Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil

Microbial transformation of soil organic matter under varying agricultural management systems in Ukraine

Introduction

This paper presents comparative studies on the content and structure of organic matter (OM) and the activity of microbiological cellulose destruction in three types of Ukrainian soils intensively used in agricultural production.

Methods

The highest content of humus in the arable layer (4.9%), OM (410 t ha-1), and total carbon (30.9 mg C g-1 soil) was determined in chernic phaeozems, which is 2.2-2.5 times higher than in albic retisols. The soil of natural ecosystems is characterised by a high content of microbial carbon (Cmic) in the carbon fraction of organic soil compounds.

Results and discussion

In arable soils, the content and reserves of humus and soil organic matter (SOM) have decreased by an average of 1.5-2 times. The most considerable loss of humus reserves in the soil profile was identified in albic retisols (1.96-1.44 times) and the smallest in chernic phaeozems (1.27-1.81 times). During the long-term systematic application of mineral fertilisers, the Corg content decreased by 8-21% in chernic phaeozems, 12-33% in greyzemic phaeozems, and 6-38% in albic retisols. A significant difference of 2.1-8.0 times was determined regarding the number of aerobic cellulolytic microorganisms and 1.3-3.3 times in the potential cellulolytic activity of the studied soils. The high number of cellulose-destroying microorganisms is characteristic of chernic phaeozems with a high content of OM in the soil; the advantage over other types of studied soils was 1.4 times and 7.8 times for greyzemic phaeozems and albic retisols, respectively. Among the studied soil types, high values of CO2 emissions were identified in chernic phaeozems. Intensive agricultural practices in Ukrainian soils have significantly altered the content and composition of organic matter, leading to reduced humus and soil organic matter reserves. The study also underscores the importance of considering the abundance of cellulose-destroying microorganisms and their potential activity in assessing soil health and sustainability.

Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata

The top-down approach of microbiome-mediated rhizosphere engineering has emerged as an eco-friendly approach for mitigating stress and enhancing crop productivity. It has been established to mitigate salinity stress in Vigna radiata using multi-passaging approach. During the process of acclimatization under increasing levels of salinity stress, the structure of rhizospheric microbial community undergoes dynamic changes, while facilitating stress mitigation in plants. In this study, using ITS-based amplicon sequencing, the dynamics of rhizosphere fungal community was unravelled over successive passages under salinity stress in V. radiata. Clear shifts were evident among the fungal community members under stress and non-stress conditions, upon application of acclimatized rhizosphere microbiome in V. radiata across successive passages. These shifts correlated with enhanced plant biometrics and reduced stress marker levels in plant. Significant changes in the fungal community structure were witnessed in the rhizosphere across specific passaging cycles under salinity stress, which possibly facilitated stress mitigation in V. radiata.

A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar

Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.

Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate

Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.

Soil Microbial Distribution Depends on Different Types of Landscape Vegetation in Temperate Urban Forest Ecosystems

Although soil microbes play an important role in the functioning of the forest ecosystem, our understanding of the spatial distribution characteristics of soil microbes among different vegetation types in urban forest ecosystems is poor. In this study, with the help of high-throughput sequencing, we examined the vegetation type preferences of soil microbes (fungi and bacteria) and then analyzed the microbe–environment (plant community, light availability, soil properties) relations in a temperate urban forest in China. Our results showed that the soil microbial (bacterial and fungal) richness of deciduous forest was higher than that of evergreen, and mixed forests. The spatial distribution of fungi was more specialized than that of bacteria among different vegetation types. The driving forces of environmental factors on soil bacteria and fungi were different. Our findings suggest that different vegetation types favor the occurrence of different microbes, and the relationships between soil microbes and environmental factors depend on different vegetation types in this temperate urban forest. These findings shed new light on the biodiversity conservation of microbes in temperate urban forests and point to the potential importance of vegetation types for microbe formation.

Phylogenetic signal of host plants in the bacterial and fungal root microbiomes of cultivated angiosperms

Root microbiomes are established through selective recruitment by host plants from pools of potential partners. However, the assembly rules of root microbiomes remain unclear. To elucidate (i) the effects of host plant phylogeny on root microbiome assembly and (ii) which microbial groups affect differences in root microbiome assemblies, the structures of bacterial and fungal root microbiomes from 20 cultivated angiosperms were compared. Surface-sterilized seeds from each species were sown in identical soil, and DNA was extracted from the plant roots after 7-8 weeks. The bacterial (16S rRNA) and fungal (ITS) communities were then examined using Illumina MiSeq. The phylogenetic distances of host plants and assembly dissimilarities of bacterial microbiomes, but not of fungal ones, were significantly correlated, as were the topologies of the host plant phylogenetic tree and the community dissimilarity tree, thereby confirming the phylogenetic conservation of bacterial root microbiomes. Furthermore, host plant phylogeny mainly affected only a few specific bacterial lineages, including the Betaproteobacteria, Gammaproteobacteria, and Chloroflexi. Burkholderia (Betaproteobacteria) taxa were more abundant in monocots than in dicots, whereas Streptomyces (Actinobacteria) taxa were less abundant. These findings suggest that bacterial root microbiomes have significantly contributed to the functional divergence of angiosperms at higher taxonomic levels.

Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia

Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e.g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.