Soil Community Research Articles

Microbiome associated to an H2-emitting zone in the São Francisco basin Brazil

BackgroundDihydrogen (H₂) natural gas is a clean and renewable energy source of significant interest in the transition to sustainable energy. Unlike conventional petroleum-based fuels, H₂ releases only water vapor upon combustion, making it a promising alternative for reducing carbon footprints in the future. However, the microbial impact on H₂ dynamics in H2-emitting zones remains unclear, as does the origin of H2 — whether it is produced at greater depths or within shallow soil layers. In the São Francisco Basin, soil hydrogen concentrations of approximately 200 ppm were identified in barren ground depressions. In this study, we investigated the microbiome associated with this area using the 16S rRNA gene sequencing, with a focus on metabolic processes related to H₂ consumption and production. Soil samples were collected from two monitored (< 1 m) depths – 10 cm and 1 m – in the emission zone, which is predominantly covered with pasture vegetation, and from an adjacent area with medium and small trees.ResultsOur findings suggest that the H2-emitting zone significantly influences the composition and function of the microbiome, with Bacillus emerging as the dominant genus. In contrast to typical Cerrado soil, we observed a higher prevalence of Actinobacteriota (∼ 40%) and Firmicutes (∼ 20%). Additionally, we identified an abundance of sporulating bacteria and taxonomic groups previously described as H2-oxidizing bacteria.ConclusionsThe H2-emitting zone in the São Francisco Basin presents a unique opportunity to deepen our understanding of the impact of H₂ on microbial communities. This study is the first to characterize a natural H2-associated bacterial community in Cerrado soil using a culture-independent approach.

Ключ для определения накипных лишайников семейства Teloschistaceae в напочвенных сообществах на территории России

Here we provide a key for the identification of 39 crustose Teloschistaceae species in soil communities in Russia growing on soil, bryophytes, plant debris, twigs of small shrubs, and on thalli of other lichens.

Short-term effects of co-applied biochar and paper mill biosolids on soil microbial communities under field conditions

Biochar and paper mill biosolids (PB) are reported to improve soil fertility, crop growth and indirectly conditions for soil microbial communities. However, it is unclear how the co-application of these materials impacts soil microbial communities under field conditions. A study was initiated in 2018 in Québec, QC, Canada and fine roots and rhizosphere soil were sampled to determine the effects of co-application of wood biochar (0, 10, and 20 Mg dry wt. ha−1) and PB (0 and 30 Mg wet wt. ha−1) on the percentage of corn (Zea mays L.) and soybean (Glycine max L. Merr.) root colonization by arbuscular mycorrhizal fungi (AMF), soil microbial biomass phosphorus (MBP) and microbial (Bacteria, Fungi and AMF) diversity and community structure in a temperate loamy soil. Co-applying PB and biochar increased soil MBP compared with the control and biochar-only application. Applying PB alone or with biochar increased the level of root colonization by AMF compared with the control and biochar-only application in soybean but not in corn. Overall, biochar and PB application had no significant effect on bacterial and AMF diversity and community structure compared with the control. However, applying PB alone or with biochar decreased the fungal alpha diversity (Shannon and Simpson indices), affected several fungal taxa abundances and shifted the fungal community structure as indicated by the principal coordination analysis (PCoA). Our results provided an understanding on the short-term effects of co-applied wood biochar and PB on microbial communities of a temperate loamy soil under field conditions, as well as scientific bases for further investigation.

