Soil Bacterial Community Research Articles

Tradeoffs among yield, cadmium bioavailability, nitrous oxide emission and bacterial community stability: Effects of iron-modified woody peat and nitrification inhibitors on soil-vegetable systems

Cadmium (Cd) pollution leads to soil degradation, decreases crop yield and affects human health through the food chain. Iron-modified woody peat (IMP) is an organic passivation material that significantly affects the migration of heavy metals in soil. Nitrification inhibitors are widely used to reduce greenhouse gas emissions. This study investigated the effects of the IMP and nitrification inhibitors dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate on Cd content and form, crop yield, nitrous oxide (N2O) emission and bacterial communities in soil-lettuce systems. The simultaneous additions of IMP and DCD substantially reduced the soil available Cd content by 22.6 % and significantly promoted the lettuce yield by 42.9 %. Lettuce yield was significantly and negatively correlated with soil available Cd (correlation coefficient = −0.52). The simultaneous applications of IMP and nitrification inhibitors stimulated N2O emission risk by enhancing the soil NH4+-N contents and the relative abundances of Firmicutes, which could also decrease soil bacterial community stabilities. Therefore, tradeoffs among yield, Cd bioavailability, N2O emission and bacterial community stability should be comprehensively considered when evaluating the combined performances of IMP and nitrification inhibitors.

Deciphering the Effects of Phosphate Fertiliser on Rhizospheric Bacterial Community Structure and Potato Common Scab.

The prolonged practice of continuous potato cropping, coupled with inadequate field management, disrupts the soil bacterial community equilibrium. Such disturbances compromise the resilience of the soil ecosystem, predisposing it to an increased incidence of potato diseases. However, the effects of the phosphorus fertiliser application rate on the rhizosphere soil bacterial community composition of potatoes and the occurrence of potato common scab (CS) have not been adequately studied. Here, diseased field soils from Dingxi and Huidong Counties were collected for potting tests, and field tests were conducted in Huidong County for validation. An examination of the relationship between the bacterial community composition in the potato rhizosphere soil and potato CS under different phosphate fertiliser treatments was conducted using 16S rRNA high-throughput sequencing. The results show that a lower phosphorus fertiliser application rate was more conducive to maintaining soil bacterial community diversity under different phosphorus fertiliser treatments in different habitats. In addition, the relative abundance of the txtA gene increased significantly (p < 0.05) with the increase in the phosphate fertiliser application rate. Field trials conducted in Huidong revealed that treatments F1, F2, and F3 had respective CS incidence rates of 28.33%, 46.67%, and 59.44%, while their corresponding disease severity indices were 7.67, 17.33, and 29.44. Further analysis revealed that the relative abundance of antagonistic genera of pathogenic S. scabies decreased significantly (p < 0.05) with increases in the phosphorus fertiliser application rate. In summary, the correlation between potato CS and changes in the bacterial community of rhizosphere soil was used to determine the optimal phosphorus application rate during potato production, which can provide a scientific basis for the management of phosphorus fertiliser in potato farmland.

Varying nitrogen fertilization and soil bacterial community dynamics at three growth phases of winter wheat production

Varying nitrogen fertilization and soil bacterial community dynamics at three growth phases of winter wheat production

The Effects of Low Concentrations and Long-Term Contamination by Sodium Dodecyl Sulfate on the Structure and Function of Bacterial Communities in the Lake-Terrestrial Ecotone.

Due to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake-terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities due to its bacteriostatic properties. To investigate the effects of long-term discharge of sewage containing low concentrations of SDS on microorganisms in the lake-terrestrial ecotone, alterations in bacterial community structure, functional genes, and biomass were examined using a simulated continuous pollutant input. The results indicated the following: (1) The degradation rate of sodium dodecyl sulfate (SDS) by soil microorganisms in the lake-terrestrial ecotone under long-term and low concentrations of SDS stress ranged from 11 to 16 mg/kg·d. (2) The effects of low concentrations and long-term SDS stress on bacterial community structure and gene function in the lake-terrestrial ecotone differed significantly from those of short-term pollution. The damage to microbial-promoted material cycling in the lake-terrestrial ecotone was more severe; however, the proliferation of pathogenic bacteria remained continuously suppressed. (3) Soil bacteria in the lake-terrestrial ecotone responded to the stress of long-term and low concentrations of SDS primarily by enhancing chemotaxis and tolerance.

