Soil Bacteria Research Articles

Assessment of technogenic pollution by silver compounds on the biological properties of the soil (Model experiment)

Introduction: Silver (Ag) has increasingly become one of the priority pollutants of soils, which is accompanied by a number of consequences for humans and soil biota. To fully assess the effects of the entry of different chemical forms of Ag into soils, it is necessary to conduct experiments with different types of soils, different exposure periods, as well as a wide range of biological indicators. The purpose of the study is to assess technogenic pollution by silver compounds (silver oxide (Ag2O) and nitrate (AgNO3)) on the biological properties of the soil in model experiment of the soil in a model experiment, followed by the use of the data obtained in the normalization of the Ag content in the soil. Materials and methods: The effect of Ag2O and AgNO3 was investigatedin specific permissible concentrations of biological indicators of the state of Haplic Chernozems Calcic (HCC), Haplic Cambisols Eutric (HCE) and Haplic Arenosols Eutric (HAE). Ecotoxicity was assessed by the degree of changes in the indicators of enzymatic activity, microbiological and phytotoxic indicators of soils 10, 30 and 90 days after contamination. Activity of catalase it was determined gasometrically, dehydrogenases, peroxidase, polyphenoloxidase, ferrireductase, ascorbatoxidase, phosphatase, invertase, urease, protease was determined photocolorimetrically, the total number of bacteria by luminescent method, Azotobacter sp. abundance by the method of fouling lumps on the Ashby medium, length of shoots and roots of wheat (Triticum aestivum L.) morphometrically. Results: It was revealed that Ag ecotoxicity was determined by the content of Ag in the soil, its form, the period from the moment of contamination and soil type. In most cases, AgNO3 had a stronger ecotoxic effect on biological parameters. Phosphatase activity and number of soil bacteria are the most sensitive indicators. The activity of invertase, urease, dehydrogenases and Azotobacter sp. abundance are the most informative indicators. Conclusion: Abundance is the most informative indicator. The results obtained to assess the ecotoxicity of soils contaminated with Ag, as well as the identified sensitive and informative indicators, can be used for diagnosis and as an indicator of the ecological state of soils.

Soil microbiome bacteria protect plants against filamentous fungal infections via intercellular contacts

Bacterial-fungal interaction (BFI) has significant implications for the health of host plants. While the diffusible antibiotic metabolite-mediated competition in BFI has been extensively characterized, the impact of intercellular contact remains largely elusive. Here, we demonstrate that the intercellular contact is a prevalent mode of interaction between beneficial soil bacteria and pathogenic filamentous fungi. By generating antibiotics-deficient mutants in two common soil bacteria, Lysobacter enzymogenes and Pseudomonas fluorescens, we show that antibiotics-independent BFI effectively inhibits pathogenic fungi. Furthermore, transcriptional and genetic evidence revealed that this antibiotics-independent BFI relies on intercellular contact mediated by the type VI secretion system (T6SS), which may facilitate the translocation of bacterial toxic effectors into fungal cells. Finally, by using a "conidia enrichment" platform, we found that T6SS-mediated fungal inhibition resulting from intercellular contact naturally occurs within the soil microbiome, particularly represented by Pseudomonas fulva. Overall, these results demonstrate that bacteria from the soil microbiome can protect host plants from fungal infection through antibiotics-independent intercellular contacts, thus revealing a naturally occurring and ecologically important mode of BFI in agricultural contexts.

Fertilization Induced Soil Microbial Shifts Show Minor Effects on Sapindus mukorossi Yield

