Soil Microbes Research Articles

MicroRNA399s and strigolactones mediate systemic phosphate signaling between dodder‐connected host plants and control association of host plants with rhizosphere microbes

Summary A dodder (Cuscuta) often simultaneously parasitizes two or more adjacent hosts. Phosphate (Pi) deficiency is a common stress for plants, and plants often interact with soil microbes, including arbuscular mycorrhizal fungi (AMF), to cope with Pi stress. Little is known about whether dodder transmits Pi deficiency‐induced systemic signals between different hosts. In this study, dodder‐connected plant clusters, each composed of two tobacco (Nicotiana tabacum) plants connected by a dodder, were established, and in each cluster, one of the two tobacco plants was treated with Pi starvation. AMF colonization efficiency, rhizosphere bacterial community, and transcriptome were analyzed in the other dodder‐connected Pi‐replete tobacco plant to study the functions of interplant Pi signals. We found that dodder transfers Pi starvation‐induced systemic signals between host plants, resulting in enhanced AMF colonization, changes of rhizosphere bacterial communities, and alteration of transcriptomes in the roots of Pi‐replete plants. Importantly, genetic analyses indicated that microRNA399s (miR399s) and strigolactones suppress the systemic Pi signals and negatively affect AMF colonization in the Pi‐replete plants. These findings provide new insight into the ecological role of dodder in mediating host–host and host–microbe interactions and highlight the importance of strigolactone and miR399 pathways in systemic Pi signaling.

Isolation and characterization of halophilic Bacillus thuringiensis from local Egyptian sites and their potential against Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)

Abstract Background Bacillus thuringiensis (Bt) serves as a peculiar soil microbe that is Gram-positive, rod-shaped, spore-forming, and aerobic facultative. It endures across a range of conditions and has been demonstrated to be an effective biological pest control agent against several insect pests. The main objective of the study is to isolate and recognize Bt bacteria from saline environments in Egyptian soil for biological surveillance uses. Results Isolates three, four, five, ten, eleven, twelve, and thirteen were found to be moderately tolerant, while isolate eight showed highly tolerant, but isolate six was found to be borderline extreme halophile. On the other hand, the other isolates showed extreme halophiles. To find out the presence of crystals, a scanning electron microscope was carried out and the result showed that the crystals ranged from spherical to bi-pyramidal spherical. Molecular analysis was carried out using universal primers to confirm the presence of cry genes. The results showed that 84.6% of the isolates contain cry seven and eight, whereas cry one and four are distributed by 92.3%. Cry two genes were found to be 100 percent in all tested and isolated cultures. Cry genes were present and distribution among isolated was detected using gene-specific primers. cry3Ba1 and cry8B showed the lowest and equal distribution among the isolates, while the cry2Ab2gene frequency distribution was (84.6%) among isolated cultures. Around six cry genes were found to be absent in all isolated cultures. The bioinsecticidal activity and bioassays were carried out to check the potential effect of halophilic Bt isolates against 1st instar larvae of the Fall Armyworm (FAW) Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae). Mortality was calculated after infecting S. frugiperda with thirteen Bt isolates. The most virulent Bt isolate was isolate 7, followed by isolate 10, with LC50 values of 9.542 × 107 spores/ml and 1.289 × 108 spores/ml, respectively, after 72 h. Morphological traits of the larvae were carried out, to check the effect of Bt isolates as a biological control against the FAW. Conclusion To protect and enhance the sustainability of field crops and vegetables, especially in new high salinity lands, from disease-causing insects such as FAW, it is necessary to identify new strains of Bt from these saline lands. In this field, local isolates of Bt from several regions in Egypt known for their high levels of salinity were documented and showed an effective bioinsecticide on FAW larvae.

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.

Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects. Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants. Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.