Increased stability of a subtropic bamboo forest soil bacterial communities through integration of water and fertilizer management compared to conventional management

BackgroundConventional management (CM), substantial fertilization and flooding irrigation, has led to soil acidification, the decrease in soil bacterial diversity in bamboo forests. Integration of water and fertilizer management (IWF) can effectively improve the efficiency of water and fertilizer use, but its effect on soil environment, especially on microbial community, is still unclear.MethodsHere, we used next-generation high-throughput sequencing to compare soil properties and bacterial communities through different fertilization and irrigation methods under IWF and CM.ResultsCompared to the control group, CM significantly reduced soil pH and bacterial diversity, while IWF improved soil nutrition status, increased soil bacterial diversity and soil pH to a level similar to the control group. Compared with CM, IWF also improved the relative abundance of beneficial bacteria and copiotrophic bacteria community in the soil, and the bacterial community in IWF was similar to CK. The structure of the bacterial community was also significantly correlated with soil organic matter, total nitrogen, hydrolyzable nitrogen, and available potassium, while soil bacterial diversity was mainly associated with soil hydrolyzable nitrogen.ConclusionsIWF can play an important role in preventing soil acidification, the loss of soil bacterial diversity, and improving the structure of the bacterial community under specific conditions.

Enhanced phytoremediation of Cd-contaminated soil by Solanum nigrum L. through the addition of earthworm and organic wastes

BackgroundPhytoremediation is considered to have great development potential to deal with soil Cd contamination, and assisted measures are necessary to improve the efficiency of Cd extraction from soil by hyperaccumulator plants. Based on this, a pot experiment was conducted to determine the growth indices, physiological indices, Cd content of Solanum nigrum L. and soil bacterial community under single and combined application of earthworm and organic wastes [chili straw and spent mushroom substrate (SMS)].ResultsPot experiments revealed that adding earthworms, chili straw, or SMS alone did not affect the growth of S. nigrum. However, the combination of earthworms + chili straw and earthworms + SMS, significantly increased the total dry weight of S. nigrum by 20.94% and 74.69% compared to the control. The chlorophyll content of S. nigrum in the treatment groups with earthworms, SMS, and earthworms + SMS was also significantly higher than that in the control. Meanwhile, adding earthworms and organic wastes also reduced the malondialdehyde content in the leaves of S. nigrum and increased the activity of superoxide dismutase and peroxidase. In addition, applying earthworm + chili straw and earthworm + SMS also increased the availability of Cd in the soil, promoted the absorption of Cd by S. nigrum, and significantly increased its total extraction amount of Cd by 41.55% and 92.83%, respectively. The diversity of soil bacterial communities increased when earthworms and organic wastes coexisted. Adding earthworms and organic wastes also increased the relative abundance of Verrucomicrobia at the phylum level and of Sphingomonas, Ohtaekwangia, Saccharibacteria_genera_incertae_sedis, and Aridibacter at the genus level in the soil. At the same time, this process reduces the relative abundance of Proteobacteria and Firmicutes at the phylum level and Devosia and Bacillus at the genus level.ConclusionsThe combined application of earthworms and SMS enhanced phytoextraction of Cd-contaminated soil by S. nigrum. It also improved soil nutrient conditions and reduced external environmental stress on bacteria, increasing their diversity and restructuring the community structure, which was conducive to forming a good soil microecological environment. The results of this study can provide a scientific basis for the treatment of Cd contaminated soil, but field experiments need to be conducted for verification and optimization before practical application in the future.Graphical