Zooming in on the temporal dimensions of plant–soil feedback: Plant sensitivity and microbial dynamics

Abstract The magnitude of plant–soil feedback (PSF) can depend on the time of conditioning as well as the length of feedback. Understanding the temporal variation in PSF requires insight in the response of both soil characteristics and the plant. We examined how conspecific PSF varies with the length of conditioning and the size of the response plant using Jacobaea vulgaris, a species known to experience negative conspecific PSF. Together with reanalysis of an existing microbial sequence dataset, we tested whether the temporal variation in PSF is due to size‐dependent plant sensitivity to conditioned soil or due to compositional changes in microbial communities of conditioned soil. Further, by reanalysing another existing dataset, we examined temporal dynamics of the relative growth rates (RGR) of J. vulgaris during the feedback phase. Testing varying conditioning lengths, uncovered that J. vulgaris exhibited the strongest negative PSF at 5 weeks of conditioning, after which PSF gradually attenuated. Plant sensitivity to conditioned soil decreased with increasing plant age/size of the response plant. In the feedback phase, the RGR of J. vulgaris was first higher, then lower and at the end similar in ‘away’ soil compared to ‘home’ soil. The dissimilarity in bacterial and fungal communities in ‘home’ and ‘away’ soil significantly decreased during the feedback phase. When J. vulgaris grew in ‘away’ soil, the relative abundance of 10 (out of 80) bacterial OTUs that positively correlated with plant growth decreased over time, while 5 (out of 86) OTUs that negatively correlated with plant growth the relative abundance increased over time. Additionally, only one (out of 10) fungal OTU that negatively associated with plant growth increased over time in ‘away’ soil. Synthesis. Our findings illustrate that PSF varies with the duration of soil conditioning and of the feedback phase. During the feedback phase, changes in PSF can be attributed to both the size‐dependent plant sensitivity to conditioned soil and temporal changes in the microbial community of conditioned soil. This highlights the importance of considering the reconditioning of soil microbial communities by the test plants during the feedback phase for understanding temporal variation in PSF.

The Process of Soil Carbon Sequestration in Different Ecological Zones of Qingtu Lake in the Arid–Semi-Arid Region of Western China

As a vital component of the global carbon pool, soils in arid and semi-arid regions play a significant role in carbon sequestration. In the context of global warming, increasing temperatures and moisture levels promote the transformation of barren land into wetlands, enhancing carbon sinks. However, the overdevelopment of oases and excessive extraction of groundwater lead to the opposite effect, reducing carbon sequestration. This study examines two soil types—meadow soil (MS) and swamp soil (SS)—from Qingtu Lake, an arid lake in western China. It analyzes the sources of soil inorganic carbon, the composition and origin of dissolved organic matter (DOM), and the relationships between microbes, soil organic carbon (SOC), soil inorganic carbon (SIC), mineral composition, and soil texture. The results indicate that inorganic carbon in the study area consists of both primary carbonate minerals and secondary pedogenic carbonates. The DOM primarily consists of two components, both identified as terrestrial humic substances. In meadow soils, bacterial activity drives the weathering of plagioclase, which releases Ca2+ necessary for the formation of pedogenic carbonates. Plagioclase also provides colonization sites for microbes and, along with microbial activity, participates in the soil carbon cycle. Within the soil community, bacteria appear to play a more critical role than fungi. In contrast, microbial contributions to the carbon cycle in swamp soils are weaker, with minerals predominantly interacting with organic carbon to form mineral-associated organic matter, thus promoting the soil carbon cycle. These findings have important implications for understanding soil carbon sinks under different micro-ecological conditions in arid and semi-arid regions. Through targeted human intervention, it is possible to enhance carbon sequestration in these areas, contributing to the mitigation of global climate change.

The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil.

Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.

Applying Systems Thinking to Sustainable Beef Production Management: Modeling-Based Evidence for Enhancing Ecosystem Services

