Search Results (147)

Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed soils; however, direct soil transfer presents practical limitations for large-scale applications. An alternative strategy involves extracting microbial communities through soil washing processes, but its success highly depends on proper microbiota characterization and efficient extraction methods. This study evaluated a soil wash method using four different dispersant solutions (Tween-80, NaCl, sodium citrate, and sodium pyrophosphate) for their ability to extract the majority of microbial cells from Antarctic and Crop soils. The extracted microbiomes were analyzed using 16S rRNA gene metataxonomics to assess their diversity and abundance. We found that some treatments extracted a greater proportion of specific taxa, and, on the other hand, some extracted a lower proportion than the control treatment. In addition, these dispersant solutions showed the extraction of the relevant microbial community profile in soil samples, composed of multiple taxa, including beneficial bacteria for soil health. Our study aims to optimize DNA extraction methods for microbiome analyses and to explore the use of this technique in various biotechnological applications. The results provide insights into the effect of dispersant solutions on microbiome extractions. In this regard, sodium chloride could be optimal for Antarctic soils, while sodium citrate is suggested for the Crop soils. Full article

Environmental DNA (eDNA) is DNA isolated from environmental samples. It is distinctly different from genomic DNA, which is extracted directly from biological specimens. eDNA metabarcoding technology is a novel surveillance tool combining eDNA and second-generation high-throughput sequencing technology. Different from conventional approaches and biomonitoring techniques, eDNA metabarcoding technology (eMT) has many advantages, such as promising timeliness and accuracy, lower time consumption, and low cost, and thus is widely used in ecological and environmental monitoring, including that in rivers, lakes, oceans, soils, and sediments. As a tool, eDNA metabarcoding technology supplements the evaluation of environmental qualities by monitoring both the diversity of aquatic biology communities and target species. In addition, it is essential to understand the limitations of eDNA metabarcoding technology in practical applications. As a tool, eDNA metabarcoding technology features high efficiency, providing indicators of environmental health and allowing for the indirect estimation of the impact and extent of water pollution with respect to aquatic ecosystems. It provides new insights for aquatic environment protection. Full article

Soil salinity is a major global challenge, reducing fertility and crop productivity. This study evaluated the effects of various soil management practices on the physical, chemical, and microbial properties of saline soils. Six treatments, combining loosening, ploughing, disking, and gypsum amendment, were applied to solonetzic meadow soil with high sodium levels. Soil penetration resistance was measured using a Penetronik penetrometer, while chemical analyses included pH, total salt content, calcium carbonate (CaCO₃), humus, and exchangeable cations (Na⁺, K⁺, Ca²⁺, Mg²⁺). Microbial composition was determined through DNA extraction and nanopore sequencing. The results showed that level A had the lowest penetration resistance (333 ± 200 N/m²), indicating better conditions for plant growth. Gypsum and loosening treatment significantly improved penetration resistance (141 N/m², p < 0.001), while gypsum amendment enhanced chemical properties (p < 0.05, p < 0.01, and p < 0.001). Gypsum application balanced soil parameters and influenced microbial communities. Reduced tillage favored functionally important microbial genera but did not support fungal diversity (p > 0.05). These findings highlight the effectiveness of gypsum amendment and tillage practices, like loosening and disking, in mitigating salinity stress and fostering beneficial microbial communities. Combining gypsum with these tillage methods proved most effective in enhancing soil health, offering insights for sustainable soil management in saline environments. Full article

Salinity is one of the main abiotic stresses that limits plant growth. This study addressed how the composition and diversity of root-associated bacterial communities reacts over time to salt-induced stress conditions. To understand its adaptation to soil salinization, the microbiome was studied by total DNA extraction and sequencing, using the Illumina MiSeq platform. Additionally, we evaluated the plant metabolites associated with salt stress (oxylipins, fatty acids (FAs) and hormones) by mass spectrometry. Salinity reduced rhizosphere bacterial diversity in salt-treated plants at 7 and 14 days and triggered a progressive shift of the bacterial structure, starting 7 days after salt stress imposed. The bacterial rhizosphere community became enriched with specific bacteria associated with potential genes involved in the PGP trait and ion homeostasis. For these plants, metabolites that showed higher levels included 9-lipoxygenase (LOX) oxylipins, which were found at days 7 and 14. The results indicated that salinity seems to have induced changes in the rhizosphere bacterial community, with characteristics that may help the plant respond to the imposed stress. Furthermore, our study highlighted the role of 9-LOX oxylipins in responding to salinity stress, providing new insights into the complex plant–microbe interactions under salt stress. Full article