Investigating the Effects of Elevation on Microbial Communities and Soil Properties at Fanjing Mountain, China

Elevation is one of the most influential factors affecting soil characteristics and microbial communities in forest ecosystems. Nevertheless, there is no consensus on how soil characteristics, soil microbials, and their relationships response to the elevation of the mountain ecosystem. We investigated the soil physicochemical characteristics, the activity of soil enzymes, and the microbial community at elevational sites from 600 to 2400 m above sea level (asl) in the western slopes of the Fanjing Mountain ecosystem, China. The soil microbial communities were determined by high throughput 16S rRNA and ITS amplicon sequencing. The results demonstrated that soil total nitrogen (TN) showed a slight decrease, whereas total phosphorus (TP) and total potassium (TK) gradually tended to increase with increasing elevation. The large macroaggregates (>2 mm) accounted for the largest proportion of the aggregate fraction (66.23%–76.13%) in the 0–10 cm soil layer with elevation. The average values of the soil electrical conductivity (EC), soil organic carbon (SOC), and cation exchange capacity (CEC) concentration in the 0–60 cm layer undulated with increasing elevation, and the highest values were observed at 1500–1800 m asl and 1800–2100 m asl, respectively. The activities of soil urease, sucrase, acid phosphatase, and catalase clearly differed (p < 0.05) with increasing elevation, and the minimum values were found at 2100–2400 m asl. Interesting, with increasing soil depth, the values of these factors tended to decrease, indicating surface aggregation. In addition, the soil microbial (bacterial and fungal) community diversity exhibited a single-peak pattern with elevation. Our results also revealed that the soil bacterial and fungal communities varied significantly at different elevation sites. The bacterial communities were dominated by the phyla Acidobacteria, Pseudomonadota, and Chloroflexi, and the phyla Basidiomycota and Ascomycota dominated the fungal communities. The Pearson and redundancy analyses revealed that the SOC, TP, four soil enzymes, and soil aggregates were significant factors influencing the soil microbial community. In conclusion, soil properties and enzyme activities jointly explained the elevational pattern of the soil microbial community in the Fanjing Mountain. The results of this study provide insights into the influence of elevation on soil characteristics, microbial communities, and their relationships in the Fanjing Mountain ecosystem.

Microbial community structure in recovering forests of Mount St. Helens

IntroductionThe 1980 eruption of Mount St. Helens had devastating effects above and belowground in forested montane ecosystems, including the burial and destruction of soil microbes. Soil microbial propagules and legacies in recovering ecosystems are important for determining post-disturbance successional trajectories. Soil microorganisms regulate nutrient cycling, interact with many other organisms, and therefore may support successional pathways and complementary ecosystem functions, even in harsh conditions. Historic forest management methods, such as old-growth and clearcut regimes, and locations of small mammal enclo and clearcut forests, as well as in locations of historic short-term gopher enclosures (Thomomys talpoides), to evaluate community response to forest management practices and to examine vectors for dispersing microbial consortia to the surface of the volcanic landscape. These biotic interactions may have primed ecological succession in the volcanic landscape, specifically Bear Meadow and the Pumice Plain, by creating microsite conditions conducive to primary succession and plant establishment.Methods and resultsUsing molecular techniques, we examined bacterial, fungal, and AMF communities to determine how these variables affected microbial communities and soil properties. We found that bacterial/archaeal 16S, fungal ITS2, and AMF SSU community composition varied among forestry practices and across sites with long-term lupine plots and gopher enclosures. The findings also related to detected differences in C and N concentrations and ratios in soil from our study sites. Fungal communities from previously clearcut locations were less diverse than in gopher plots within the Pumice Plain. Yet, clearcut meadows harbored fewer ancestral AM fungal taxa than were found within the old-growth forest.DiscussionBy investigating both forestry practices and mammals in microbial dispersal, we evaluated how these interactions may have promoted revegetation and ecological succession within the Pumice Plains of Mount St. Helens. In addition to providing evidence about how dispersal vectors and forest structure influence post-eruption soil microbiomes, this project also informs research and management communities about belowground processes and microbial functional traits in facilitating succession and ecosystem function.