We used systems thinking (ST) to identify the critical components of beef cattle production through the lens of ecosystem services (ES), offering a holistic approach to address its adverse externalities. We identified eight critical feedback loops in beef production systems: (i) grazing and soil health, (ii) manure management and soil fertility, (iii) feed efficiency and meat production, (iv) water use and soil moisture, (v) cultural services and community engagement, (vi) energy use, (vii) carbon sequestration and climate regulation, and (viii) environmental impact. Our analysis reveals how these interconnected loops influence each other, demonstrating the complex nature of beef production systems. The dynamic hypothesis identified through the loops indicated that improved grazing and manure management practices enhance soil health, leading to better vegetation growth and cattle nutrition, which, in turn, have a positive impact on economic returns to producers and society, all of which encourage the continuation of interlinked beef and ecosystem stewardship practices. The management of beef production ES using ST might help cattle systems across the globe to contribute to 9 of the 17 different United Nations’ Sustainable Development Goals, including the “zero hunger” and “climate action” goals. We discussed the evaluation framework for agrifood systems developed by the economics of ecosystems and biodiversity to illustrate how ST in beef cattle systems could be harnessed to simultaneously achieve the intended environmental, economic, social, and health impacts of beef cattle systems. Our analysis of the literature for modeling and empirical case studies indicates that ST can reveal hidden feedback loops and interactions overlooked by traditional practices, leading to more sustainable beef cattle production outcomes. ST offers a robust framework for enhancing ES in beef cattle production by recognizing the interconnectedness of ecological and agricultural systems, enabling policymakers and managers to develop more effective and sustainable strategies that ensure the long-term health and resilience of humans and ES.

Shift of bacterial and fungal communities upon soil amelioration is driven by carbon degradability of organic amendments

The structural response of bacterial and fungal soil communities to four carbon-rich organic amendments of increasing recalcitrance was investigated. Wheat straw, green compost, a mixed product based on biogas residues, and a fermented biochar were applied to a sandy agricultural soil of low organic carbon content. After laboratory incubation for 6 months, the community structure was investigated via DNA sequencing. All amendments caused changes in the communities of bacteria and fungi, but to different extents, with the communities exposed to more recalcitrant amendments showing the least variation compared to the non-amended soil. Changes in species composition as well as their relative abundances were observed. While the straw had a pronounced effect on bacteria (e.g., the highest number of indicator species), effects of the composted, fermented, or pyrolyzed materials were minor. Hierarchical clustering showed that the fungal communities were more different from each other than the bacterial ones with the straw-soil being most different and the biochar-soil least different from the non-amended soil. While the abundant fungal species in biochar-soil and non-amended soil were very alike, especially rare fungal species shifted upon addition of biochar. An indicator species analysis identified specific taxonomic groups which were triggered by the different organic materials. We conclude that bacterial and fungal communities strongly change upon input of degradable carbon (straw), while fungi in particular respond to the application of processed organic materials. With this study, we report the consequences of applying organic materials for the microbial community in one soil. We provide these data for meta-analyses that are required to unravel all relevant interactions across different soils, organic materials, and time. This will allow to better understand and predict the effects of organic soil amelioration measures on soil microorganisms.

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions.

Effects of warming and fertilization on nirK-, nirS- and nosZ-type denitrifier communities in paddy soil

The effects of fertilization on soil denitrifying microorganisms are well-documented. However, the impact of global warming on these microorganisms, particularly regarding the interaction with fertilization, remains poorly understood. Here, a 4-year field warming experiment that included experimental warming (ET) and ambient temperature control (AC), with nitrogen (N) fertilizer applied (CF) or without N fertilizer (CK), was employed to assess the response of the abundance and community of nirK-, nirS- and nosZ- type denitrifiers to warming and fertilization in paddies, and to understand their relationship with potential denitrification rate (PDR). The results showed that warming amplified the positive effect of fertilization on abundance of nirK and nirS genes, while the abundance of nosZ remained unaffected. The copies of nirK and nirS under the ET-CF treatment were notably higher than in the other treatments. In the terms of biodiversity, warming diminished the effect of fertilization on the α-diversity of nirK and nirS, but it did not influence the α-diversity of nosZ. Besides, warming intensified the effect of fertilization on the β-diversity of nirK, while the β-diversity of nirS and nosZ remained unchanged in response to fertilization. Additionally, the community structure of denitrifiers varied with warming and/or fertilization. Specifically, Mesorhizobium (nirK), Proteobacteria (nirS) and Rhizobiales (nosZ) were dominant in AC-CK treatment. In the AC-CF treatment, Proteobacteria (nirK/S), Rhizobiales (nosZ) were the main taxa. For the ET treatments (ET-CF, ET-CK), Bradyrhizobiaceae (nirK), Proteobacteria (nirS) and Alphaproteobacteria (nosZ) were predominant. Correlation analysis revealed that soil pH, carbon and N content were the primary factors influencing nirK-, nirS-and nosZ- type denitrifiers. Moreover, PDR showed a positive relationship with nirK abundance, α-diversity of nosZ, and SOC. Overall, the results demonstrate that warming can modify the response of denitrifiers to fertilization, subsequently affecting denitrification rates, a phenomenon that merits attention.

Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

BackgroundUnderstanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome are unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: (i) crop yields; (ii) disease development (blackleg or common scab); and (iii) soil microbial community dynamics.MethodsWe used stocks of seed potatoes with varying natural levels of Pectobacterium (Jelly [high load], Jelly [low load] and Estima [Zero – no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and at harvest. Generalised linear latent variable models and an annotation-free mathematical framework approach (ensemble quotient analysis) were then used to show the interacting microbes with irrigation regime and Pectobacterium pathogen levels.ResultsIrrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22–34%) but not in the zero stock (2–6%). However, withholding irrigation increased common scab symptoms (2–5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted the Anaerolinea taxa were highly associated with high levels of Pectobacterium in the seed stock and blackleg symptoms in the field.ConclusionsWe conclude that planting seed stocks with a high Pectobacterium burden alters the abundance of specific microbial species within the soil microbiome and suggest that managing pathogen load in seed stocks could substantially affect soil communities, affecting crop health and productivity.BWvw4eepooU5poSUC2MUy8Video

Revealing the characteristics of myxobacterial communities in rhizosphere and non-rhizosphere soils of halophytic plants following wetland degradation using high-throughput sequencing

Myxobacteria represent a distinct group in soil microbial communities, with their predatory capabilities playing a vital role in regulating and stabilizing these communities. However, the characteristics of myxobacterial communities in the soils of Karelinia caspia (KC), a halophytic plant growing in degraded wetlands, remain unclear. In this study, we investigated myxobacterial communities in rhizosphere and non-rhizosphere soils from nine KC’ sampling sites in saline-alkaline land formed after wetland degradation using high-throughput sequencing. A total of 486 myxobacterial ASVs were identified from both rhizosphere and non-rhizosphere soil samples, comprising 2.68% of the total bacterial community. The dominant genera at the genus level were Unclassified_g_bacteriap25 and Haliangium. FAPROTAX functional predictions indicated that myxobacteria in rhizosphere soils performed various ecological functions, such as predation, organic matter decomposition, and cellulose degradation, while in non-rhizosphere soils, they primarily displayed predatory functions. The high proportion of unclassified functions suggests that many aspects of myxobacteria in soil remain unexplored. Correlation analysis showed that electrical conductivity, soil moisture, and total nitrogen significantly affected myxobacterial diversity and abundance. Co-occurrence network analysis revealed multiple associations between myxobacteria and other bacterial groups, highlighting their crucial role in maintaining the dynamic equilibrium of soil bacterial communities. These findings deepen our understanding of the relationship between microbial community dynamics and environmental factors, laying a strong foundation for future research in soil microbial ecology and conservation strategies.

Study on the Changes in the Microbial Community in Rhizosphere Soil of Blueberry Plants at Different Growth Stages

