Perspectives of using Illumina MiSeq for identification of arbuscular mycorrhizal fungi

Diversity of Arbuscular Mycorrhizal Fungi of the Rhizosphere of Lycium barbarum L. from Four Main Producing Areas in Northwest China and Their Effect on Plant Growth

Arbuscular mycorrhizal fungi (AMF) can help plants absorb more mineral nutrients after they colonize plant roots, and the mycelia harmonize the soil structure and physical and chemical properties by secreting compounds. AMF species co-evolve with their habitat's geographic conditions and hosts; this gradually causes differences in the AMF species. By using Melzer's reagent to analyze the morphology and using Illumina Miseq sequencing technology to perform the molecular identification of AMF communities among the four typical L. barbarum planting areas (Zhongning, Guyuan, Jinghe, and Dulan) investigated, the variety of L. barbarum roots and rhizosphere AMF communities was greater in the Zhongning area, and every region additionally had endemic species. The successfully amplified AMF was re-applied to the L. barbarum seedlings. We found that the total dry weight and accumulation of potassium increased significantly (p < 0.05), and the root volume and number of root branches were significantly higher in the plants that were inoculated with Paraglomus VTX00375 in the pot experiment, indicating that AMF improves root development and promotes plant growth. We have investigated AMF germplasm species in four regions, and we are committed to the development of native AMF resources. The multiplication and application of AMF will be conducive to realizing the potential role of biology in the maintenance of agroecology.

Evaluation of the Presence of Arbuscular Mycorrhizae and Cadmium Content in the Plants and Soils of Cocoa Plantations in San Martin, Peru

Cocoa (Theobroma cacao L.) is an important crop in Peru. International regulations require products derived from cocoa to be free of heavy metals (HMs), such as cadmium. Arbuscular mycorrhizae (AM) contribute to reduced HM content in the plant, preventing its accumulation in the fruit and facilitating the rhizodeposition of HMs through glomalin-related soil proteins (GRSP). We studied the presence of mycorrhizal symbiosis in cocoa plants and cadmium in three plantations in San Martín, Peru. The maximum Cd content detected in soils was 1.09 (mg/kg), an amount below the tolerable limit for agricultural soil (≥1.4 mg/kg). Cocoa roots showed 68–86% active mycorrhizal colonization; agronomic management did not cause differences between plantations. Levels of GRSP were between 7.67 (GRSP-EE) and 13.75 (GRSP-T) mg protein g soil−1. Morphological and molecular analysis of Glomeromycota fungi showed the presence of families Claroideoglomeraceae, Paraglomeraceae, Gigasporaceae, Glomeraceae, Acaulosporaceae, Archaeosporaceae, and Diversisporaceae. Our results show the presence of arbuscular mycorrhizal symbiosis in cocoa plantations and suggest that T. cacao may phytostabilize HM in its rhizosphere through the production of GRSP. The presence of mycorrhizal symbiosis indicates the potential for the preparation of biofertilizers for cocoa since the production of GRSP is promissory for the biostabilization of soil HMs.

Illumina MiSeq Sequencing Reveals Correlations among Fruit Ingredients, Environmental Factors, and AMF Communities in Three Lycium Barbarum Producing Regions of China

The symbiotic relationship of arbuscular mycorrhizal fungi (AMF) is important for Lycium barbarum, a highly nutritious and medicinal crop. However, the influence of environmental factors on AMF communities remains largely elusive. Based on MiSeq sequencing, we analyzed AMF communities in rhizosphere soils of L. barbarum with growth synchronization in three typical L. barbarum cultivation sites in China. The Zhongning region has poor soils with a high richness of AMF communities. Geographical environmental variances lead to differences in AMF communities which in turn affects the active ingredients of L. barbarum fruit. Furthermore, different genera of AMF showed significant correlations with environmental factors and fruit ingredients. The three genera, Claroideoglomus, Dominikia, and Funneliformis correlated to environmental factors and fruits ingredients in a similar manner affecting the whole sugar (TS) and flavonoids (FLA) contents in the fruits of L. barbarum. Also, these showed a significantly positive correlation with soil pH. This fact was unknown so far due to different soil acidity/alkalinity in different studies. IMPORTANCE The climatic and ecological environment is a complex phenomenon, involving various environmental factors that regulate the diversity and population distribution structure of AMF communities affecting plant growth, crop composition, and yield. Current studies on the effects of environmental factors on AMF communities have mainly focused on soil conditions and host plants. Fewer studies have been conducted on the correlation between temperature, enzyme activity, plant fruiting, and AMF communities. The present study investigated the diversity of AMF communities and the influence of environmental factors on their distribution patterns, which showed similar effects on some AMF species. The results suggest that screening AMF fungicides that meet the target may significantly help soil restoration reducing the use of chemical fertilizers and a large amount of human and material resources.

Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture

Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.

A next-generation probiotic: Akkermansia muciniphila ameliorates chronic stress-induced depressive-like behavior in mice by regulating gut microbiota and metabolites

Major depressive disorder (MDD) is a neurasthenic disease, which is the second-largest burden of disease globally. Increasing studies have revealed that depression is associated with abnormalities in gut microbiota and metabolites. Several species of bacteria have been classified as psychobiotics, which confer mental health benefits through interactions with commensal gut microbiota. Therefore, it is essential to identify new psychobiotics and elucidate their mechanisms in the treatment of depression. This study aims to evaluate the antidepressant effect of Akkermansia muciniphila (AKK) in a mouse model of depression induced by chronic restraint stress (CRS). C57BL/6 male mice were divided into three groups: mice subjected to CRS, mice not subjected to CRS, and mice treated with AKK for 3 weeks. Behavioral tests were performed, and hormone, neurotransmitter, and brain-derived neurotrophic factor (BDNF) levels were measured. Cecal microbiota was analyzed using 16S rRNA gene sequencing, and serum metabolites were detected using untargeted metabolomics. In addition, correlations between altered gut microbiota and metabolites with significant variations in serum associated with AKK ameliorating depression were analyzed using Pearson's correlation coefficient. The results revealed that AKK significantly ameliorated depressive-like behavior and restored abnormal variations in depression-related molecular (corticosterone, dopamine, and BDNF). Moreover, AKK altered chronic stress-induced gut microbial abnormalities. Untargeted metabolomics analysis revealed 23 potential biomarkers in serum that could be associated with the mechanisms underlying CRS-induced depression and the therapeutic effects of AKK. Pearson's correlation coefficient analysis revealed that AKK predominantly upregulated β-alanyl-3-methyl-L-histidine and edaravone to relieve depression. Furthermore, β-alanyl-3-methyl-L-histidine and edaravone exhibited the antidepressant phenotype in mice subjected to CRS. In conclusion, the study demonstrated that AKK ameliorates chronic stress-induced depressive symptoms in mice by regulating gut microbiota and metabolites. KEY POINTS: • AKK reduces depressive-like behaviors induced by chronic stress. • AKK regulates the gut microbial structure and metabolomics of serum under the chronic stress. • Antidepressant effect of AKK correlates with the increase of β-alanyl-3-methyl-l-histidine and edaravone.

Identification of arbuscular mycorrhizal fungi in soils of the North Caucasus based on Illumina MiSeq data for ITS1 and ITS2 regions

The objective of our research was to analyze the efficiency of identification of arbuscular mycorrhizal fungi (AMF) for 2 regions: ITS1 and ITS2 regions of AMF DNA isolated from the soils of the North Caucasus (Karachay-Cherkessia). For the first time the necessity of different AMF species identification using both ITS regions was revealed, but not one region. The research demonstrated: 1) the set of taxa is different using ITS1- and ITS2-based identification; 2) analysis of the ITS1 region reveals a greater number of operational taxonomic units; 3) ITS2 allows identification of AMF at the species level more often. Sample preparation for Illumina MiSeq analysis was optimized. Obligatory stages in the sample preparation were the purification of DNA in the agarose gel in Silica after isolation, as well as separate amplification of ITS1 and ITS2 followed by combining and joint sequencing for each sample. The results showed the highest AMF biodiversity for the 176Te sample from the ecosystem of the subalpine meadow of the southeastern slope of Malaya Hatipara mountain (43°25′48.0″N 41°42′31.0″E; 2401 m above sea level), in which 8 species of AMF were identified (Archaeospora spainiae, Claroideoglomus claroideum, Diversispora versiformis, Entrophpora infrequens, Funneliformis mosseae, Glomus indicum, Paraglomus laccatum, Rhizophagus irregularis).