Plant-Guided Microbiome Selection Produces Transient Effects on Insect Performance and Rhizosphere Community Assembly

Microbial communities are essential for plant health, but using these relationships to enhance growth and pest protection is challenging. Leveraging the natural mechanisms plants employ to manage relationships with microbes is one promising means to selectively engineer whole microbial communities with beneficial properties. This approach, known as host-guided selection, has been successful in some model species targeting performance traits (e.g., biomass). However, few studies use crop plants or focus on defensive traits (e.g., pest resistance). Our goal was to naturally engineer tomato root-associated microbiomes that increase resistance to insect pests. First, we used an iterative soil microbial inoculation process to engineer insect-suppressive rhizosphere soil microbiomes that reduce damage from aphid feeding ( Macrosiphum euphorbiae) or caterpillar defoliation ( Manduca sexta, Spodoptera exigua). We then characterized the bacterial and fungal microbial communities of soils associated with differences in insect performance using metabarcoding approaches. Overall, soil microbiome selection produced transient differences in aphid performance, but caterpillar growth was unaffected. In four of nine generations, the aphid population growth rate was significantly lower on plants with rhizospheres selected for “low” insect performance, where abundance was reduced by up to 20%. Correspondingly minor shifts in fungal and bacterial relative abundance occurred in insect-suppressive communities. However, network analysis indicated that aphid feeding disrupted rhizosphere microbiome assembly, resulting in lower community complexity and connectivity and fewer structurally important taxa compared with uninfested controls. Overall, our results highlight critical factors for successful engineering of beneficial microbiomes, particularly insect feeding guild and microbial community stability.

Microbial Basis for Suppression of Soil-Borne Disease in Crop Rotation.

The effect of crop rotation on soil-borne diseases is a representative case of plant-soil feedback in the sense that plant disease resistance is influenced by soils with different cultivation histories. This study examined the microbial mechanisms inducing the differences in the clubroot (caused by Plasmodiophora brassicae pathogen) damage of Chinese cabbage (Brassica rapa subsp. pekinensis) after the cultivation of different preceding crops. It addresses two key questions in crop rotation: changes in the soil bacterial community induced by the cultivation of different plants and the microbial mechanisms responsible for the disease-suppressive capacity of Chinese cabbage. Twenty preceding crops from different plant families showed significant differences in the disease damage, pathogen density, and bacterial community composition of the host plant. Structural equation modelling revealed that the relative abundance of four key bacterial orders in Chinese cabbage roots can explain 85% and 70% of the total variation in pathogen density and disease damage, respectively. Notably, the relative dominance of Bacillales and Rhizobiales, which have a trade-off relationship, exhibited predominant effects on pathogen density and disease damage. The disease-suppressive soil legacy effects of preceding crops are reflected in compositional changes in key bacterial orders, which are intensified by the bacterial community network.

Effect of Compound Fertilizer on Foxtail Millet Productivity and Soil Environment.

The effects of balanced fertilization with nitrogen, phosphorus, and potassium (NPK) on foxtail millet productivity and the soil environment under the same conditions of total nutrients have received limited research attention. Therefore, in this study, three balanced fertilization patterns of 27-14-10 (T1), 27-17-7 (T2), and 30-10-11 (T3), and one no fertilization treatment (CK), a total of four treatments, were set up through a two-year field experiment to study the effects of balanced fertilization patterns on foxtail millet yield and soil environment. Mantel analysis was conducted to reveal the correlation between soil environmental factors and the community and their contribution to productivity. The results showed that: (1) all balanced fertilization treatments significantly increased foxtail millet yield, with the highest yield in the T1 treatment. (2) The contents of EC, available K, available P, and alkaline-hydrolyzable nitrogen in the soil of the two-year TI treatments were higher than those of the other treatments and increased by 7.20-9.36%, 24.87-52.35%, 55.83-56.38%, and 21.05-43.95%, respectively, compared with CK. (3) Soil urease activity in the T1 treatment increased significantly by 26.67% and 9.00% compared with the control over the two years. Sucrase activity increased by 36.27% and 23.88% in the T1 treatment compared to CK, and glutaminase activity increased by 33.33% and 19.23% in the T1 treatment compared to CK. (4) T1 treatment significantly increased the OUT number and diversity index of the soil bacterial community. (5) Mantel analysis and principal component analysis showed that available soil nutrients and soil enzymes were positively correlated, and soil enzymes and soil nutrients contributed more to foxtail millet productivity. In this study, the 27-14-10 balanced fertilization pattern was more effective, providing a theoretical basis for the research and development of special fertilizers for foxtail millet and offering technical guidance for realizing the light simplified cultivation of foxtail millet and sustainable development of cost-saving and increased efficiency.

