Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops

Diversity and Correlation Analysis of Endophytes and Top Metabolites in Phlomoides rotata Roots from High-Altitude Habitats

Phlomoides rotata, a traditional medicinal plant, always grows on the Tibetan Plateau at a high altitude of 3100-5200 m. The major active ingredients in P. rotata were used in medicines due to their diverse pharmacological effects, including hemostatic, anti-inflammatory, antitumor, immuno-modulatory, and antioxidant activities. This study screened 15 top endophytic genus through the analysis of OTUs and the top 30 metabolites with relatively high content in P. rotata roots from four different habitats (HN, GL, YS, and CD regions) in Qinghai Province. Twelve physicochemical indicators were measured and analyzed in the rhizosphere soils of P. rotata habitats. The results indicated that the top 30 metabolites compounds included 7 amino acids, 5 sugars and alcohols, 4 phenylpropanoids, 3 Organic acids, and 3 Alkaloids. Four endophytic bacteria (Acidibacter, Sphingomonas, Variovorax, and Sphingobium) and three endophytic fungi (Tetracladium, Cadophora, and Minimelanolocus) were dominant genera in P. rotata roots from four habitats. There were 109 positive significant correlations and 57 negative correlations between OTUs of endophytic bacteria and contents of top 30 metabolites, and 59 positive significant correlations and 58 negative correlations between OTUs of endophytic fungus and contents of top 30 metabolites. The OTUs of Acidibacter were significantly positively correlated with the content of 5 soil physicochemical indicators (total phosphorus, amylase, sucrase, total potassium, or soil organic carbon) and significantly negatively correlated with the content of acid protease. OTUs of Tetracladium or Cadophora showed a positive correlation with the content of total phosphorus and a negative correlation with that of alkaline phosphatase. This study provides a theoretical basis for the study of the correlation between endophytes and metabolites in P. rotata roots.

Effects of Deep Tillage on Wheat Regarding Soil Fertility and Rhizosphere Microbial Community

Wheat production is intrinsically linked to global food security. However, wheat cultivation is constrained by the progressive degradation of soil conditions resulting from the continuous application of fertilizers. This study aimed to examine the effects of deep tillage on rhizosphere soil microbial communities and their potential role in improving soil quality, given that the specific mechanisms driving these observed benefits remain unclear. Soil fertility in this research was evaluated through the analysis of various soil parameters, including total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium, among others. The high-throughput sequencing technique was utilized to examine the rhizosphere microbial community associated with deep tillage wheat. The findings indicated that deep tillage cultivation of wheat led to reduced fertility levels in the 0-20 cm soil layer in comparison with non-deep tillage cultivation. A sequencing analysis indicated that Acidobacteria and Proteobacteria are the dominant bacterial phyla, with Proteobacteria being significantly more abundant in the deep tillage group. The dominant fungal phyla identified were Ascomycota, Mortierellomycota, and Basidiomycota. Among bacterial genera, Arthrobacter, Bacillus, and Nocardioides were predominant, with Arthrobacter showing a significantly higher presence in the deep tillage group. The predominant fungal genera included Mortierella, Alternaria, Schizothecium, and Cladosporium. Deep tillage cultivation has the potential to enhance soil quality and boost crop productivity through the modulation of soil microbial community structure.

Kiwifruit-Agaricus blazei intercropping effectively improved yield productivity, nutrient uptake, and rhizospheric bacterial community

Intercropping systems have garnered attention as a sustainable agricultural approach for efficient land use, increased ecological diversity in farmland, and enhanced crop yields. This study examined the effect of intercropping on the kiwifruit rhizosphere to gain a deeper understanding of the relationships between cover plants and kiwifruit in this sustainable agricultural system. Soil physicochemical properties and bacterial communities were analyzed using the Kiwifruit-Agaricus blazei intercropping System. Moreover, a combined analysis of 16S rRNA gene sequencing and metabolomic sequencing was used to identify differential microbes and metabolites in the rhizosphere. Intercropping led to an increase in soil physicochemical and enzyme activity, as well as re-shaping the bacterial community and increasing microbial diversity. Proteobacteria, Bacteroidota, Myxococcota, and Patescibacteria were the most abundant and diverse phyla in the intercropping system. Expression analysis further revealed that the bacterial genera BIrii41, Acidibacter, and Altererythrobacter were significantly upregulated in the intercropping system. Moreover, 358 differential metabolites (DMs) were identified between the monocropping and intercropping cultivation patterns, with fatty acyls, carboxylic acids and derivatives, and organooxygen compounds being significantly upregulated in the intercropping system. The KEGG metabolic pathways further revealed considerable enrichment of DMs in ABC transporters, histidine metabolism, and pyrimidine metabolism. This study identified a significant correlation between 95 bacterial genera and 79 soil metabolites, and an interactive network was constructed to explore the relationships between these differential microbes and metabolites in the rhizosphere. This study demonstrated that Kiwifruit-Agaricus blazei intercropping can be an effective, labor-saving, economic, and sustainable practice for reshaping bacterial communities and promoting the accumulation and metabolism of beneficial microorganisms in the rhizosphere.

