Changes In Soil Bacterial Composition Research Articles

Effects of grazing in different intensities and 10‐year grazing exclusion on soil bacterial community composition and interaction complexity in alpine grasslands of the Qinghai‐Tibet Plateau

AbstractTo decrease the detrimental consequences of overgrazing on the sustainability of grassland ecosystems, many countries have developed policies on grazing exclusions. However, compared with grazing, how grazing exclusion modifies soil bacterial community and the associated environmental drivers is inadequately understood. Here, we studied the effects of grazing in different intensities (no grazing, light, moderate, and heavy grazing) and 10 years' grazing exclusion on soil bacteria community and associated environmental factors in the grassland of the Qinghai‐Tibet Plateau. The results showed significant changes in soil bacterial composition among all the treatments. After 10 years' grazing exclusion, the composition of the bacterial community rather than bacterial diversity was significantly different from that in grassland without grazing treatment. Under grazing exclusion, bacterial community composition was regulated by the total nitrogen and nitrate nitrogen. Grazing treatments decreased the complexity of the bacterial co‐occurrence network, but 10 years' grazing exclusion increased the complexity. This study found that grazing in different intensities substantially affected bacterial community structure and diversity, but 10 years' grazing exclusion hardly alleviated the historical grazing effects on the bacterial community structure. The findings of the study extended the understanding of how bacterial communities in grasslands respond to grazing in different intensities and grazing exclusion, providing a crucial scientific foundation for evaluating sustainable grazing management.

Effect of long-term conservation tillage management on microbial diversity under Mediterranean rainfed conditions

Conservation Agriculture has been the subject of numerous studies for decades. However, its impact on the soil microbial community has often been overlooked. Recent studies have shed light on the changes in soil bacterial composition resulting from modifications in tillage practices, particularly when compared to conventional tillage methods. However, there is a lack of soil microbial community analysis conducted under conservation tillage and rainfed conditions in the Mediterranean basin. A metataxonomic approach was employed to assess the influence of 19 years (2004–2022) of minimum tillage (MT) and no-till (NT) practices, along with crop rotation, on the soil bacterial community at upper layers (15 cm depth). This field study involved three different seasonal moments throughout the year. Results revealed that both sampling time and tillage management significantly influenced the structure of the bacterial community, whereas no effect was observed due to the crop. May showed a higher taxonomic diversity than July and December, showing differences in some o fthe most abundant phyla, such as Actinobacteria, Firmicutes and Proteobacteria. On the other hand, the long-term application of NT was found to lead to a significant decrease in bacterial diversity, with lower abundances of the phyla Chloroflexi, Gemmatimonadetes, and Armatimonadota, as well as an increase in k-strategist bacteria compared to MT. However, no significant effect on alpha diversity was observed as a result of tillage. no variations in phyla composition were observed attributable to crop, as the primary distinctions were identified among legume crops, which were associated with different sampling times. Therefore, our conclusion is that over this period, NT did not promote microbial diversity in the upper soil layers, despite notable shifts in bacterial composition occurring across seasonal time points in both tillage management systems.

Ramifications of crop residue loading for soil microbial community composition, activity and nutrient supply

AbstractVariable results have been reported on the effects of crop residue loads on soil microbial properties. We investigated changes in soil bacterial composition, β‐glucosidase enzyme activity and nutrient bioavailability in response to wheat residue loading. The treatments included three levels of above‐ground wheat residues (removed, retained or supplemented), with or without fertilizer N. Bacteroidetes, Firmicutes and Verrucomicrobia (the first two are copiotrophs) were less abundant where residues were removed than where residues were retained or supplemented, but the reverse was true for Actinobacteria, Cyanobacteria, Chloroflexi and Nitrospirae (all oligotrophs, although some Actinobacteria can be copiotrophic). Actinobacteria were also less abundant where fertilizer N was applied, and the abundances of their genera (including Arthrobacter and Mycobacterium) increased where residues were removed, confirming that they were oligotrophic in this study. β‐diversity showed similar differences in the bacterial community structures because of residue management, but α‐diversity was not affected by residue management or N fertilizer. β‐glucosidase enzyme activities increased as C inputs increased with residue manipulation and N fertilizer. The enzyme activities increased with increasing residue loading in the 0–15 cm soil depth, but decreased with soil depth. Soil K supply increased with increasing residue loading, but nitrate‐N supply was highest with residue retention. These results demonstrate remarkable resilience of soil microbial functioning under a wide range of crop residue inputs, without adverse effects on enzyme activity attributable to inorganic N fertilizer. The increasing β‐glucosidase activity with increasing residue loading probably explains why crop residue return does not always increase soil C stocks.

