Search Results (8)

Ziziphus lotus (L.) Lam. (Rhamnaceae), a key shrub species native to North Africa, is commonly found in arid and semi-arid regions. Renowned for its resilience under harsh conditions, it forms vegetation clusters that influence the surrounding environment. These clusters create microhabitats that promote biodiversity, reduce soil erosion, and improve soil fertility. However, in agricultural fields, Z. lotus is often regarded as an undesirable species. This study investigated the bacterial diversity and community composition along spatial gradients around Z. lotus patches in barley-planted and non-planted fields. Using 16S rRNA gene sequencing, 84 soil samples were analyzed from distances of 0, 3, and 6 m from Z. lotus patches. MiSeq sequencing generated 143,424 reads, representing 505 bacterial ASVs across 22 phyla. Alpha-diversity was highest at intermediate distances (3 m), while beta-diversity analyses revealed significant differences in community composition across distances (p = 0.035). Pseudomonadota dominated close to the shrub (44% at 0 m) but decreased at greater distances, whereas Bacillota and Actinobacteriota displayed distinct spatial patterns. A core microbiome comprising 44 ASVs (8.7%) was shared across all distances, with the greatest number of unique ASVs identified at 3 m. Random forest analysis highlighted Skermanella and Rubrobacter as key discriminatory taxa. These findings emphasize the spatial structuring of bacterial communities around Z. lotus patches, demonstrating the shrub’s substantial influence on bacterial dynamics in arid ecosystems. Full article

Biological nitrogen (N) fixation is an ecological method used to provide nutrition for crops and reduce fertilizer application in terrestrial ecosystems. Silver nanoparticles (AgNPs) are becoming environmental contaminants, and, thus, could negatively affect the activity and diversity of soil diazotrophs. To test this, a greenhouse pot experiment for growing maize was performed under different concentrations of AgNPs (0, 1, 5, 10, 20 mg kg⁻¹). We measured the N₂-fixation activity and abundance of nifH gene encoding the nitrogenase reductase subunit and analyzed the diversity, composition and co-occurrence networks of diazotrophic communities in maize rhizospheric soil. Results showed that a lower dose of AgNPs did not show significant influence on soil diazotrophs, while a higher dose of AgNPs decreased both soil N₂-fixation activity and nifH gene abundance, though diazotrophic diversity remained unchanged. AgNPs at 10 mg kg⁻¹ and 20 mg kg⁻¹ strongly shifted the community composition of diazotrophs, increasing the proportions of Bradyrhizobium and Paenibacillus, while decreasing Azospirillum and Rhizobium. Network analysis revealed weakened negative associations among species under AgNPs, with keystone taxa shifting from Bradyrhizobium, Geobacter, Azospirillum and Burkholderia to Bradyrhizobium, Paenibacillus and Skermanella under AgNPs. Soil-soluble Ag, dissolved organic carbon and soil pH were identified as the factors most closely driving the diazotrophic community composition. In conclusion, higher doses of AgNPs could inhibit N₂-fixation activity and shape the diazotrophic communities. These findings provide empirical evidence of AgNPs’ ecological impacts on soil microbial functions. Full article

Biological soil crusts (referred to as biocrusts) constitute prominent components within the ecosystem of tropical coral islands in the South China Sea, covering approximately 6.25% of the island’s terrestrial surface. Biocrusts are the key to the restoration of the island ecosystem. It is widely acknowledged that phototrophic microorganisms profoundly contribute to biocrust formation and development. They provide fixed carbon and nitrogen and produce exopolysaccharides for the BSC ecosystems. Although aerobic anoxygenic phototrophic bacteria (AAPB) are an important functional group of phototrophic microorganisms, the community characteristics of AAPB in coral island biocrusts and their role in the formation of biocrusts have rarely been reported. In this study, we employed amplifications of the pufM gene to characterize the AAPB communities of biocrusts on a tropical coral island. The outcomes revealed a discernible augmentation in both the abundance and richness of AAPB concurrent with the formation of biocrusts, concomitantly with a decrement in diversity. Within the AAPB communities, the Pseudomonadota (Proteobacteria) phylum emerges as the prevailing dominion, indicating marked differentiations in terms of family and genus compositions between the biocrust and bare soil. Canonical correlation analysis has unveiled a robust and meaningful correlation between the AAPB composition and the attributes of the soil, including total nitrogen, total organic carbon, total phosphorus, pH, and calcium content. Furthermore, co-occurrence network patterns shift with biocrust formation, enhancing stability. Meanwhile, keystone taxa analysis revealed specific OTUs associated with each soil type, with genus Brevundimonas as the main group. Furthermore, pure-culture AAPB strains isolated from biocrusts exhibited a panorama of diversity, predominantly belonging to Pseudomonadota. Particularly, the Skermanella and Erythrobacter genera demonstrated strong exopolysaccharide secretion and sand-binding capabilities. This study sheds light on the significant functional role of AAPB in tropical coral island biocrusts, expanding our understanding of their contribution to ecosystem services, and providing valuable insights for ecological restoration efforts on coral islands. Full article