Effects of Different Wheat Varieties on Soil Bacterial and Fungal Communities

ABSTRACTThe diversity and stability of soil microbial communities are indispensable components for maintaining the functions and services of agricultural ecosystems and play crucial roles in wheat production. However, the effects of different wheat varieties on soil microbial diversity, network complexity, stability, and assembly mechanisms remain largely unexplored. To bridge this research gap, we conducted field experiments in Chuzhou, China, to study the yield and soil microbial community composition of six different wheat varieties. The soil bacterial and fungal communities were investigated using high‐throughput sequencing of the 16S rRNA and ITS gene regions. Our findings indicated that, compared to common wheat, high‐yielding and disease‐resistant (HD) wheat increased both bacterial and fungal α‐diversity by regulating soil nitrogen and phosphorus concentrations, significantly affecting community structure (Adonis, p < 0.001). HD wheat significantly altered the co‐occurrence network patterns of soil microbial communities. Network analyses revealed that HD wheat increased the complexity of fungal networks while exhibiting the opposite trend for bacterial networks. However, both the bacterial and fungal networks demonstrated increased stability. Furthermore, HD wheat may increase microbial migration rates, influencing assembly processes by promoting stochastic processes in bacterial and fungal communities. Overall, this study provides valuable insights into the ecological functions and driving factors of soil microbes, offering information for the development of ecological management strategies to achieve sustainable wheat cultivation and improve soil quality. Furthermore, HD wheat significantly modified the co‐occurrence network patterns of the soil microbial communities. Network analysis revealed increased fungal network complexity in HD wheat, whereas bacterial networks showed the opposite trend. However, both the bacterial and fungal networks exhibited enhanced stability. Additionally, HD wheat likely increased microbial migration rates, influencing assembly processes by promoting stochastic processes in both bacterial and fungal communities. Overall, this study provides valuable insights into the ecological functions and driving factors of soil microbes, providing information for the development of ecological management strategies to achieve sustainable wheat cultivation and improve soil quality.

Microbes in Agriculture: Prospects and Constraints to Their Wider Adoption and Utilization in Nutrient-Poor Environments

Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant growth promotion include mycorrhizal fungi, associative diazotrophs, and the N2-fixing rhizobia belonging to the α, β and γ class of Proteobacteria. Mycorrhizal fungi generally contribute to increasing the surface area of soil-root interface for optimum nutrient uptake by plants. However, when transformed into bacteroids inside root nodules, rhizobia also convert N2 gas in air into ammonia for use by the bacteria and their host plant. Thus, nodulated legumes can meet a high proportion of their N requirements from N2 fixation. The percentage of legume N derived from atmospheric N2 fixation varies with crop species and genotype, with reported values ranging from 50–97%, 24–67%, 66–86% 27–92%, 50–92%, and 40–75% for soybean (Gycine max), groundnut (Arachis hypogea), mung bean (Vigna radiata), pigeon pea (Cajanus cajan), cowpea (Vigna unguiculata), and Kersting’s groundnut (Macrotyloma geocarpum), respectively. This suggests that N2-fixing legumes require little or no N fertilizer for growth and grain yield when grown under field conditions. Even cereals and other species obtain a substantial proportion of their N nutrition from associative and endophytic N2-fixing bacteria. For example, about 12–33% of maize N requirement can be obtained from their association with Pseudomonas, Hebaspirillum, Azospirillum, and Brevundioronas, while cucumber can obtain 12.9–20.9% from its interaction with Paenebacillus beijingensis BJ-18. Exploiting the plant growth-promoting traits of soil microbes for increased crop productivity without any negative impact on the environment is the basis of green agriculture which is done through the use of biofertilizers. Either alone or in combination with other synergistic rhizobacteria, rhizobia and arbuscular mycorrhizal (AM) fungi have been widely used in agriculture, often increasing crop yields but with occasional failures due to the use of poor-quality inoculants, and wrong application techniques. This review explores the literature regarding the plant growth-promoting traits of soil microbes, and also highlights the bottle-necks in tapping this potential for sustainable agriculture.