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

BACKGROUND

Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS

Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION

Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.

Influence of weeding methods on rhizosphere soil and root endophytic microbial communities in tea plants

Introduction

Polyethylene mulch is a kind of inorganic mulch widely used in agriculture. The effects of plastic mulch debris on the structure of plant soil and root growth have been fully studied, but their effects on endophytic microbial communities have not been explored to a large extent.

Methods

In this study, High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences were used to analyze microbial community structure and composition in rhizosphere soil and root endophytic of tea plant under three different weeding methods: polyethylene mulching, hand weeding and no weeding (CK).

Results

The results showed that the weeding methods had no significant effect on the rhizosphere and root endophytic microbial abundance, but the rhizosphere bacterial structure covered by polyethylene mulch was significantly different than hand weeding and CK. The rhizosphere fungal diversity was also significantly higher than the other two analyzed treatments. The community abundance of rhizosphere microorganisms Acidobacteria, Candidatus Rokubacteria and Aspergillus covered by polyethylene mulch decreased significantly, whereas Bradyrhizobium, Solirubrobacterales and Alphaproteobacteria increased significantly. The abundance of bacteria Ktedonobacter, Reticulibacter, Ktedonosporobacter and Dictyobacter communities covered by polyethylene mulch was significantly changed, and the abundance of Fusarium and Nitrobacteraceae was significantly increased. Rhizosphere dominant bacteria were negatively correlated with soil available nitrogen content, while dominant fungi were significantly correlated with soil pH, total nitrogen and total potassium.

Discussion

Polyethylene mulch forms an independent micro-ecological environment. At the same time, the soil nutrient environment was enriched by affecting the nitrogen cycle, and the composition of microbial community was affected. This study elucidated the effects of polyethylene mulch on soil microbial community in tea garden and provided a new theoretical understanding for weed management.

Effects of Short-Term Nitrogen Addition on Soil Fungal Community Increase with Nitrogen Addition Rate in an Alpine Steppe at the Source of Brahmaputra

The soil fungal community plays a crucial role in terrestrial decomposition and biogeochemical cycles. However, the responses of the soil fungal community to short-term nitrogen addition and its related dominant drivers still remain unclear. To address this gap, we conducted an experiment to explore how different levels of nitrogen addition (five levels: 0, 2.5, 5, 10, and 20 g N m-2 y-1) affected the soil fungal community in an alpine steppe at the source of Brahmaputra. Results showed that the reduced magnitudes of soil fungal species and phylogenetic α-diversity increased with the increasing nitrogen addition rate. Nitrogen addition significantly changed the community composition of species, and the dissimilarity of the soil fungal community increased with the increasing nitrogen addition rate, with a greater dissimilarity observed in the superficial soil (0-10 cm) compared to the subsurface soil (10-20 cm). Increases in the soil nitrogen availability were found to be the predominant factor in controlling the changes in the soil fungal community with the nitrogen addition gradient. Therefore, short-term nitrogen addition can still cause obvious changes in the soil fungal community in the alpine grassland at the source of Brahmaputra. We should not underestimate the potential influence of future nitrogen deposition on the soil fungal community in the high-altitude grassland of the Qinghai-Tibet Plateau. Adverse effects on the soil fungal community should be carefully considered when nitrogen fertilizer is used for ecosystem restoration of the alpine grassland of the Qinghai-Tibet Plateau.

The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.

Characterization of Functional Microorganisms in Representative Traditional Fermented Dongcai from Different Regions of China

Dongcai is loved for its delicious flavor and nutritional value. The microorganisms in Dongcai play a vital role in their flavor, quality, and safety, and the microbial communities of Dongcai vary greatly from region to region. However, it remains unknown what the predominant microorganisms are in different traditional Dongcai and how they affect its flavor. The objective of this study is to explore the microbial diversity of traditional fermented Dongcai in three representative Chinese regions (Tianjin, Sichuan, and Guangzhou) and further assess their microbial functions. The microbial diversity of fermented Dongcai in Guangdong has the lowest diversity compared to fermented Dongcai in Sichuan, which has the highest. The distribution of the main genera of fermented Dongcai varies from region to region, but Carnimonas, Staphylococcus, Pseudomonas, Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, and Rhodococcus are the dominant genera in common. In addition, halophilic bacteria (HAB, i.e., Halomonas Bacillus, Virgibacillus, etc.) and lactic acid bacteria (LAB, i.e., Weissella and Lactobacillus) are also highly abundant. Of these, Burkholderia-Caballeronia-Paraburkholderia, Rhodococcus, Sphingomonas, Ralstonia, and Chromohalobacter are dominant in the Sichuan samples. In the Tianjin samples, Lactobacillus, Weissella, Virgibacillus, Enterobacter, Klebsiella, and Pseudomonas are the most abundant. Predictions of microbial metabolic function reveal that carbohydrates, amino acids, polyketides, lipids, and other secondary metabolites are abundantly available for biosynthesis. In addition, the different flavors of the three types of Dongcai may be due to the fact that the abundance of HAB and LAB shows a significant positive correlation with the amounts of important metabolites (e.g., salt, acid, amino nitrogen, and sugar). These results contribute to our understanding of the link between the distinctive flavors of different types of Dongcai and the microorganisms they contain and will also provide a reference for the relationship between microbial communities and flavor substances in semi-fermented pickles.

