Rhizosphere Microenvironments of Eight Common Deciduous Fruit Trees Were Shaped by Microbes in Northern China

Effects of Substrate Composition on the Growth Traits of Grafted Seedling in Macadamia (Macadamia integrifolia) Nuts

Macadamia nut plantings in China are expanding year by year. In order to breed and promote superior varieties, this study analyzed the effects of different rootstocks and scions on the survival rate of grafted seedlings, and then selected the best substrate composition for plant growth. The results showed that the survival rate of the HAES788 variety as rootstock and Guire No. 1 as scion was the highest, reaching 96%. The optimal grafting time in December was better than that in March. Furthermore, among 16 substrate formulations, T12, T13, T15, and T16 had advantages of agglomerated soil and more well-developed root systems compared to the CK made of loess. The plant height, stem diameter, leaf length, leaf width, and dry weight of the aboveground and underground parts of the grafted seedlings planted in these substrate formulations were significantly higher than those plants planted in the CK. In addition, the substrate formulations T12, T13, T15, and T16 significantly improved the organic matter, total nitrogen, and total potassium content of the substrate soils, but little improvement was observed for total phosphorus content after 13 months. Overall, macadamia grafting times are best in December, with HAES788 and Guire No. 1 being the best rootstock and scion. The optimal substrate formulations are T12, T13, T15, and T16. This study provides a solid foundation for the production of high-quality macadamia plants.

Effects of Male and Female Strains of Salix linearistipularis on Physicochemical Properties and Microbial Community Structure in Saline-Alkali Soil

The woody plant gender difference may lead to alteration in rhizosphere microbial communities and soil physicochemical properties. In this study, we investigated the differences in rhizosphere soil properties and microbial community structures of S. linearistipularis. Rhizosphere microorganisms were analyzed by high-throughput sequencing technology. The results showed that there were significant differences in rhizosphere soil nutrition between male and female S. linearistipularis plants in saline-alkali soil. The female S. linearistipularis plants significantly reduce soil pH values and significantly increase the soil water content (SWC), available total nitrogen (TN), soil organic matter (SOM), and soil urease activity (S-UE) compared to the male plant. The ACE, Chao, and Shannon index of the female plant was significantly higher than that of the male strain. At the level of Bacteriophyta, the relative abundance of Actinobacteriota in male and female S. linearistipularis was the highest, with 34.26% and 31.03%, respectively. Among the named bacterial genera, the relative abundance of Defluviicoccus of male and female plants was the highest, with 2.67% and 5.27%, respectively. At the level of Eumycophyta, the relative abundance of Ascomycetes in male and female plants was the highest, with 54.93% and 52.10%, respectively. Among the named fungi genera, the relative abundance of male and female plants of Mortierella was the highest, with 6.18% and 9.31%, respectively. In addition, soil pH, SOM, SWC, and S-UE activities were the main driving factors of soil microbial community structures. In the process of restoring saline-alkali land in the Songnen Plain, we may prioritise the planting of female S. linearistipularis, which also provides a theoretical basis for the microorganisms restoration of saline-alkali land in the Songnen plain.

Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a 'Red Jonaprince' apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches.

Stochastic processes drive the soil fungal communities in a developing mid-channel bar

Intricate associations between rhizosphere microbial communities and plants play a critical role in developing and maintaining of soil ecological functioning. Therefore, understanding the assembly patterns of rhizosphere microbes in different plants and their responses to environmental changes is of great ecological implications for dynamic habitats. In this study, a developing mid-channel bar was employed in the Yangtze River to explore the assembly processes of rhizosphere fungal communities among various plant species using high-throughput sequencing-based null model analysis. The results showed a rare significant variation in the composition and alpha diversity of the rhizosphere fungal community among various plant species. Additionally, the soil properties were found to be the primary drivers instead of plant species types. The null model analysis revealed that the rhizosphere fungal communities were primarily driven by stochastic processes (i.e., undominated processes of ecological drift), and the predominance varied with various plant species. Moreover, the assembly processes of rhizosphere fungal communities were significantly related to the changes in soil properties (i.e., soil total carbon, total nitrogen, organic matter, and pH). The co-occurrence network analysis revealed that many keystone species belonged to unclassified fungi. Notably, five network hubs were almost unaffected by the measured soil properties and aboveground plant traits, indicating the effect of stochastic processes on the rhizosphere fungal community assembly. Overall, these results will provide insights into the underlying mechanisms of fungal community assembly in the rhizosphere soils, which are significant for maintaining the functional stability of a developing ecosystem.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Response of physiological characteristics of ecological restoration plants to substrate cement content under exogenous arbuscular mycorrhizal fungal inoculation