Nitrogen addition alleviates the negative effects of reduction in precipitation on soil multifunctionality in a typical steppe

The increasing frequency of drought events and nitrogen deposition have fundamentally changed soil microbial functions in terrestrial ecosystems. However, most studies have mainly concentrated on the impact of a single environmental factor on ecosystem functions; how drought and nitrogen enrichment interactively affect soil multifunctionality remains largely unknown. In this study, the effects of different drought scenarios [intense drought (ID), chronic drought (CD), and reduced rainfall frequency (RF)] and nitrogen addition on soil microbial biomass, and soil multifunctionality (determined using soil enzyme activity) were examined in the fourth year of a field manipulative experiment conducted in a typical steppe in northern China. The results demonstrated that both ID and CD significantly reduced soil multifunctionality, microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). The CD treatment also decreased the ratio of MBC to MBN, while RF had less impacts on soil multifunctionality and the biomass of soil microbes. In contrast, nitrogen addition enhanced soil multifunctionality, MBC and MBN. Structural equation modeling analysis demonstrated that drought decreased soil multifunctionality directly and indirectly by reducing MBN and soil water content, whereas nitrogen addition increased soil multifunctionality mainly by increasing MBN and soil inorganic nitrogen. This study provides the first experimental evidence of the opposing impacts of reduction in precipitation and nitrogen enrichment on soil microbial biomass and soil multifunctionality in a semiarid typical steppe, and suggests that nitrogen fertilization could be an effective measure to alleviate the negative effects of climate drought on soil functions in nitrogen- and water-limited grassland ecosystems.

Arbuscular mycorrhizal fungi influence belowground interactions between a specialist root-feeder and its natural enemy

As primary producers, plants play a central role in mediating interactions across trophic levels. Although plants are the primary food source for herbivorous insects, they can protect themselves from herbivore damage. Many plants produce toxic compounds that directly reduce herbivore feeding, but plants also protect themselves indirectly by attracting natural enemies of the attacking herbivore through volatile signaling. These so-called tri-trophic interactions have historically been documented aboveground in aerial plant parts but are also known to occur belowground in root systems. In addition to herbivores, plants directly interact with other organisms, which can influence the outcomes of tri-trophic interactions. Arbuscular mycorrhizal fungi (AMF) are symbiotic soil microbes that colonize the roots of plants and facilitate nutrient uptake. These microbes can alter plant chemistry and subsequent resistance to herbivores. Few studies, however, have shown how AMF affect tri-trophic interactions above- or belowground. This study examines how AMF colonization affects the emission of root volatiles when plants are under attack by western corn rootworm, a problematic pest of corn, and subsequent attraction of entomopathogenic nematodes, a natural enemy of western corn rootworm. Mycorrhizal fungi increased rootworm survival but decreased larval weight. Differences were detected across root volatile profiles, but there was not a clear link between volatile signaling and nematode behavior. Nematodes were more attracted to non-mycorrhizal plants without rootworms and AMF alone in soil, suggesting that AMF may interfere with cues that are used in combination with volatiles which nematodes use to locate prey.

Salinity drives niche differentiation of soil bacteria and archaea in Hetao Plain, China

Soil salinization is a critical environmental issue that limits plant productivity and disrupts ecosystem functions. As important indicators of soil environment, soil microbes play essential roles in driving nutrient cycling and sustaining ecosystem services. Therefore, understanding how microbial communities and their functional potentials respond to varying levels of soil salinization across different land use types is crucial for the restoration and management of salt-affected ecosystems. In this study, we randomly selected 63 sites across the Hetao Plain, covering an area of ∼2500 km2. Our results showed that both salinity- and fertility-related soil parameters were significantly correlated with bacterial and archaeal diversities, with soil salinity emerging as the stronger predictor of prokaryotic diversity. Intriguingly, bacterial and archaeal communities were tightly interlinked but displayed opposite trends in response to environmental factors, indicating a clear microbial niche differentiation driven by soil salinity. Moreover, the generalist functions of bacteria and archaea (e.g., chemoheterotrophy) exhibited contrasting responses to environmental parameters, while their specialist functions (e.g., nitrification) responded consistently. These findings highlight the pivotal role of soil salinity in shaping the niche differentiation of bacterial and archaeal communities in saline soils, providing insights to guide salinity-centered restoration strategies for effective marginal land management.