In order to clarify the relationship between mineral nutrients and rhizosphere microorganisms at different growth and development stages of blueberry (Vaccinium spp.), this work studied the dynamic changes in element content and microbial quantity in different parts of blueberry plants. The test material was a 12-year-old half-highbush blueberry variety (‘Beilu’). The changes in the mineral nutrient elements in leaves, branches and the soil of blueberry plants were studied at the full bloom stage (T1), green fruit stage (T2), mature stage (T3) and late mature stage (T4), and the correlations of the average contents of mineral elements in the four periods were studied. The bacterial community in the rhizosphere soil was determined and analyzed using 16S rRNA high-throughput sequencing technology. The results showed that the changes in other mineral elements in various parts of blueberry plants varied in different periods. Nitrogen (N) showed a downward trend in branches, leaves and soil, especially in leaves (p &lt; 0.05). The N contents in T2, T3 and T4 decreased by 9.9%, 26.4% and 29.9%, respectively. The N contents in the leaves and branches showed a downward trend at different growth stages, especially in leaves. The phosphorus (P) content in leaves showed a trend of increasing first and then decreasing, while it continued to increase in branches. The content of potassium (K) in leaves changed significantly, where it increased first and then decreased. The content of calcium (Ca) in leaves decreased first and then increased, while the content of magnesium (Mg) in branches and leaves decreased first and then increased, and the relative change was significant. The contents of iron (Fe) and zinc (Zn) in leaves decreased first and then increased, while the contents of manganese (Mn) and copper (Cu) were relatively stable. Cu decreased first and then increased in leaves and soil, and it increased first and then decreased in branches. The mineral nutrients in different growth stages of blueberry showed significant correlation in leaves, branches and soil. Mn in leaves was significantly positively correlated with P, Ca, Mg, Mn, Cu and Zn in soil (p &lt; 0.01). Nitrogen and calcium in leaves were significantly correlated with manganese and phosphorus in soil, respectively. Ca in branches was significantly positively correlated with N and K in soil and was significantly positively correlated with Zn in soil (p &lt; 0.01). Magnesium was significantly negatively correlated with iron in soil. The bacterial community structure of the blueberry rhizosphere soil changed significantly over time (p &lt; 0.05), and the relative abundance showed the following trend: T4 &gt; T2 &gt; T3 &gt; T1. At the phylum level, Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi and Verrucomicrobia were the dominant bacteria in different periods. Candidatus solibacter and Bryobacter were significantly higher in T1 and T3 than in T1 and T4. Bradyrhizobium flora increased significantly at T3. Sphingomonas increased significantly at T1 (p &lt; 0.05).

The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent

BackgroundIn addition to their role as endosymbionts for plant roots, arbuscular mycorrhizal fungi (AMF) engage in complex interactions with various soil microorganisms, the rhizosphere, and the root endosphere of host plants. They also host diverse prokaryotic groups within their mycelia, contributing to what is termed multipartite symbiosis. In this study, we examined the impact of three AMF species—Rhizophagus irregularis, R. clarus, and R. cerebriforme—combined with microbial bioaugmentation on the diversity and composition of bacterial communities in the mycelia and hyphosphere. Using a microcosm design to separate the influence of host plant roots from AMF mycelia and Illumina MiSeq amplicon sequencing to analyze the bacterial communities.ResultsOur results revealed that, while AMF identity and microbial bioaugmentation did not affect the structure of bacterial communities in the hyphosphere soil, they significantly altered the communities associated with their mycelia. Although all three AMF species belong to the same genus, with R. irregularis and R. clarus being closely related compared to R. cerebriforme, we observed variations in the bacterial communities associated with their mycelia. Interestingly, the mycelial bacterial community of R. cerebriforme contained 60 bacteriome core taxa exclusive to it, while R. clarus and R. irregularis had 25 and 9 exclusive taxa, respectively.ConclusionThis study suggests that organismal phylogeny influences the bacterial communities associated with AMF mycelia. These findings provide new insights into AMF and bacterial interactions, which are crucial for the successful deployment of AMF inoculants. The taxonomic diversity of AMF inoculants is important for engineering the plant microbiome and enhancing ecosystem services.

Soil animal communities demonstrate simplification without homogenization along an urban gradient.

Urbanization profoundly impacts biodiversity and ecosystem function, exerting an immense ecological filter on the flora and fauna that inhabit it, oftentimes leading to simplistic and homogenous ecological communities. However, the response of soil animal communities to urbanization remains underexplored, and it is unknown whether their response to urbanization is like that of aboveground organisms. This study investigated the influence of urbanization on soil animal communities in 40 public parks along an urbanization gradient. We evaluated soil animal abundance, diversity, and community composition and related these measures to urban and soil characteristics at each park. The most urbanized parks exhibited reduced animal abundance, richness, and Shannon diversity. These changes were influenced by many variables underscoring the multifaceted influence of urbanization on ecological communities. Notably, contrary to our expectation, urbanization did not lead to community homogenization; instead, it acted stochastically, creating unique soil animal assemblages. This suggests that urban soil animal communities are concomitantly shaped by deterministic and stochastic ecological processes in urban areas. Our study highlights the intricate interplay between urbanization and soil animal ecology, challenging the notion of urban homogenization in belowground ecosystems and providing insight for managing and preserving belowground communities in urban areas.