Fertilization can improve soil nutrition and increase the yield of Sapindus mukorossi, but the response of soil microbial communities to fertilization treatments and their correlation with soil nutrition and Sapindus mukorossi yield are unclear. In order to investigate the characteristics of soil physicochemical qualities and the bacterial community, we carried out a field experiment comparing various quantities of nitrogen (N), phosphorus (P), and potassium (K) fertilizers to the unfertilized control treatments and the yield of Sapindus mukorossi in raw material forests in response to different applications of fertilizers and to try to clarify the interrelation among the three. Results showed that (1) there are significant differences in the effects of different fertilization treatments on the soil properties of Sapindus mukorossi raw material forests. The increase in the application rates of nitrogen or phosphorus fertilizers significantly reduced the soil pH value. (2) Compared with control, the α-diversity of bacterial communities was significantly lower in N3P2K2 and N1P1K2 treatments. Among the dominant groups of soil bacteria at the phylum level, the relative abundance of Chloroflexi showed an increase and then a decrease trend with the increase in N application. The relative abundance of Firmicutes, Bacteroidota, and Fusobacteriota was positively correlated with the application of P and K fertilizers, while the relative abundance of Acidobacteriota and Verrucomicrobiota decreased with the increase in P and K fertilizers. (3) The N2P2K2 treatment produced the highest sapindus yield (1464.58 kg/ha), which increased by 258.67% above the control. (4) Redundancy analysis (RDA) showed that the primary determinants of bacterial community structure were soil pH, total K, and effective P concentration. (5) Structural equation modeling (SEM) showed that soil nutrient content was the main direct factor driving the yield of Sapindus mukorossi, whereas the bacterial community attributes (e.g., diversity and structure) had minor effects on the yield. In summary, the rational use of formulated fertilization can change the bacterial community structure, improve the bacterial diversity, and increase the soil nutrient content, with the latter exerting a significant effect on the improvement of the yield of Sapindus mukorossi.

Towards repeated clear-cutting of boreal forests - a tipping point for biodiversity?

Boreal forests are important carbon sinks and host a diverse array of species that provide important ecosystem functions. Boreal forests have a long history of intensive forestry, in which even-aged management with clear-cutting has been the dominant harvesting practice for the past 50-80 years. As a second cycle of clear-cutting is emerging, there is an urgent need to examine the effects of repeated clear-cutting events on biodiversity. Clear-cutting has led to reduced numbers of old and large trees, decreased volumes of dead wood of varied decay stages and diameters, and altered physical and chemical compositions of soils. The old-growth boreal forest has been fragmented and considerably reduced. Here, we review short- and long-term (≥50 years) effects of clear-cutting on boreal forest biodiversity in four key substrates: living trees, dead wood, ground and soil. We then assess landscape-level changes (habitat fragmentation and edge effects) on this biodiversity. There is evidence for long-term community changes after clear-cutting for several taxa: epiphytic lichens; saproxylic fungi, bryophytes and insects; epigeic bryophytes; and soil snails, bacteria, and ectomycorrhizal fungi. Long-term declines in species richness were found for saproxylic fungi, bryophytes and true flies. However, for the majority of taxa, long-term effects of clear-cutting are not well understood. On the landscape level, reduced connectivity to old-growth forests has negative effects on several species of fungi, lichens, bryophytes and insects, notably among Red-Listed species. Furthermore, altered microclimate near clear-cut edges negatively affects epiphytic lichens and epigeic arthropods, implying complex effects of habitat fragmentation. Repeated cycles of clear-cutting might pose even stronger pressures on boreal forest biodiversity due to continued fragmentation of old-growth forests and accumulation of extinction debts. Examining the broad effects of forestry on biodiversity across the boreal biome is crucial: (i) to increase our knowledge of long-term and landscape-level effects of former clear-cutting; and (ii) to gain a better understanding of how forestry will affect biodiversity and, subsequently, ecosystem functioning, with repeated cycles of clear-cutting.

Isolation and Bioactivity of Natural Products from Streptomyces sp. MA37

The isolation and characterization of bioactive metabolites from Streptomyces species continue to represent a vital area of research, given their potential in natural product drug discovery. In this study, we characterize a new siderophore called legonoxamine I, together with a known compound, streptimidone, from the talented soil bacterium Streptomyces sp. MA37, using chromatographic techniques and spectroscopic analysis. Legonoxamine I is a new holo-siderophore, which is likely to be a derailed product from the biosynthetic pathway of legonoxamine A. We also demonstrate that legonoxamine A possesses potent anticancer activity (IC50 = 2.2 µM), exhibiting a remarkable ~30-fold increase in potency against MCF-7 ATCC HTB-22 breast cancer cells compared to desferrioxamine B, a structural analogue of legonoxamine A (IC50 = 61.1 µM). Comparing the structural difference between legonoxamine A and desferrioxamine B, it is deduced that the phenylacetyl moiety in legonoxamine A may have contributed significantly to its enhanced potency. Our findings contribute to the growing library of Streptomyces-derived metabolites and underscore the genus’ potential as a promising source of lead compounds.