Continuous cropping obstacles pose significant constraints and urgent challenges in the production of Tussilago farfara L. This experiment investigated the effects of consecutive cropping on T. farfara over periods of 1, 2, and 3 years. It assessed the yield and quality of T. farfara flower buds, in addition to the physicochemical properties of the rhizosphere soil. The microbial community in the rhizosphere was analyzed through 16S rDNA and ITS sequencing using Illumina Novaseq high-throughput sequencing technology, while also examining the correlations among these factors. The results reveal that as the duration of continuous cropping increases, the yield of T. farfara flower buds, along with the contents of extract, tussilagone, and total flavonoids, steadily decreased; soil pH, organic matter, available phosphorus, available potassium, alkaline nitrogen, and the activities of sucrose, catalase, and alkaline phosphatase markedly decreased. As the duration of consecutive cropping increases, the quantity and diversity of bacteria in the rhizosphere soil initially increase and then decrease, while the number of fungal species increases by 22.5%. Meanwhile, continuous cropping of T. farfara contributes to a gradual reduction in the relative abundance of beneficial genera such as Ralstonia, Nitrospira, and Trichoderma in the rhizosphere soil, while harmful genera such as Mortierella, Fusarium, and Tricharina accumulate significantly. Correlation analysis shows that changes in microbial communities notably influence the growth of T. farfara and soil quality. This study elucidates the impacts of continuous cropping on the yield and quality of T. farfara flower buds, soil physicochemical properties, and the microbial communities in the rhizosphere, providing a scientific basis for further research on continuous cropping barriers and the selection of beneficial microbial genera for the growth of T. farfara. Full article

Microalgal biomass offers a promising biofertilizer option due to its nutrient-rich composition, adaptability, and environmental benefits. This study evaluated the potential of microalgal-based biofertilizers—microalgal Chlorella biomass, de-oiled microalgal biomass (DMB), and de-oiled and de-aqueous extract microalgal biomass (DAEMB)—in enhancing lettuce growth, soil nutrient dynamics, and microbial community composition. Lettuce seedlings were cultivated with these biofertilizers, and plant growth parameters, photosynthetic pigments, and nitrogen uptake were assessed. Soil incubation experiments further examined nutrient mineralization rates, while DNA sequencing analyzed shifts in rhizosphere microbial communities. Lettuce grown with these biofertilizers exhibited improved growth parameters compared to controls, with Chlorella biomass achieving a 31.89% increase in shoot length, 27.98% in root length, and a 47.33% increase in fresh weight. Chlorophyll a and total chlorophyll levels increased significantly in all treatments, with the highest concentrations observed in the Chlorella biomass treatment. Soil mineralization studies revealed that DMB and DAEMB provided a gradual nitrogen release, while Chlorella biomass exhibited a rapid nutrient supply. Microbial community analyses revealed shifts in bacterial and fungal diversity, with increased abundance of nitrogen-fixing and nutrient-cycling taxa. Notably, fungal diversity was enriched in biomass and DAEMB treatments, enhancing soil health and reducing pathogenic fungi. These findings highlight microalgal biofertilizers’ potential to enhance soil fertility, plant health, and sustainable resource use in agriculture. Full article

