata 13, M. eximia SM, and M. importuna Y2) through a confrontation culture method. The successful establishment of artificial endosymbiosis was confirmed by PCR assay, green fluorescent protein gene (gfp) localisation, and the cryo‐preparation system conjunction with high‐resolution field emission scanning electron microscopy. Laboratory assay indicated that artificial endosymbiosis of the bacterium significantly enhanced morel's growth potential, resistance to allelochemicals of 4‐coumaric acid and antagonistic capability against the pathogenic fungus Fusarium oxysporum and soil‐dominant fungus Chaetomium globosum. Moreover, the outdoor planting experiment showed significant increase in productivity among the endosymbiotic morel strains. The study provides an additional tool to improve Morchella strains with high yield and strong stress resistance.

Comparison of microbial community structures in rhizosphere soils of different plants in riverine wetland.

Bacterial communities play an important role in nutrient cycling in riverine wetland ecosystems, and the study of rhizosphere microbial community composition of different plants is of great scientific significance in revealing the relationship between microorganisms and plant interactions in riverine wetlands. In this study, samples were collected from four plant congeries dominated by Artemisia argyi (AH), Acorus calamus (CP), Miscanthus sacchariflorus (DC), and Paspalum distichum (QB), respectively. High-throughput sequencing technology was employed to investigate the rhizosphere microbial community structures associated with these distinct plant species. The results showed that soil water content could effectively regulate the functional diversity of soil microbial communities. Different plant congeries types significantly affected soil bacterial community diversity, and at the phylum level, both Proteobacteria and Acidobacteria were absolutely dominant groups, followed by Bacteroidetes. At the genus level, Flavobacterium, Sphingomonas, Gp6 and Gp4 were the dominant bacteria in the rhizosphere soil of plants along the river. Soil pH, water content, NO3-N, NO2-N and TOC were the main factors affecting the composition of microbial communities. This study broadens our understanding of the composition of rhizosphere microbial communities in the river buffer zone, and provide data support for river ecological environment protection.

Humic substance turnover by bacterial decomposers in the maritime Antarctic soil

Context Soil fungi and bacteria play a crucial role in decomposing soil organic matter (SOM) and providing nutrients to terrestrial ecosystems. However, in polar environments, their relative contributions to decomposition remain unclear. Aims This study aimed to determine whether fungi or bacteria contributes more to humic substances (HS) decomposition (the largest constituent of SOM) in maritime Antarctic soils under controlled laboratory conditions with elevated temperature and moisture levels. Methods Soil culturing method was used to select for soil microbes that efficiently degrade HS. During culturing at 18°C for 30 days, Antarctic soils were treated with selective antimicrobials to manipulate microbial communities. After culturing, HS degradation and bacterial communities were analysed. The effects of soil culturing on plant growth were also evaluated using Arabidopsis thaliana as a surrogate for Antarctic plants. Key results HS decomposition and solubilisation were more pronounced in antifungal-treated soils compared to antibacterial-treated soils. Antifungal treatment reduced bacterial alpha diversity, altered bacterial composition, and increased the abundance of rhizosphere-associated Saccharibacteria. Bacterial growth resumed quickly after antibacterial treatment indicating resilience to antimicrobials. Soil culturing resulted in a higher water-soluble HS fraction, which significantly enhanced the fresh and dry weights of A. thaliana. Conclusions Antarctic bacteria exhibit higher degradative activity and resilience to antimicrobials compared to fungi, promoting HS decomposition and solubilisation. This indicates that bacteria have a greater impact on Antarctic soil functioning than fungi. Implications These findings highlight the critical role of bacteria in nutrient cycling and plant growth in polar ecosystems.

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation.

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation.

Characteristics of airborne bacteria over inland and coastal atmosphere influenced by systemic air mass in northern China.

Characteristics of airborne bacteria over inland and coastal atmosphere influenced by systemic air mass in northern China.

Golden Rice: a quarter-century of innovation, challenges, and the promise of better nutrition.

Golden Rice: a quarter-century of innovation, challenges, and the promise of better nutrition.

Degradation of biodegradable plastic films in soil: microplastics formation and soil microbial community dynamics.

Degradation of biodegradable plastic films in soil: microplastics formation and soil microbial community dynamics.

Inter-root soil bacterial community composition and its driving factors in Ulmus pumila L. of different ages

Ulmus pumila L: is the primary tree species in the Hunshandake Sandy Land and plays a crucial role in controlling wind and sand movement and stabilizing the soil. Currently, Ulmus pumila L. is aging severely, and the inter-root bacterial community structure directly affects its resistance and nutrient uptake. Therefore, it is crucial to investigate the composition of the inter-root soil bacterial community and its driving factors during elm growth. In this study, high-throughput sequencing technology was utilized to determine the bacterial community composition and reveal the relationship between the inter-root bacterial community composition of U. pumila L. of different ages and microenvironmental factors based on basic soil properties and enzyme activities. The results showed that alkaline phosphatase and soil invertase levels increased with the increasing stand age. Compared with young forests (YF), soil total nitrogen, total phosphorus, and organic carbon in mature forests (MF) increased by 32.20%, 33.73%, and 17.65%, respectively. The contents of soil available nitrogen (AN) and available phosphorus showed the same trend in different forest ages. The variation trends of the total number of species and specific species of inter-root soil bacteria in U. pumila L. were consistent, and both showed a downward trend. Actinobacteria were significantly more abundant in young forests than in the others (P &amp;lt; 0.05). It showed a decreasing trend, and mature forests decreased by 29.23% compared to YF, while the abundance of Firmicutes increased. The results of the RDA analysis suggested that available nitrogen explained the most changes in soil bacterial community structure. AK and AN were strongly negatively correlated with Firmicutes but positively correlated with all other bacteria. This study provides useful information for the conservation and utilization of sparse elm forests and also helps provide a vital theoretical basis for understanding the ecological environment construction in the Hunshandake Sandy Land.

Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons.

Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons.

Development and validation of a stability-indicating high performance liquid chromatography method based on a core-shell octadecyl column to determine Avermectin and its related substances in bulk Avermectin batches.

Development and validation of a stability-indicating high performance liquid chromatography method based on a core-shell octadecyl column to determine Avermectin and its related substances in bulk Avermectin batches.