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

Different Flooding Conditions Affected Microbial Diversity in Riparian Zone of Huihe Wetland

The soil microbiome plays an important role in wetland ecosystem services and functions. However, the impact of soil hydrological conditions on wetland microorganisms is not well understood. This study investigated the effects of wetted state (WS); wetting–drying state (WDS); and dried state (DS) on the diversity of soil bacteria, fungi, and archaea. The Shannon index of bacterial diversity was not significantly different in various flooding conditions (p > 0.05), however, fungal diversity and archaeal communities were significantly different in different flooding conditions (p < 0.05). Significant differences were found in the beta diversity of bacterial, fungal, and archaeal communities (p < 0.05). Additionally, the composition of bacteria, fungi, and archaea varied. Bacteria were predominantly composed of Proteobacteria and Actinobacteria, fungi mainly consisted of Ascomycota and Mucoromycota, and archaea were primarily represented by Crenarchaeota and Euryarchaeota. Bacteria exhibited correlations with vegetation coverage, fungi with plant diversity, and archaea with aboveground vegetation biomass. The pH influenced bacterial and archaeal communities, while soil bulk density, moisture, soil carbon, soil nitrogen, and plant community diversity impacted fungal communities. This study provides a scientific basis for understanding the effects of different hydrological conditions on microbial communities in the Huihe Nature Reserve; highlighting their relationship with vegetation and soil properties, and offers insights for the ecological protection of the Huihe wetland.

Responses of Soil Microbial Communities to Abandoned Paddy Fields With Different Fertilization Histories

ABSTRACTThe abandonment of cultivated fields notably affects soil characteristics. However, its impact on soil microbial community composition, particularly under different fertilization regimes, remains poorly understood. Therefore, we evaluated the effects of abandoned paddy fields with different fertilization histories (no fertilization, NK, NP, and NPK) on the abundance, composition, and their predicted function of soil bacteria and fungi. Our findings revealed that the abandonment led to a considerable decrease in soil bacterial and fungal biomass. Fertilization history and abandonment each significantly affected on the bacterial community, resulting in increased relative proportions of Acidobacteria and decreased relative proportions of Proteobacteria in the NP and NPK treatments compared to those in the CK and NK treatments. The fungal community only exhibited a notable response to abandonment, with variations in the relative abundance of Ascomycota, Mucoromycota, and Basidiomycota. Canonical correspondence analysis revealed the significant association between soil bacterial community and pH, total phosphorus, and available phosphorus, whereas the pH and NO3−–N were key drivers of fungal community variations in abandoned soils. Network analysis indicated that abandonment enhanced the complexity but decreased the stability of the bacterial community, while fungi exhibited the opposite trend. Our findings highlight that changes in bacterial functions caused by residual nutrients, particularly high residual phosphorus, may accelerate soil organic C decomposition. Overall, this study provides a novel insight into the shifts in soil bacterial and fungal communities and their ecological functions after the abandonment of cultivated fields.

Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome.

Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures. This study developed a machine-learning approach that integrates the properties of chemical structures with the diversity of soil bacteria and functions to predict the impact of heterocyclic compounds on the microbial community and improve the design of eco-friendly heterocyclic compounds. We screened the key chemical structures of heterocyclic compounds─particularly those with topological polar surface areas (<74.2 Å2 or 111.3-154.1 Å2), carboxyl groups, and dissociation constant, which maintained high soil bacterial diversity and functions, revealing threshold effects where specific structural parameters dictated microbial responses. These eco-friendly compounds stabilize communities and increase beneficial carbon and nitrogen cycle functions. By applying these design parameters, we quantitatively assessed the eco-friendliness scores of 811 heterocyclic compounds, providing a robust foundation for guiding future applications. Our study disentangles the critical chemical structure-related properties that influence the soil microbial community and establishes a computational framework for designing eco-friendly compounds with ecological benefits from an ecological perspective.