Different responses of soil bacterial species diversity and phylogenetic diversity to short-term nitrogen input in an alpine steppe at the source of Brahmaputra

The Qinghai-Tibet Plateau has experienced an increase in N deposition/input due to global change. However, it remains unclear how the responses and whether the responses of soil bacterial diversity to short-term N input are consistent at different levels. Here, we investigated soil bacterial species and phylogenetic α-diversity and community composition based on a short-term nitrogen input experiment (five levels: 0, 2.5, 5, 10, and 20 g N m−2 y−1) in an alpine steppe at the source of Brahmaputra, using high-throughput sequencing technology. Short-term nitrogen input did not affect the species α-diversity and β-diversity of soil bacteria. However, soil bacterial phylogenetic α-diversity and dissimilarity increased with increasing nitrogen input. Different relative contributions and correlations of primary factors to species and phylogenetic diversity under short-term nitrogen input may result in different responses, in which ecological processes also play a role. Therefore, studying the response of soil bacteria to short-term nitrogen input should take into account not only the species level but also the phylogenetic level. We should pay close attention to the potential influence of short-term nitrogen deposition/fertilization on the soil bacterial community in the alpine steppe on the Tibetan Plateau.

Activity-Based Screening of Soil Samples from Nyingchi, Tibet, for Amylase-Producing Bacteria and Other Multifunctional Enzyme Capacities

Despite the interest in Tibetan soil as a promising source of functional enzymes with potential biotechnological applications, few studies have considered the screening and identification of amylase producing bacteria from Tibetan soil. Amylase has many applications in the food and feed industries, textile and biofuel production, and biomedical engineering. The area of amylase with specific properties is attracting growing attention because of its better application to various industrial conditions. This study aims to screen and identify amylase-producing strains from soil samples collected in Nyingchi, Tibet, and then explore whether the bacterial isolates are superior for unique enzymes. In this paper, a total of 127 amylase producing bacteria were isolated by activity-based screening of six Tibetan soil samples. The 16S rRNA gene survey then identified four major phyla, namely, firmicutes, bacteroidetes, proteobacteria, and actinobacteria, which were differentiated into twelve genera with a dominance of Bacillus (67.72%), followed by Pseudomonas (8.66%). Microbial diversity analysis revealed that the amylase-producing bacterial community of the Kadinggou forest soil sample showed the best variety (the Simpson index was 0.69 and the Shannon index was 0.85). The amylase activity assay of the bacterial isolates showed a mean of 0.66 U/mL at 28°C and pH 5.2. Based on the effect of temperatures and pHs on amylase activity, several bacterial isolates can produce thermophilic (50°C), psychrophilic (10°C), acidophilic (pH 4.2), and alkaliphilic (pH 10.2) amylases. Furthermore, four bacterial isolates were screened for amylase, protease, and esterase activities, which indicated multifunctional enzyme capacities. The present study is expected to contribute to our understanding of Tibetan microbial resources and their potential for scientific research and industrial applications.

Trypoxylus dichotomus Gut Bacteria Provides an Effective System for Bamboo Lignocellulose Degradation

Fast-growing bamboo may be a source of high-quality cellulose with the potential to contribute to energy sustainability, if an efficient and low-cost solution to bamboo cellulose decomposition can be developed. This study compared the gut microbiomes of rhinoceros beetle (Trypoxylus dichotomus) feeding on bamboo and wood fiber. The results revealed that diet has a distinctive effect on microbial composition in the midgut, including its most abundant microorganisms that in the fermentation and chemoheterotroph pathways. After identifying the 13 efficient bacterial isolates, we constructed a natural bacterial system based on the microbial relative abundance and an artificial bacterial system with equal proportions of each isolate to catabolize bamboo lignocellulose. The isolate Enterobacter sp. AZA_4_5 and the natural system showed higher degradation efficiency than other single strains or the artificial system. The results can thus serve as important reference for further research and development of a synthetic bacterial consortium to maximize lignocellulolytic ability. IMPORTANCE Bamboo produces a great yield of lignocellulosic biomass due to its high efficiency in carbon fixing. The gut microbiome of Trypoxylus dichotomus differed between bamboo and wood fiber diets. The lignocellulosic pathways were enriched in the gut bacteria of the bamboo diet. The highly efficient bacterial isolates were identified from midgut, whereas the natural bacterial system as well as one isolate showed the higher degradation efficiency of bamboo lignocellulose. The results indicate that the gut bacteria could provide an effective system to utilize the bamboo lignocellulosic biomass.