Litter Removal Counteracts the Effects of Warming on Soil Bacterial Communities in the Qinghai-Tibet Plateau.

Climate warming and high-intensity human activities threaten the stability of alpine meadow ecosystems. The stability of the soil microbial community is crucial for maintaining ecological service function. However, the effects of warming and litter removal on microbial interactions, community-building processes, and species coexistence strategies remain unclear. In this study, we used a fiberglass open-top chamber to simulate global change, and moderate grazing in winter was simulated by removing above-ground litter from all plants in the Qinghai-Tibet Plateau, China, to investigate the effects of warming, litter removal, and interactions on soil microbial communities. The treatments included (1) warming treatment (W); (2) litter removal treatment (L); (3) the combined treatment (WL); and (4) control (CK). The results show that compared with the control treatment, warming, litter removal, and the combined treatments increased bacterial Shannon diversity but reduced fungal Shannon diversity, and warming treatment significantly changed the bacterial community composition. Warming, litter removal, and the combined treatments reduced the colinear network connectivity among microorganisms but increased the modularity of the network, and the average path distance and average clustering coefficient were higher than those in the control group. Stochastic processes played a more important role in shaping the microbial community composition, and soil-available phosphorus and soil ammonium contributed more to the βNTI of the bacterial community, while total phosphorus and NAG enzyme in the soil contributed more to the βNTI of the fungal community. Notably, litter removal counteracts the effects of warming on bacterial communities. These results suggest that litter removal may enhance bacterial community stability under warming conditions, providing insights for managing alpine meadow ecosystems in the context of climate change.

Ecological impacts of diversified agroforestry on soil nutrients and bacterial communities in Pinus massoniana plantations in the southern subtropics

Converting forests from single-species to mixed-species planting affects soil chemical and biological properties, yet its impacts within medicinal plant-based agroforestry systems remain largely unexamined. This research assessed the soil nutrient spectrum and bacterial community composition in a monoculture Pinus massoniana (CK) and various agroforestry models: (M1) Pinus massoniana and Alpina oxyphylla, (M2) Pinus massoniana and Ficus simplicissima, (M3) Pinus massoniana and Amomum villosum, and (M4) Pinus massoniana and Curcuma longa, within both field soil and rhizosphere environments. Results showed significant (p < 0.05) improvements in soil pH and cation exchange capacity (CEC) in agroforestry systems. Agroforestry models exhibited greater variability in soil macronutrient distribution, including nitrogen, potassium, calcium, magnesium, and sulfur (N, K, Ca, Mg, S), compared to monocultures. Specifically, Curcuma longa (M4C.RS) had 46.12 % higher total N content than monoculture Pinus massoniana. Micronutrients were higher in agroforestry rhizospheres, except for total zinc, which was higher in monoculture Pinus massoniana. Bacterial community analysis revealed dominant phyla including Acidobacteriota, Proteobacteria, Actinobacteria, and Chloroflexi. Agroforestry models had higher abundance of Proteobacteria, while monoculture had higher Acidobacteriota. Alpha diversity metrics, including Chao1 and Shannon indices, indicated higher species richness and evenness in agroforestry models, particularly in the rhizosphere of Amomum villosum (M3A.RS) and Curcuma longa (M4C.RS). Phylogenetic analysis indicated greater genetic diversity in agroforestry models, in terms of species richness and phylogenetic variation especially for Proteobacteria. Cluster analysis and NMDS revealed close grouping of agroforestry models, with dbRDA showing significant associations between environmental variables (pH, CEC, and nutrient profile), emphasizing their critical role in shaping bacterial community composition, supported by Spearman correlation. Functional prediction (PICRUSt2) indicated metabolism as the predominant functional category. Therefore, transition from monoculture to agroforestry, especially with Curcuma longa (M4), significantly enhanced soil fertility and ecosystem sustainability.

Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure.

Chemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology. The fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum. The results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm2). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.

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 (&gt;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 &lt; 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.

Microencapsulated Microbial Seed Coating Could Improve Soil Environment and Maize Grain Yield in Saline Soil.

Soil salinization is one of the major challenges for modern agriculture, posing a great threat to soil health and food security. Field experiments were conducted to evaluate the effect of seed coating on soil environment and maize growth in saline soils. Three treatments were applied to maize seeds: coating with a microencapsulated microbial agent (ME), coating with microbial only (MB), and no coating (CK). High-throughput sequencing of soil bacterial and fungal 16S and ITS rRNA genes was performed using the Illumina HiSeq platform to analyze the effects of these treatments on soil bacterial and fungal diversity and community structure. Additionally, the influence of different treatments on endogenous hormones and yield of maize were investigated. It was found that the coating with a microencapsulated microbial agent led to decreases in pH and electrical conductivity (EC), while increasing the content of soil available phosphorus. This coating improved soil microbial diversity, significantly increasing the relative abundance of the main bacteria genera, Bacillus (34.9%), and the main fungal genera, Mortierella (190.4%). The treatment also significantly enhanced indole-3-acetic acid (IAA) by 51.2%, contributing to improvements in resistance to salt stress. The germination rate increased by 22.9%, the 100-grain weight increased by 12.7%, and grain yield increased by 14.3%. The use of the microencapsulated microbial agent effectively mitigated the adverse effects of salt stress on maize plants. This approach is beneficial for promoting sustainable agriculture in saline soils.

Grazing disturbance reduces biocrust-related cyanobacteria and N-fixer abundance but increases bacterial diversity: Implications for biocrust restoration in degraded drylands

Overgrazing is a major driver of dryland degradation, however, so far, there is limited understanding on how this process affects biocrust-related microbial community, and especially how the key groups respond to grazing disturbance. In this study, quantitative polymerase chain reaction (qPCR) and high throughout sequencing technologies were used to investigate the bacterial community abundance and diversity in the Horqin Sandland (China) experiencing different livestock grazing disturbances, in order to examine whether a shift in bacterial community (in particular the key biocrust components, cyanobacteria) was involved, and how this was related to biocrust development and altered soil carbon and nitrogen level. Our results revealed that a clear heterogeneous soil bacterial community was associated with grazing disturbance, which inhibited biocrust development. The decreased photosynthetic cyanobacterial abundance (81.81 % in relative abundance and 98.83 % in absolute abundance) and nitrogen-fixing genes (87.72 %), associated with the lower total carbon and nitrogen content (P<0.05), illustrated a low soil carbon and nitrogen-fixing capability and nutrient level in the grazing-disturbed soils. In particular, a switch of nitrogen-fixing dominance from cyanobacteria to proteobacteria was induced by the grazing disturbance. Compared to the grazing-disturbed soils, higher dominant cyanobacterial operational taxonomic units (OTUs) (especially the species of Nostoc and Scytonema) and lower bacterial diversity (e.g., Shannon, Ace, and Chao index) were observed in the undisturbed biocrust soils, highlighting that the dominants rather than diversity played more important roles in biocrust development. Collectively, our results demonstrate that cyanobacteria are very sensitive (even more than others, e.g., proteobacteria and actinobacteria) to grazing disturbance, therefore, we propose that cyanobacterial inoculation is likely an effective approach to supplement soil cyanobacterial abundance, which is expected to induce biocrust development and increase carbon and nitrogen level in the disturbed drylands.