The soil bacterium Lysobacter capsici attaches to the nematode surface, and triggers induced systemic resistance in barley, impairing the invasion of root‐lesion nematodes

The soil bacterium <i>Lysobacter capsici</i> attaches to the nematode surface, and triggers induced systemic resistance in barley, impairing the invasion of root‐lesion nematodes

Differential diversity and structure of autotrophs in agricultural soils of Qinghai Province.

Agricultural soil plays important roles in carbon fixation during carbon capture and storage. Autotrophic bacteria that utilize inorganic compounds as electron donors for growth fix CO2 photosynthetically or chemo-autotrophically in diverse ecosystems and affect soil organic carbon sequestration. Soil properties, agronomic management measures, and environmental factors can influence the community composition, abundance, and activity of CO2-assimilating bacteria. This study aims at evaluating the effects of different regions and crop types on the abundance, composition, and activity of CO2-fixing bacteria in agricultural soil.

Assessment In Depth on the Anti‐seasonal Water Fluctuations and Vegetation Dynamic Trends in a Plateau Lake, Southern China

ABSTRACTHuman activities, such as dam construction for flow regulation, modify the natural hydrological regimes of lakes and rivers. The altered flow regimes substantially influence plant growth in the water level fluctuation zone, impacting both vegetation patterns and success. The relationships among above‐ground vegetation, soil seed bank and soil microorganisms remain unexamined. This study was performed in Lashi Lake, a plateau lake in southern China characterized by anti‐seasonal water level fluctuations, and Jizi Reservoir, a reference site exhibiting natural seasonal water level variations. The primary aim was to assess the distribution pattern of plant, soil seed bank and their corresponding soil microorganism over the three flood gradients, and the relationships among them were analysed simultaneously. The findings indicated that both plant community variety and seed bank diminished as the area of soil flooding increased. The soil seed bank was a strong indication of community diversity, particularly throughout late spring and late summer. Additionally, significant correlations between the alpha diversity of soil microorganisms and the concentrations of soil carbon, nitrogen and moisture were found across the flooding gradients. The organization and diversity of soil microbial communities were significantly correlated with the alpha diversity of the plant community and the soil seed bank. The findings demonstrate that both seed banks and soil bacteria play a dynamic role in the restoration of vegetation in areas experiencing anti‐seasonal water fluctuations.

Mercury tolerance and bioremediation potential of mountain soil bacteria: Insights from Darjeeling, containing elevated levels of mercury.

More and more research is now being focused on the mercury contamination of remote mountain environments. This study aimed to explore the mountain soil of Tiger Hill, Darjeeling, through the lens of its mercury tolerant bacterial microbiome to characterize regional mercury pollution and isolate strains with mercury bioremediation potential. The soil bacteria isolated from the region displayed an extreme tolerance to mercury at previously unseen levels of up to 7mg/mL. The mercury removal capacity of the two best isolates, MTD11C and MTD11E, identified as strains of Brevundimonas naejangsanensis and Staphylococcus arlettae, exhibited a mercury removal capacity of 99.74% and 99.56 %, respectively. As per our research, such extreme tolerance to mercury as demonstrated by the bacterial strains has not been reported thus far. The prevalence of such tolerance in the microbiota of a region may well be an indication of the degree of mercury pollution harbored by it. Their tolerance to other heavy metals and antibiotics, as well as active plant growth promotion traits, were also characterized in this study. The topsoil of this region was estimated to contain elevated levels of mercury at around 0.52-2.39mgkg-1. Ecological risk assessment further showed the potential for harm to the environment posed by the level of mercury. Collected vegetation samples from tea plantations surrounding Tiger Hill displayed an accumulation of mercury in the leaves and roots of the tea plants as well, suggesting rampant mercury pollution that needs to be addressed.

Characteristics of the Bacterial Community in Alpine Meadows in Response to Altitude and Aspect in the Qilian Mountains, Northwest China.