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Beneficial soil fungi enhance tomato crop productivity and resistance to the leaf-mining pest Tuta absoluta in agronomic conditions

Research has shown that soil-borne beneficial microorganisms can enhance plant growth, productivity, and resistance against pests and pathogens and could thus serve as a sustainable alternative to agrochemicals. To date, however, the effect of soil-beneficial microbes under commercial crop production has been little assessed. We here investigated the effect of root inoculation with nine well-characterized bacterial and fungal strains and two consortia on tomato performance under intensive tomato crop management practices. We measured the impact of these root inoculations on plant growth, fruit quality, yield, and pest and pathogen incidence. While most microbial strains showed weak effects, we found that the fungal strains Trichoderma afroharzianum T22 and Funneliformis mosseae significantly increased marketable tomato yield. Moreover, we found that inoculation with most of the fungal strains led to a significant reduction in the incidence of the devastating leaf-mining pest Tuta absoluta, while this effect was not observed for bacterial inoculants. In addition, we found that microbial inoculations did not impact the incidence of introduced natural pest enemies, supporting their compatibility with well-established integrated pest management strategies in horticulture. In summary, the observed general positive effects of soil microbes on tomato yield and resistance reinforce the move toward broader adoption of microbial inoculants in future crop production, ultimately improving agricultural sustainability.

Potential of biochar to restoration of microbial biomass and enzymatic activity in a highly degraded semiarid soil

Biochar is an effective material for enhancing soil ecosystem services. However, the specific impacts of biochar on microbial indicators, particularly in degraded soils, remain poorly understood. This study aimed to evaluate the effects of biochar produced from cashew residues and sewage sludge, in a highly degraded soil, on microbial indicators. We analyzed soil chemical composition and microbial biomass C and N, enzyme activity, and stoichiometry. Cashew biochar increased soil respiration, indicating a higher availability of C to microorganisms compared to sewage sludge biochar and a better adaptation of soil microbial communities to C-rich organic material obtained from a native plant. Although the biochar differentially impacted microbial biomass C, both significantly increased N in the microbial biomass. Arylsulphatase activity did not respond to biochar application, while β-glucosidase, urease, and phosphatases showed significant changes with biochar treatments. Importantly, stoichiometry and vector analysis revealed that both types of biochar increased P limitation for soil microbes. Conversely, both biochar alleviated C and N limitations for the soil microbes. Thus, biochar applications in highly degraded soils should be supplemented with external P sources to maintain soil functions, mainly for cashew residues. Our results provide evidence that biochar can restore soil biological properties and enhance the availability of C and N to microorganisms. These findings have significant implications for restoration practices in degraded lands of semiarid regions.

Dynamics of major plant nutrients and enzymatic activities in soil influenced by application of biochar and organic waste.

The concentration of salt ions influences the availability and plant nutrients dynamics in the soil. Proper management of these ions can enhance food grain production, helping to feed the growing population. In this experiment, nine fertility combinations were followed to enhance the soil organic carbon and reduce the salt toxicity and monitor the plant nutrient availability. An incubation experiment was conducted for the period of one year with different organic soil amendments in combinations including biochar (BC), pressmud (PM), and farm yard manure (FYM) as follow: T1-control, T2-RDF, T3-FYM (10 t/ha), T4-PM (10 t/ha), T5-BC (10 t/ha), T6-FYM (5 t/ha) + PM (5 t/ha), T7-FYM (5 t/ha) + BC (5 t/ha), T8-PM (5 t/ha) + BC (5 t/ha), T9-FYM (5 t/ha) + BC (2.5 t/ha) + PM (2.5 t/ha). Results showed that addition of organic substance (10 t/ha) significantly (p < 0.05) affected soil pH and electric conductivity. Plant nutrient availability (N, K, and S) was also influenced by application of organic substance (10 t/ha). Organic C and available N were recorded the highest in the treatment T7 (FYM-5 t/ha + BC -5 t/ha); whereas, the highest available K and S were observed in treatment T5 (BC-10 t/ha). The microbial soil fertility indicators (alkaline phosphatases, arylsulphatase, dehydrogenase activity and microbial biomass carbon) were measured the highest in FYM (5 t/ha) + BC (5 t/ha) applied treatment. In conclusion, application of organic substance 10 t/ha (biochar alone or with FYM) improved the plant nutrient availability and soil microbial activities in saline soil. It could be a suitable option for enhancing the soil fertility in saline soils.