Biocontrol Agents Inhibit Banana Fusarium Wilt and Alter the Rooted Soil Bacterial Community in the Field.

Banana is an important fruit and food crop in tropical and subtropical regions worldwide. Banana production is seriously threatened by Fusarium wilt of banana (FWB), a disease caused by Fusarium oxysporum f. sp. cubense, and biological control is an important means of curbing this soil-borne disease. To reveal the effects of biocontrol agents on inhibiting FWB and altering the soil bacterial community under natural ecosystems, we conducted experiments at a banana plantation. The control efficiency of a compound microbial agent (CM), Paenibacillus polymyxa (PP), Trichoderma harzianum (TH), and carbendazim (CA) on this disease were compared in the field. Meanwhile, the alterations in structure and function of the rooted soil bacterial community in different treatments during the vigorous growth and fruit development stages of banana were analyzed by microbiomics method. The results confirmed that the different biocontrol agents could effectively control FWB. In particular, CM significantly reduced the incidence of the disease and showed a field control efficiency of 60.53%. In terms of bacterial community, there were no significant differences in the richness and diversity of banana rooted soil bacteria among the different treatments at either growth stage, but their relative abundances differed substantially. CM treatment significantly increased the ratios of Bacillus, Bryobacter, Pseudomonas, Jatrophihabitans, Hathewaya, and Chujaibacter in the vigorous growth stage and Jatrophihabitans, Occallatibacter, Cupriavidus, and 1921-3 in the fruit development stage. Furthermore, bacterial community function in the banana rooted soil was affected differently by the various biocontrol agents. CM application increased the relative abundance of multiple soil bacterial functions, including carbohydrate metabolism, xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, lipid metabolism, and metabolism of other amino acids. In summary, our results suggest that the tested biocontrol agents can effectively inhibit the occurrence of banana Fusarium wilt and alter the soil bacterial community in the field. They mainly modified the relative abundance of bacterial taxa and the metabolic functions rather than the richness and diversity. These findings provide a scientific basis for the use of biocontrol agents to control banana Fusarium wilt under field conditions, which serves as a reference for the study of the soil microbiological mechanisms of other biocontrol agents.

Diversity Patterns and Drivers of Soil Bacterial and Fungal Communities in a Muddy Coastal Wetland of China.

Elucidating the dynamics of soil microbial diversity in coastal wetlands is essential for understanding the changes in ecological functions within these ecosystems, particularly in the context of climate change and improper management practices. In this study, the diversity patterns and influencing factors of soil bacterial and fungal communities in a muddy coastal wetland in China were investigated using Illumina sequencing of 16S rRNA and ITS1, across wetlands dominated by different vegetations and varying proximity to the coastline. The wetlands include four plots dominated by Spartina alterniflora (SA1), four plots dominated by Suaeda glauca (SG2), additional four plots of Suaeda glauca (SG3), and four plots dominated by Phragmites australis (PA4), ranging from the nearest to the coast to those farther away. The results revealed significant differences in bacterial richness (Observed_species index) and fungal diversity (Shannon index) across different wetlands, with SG3 demonstrating the lowest bacterial Observed_species value (1430.05), while SA1 exhibited the highest fungal Shannon value (5.55) and PA4 showing the lowest fungal Shannon value (3.10). Soil bacterial and fungal community structures differed significantly across different wetlands. The contents of soil available phosphorus and total phosphorus were the main drivers for fungal Observed_species and Shannon index, respectively. Soil organic carbon, pH, and salinity were indicated as the best predictors of bacterial community structure, accounting for 28.1% of the total variation. The total nitrogen content and soil salinity contributed mostly to regulating fungal community structure across different wetlands, accounting for 19.4% of the total variation. The results of this study offer a thorough understanding of the response and variability in soil microbial diversity across the muddy coastal wetlands in China.