(1) Background: Rhizobia can promote plant growth by providing essential nutrients such as NH₄⁺ and PO₄³⁻; thus, rhizobia that can tolerate the stress of heavy metals will be conducive to the phytoremediation of heavy-metal-contaminated soils. Therefore, understanding the dominant heavy-metal-tolerant rhizobia that can be cultured is important for the establishment of an indigenous legume–rhizobia symbiotic remediation system; (2) Methods: Here, we investigated nifH gene diversity in culturable rhizobia from black locust (Robinia pseudoacacia L.) grown in cadmium (Cd)-contaminated soils using high-throughput sequencing.; (3) Results: A total of 16 genera and 26 species were identified from the cultures of root nodules of black locust exposed to five Cd levels. Cadmium did not show a significant effect on the abundance, diversity, and evenness of the culturable rhizobia community. However, Cd significantly affected the community structure of culturable rhizobia containing nifH. Mesorhizobium, Sinorhizobium, and Rhizobium were the absolute dominant genera present in the cultures under five Cd treatments. Additionally, Cd significantly affected the relative abundance of Azohydromonas, Xanthobacter, Skermanella, Bradyrhizobium, Paenibacillus, and Pseudacidovorax in the cultures. Soil pH, total Cd, DTPA-Cd, and C/H ratio were the significant factors on culturable rhizobia community.; (4) Conclusions: Cd showed a negative effect on nifH gene community of culturable rhizobia from black locust, which will provide insight into the selection of excellent strains that can promote phytoremediation of heavy-metal-contaminated soils. Full article

The genus Skermanella comprises important soil bacteria that are often associated with the crop rhizospheres, but its physiological traits remain poorly understood. This study characterizes Skermanella sp. TT6^T, isolated from human skin, with a focus on its metabolic and environmental adaptations. Genome sequencing and phylogenomic analyses revealed that the strain TT6^T is most closely related to S. rosea M1^T, with average nucleotide identity and digital DNA–DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. Comparative genomic analysis showed that the strains TT6^T, S. rosea M1^T and S. mucosa 8-14-6^T share the Calvin cycle, and possess photosynthetic genes associated with the purple bacteria-type photosystem II. The strains TT6^T and S. rosea M1^T exhibited growth in a nitrogen-free medium under microaerobic conditions, which were generated in test tubes containing 0.1% soft agar. Under these conditions, with nitrate as a nitrogen source, S. rosea M1^T formed gases, indicating denitrification. Strain TT6^T also contains gene clusters involved in trehalose and carotenoid biosynthesis, along with salt-dependent colony morphology changes, highlighting its adaptive versatility. Genomic analyses further identified pathways related to hydrogenase and sulfur oxidation. Phenotypic and chemotaxonomic traits of strain TT6^T were also compared with closely related type strains, confirming its genotypic and phenotypic distinctiveness. The new species, Skermanella cutis sp. nov., is proposed, with TT6^T (=KCTC 82306^T = JCM 34945^T) as the type strain. This study underscores the agricultural and ecological significance of the genus Skermanella. Full article