Effect of Vermicompost Application on the Soil Microbial Community Structure and Fruit Quality in Melon (Cucumis melo)

Melon (Cucumas melon) is widely cultivated and popular because of its quality value and unique flavor. However, the continuous cropping of melons in greenhouses has various negative effects on the soil environment, melon growth, and quality. Recently, farmers have utilized organic fertilization, especially vermicompost, for melons to resist the harmful effects of continuous cropping. A field experiment was conducted to explore the effects of vermicompost on soil microbes and melon fruit quality via high throughput sequencing and chemical sequencing methods. The results showed that the application of vermicompost decreased (p &lt; 0.05) soil pH and increased organic matter, available phosphorus, biomass, urease, catalase, peroxidase, and alkaline phosphatase. A total of 3447 bacterial and 718 fungal operational taxonomic units were identified in all soil samples. Application of vermicompost decreased (p &lt; 0.05) the relative abundances of Acidobacteriota, Gemmatimonadota, Actinobacteriota, and unclassified and increased the relative abundance of Planctomycetota. Compared with the control soil, vermicompost application resulted in significantly higher bacterial Chao indices and a significantly lower Chao index under vermicompost of 60 t ha−1 based on farmers’ normal fertilizer and significantly lower diversity under vermicompost of 90 t ha−1. Otherwise, vermicompost application increased the photosynthetic rate and chlorophyll content of melon leaves and increased the total sugar, soluble solids, vitamin C, soluble protein, and organic acid contents of melon. The results of redundancy analysis indicated that Proteobacteria exhibited a positive correlation with soil ammonium nitrogen (AN) and pH, while showing a negative association with soil available phosphorus and organic matter. Spearman’s correlation analysis revealed that both total sugar content and central soluble solid content in melon had a significant positive correlation (p &lt; 0.05) with Patescibacteria. This study demonstrates that the application of vermicompost alters the microbial community structure in melon cultivation, enhancing fruit quality; this not only promotes a healthier soil ecosystem but also contributes to sustainable and productive practices in melon farming.

Exploring cadmium tolerance in soil microbes: Isolation and identification of resistant strains

Cadmium poses detrimental effects on our surrounding environment and causes various health hazards. In this research, the bacterial diversity of soil samples procured from the contaminated sites of Coimbatore, Tamil Nadu, India was investigated and their cadmium removal potential was assessed. 16S rRna sequencing was followed for the identification of two isolates, which belong to the same genus, Cupriavidus sp. This genus was used for assessing the cadmium bioremediation potential. It was found that the strain S1CL (Cupriavidus necator) exhibited a high ability to remove cadmium (9 %) compared to S3CL (Cupriavidus alkaliphilus), which removed 2 %. The strains were compatible to each other and exhibited 1 2% removal efficiency in combination. The results revealed that Cupriavidus necator possessed a great potential for the cadmium bioremediation process.

Effects of Microbial Organic Fertilizer, Microbial Inoculant, and Quicklime on Soil Microbial Community Composition in Pepper (Capsicum annuum L.) Continuous Cropping System