Controlled natural selection of soil microbiome through plant-soil feedback confers resistance to a foliar pathogen

Background and aimsThe rhizosphere microbiome has been shown to contribute to nutrient acquisition, protection against biotic and abiotic stresses and, ultimately, to changes in the development and physiology of plants. Here, using a controlled natural selection approach, we followed the microbial dynamics in the soil of Arabidopsis thaliana plants infected with the foliar pathogen Pseudomonas syringae DC3000 (Pst).MethodsPlants were iteratively cultivated on a pasteurised soil inoculated with the soil microbial community of the previous iteration isolated from the rhizosphere of plants infected with Pst (pst-line) or not (mock-line). Modification of soil microbial communities was assessed through an amplicon-based metagenomic analysis targeting bacterial and fungal diversity. Plant fitness and transcript abundance of stress hormone related genes were also analysed.ResultsAt the tenth and eleventh iterations respectively, we observed a reduction in disease severity of 81% and 85% in pst-lines as compared to mock-lines. These changes were associated with (i) an early induction of defence mechanisms mediated by salicylic acid, in pst-line as compared to mock-line, shown by the decrease in transcript abundance of salicylic acid related genes, whereas jasmonic acid, ethylene or abscisic acid related genes remained unchanged and (ii) a shift in soil bacterial, and not in fungal, composition.ConclusionsOur study suggests that these changes in soil bacterial composition are mediated by plant-soil feedback in response to Pst and resulted in an activation of SA-related immune response in the plant. This supports the concept of applying plant-soil feedbacks to enhance soil suppressiveness against foliar pathogens.

The Response of Soil Bacterial Communities to Land-use Types in a Subtropical Mountainous Region, Southwestern China

In this study, the characteristics of soil bacterial composition and diversity were investigated under four land-use types (afforestation land, FL; abandoned land, SL; native grassland, GL; cultivated land, CL) to explore correlations between land-use types and the bacterial communites in soil in a subtropical mountainous region of southwestern China. The results showed that the dominant taxonomic genera were Actinobacteria and Proteobacteria. Land-use type influenced the bacterial richness and diversity, and ranked as follows: FL>CL>SL>GL. Marked differences in the distribution of taxon assemblages among the different land-use types in soil were found. The relative abundances of Acidobacteria in SL, Proteobacteria in FL, and Chloroflexi in GL presented as being higher than in other land-use types. Among all the physicochemical properties, significant pearson linear correlations between soil bacterial taxonomic genera (Flavobacterium, Sphingomonas, Blastocatella, Zymomonas, Pedomicrobium, Reyranella, Rhodanomonas, Flavisolibacter, Candidatus and Telmatobacter ) and physicochemical properties (pH, TP and LAP) were observed. These findings suggested that land-use type is a major factor that affects the bacterial composition and diversity, and that changes in soil bacterial composition and diversity are associated with shifts in physicochemical properties.

Synergistic Effect of Rhamnolipids and Inoculation on the Bioremediation of Petroleum-Contaminated Soils by Bacterial Consortia.

Crude oil is a serious soil pollutant, requiring large-scale remediation efforts. Bacterial consortia in combination with rhamnolipids can be an effective bioremediation method. However, the underlying mechanisms and associated changes in soil bacterial composition remain uncharacterized. Therefore, this study sought to evaluate the effectiveness of rhamnolipids in petroleum hydrocarbon removal, and the associated bacterial community dynamics during bioremediation of petroleum-contaminated soils. Contaminated soils were subjected to natural attenuation, bioremediation with rhamnolipids, bioremediation with bacterial consortia, or bioremediation with bacterial consortia supplemented with rhamnolipids (BMR). High-throughput sequencing of bacterial sample partial 16S rRNA sequences was performed. Additionally, the n-alkanes and aromatic fractions were analyzed by gas chromatography-mass spectroscopy. The results showed that rhamnolipid supplementation increased the rate and extent of total petroleum hydrocarbon biodegradation to a maximum of 81% within 35days. Further, phylogenetic analysis revealed that the bacterial community was composed of 14 phylotypes (similarity level = 97%). Actinobacteria and Proteobacteria were the two core phyla in all samples, accounting for 63-89%, but Proteobacteria was the most dominant phylum in the BMR sample (~ 53%). Among the top 20 genera, Pseudomonas, Pseudoxanthomonas, Cavicella, Mycobacterium, Rhizobium, and Acinetobacter were more abundant in BMR samples compared to other samples. Predicted functional profiles revealed that rhamnolipid addition also induced changes in gene abundance related to hydrocarbon metabolic pathways. This study provided comprehensive insights into the synergistic effect of rhamnolipids and bacterial consortia for altering bacterial populations and specific functional traits, which may serve to improve bacteria-mediated petroleum hydrocarbon biodegradation in contaminated soils.

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