INTRODUCTION

In order to solve the inhibition of alkaline environment on plants growth at the initial stage of Eco-restoration of vegetation concrete technology, introducing AMF into vegetation concrete substrate is an effective solution.

METHODS

In this study, Glomus mosseae (GM), Glomus intraradices (GI) and a mixture of two AMF (MI) were used as exogenous inoculation agents. Festuca elata and Cassia glauca were selected as host plants to explore the relationship between the physiological characteristics of plants and the content of substrate cement under exogenous inoculation of AMF.

RESULTS

The experiment showed that, for festuca elata, the maximum mycorrhizal infection rates of inoculation with GM, MI were when the cement contents ranged 5-8% and that of GI inoculation was with the cement contents ranging 5-10%. Adversely, for Cassia glauca, substrate cement content had little effect on the root system with the exogenous inoculation of AMF. Compared with CK, the effects of AMF inoculation on the physiological characteristics of the two plants were different. When the cement content was the highest (10% and 8% respectively), AMF could significantly increase(p<0.05) the intercellular CO₂ concentration (Ci) of Festuca elata. Moreover, for both plants, single inoculation was more effective than mixed inoculation. When the cement content was relatively low, the physiological characteristics of Cassia glauca were promoted more obviously by the inoculation of GI. At higher cement content level, inoculation of GM had a better effect on the physiological characteristics of the two plants.

CONCLUSION

The results suggest that single inoculation of GM should be selected to promote the growth of Festuca elata and Cassia glauca in higher alkaline environment.

Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars

Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20-34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon-Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.

Differences in Microbial Communities Stimulated by Malic Acid Have the Potential to Improve Nutrient Absorption and Fruit Quality of Grapes

Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson's correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae. Furthermore, Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae were closely related to grape nutrient absorption and fruit quality. Bacillaceae and Woeseiaceae were positively correlated with total soluble sugar, while Planococcaceae and Rhodobacteraceae were positively correlated with titratable acid. Hence, Bacillaceae and Woeseiaceae were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.

Deyeuxia angustifolia Kom. encroachment changes soil physicochemical properties and microbial community in the alpine tundra under climate change

Plant encroachment in alpine regions, caused by global changes and human activities, has been well documented. However, our knowledge of the effects of plant encroachment on belowground microbial communities is limited. Here, we investigated soil physicochemical properties and microbial community structures under the impact of plant encroachment along an elevation gradient in the alpine tundra of the Changbai Mountain, China. We found that plant encroachment had insignificant (P > 0.05) and inconsistent effects on the α-diversity (number of observed OTUs, Shannon, Chao1, Faith's PD) of soil microbial communities. Plant encroachment indirectly influenced soil microbial community structures by altering soil physicochemical properties, which differed between elevations and plant types (P < 0.05). In all, 40 bacterial indicator taxa and 57 fungal indicator taxa significantly shifted in response to plant encroachment, some of which were involved in soil biogeochemical cycle. Overall, our results documented the impacts of plant encroachment on soil microbial diversity and community composition, and provided a scientific basis for predicting future changes in alpine ecosystem structure and function and its subsequent feedbacks to global change.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris)

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Pecan agroforestry systems improve soil quality by stimulating enzyme activity

BACKGROUND

Forest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and chemical properties of the soil.