Elevated Atmospheric Co2 Levels Impact Soil Protist Functional Core Community Compositions

Protists, known as microeukaryotes, are a significant portion of soil microbial communities. They are crucial predators of bacteria and depend on bacterial community dynamics for the growth and evolution of protistan communities. In parallel, increased levels of atmospheric CO2 significantly impact bacterial metabolic activity in rhizosphere soils. In this study, we investigated the effect of elevated atmospheric CO2 levels on the metabolically active protist community composition and function and their co-occurrences with bacteria from bulk and rhizosphere soils from the Giessen Free-Air CO2 enrichment grassland experiment. Metabarcoding sequencing data analyses of partial 18S rRNA from total soil RNA showed that elevated CO2 concentrations stimulated only a few ASVs of phagotrophic predators of bacteria and other microeukaryotes, affecting protist community composition (P = 0.006, PERMANOVA). In parallel, phagotrophic and parasitic lineages appeared slightly favoured under ambient CO2 conditions, results that were corroborated by microbial signature analyses. Cross-comparisons of protist-bacteria co-occurrences showed mostly negative relations between prokaryotes and microeukaryotes, indicating that the ongoing increase in atmospheric CO2 will lead to changes in microbial soil communities and their interactions, potentially cascading to higher trophic levels in soil systems.

Dispersal of microbes from grassland fire smoke to soils.

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of fields including agriculture, restoration, plant disease, and biodiversity.

Semiconducting minerals participated extracellular electron transfer in red soil of Ningxia Plain, China

In recent years, exploring interactions between sunlight, semiconducting minerals and microorganisms in nature has attracted great attention. However, relatively little research has been conducted on the interaction between minerals and microorganisms in the plain areas of the Yellow River Basin under sunlight. In this study, the mineral composition and microbial community of red soil from the Ningxia Plain, China were analyzed. X–ray diffraction (XRD) results showed that red soil contained semiconducting minerals such as birnessite, hematite and goethite. 16S rRNA analysis found that electroactive microorganisms such as Proteobacteria, Firmicutes and Actinobacteriota were enriched in in–situ microbial community of red soil. Afterwards, electrochemical tests such as linear sweep voltammetry (LSV) and I–t curves, indicated that red soil exhibited good semiconducting properties under light irradiation. Finally, a dual chamber system and electrochemical techniques were used to explore the electron transfer relationship between red soil and microorganisms. The open circuit voltage (350 mV) and maximum power density (1242.72 mW/m2) of red soil cathode system were significantly improved compared to blank graphite electrode, indicating that red soil could serve as electron acceptors for microbial extracellular respiration. Red soil electrode in live bacteria exhibited the highest photocurrent density (0.29 μA/cm2) and the lowest charge transfer resistance (Rct) (223 Ω) under light conditions, indicating that red soil accelerated the rapid transfer of electrons, reduced polarization loss, and enhanced extracellular electron transfer (EET) process under light conditions. This study demonstrated that the participation of semiconducting minerals in microbial EET processes under sunlight in the Ningxia Plain, China.

Assessment of Chinese Medicinal Herbal Wastes Compost Inoculated with Antagonistic Fungi: Nitrogen Retention and Microbial Community in Phytopathogenic Soil

Assessment of Chinese Medicinal Herbal Wastes Compost Inoculated with Antagonistic Fungi: Nitrogen Retention and Microbial Community in Phytopathogenic Soil

Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland

Background The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem. Methods High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure. Results S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors. Conclusions Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.