As one of the most sensitive and fragile alpine ecosystems in the Qilian Mountains, the alpine meadow holds significant scientific importance in understanding the changes in the characteristics of soil bacterial community in response to altitude and aspect variations. In our study, we analyzed the composition, diversity, and function of soil bacterial communities in alpine meadows at different altitudes and aspects and their relationship with environmental factors. Our results indicate that altitude and aspect orientation significantly influences the diversity index and composition of soil bacterial communities. Specifically, the Shannon and Chao1 indices of soil bacteria initially increased and then decreased with increasing altitude, with the Shannon index being lower in shady aspects compared to sunny aspects, and the Chao1 index being lower in sunny aspects above an altitude of 3400 m compared to shady aspects at the exact altitudes. Using Linear Discriminant Analysis Effect Size analysis, we identified 77 bacterial species in the research area, with key ecological functions primarily associated with nitrification, aerobic ammonia oxidation, and chitinolysis. Furthermore, we found that soil water content and Urease were the main factors influencing bacterial community composition. Our findings underscore the significant impact of altitude orientation on bacterial communities in alpine grasslands, emphasizing the importance of considering bacterial differences in evaluating alpine grassland health.

A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.

Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.

Composition and functional diversity of soil and water microbial communities in the rice-crab symbiosis system.

Rice-crab co-culture is an environmentally friendly agricultural and aquaculture technology with high economic and ecological value. In order to clarify the structure and function of soil and water microbial communities in the rice-crab symbiosis system, the standard rice-crab field with a ring groove was used as the research object. High-throughput sequencing was performed with rice field water samples to analyze the species and abundance differences of soil bacteria and fungi. The results showed that the OTU richness and community diversity in soil were significantly higher than those in water, while there were significant differences in soil microbial diversity and OTU richness in water sediments. The dominant species at the bacterial phylum level were Amoebacteria, Cyanobacteria, Actinomycetes, Synechococcus and Greenbacteria, and at the genus level the dominant species were norank_f_norank_o_Chloroplast, unclassified_f_Rhodobacteraceae, LD29, Cyanobium_PCC-6307, and norank_f_MWH-UniP1_aquatic_group. The dominant species at the fungal phylum level are unclassified_k_Fungi, Ascomycota, Rozellomycota, Phaeomycota and Stenotrophomonas, and at the genus level the dominant species are unclassified_k_Fungi, unclassified_p_Rozellomycota, Metschnikowia, Cladosporium, unclassified_p_Chytridiomycota. The dominant phylum may rely on mechanisms such as organic matter catabolism, secretion of secondary metabolites and phototrophic autotrophy, as predicted by functional gene analysis. The main functional genes are related to metabolic functions, including secondary product metabolism, energy metabolism, and amino acid metabolism.

A single-plasmid-based, easily curable CRISPR/Cas9 system for rapid, iterative genome editing in Pseudomonas putida KT2440

BackgroundPseudomonas putida KT2440, a non-pathogenic soil bacterium, is a key platform strain in synthetic biology and industrial applications due to its robustness and metabolic versatility. Various systems have been developed for genome editing in P. putida, including transposon modules, integrative plasmids, recombineering systems, and CRISPR/Cas systems. However, rapid iterative genome editing is limited by complex and lengthy processes.ResultsWe discovered that the pBBR1MCS2 plasmid carrying the CRISPR/Cas9 module could be easily cured in P. putida KT2440 at 30 oC. We then developed an all-in-one CRISPR/Cas9 system for yqhD and ech-vdh-fcs deletions, respectively, and further optimized the editing efficiency by varying homology arm lengths and target sites. Sequential gene deletions of vdh and vanAB were carried out rapidly using single-round processing and easy plasmid curing. This system’s user-friendliness was validated by 3 researchers from two labs for 9 deletions, 3 substitutions, and 2 insertions. Finally, iterative genome editing was used to engineer P. putida for valencene biosynthesis, achieving a 10-fold increase in yield.ConclusionsWe developed and applied a rapid all-in-one plasmid CRISPR/Cas9 system for genome editing in P. putida. This system requires less than 1.5 days for one edit due to simplified plasmid construction, electroporation and curing processes, thus accelerating the cycle of genome editing. To our knowledge, this is the fastest iterative genome editing system for P. putida. Using this system, we rapidly engineered P. putida for valencene biosynthesis for the first time, showcasing the system’s potential for expanding biotechnological applications.