The additions of microbial organic fertilizer (MOF), a microbial inoculant (MI), and quicklime (Q) are considered to be sustainable practices to restore land that has been damaged by continuous cropping of pepper (Capsicum annuum L.). However, the combined effects of these three additives on pepper yield, soil chemical properties, and soil microbial communities were unclear. The experimental design consists of 13 treatment groups: the untreated soil (control); soil amended solely with three treatments for each of MOF (1875–5625 kg ha−1), MI (150–450 mL plant−1), and Q (1500–4500 kg ha−1); and soil amended with combinations of MOF, MI, and Q at three comparable concentrations. A significant increase in pepper fruit diameter, length, yield, and soil available nitrogen, phosphorus, and potassium contents occurs upon exclusive and combined applications of MOF, MI, and Q. Pepper yield was greatest (29.89% more than control values) in the combined treatment with concentrations of 1875 kg ha−1 MOF, 150 mL plant−1 MI, and 1500 kg ha−1 Q. The application of Q increased soil pH and reduced soil–fungal richness. The application of MOF, MI, and Q increased the relative abundance of bacterial genera and the complexity of bacterial and fungal co-occurrence networks compared with control levels. The combined application of MOF, MI, and Q resulted in the greatest microbial network complexity. A Mantel test revealed the key role of soil available nitrogen content and bacterial diversity in the regulation of pepper growth and yield. We conclude that the combined application of MOF, MI, and Q improves soil nutrient availability and modifies soil microbial community composition, significantly promoting plant growth and pepper yield during continuous cultivation.

Soil microbial biodiversity supports the delivery of multiple ecosystem functions under elevated CO2 and warming

The contribution of the soil microbes to agroecosystem multifunctionality under global change remains poorly understood. Here, based on data from a field experiment involving elevated carbon dioxide (CO2) and warming in a rice-wheat agroecosystem, we found that soil microbes influence the impact of climate change on agroecosystem functions. The stability of food production during the rice season increased under elevated CO2 but decreased under warming, with no significant changes in the wheat season. The interactive influences of elevated CO2 and warming on agroecosystem multifunctionality were found to be minimal. The abundance of soil fungi and nematode was associated with agroecosystem stability during the rice and wheat seasons, respectively. Soil archaeal diversity and bacterial abundance were linked to agroecosystem multifunctionality in the rice and wheat seasons, respectively. Our work proves the positive effects of soil microbes on agroecosystem functions and highlights the implications of maintaining microbial diversity for agroecosystem health under climate change.

Exploring the Relationship Between Biochar Pore Structure and Microbial Community Composition in Promoting Tobacco Growth.

The potential benefits of biochar, a carbon-rich substance derived from biomass, for enhancing agricultural yield and soil health have drawn increasing interest. Nevertheless, owing to the lack of specialized studies, the role of its poly-spatial structure in the success of fostering plant growth remains unclear. This study aimed to assess the effects of various biochar pore shapes on tobacco growth and the underlying microbiological processes. Three pyrolysis temperatures (250 °C, 400 °C, and 550 °C) were used to produce biochar from tobacco stems, resulting in different pore structures (T3 > T2 > T1). We then used BET-specific surface area (BET), t.Plot micropore specific surface area (t.Plot), mesopore specific surface area (MSSA), specific pore volume (SPV), average pore size (AP), and mesopore pore volume (MPV) measurements to evaluate the effects of these biochars on tobacco growth and biomass accumulation, and microbial analyses were performed to investigate the underlying mechanisms. When applied to plants, biochar increased their growth compared to untreated controls. The most notable improvement in tobacco growth was observed in the biochar produced at 400 °C (T3), which possessed the largest and most advantageous pore structure among all treatments. Further studies demonstrated that biochars with greater specific surface areas (BET, t.Plot, and MSSA) positively altered the abundance of key microbial taxa (e.g., Stenotrophobacter, Ensifer, Claroideoglomus) and community composition, thereby encouraging plant development and biomass accumulation. Conversely, greater pore volumes (SPV, AP, and MPV) inhibited microbial activity and significantly affected growth and biomass accumulation. Structural equation modeling further demonstrated that the pore structure of biochar greatly affected plant growth by changing the relative abundance and community composition of soil microbes. Maximizing the benefits of biochar in stimulating plant growth and improving soil microbial communities depends on optimizing the material's pore structure, particularly by increasing the specific surface area. These findings will help expand the use of biochar in sustainable agriculture.

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems.

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)-cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.