A total of 34 strains of bacteria were isolated from peanut rhizosphere soil, and all showed some in vitro inhibition of the pathogen Sclerotium rolfsii in co-culture. Strain YB-1632 produced the highest level of inhibition and also produced relatively high levels of biofilm in culture. Cell-free culture extracts and volatiles from it were also inhibitory to S. rolfsii. Based on 16S rDNA, gyrA, and gyrB sequences, it was identified as Bacillus siamensis. In the greenhouse, seed treatment resulted in a level of control of peanut sclerotium blight (PSB) comparable to that of a standard fungicide seed treatment. In addition to its antifungal activity, YB-1632 could induce disease resistance in peanut seedlings based on increasing peanut defense enzyme activities and gene expression. The priming of defense gene expression against a necrotrophic pathogen is consistent with Induced Systemic Resistance (ISR). In addition, YB-1632 produced enzyme activities in culture associated with root colonization and plant growth promotion. In the greenhouse, it increased peanut seedling growth, indicating the YB-1632 is a plant growth-promoting rhizobacterium (PGPR). In summary, YB-1632 is a promising novel PSB biocontrol agent and PGPR of peanut. Full article

Soil is the most dynamic matrix in the environment and where biogeochemical cycles take place through the activities of microorganisms such as bacteria. A 16S rRNA sequence analysis of seven different soil samples from different geographical locations in the northeastern part of the United States of America was conducted in order to determine bacterial community composition and diversity and whether geographical distance affects community composition. Microbial DNA was extracted from each soil sample and next generation sequencing was performed. Overall, the predominant bacterial phyla with high relative abundance in each soil were found to be members of Pseudomonadota, Actinomycetota, Acidobacteriota, Chloroflexota, and Bacteroidota which comprised the core microbiome in all 7 soils analyzed. At the order level, the top four bacteria belonged to Rhizobiales, Actinomycetales, Gaiellales, and Solirubrobacterales. Bacterial identification at the genus level were predominantly unclassified with an average of 58%. However, when identification was possible, the most abundant genera detected were Bradyrhizobium and Rhodoplanes. Surface soil samples from the states of New York, Maryland, and Delaware showed the lowest bacterial diversity when compared to suburban soil samples from the state of New Jersey. Similarity between bacterial communities decreased with increasing distance, indicating the dispersal limitations of some bacteria to colonize different habitats where some types show high relative abundance and others did not. However, in some samples, deterministic factors such as land management and possible vehicle emissions probably affected the assemblage and diversity of bacterial communities. Stochastic and deterministic processes might have determined the biogeographical distribution of bacteria in soils influencing the community structure and diversity. Full article

Drought and salinity are major environmental constraints that severely limit crop production, particularly in arid and semi-arid zones. We investigated the genetic diversity of arbuscular mycorrhizal fungi isolated from the rhizosphere of Vachellia seyal in three different soils from Senegal with varying levels of salinity. Soil and root samples were collected from under V. seyal and in the vicinity of the trees. After DNA extraction, nested PCR, and sequencing of the large subunit region of the rRNA gene, different phylotypes from rhizospheric soils, roots, and spores were compared by phylogeny in order to investigate the role of salinity in arbuscular fungal diversity. This study revealed several unidentified arbuscular fungi and a particularly high host specificity in V. seyal roots. The vast majority of operational taxonomic units (OTUs) isolated in this study had no homologous sequences in the databases. Full article

Background: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies. Methodology: In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups. Results: In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment. Conclusions: Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments. Full article

Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity. Full article

The prevalence of plant parasitic nematodes (PPN) in the Irish peatlands was investigated in five different peatland habitats—raised bog, cutover scrub/woodlands, fens and peat grasslands, which were further sub-categorised into fourteen different sub-habitats. Within the raised bog habitat were healthy bog hummock (HBH), healthy bog lawn (HBL), degraded bog hummock (DBH) and degraded bog lawn (DBL) and the fen habitats were fen peat (FP) and rich fen peat (R-FP). Cutover scrub or woodland habitat included cutover scrub rewetted (C-RW), cutover scrub non-rewetted (C-NRW), woodlands rewetted (W-RW) and woodlands non-rewetted (W-NRW). Grassland included wasted peat (WP), rough grazing (RG-I) and improved fen peat grassland (IFPG-RW and IFPG-NRW). Soil samples from peatlands were all collected between July and December 2023 when the temperature ranged from 12 to 20 °C. One half of each sample was used for molecular nematode analysis and the other half for morphological identification of nematodes. For the morphological identification, a specific nematode extraction protocol was optimised for peatland soils, and the extracted nematodes were fixed onto slides to be studied under a high-power light microscope. Subsequently, the other part of the soil was processed to isolate total DNA, from which the 18S rRNA gene was sequenced for the identification of nematode taxa. The extracted DNA was also used for randomly amplified polymorphic DNA (RAPD) fingerprinting analysis to determine banding patterns that could classify different bog habitats based on PPN random primers. Compared to that in the climax habitats (HBH, HBL, DBH, DBL, FP, R-FP), PPN prevalence was recorded as being higher in grasslands (WP, RG-I, IFPG-RW and IFPG-NRW) and scrub/woodland ecosystems (C-RW, C-NRW, W-RW, W-NRW). The results indicate that nematode populations are different across the various bog habitats. Emerging and current quarantine PPN belonging to the families Pratylenchidae, Meloidogynidae, Anguinidae and Heteroderidae were noted to be above the threshold limits mentioned under EPPO guidelines, in grassland and wooded peatland habitats. Future actions for PPN management may need to be considered, along with the likelihood that these PPN might impact future paludiculture and other crops and trees growing in nearby agricultural lands. Full article

Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61–66 (ZymoBIOMICs) up to 80–82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs. Full article

The stubby root nematode, Paratrichodorus allius, is one of the most important plant-parasitic nematodes. Besides root feeding, P. allius also transmits the Tobacco rattle virus in potatoes, which causes corky ringspot disease. Rapid detection of P. allius is key for efficient management. This study was conducted to develop a real-time recombinase polymerase amplification (RPA) assay that is capable of detecting P. allius directly in DNA extracts from soil using a simple portable device in real time. A fluorophore-attached probe was designed to target the internal transcribed spacer (ITS)-rDNA of P. allius and was used along with primers designed previously. The real-time RPA assay had the ability to detect P. allius DNA extracted directly from infested soil with a sensitivity of one-sixteenth portion of a single nematode. This RPA assay was specific, as it did not produce positive signals from non-target nematodes tested. The real-time RPA was found to be rapid as it could even detect P. allius in as little as 7 min. Testing with 15 field soil samples validated the RPA assay developed in this study. This is the first report of P. allius detection directly from soil DNA using real-time RPA and is the fastest method for P. allius detection in soil to date. Full article

Endophytic bacteria from pea (Pisum sativum L.) plants play important roles in regulating plant growth, health, and nutrition. To enhance the understanding of endophytic bacteria in peas, twenty pea cultivars, two chickpeas, and two broad bean cultivars were planted into artificial soils for 4 weeks. Leaves and roots were collected from plants and sterilized. Endophytic bacterial DNAs were isolated from sterilized materials (leaves, roots, and seeds) and used as templates to detect the bacterial diversity by amplifying the 16S V3–V4 region. The Remel Tryptose Soya Agar (TSA) medium, the aluminum sec-butoxide (ASb) medium, and the yeast extract mannitol agar (YMA) medium were used to isolate bacteria from sterilized leaves and roots, respectively. The plant growth-promoting (PGP) properties of these isolated bacteria, such as the solubilization of phosphorus and potassium and the production of Indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, nitrogenase, pectinase, and cellulose, were studied in vitro. Bacterial isolates were processed for 16S rDNA gene sequencing and performed molecular identification by reconstruction of the phylogenetic tree using the neighborhood association approach in the software MEGA X. Results indicated that the majority of the bacterial communities were shared among leaves, roots, and seeds of pea plants. In both the leaves and roots of pea plants, the prominent phyla identified were Pseudomonadota, Bacteroidota, and Bacillota, with dominant genera such as Rhizobium, Bacteroides, Blautia, and Prevotella prevailing at the genus level. The samples from leaves and roots had unique dominant bacterial genera. In total, 48 endophytic bacteria strains were isolated from leaves and roots, of which 16 strains were from roots and 32 strains were from leaves. The majority of the isolates from leaves (78.13%) and roots (75%) had the ability to produce indole-3-acetic acid (IAA). Moreover, isolates from roots also had greater ability to produce 1-amino-cyclopropane-1-carboxylic acid (ACC) deaminase (81.25%) than those from leaves (62.5%). This study demonstrated the unique distribution of endophytes in leaves and roots of pea, which can have great potential in pea production. Full article