METHODS

The treatments for this study included a single cultivation (CK) pecan control and three agroforestry systems (pecan + Paeonia suffruticosa + Hemerocallis citrina, pecan + Paeonia suffruticosa, and pecan + Paeonia lactiflora). Soil samples were categorized according to the sampling depth (0-20 cm, 20-40 cm, 40-60 cm).

RESULTS

The results demonstrated that the bulk density (BD) of soil under the pecan agroforestry system (PPH and PPL) was reduced by 16.13% and 7.10%, respectively, and the soil moisture content (MC) and total soil porosity (TPO) increased. Improvements in the physical properties of the soil under the PPS agroforestry system were not obvious when compared with the pecan monoculture. The soil total phosphorus (TP), total nitrogen (TN), available potassium (AK), and total carbon (TC) increased significantly, while the soil urease (S-UE), alkaline phosphatase (S-AKP), and 1,4-β-N-acetylglucosamines (S-NAG) enzyme activity also increased significantly, following agroforestry. Overall, the pecan agroforestry system significantly improved the physical properties of the pecan plantation soil, enriched the soil nutrients, and increased the activity of soil enzymes related to TC, TN, and TP cycles.

Changes of the agrochemical soil characteristics in the stone fruit orchard with the permanent application of nitrogen and potash fertilizers

The purpose of the research was to evaluate the changes in the agrochemical properties of the sour cherry orchard soil after the permanent soil fertilization with urea and potassium sulfate. The field experiment was conducted during 2017-2021 in the soil and climatic conditions of the Central Russian Upland (Oryol region). ‘Turgenevka’ sour cherry trees grafted on the rootstock V-2-180 were planted in 2015 at a distance of 5x3 m. The soil of the orchard is loamy Haplic Luvisol with the following parameters: pHKCl - 5.8, organic matter content - 2.8%, available phosphorus - 383 mg/kg, exchange potassium -120 mg/kg, alkali-hydrolysable nitrogen - 108 mg/kg. Experimental scheme: 1. Control (no fertilizers); 2. N30К40; 3. N60К80; 4. N90K120; 5. N120K160. Fertilizers were applied once a year in early spring. The annual use of fertilizers in N90K120 dose or more contributed to an increase in the reserves of mobile phosphorus, exchange potassium, and alkali-hydrolysable nitrogen in the orchard soil, but did not have a stable effect on the tree productivity. At the same time, there was an increase of soil acidity and loss of exchange calcium under the influence of fertilizers, which indicates the beginning of degradation processes.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Characterizing the Intra-Vineyard Variation of Soil Bacterial and Fungal Communities

Vineyard soil microbial communities potentially mediate grapevine growth, grape production as well as wine terroir. Simultaneously assessing shifts of microbial community composition at the intra-vineyard scale allows us to decouple correlations among environmental variables, thus providing insights into vineyard management. Here we investigated bacterial and fungal community compositions and their relationships with edaphic properties in soils collected from a commercial vineyard at four different soil depths (0-5, 5-10, 10-20, and 20-40 cm). Soil organic carbon (SOC) content, invertase activity and phosphatase activity decreased along depth gradient in the 0-20 cm soil fraction (P < 0.001). The soil bacterial biomass and α-diversity were significantly higher than those of fungi (P ≤ 0.001). Statistical analyses revealed that SOC content, pH, C/N ratio and total phosphorus (TP) were significant determinants of soil bacterial (R = 0.494, P = 0.001) and fungal (R = 0.443, P = 0.001) community structure. The abundance of dominated bacterial phyla (Proteobacteria, Acidobacteria and Actinobacteria) and fungal phyla (Ascomycota, Zygomycota and Basidiomycota) slightly varied among all soil samples. Genus Lactococcus, which comprised 2.72% of the soil bacterial community, showed increasing pattern with depth. Importantly, Candidatus Nitrososphaera, Monographella and Fusarium were also detected with high abundances in soil samples, indicating their ecological function in soil nitrogen cycle and the potential risk in grapevine disease. Overall, this work detected the intra-vineyard variation of bacterial and fungal communities and their relationships with soil characteristics, which was beneficial to vineyard soil management and grapevine disease prevention.