Different fertilization measures affect the soil’s physical and chemical properties and bacterial community structure, which in turn affects the growth environment and yield of maize seed production. Therefore, rational fertilization measures are important in maintaining and improving soil fertility and promoting maize crop growth. Research on fertilization practices in maize fields for seed production can help to increase agricultural productivity while protecting and enhancing soil health and achieving sustainable agricultural development. To clarify the effects of different fertilization measures on soil bacterial communities in seed corn fields, 16S rRNA high-throughput sequencing technology and PICRUSt method were used to explore the soil under different fertilization measures (CK as control, effects of single application of liquid organic fertilizer (M), single application of bacterial agents (BF), and combined application of liquid organic fertilizer and bacterial agents (M + BF)) on soil bacterial community structure characteristics and ecological functions. Proteobacteria (20.14–25.30%), Actinobacteriota (18.21–20.47%), Actinobacteriota (13.55–22.00%), and Chloroflexi (14.24–17.59%) were the dominant phyla. Bacillus, RB41, Arthrobacter, and Sphingomonas were the dominant genera. M + BF treatment significantly increased the relative abundance of Planctomycetota. The relative abundance of Bacillus and PaeniBacillus in M treatment decreased considerably, while the relative abundance of Turicibacter increased significantly. The relative abundance of Sphingomonas was reduced considerably in M and M + BF treatments. The relative abundance of Subgroup 10 decreased significantly after BF and M + BF treatments. BF treatment significantly increased the relative abundance of Skermanella. Redundancy analysis showed that alkali-hydrolyzed nitrogen (p = 0.044) was the main environmental factor affecting soil bacterial communities under different fertilizer treatments. PICRUSt function prediction results showed that metabolism was the main functional component of bacteria, accounting for 78.45–78.94%. The abundance of functional genes for terpenoid and polyketone metabolism, the endocrine system, the excretory system, and the immune system of the soil bacterial community was significantly increased under M treatment, while the abundance of functional genes for the digestive system was decreased considerably. Different fertilizer cultivation measures changed soil bacterial community composition and ecological function in maize fields. These results can provide a theoretical reference for the study of bacterial community succession characteristics in maize fields and the determination of appropriate fertilizer cultivation measures. Full article

Microbial communities are known to play a principal role in petroleum degradation. This study tries to determine the composition of bacteria in selected crude oil-contaminated soil from Tabasco and Tamaulipas states, Mexico. We determined the microbial populations living under these conditions. We evaluated the structure and diversity of bacterial communities in the contaminated soil samples. The most abundant phylum is proteobacteria. Next Generation Sequencing (NGS) analysis of the sampled soils from both states revealed that this phylum has the most relative abundance among the identified bacteria phyla. The heatmap represented the relative percentage of each genus within each sample and clustered the four samples into two groups. Moreover, this allowed us to identify many genera in alkaline soil from Tamaulipas, such as Skermanella sp., Azospirillum sp. and Unclassified species from the Rhodospirillaceae family in higher abundance. Meanwhile, in acidic soil from Tabasco, we identified Thalassospira, Unclassified members of the Sphingomonadaceae family and Unclassified members of the Alphaproteobacteria class with higher abundance. Alpha diversity analysis showed a low diversity (Shannon and Simpson index); Chao observed species in both Regions. These results suggest that the bacteria identified in these genera may possess the ability to degrade petroleum, and further studies in the future should elucidate their role in petroleum degradation. Full article

Relict charcoal hearths (RCHs) increases soil fertility in forest ecosystems. However, the effects of RCHs on the activity and abundance of soil microorganisms remain unknown. In this paper, we analysed the impact of relict charcoal production on the soil enzymatic activity and composition of soil bacterial and fungal communities in Scots pine forests of the Manowo Forest District in northern Poland. Moreover, we determined the effect of relict charcoal production on the soil properties. Our research was conducted by comparing the physical, chemical, enzymatic and microbiological properties of charcoal-enriched and charcoal-free soils. Significant differences in physical properties were found between these two soil types in terms of their structure and water holding capacity. As expected, horizons enriched with charcoal were characterised by a significantly higher organic carbon content (4.7% on average compared to 2.2% in control horizons), and also by a considerably higher content of available phosphorus (an average of 64.07 mg·kg⁻¹ compared to 36.21 mg·kg⁻¹ in the control). Similarly, RCH horizons displayed a higher pH and higher contents of Ca and Na cations. These results indicated that RCH soils provided more favourable conditions for the soil microbiome, as reflected by the higher enzymatic activity and diversity of the microorganisms. Moreover, bacterial and fungal communities in RCH soils were more diverse and had greater species/genera richness, especially in the case of fungi. Members of the genus Rhodoplanes dominated the bacterial community at both RCH and non-RCH sites, followed by Streptomyces, Burkholderia, Skermanella, Tsukamurella and Candidatus Solibacter. Both culture- and next generation sequencing (NGS)-based analyses showed that soil fungal communities were dominated by Ascomycota, with Penicillium as the most abundant genus. Our results showed that hearth soils may represent a significant C pool in the forest ecosystem. This study supports the strategy of safeguarding such charcoal-enriched soils as precious C reservoirs and ecologically important biodiversity hotspots. Moreover, the application of charcoal may effectively increase the microbial diversity of forest soils, especially during the reforestation or re-cultivation of disturbed habitats. Full article