Effect of Temperature on the Biodegradation of Glyphosate by Soil Bacteria

Glyphosate, a broad-spectrum systemic herbicide, is widely used in agriculture to control weeds. Its extensive use has raised concerns about its environmental impact and persistence in ecosystems. Understanding the biodegradation of glyphosate is crucial for evaluating its long-term effects and developing effective remediation strategies. Biodegradation is the process by which microorganisms break down substances and plays a vital role in mitigating the accumulation of harmful compounds in the environment. Therefore, this study investigates the effect of temperature on glyphosate degradation by soil bacteria, which is crucial for understanding its breakdown in soil ecosystems. Soil bacteria have shown potential in degrading glyphosate, but the impact of temperature remains understudied. The research aims to study the effect of temperature conditions on glyphosate degradation by soil bacteria. Soil samples were collected from Mardi Bachok, Kelantan, and their coordinates, pH, and temperature were recorded. Soil samples were incubated in Mineral Salts Medium (MSM) containing 100 mg/L glyphosate at 28°C and 37°C for seven days, with optical density measured every 24 hours. Both temperature treatments showed microbial communities capable of thriving in glyphosate-supplemented MSM, utilizing it as a sole carbon and phosphate source. Statistical analysis revealed no significant difference in microbial growth between the two temperatures. These results suggest that soil bacteria are capable of thriving in a range of temperature conditions while effectively degrading glyphosate. Understanding these dynamics is essential for developing effective bioremediation strategies and predicting the environmental fate of glyphosate in various climatic conditions. Future research should explore additional environmental factors and microbial interactions to further elucidate the complexities of glyphosate biodegradation in soil ecosystems.

Microbial diversity and biogeochemical interactions in the seismically active and CO2- rich Eger Rift ecosystem.

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2 concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2 during earthquakes may provide substrates for methanogenic and chemolithoautotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 238m deep drill core, running across six lithostratigraphic zones. We evaluated the diversity and distribution of bacterial and archaeal communities. Our investigation revealed a distinct low-biomass community, with a surprisingly diverse archaeal population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis demonstrated that ion concentrations (mostly sodium and sulfate) were highest in sediments from 50 to 100m depth and in weathered rock below 200m, indicating an elevated potential for ion solution in these areas. Microbial communities were dominated by common soil and water bacteria. Together with the occurrence of freshwater cyanobacteria at specific depths, these observations emphasize the heterogenous character of the sediments and are indicators for vertical groundwater movement across the Eger Rift subsurface. Our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur-cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100m. The detection of methanogenic, halophilic, and ammonia-oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2 and, when available, H2, as a primary energy source.

Influence of Mikania micrantha Kunth Flavonoids on Composition of Soil Microbial Community

Mikania micrantha, one of the world’s most destructive invasive species, is known for causing significant ecological and economic harm. While extensive research has focused on its growth characteristics, secondary metabolites, and control measures, its chemical interactions with the environment—particularly the role of flavonoids in shaping soil microbial communities—remain underexplored. In this study, we identified and quantified ten flavonoids from M. micrantha root exudates using UPLC-MS, including Hispidulin, Isorhamnetin, and Mikanin. To examine their impact, crude flavonoid extracts were applied to soil in potted experiments, which demonstrated that these compounds significantly increased soil fungal diversity and boosted the relative abundance of arbuscular mycorrhizal fungi (AMF). Furthermore, KEGG pathway analysis revealed that flavonoid addition elevated the copy numbers of genes involved in nitrogen cycling and metabolic functions, enhancing nutrient availability and microbial activity. Additionally, crude flavonoid extracts promoted the relative abundance of beneficial soil bacteria, such as Achromobacter, as well as AMF, both of which contribute to nutrient acquisition, plant growth, and soil health. These findings indicate that M. micrantha’s flavonoids can alter soil microbial community composition, thereby creating a favorable environment that reinforces its competitive edge over native plants.