Investigating the effects of various irrigation methods on bacterial communities in paddy soil

Different irrigation methods can impact the micro-ecological environment of paddy soil, affecting crop growth. This study focuses on County A, a key grain production area on China’s East Coast, where 20 plots each of intermittent and flood irrigation were selected and labeled as Group I and Group F, respectively. Soil's basic physicochemical properties and heavy metal content were measured in the laboratory, and high-throughput sequencing was used to analyze soil bacterial communities. The study evaluated the impact mechanisms of different irrigation methods on these bacterial communities. Results indicate: (1) Intermittent irrigation significantly increased bacterial richness, evenness, and diversity, enhancing microbial community diversity and stability. (2) Intermittent irrigation notably raised the abundance of 9 bacterial genera (e.g., Nitrospira, H16) while reducing the abundance of 7 genera (e.g., Geobacter, Sphingomonas). (3) The soil environment in Group I was stable, with bacterial communities influenced by SMC, pH, and Cu; Group F was affected by multiple environmental factors. Intermittent irrigation provides a stable environment that supports bacterial diversity and abundance, contributing to a richer community structure. (4) Intermittent irrigation optimizes moisture, significantly enhancing bacterial functions such as energy production, cell wall biosynthesis, repair, and signal transduction. These findings suggest that intermittent irrigation improves bacterial community stability and diversity, which is crucial for enhancing the overall quality of paddy fields.

Soil Bacteria in Archaeology: What Could Rank Abundance Functions Tell Us About Ancient Human Impacts on Microbial Communities?

Metagenomic analysis of soil bacterial communities based on 16S rRNA reflects a typical community composition containing a low number of high-abundance types and a very high number of low-abundance types. Here, the formation of characteristic rank order functions of bacterial abundance is investigated by modelling the dynamics of soil bacterial communities, assuming a succession of different bacterial populations that grow rapidly and decay more slowly. We found that the characteristic shape of typical rank order functions is well reflected by simulations. In addition, our model allowed us to investigate strong disturbances in the soil, which could be expected in cases of strongly changing local environmental conditions in soil, e.g., after translocation and covering of soil material. Such events could lead to the formation of shoulders in the rank order functions. Abundance rank orders observed in cases of some archaeological soil samples do indeed show such a shoulder and could be well interpreted by simulated rank order functions. As a result, it can be concluded that the investigations herein support our hypothesis that abundance rank orders contain information about the temporal order of developing bacterial types in changing communities and thus store information about local environmental conditions in the past, including ancient humans' impact on soil. This information can be used for interpretation of archeological findings and for reconstruction of different former human activities, as well as knowledge on the translocation of soil material in the past.

Wastewater biotreatment and bioaugmentation for remediation of contaminated sites at an oil recycling plant

ABSTRACT This work focused on the biotreatment of wastewater and contaminated soil in a used oil recycling plant located in Bizerte. A continuous stirred tank reactor (CSTR) and a trickling filter (TF) were used to treat stripped and collected wastewater, respectively. The CSTR was started up and stabilized for 90 days. Over the following 170 days, the operational organic loading rates of the TF and the CSTR were around 1,200 and 3,000 mg chemical oxygen demand (COD) L−1 day−1, respectively. The treatment efficiency was 94% for total petroleum hydrocarbons, 89.5% for COD, 83.34% for biological oxygen demand (BOD5), and 91.25% for phenol. Treated industrial wastewater from the TF was used for bioaugmentation (BA) of contaminated soil. The assessment of the soil took 24 weeks to complete. The effectiveness of the soil BA strategy was confirmed by monitoring phenolic compounds, aliphatic and polycyclic aromatic hydrocarbons, heavy metals, and germination index. The biodegradation rate of contaminants was improved and the time required for their removal was reduced. The soil bacterial communities were dominated by species of the genera Mycobacterium, Proteiniphilum, Nocardioides, Luteimicrobium, and Azospirillum, which were identified as hydrocarbon and phenol-degrading bacteria.