Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community

Effects of aftercrop tomato and maize on the soil microenvironment and microbial diversity in a long-term cotton continuous cropping field

Long-term continuous cropping affects the soil microecological community and leads to nutrient imbalances, which reduces crop yields, and crop rotation can increase soil productivity. To study the effects of the cultivation of tomato (Solanum lycopersicum) and corn (Zea mays) on the microbial community, physical and chemical factors and the structure of aggregates in cotton (Gossypium hirsutum) long-term continuous cropping soils were examined. Four cropping patterns were established, including one continuous cropping pattern and three crop rotation patterns, and the diversity of the soil microecological community was measured using high-throughput sequencing. The physical and chemical properties of different models of soil were measured, and the soil aggregate structure was determined by dry and wet sieving. Planting of aftercrop tomato and corn altered the bacterial community of the cotton continuous soil to a lesser extent and the fungal community to a greater extent. In addition, continuous cropping reduced the diversity and richness of the soil fungal community. Different aftercrop planting patterns showed that there were very high contents of soil organic carbon and organic matter in the cotton-maize rotation model, while the soil aggregate structure was the most stable in the corn-cotton rotation model. Planting tomato in continuous cropping cotton fields has a greater effect on the soil microbial community than planting maize. Therefore, according to the characteristics of different succeeding crop planting patterns, the damage of continuous cropping of cotton to the soil microenvironment can be alleviated directionally, which will enable the sustainable development of cotton production.

Influence of rice-wheat and sugarcane-wheat rotations on microbial diversity and plant growth promoting bacteria: Insights from high-throughput sequencing and soil analysis

Wheat is a staple food crop, primarily grown in India's Indo-Gangetic plains, crucial for sustaining the region. Soil quality, vitality, and microbial inhabitants' interplay are pivotal. However, very little information is available on the impacts of agricultural practices, such as crop rotation and cropping systems, on the diversity of both bulk soil (BS) and rhizospheric soil (RS) microbiota. The impact of two different cropping systems, rice-wheat (RW) and sugarcane-wheat (SW) on soil properties, microbial diversity, and plant growth-promoting bacteria (PGPB) in wheat cultivation was investigated in the Indo-Gangetic plains of India. Microbial richness and diversity were analyzed using 16S rRNA sequencing, which reveals distinct clustering patterns between RS and BS, with higher diversity in BS of RW and higher richness in RS of SW. Notably, Proteobacteria dominated across all samples, along with Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Firmicutes, Planctomycetes, candidate division TM7, Cyanobacteria, and Nitrospirae. Intriguingly, the RS associated with the SW system exhibited the presence of 67 distinct genera, whereas the RS under the RW system showed 48 such genera. Within the realm of specific microbial genera exhibiting plant growth-promoting (PGP) activity, a higher abundance was noted in the RS (17.48%), as opposed to the BS (15.21%). Moreover, certain genera such as Haliangium, Iamia, Bacillus, Gaiella, Candidatus_Entotheonella, Anaerolinea, and Anaeromyxobacter, were found to be positively correlated with the availability of nitrogen, phosphorus, potassium, iron, and sulfur. The study sheds light on the intricate relationships between cropping practices, soil properties, and microbial dynamics, contributing to the development of sustainable agricultural practices for wheat cultivation.

Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities

Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.

Dynamic changes of soil microorganisms in rotation farmland at the western foot of the Greater Khingan range

Crop rotation and other tillage systems can affect soil microbial communities and functions. Few studies have reported the response of soil spatial microbial communities to rotation under drought stress. Therefore, the purpose of our study was to explore the dynamic changes of the soil space microbial community under different drought stress-rotation patterns. In this study, two water treatments were set up, control W1 (mass water content 25%-28%), and drought W2 (mass water content 9%-12%). Four crop rotation patterns were set in each water content, spring wheat continuous (R1), spring wheat-potato (R2), spring wheat-potato-rape (R3) and spring wheat-rape (R4), for a total of eight treatments (W1R1, W1R2, W1R3, W1R4, W2R1, W2R2, W2R3, W2R4). Endosphere, rhizosphere and bulk soil of spring wheat in each treatment were collected, and root space microbial community data were generated. The soil microbial community changed under different treatments and their relationship with soil factors were analyzed using a co-occurrence network, mantel test, and other methods. The results revealed that the alpha diversity of microorganisms in the rhizosphere and bulk soil did not differ significantly, but it was significantly greater than in the endosphere. The bacteria community structure was more stable, fungi alpha-diversity significant changes (p < 0.05), that were more sensitive to the response of various treatments than bacteria. The co-occurrence network between fungal species was stable under rotation patterns (R2, R3, R4), while the community stability was poor under continuous cropping pattern (R1), and interactions were strengthened. Soil organic matter (SOM), microbial biomass carbon (MBC), and pH value were the most important factors dominating the bacteria community structural changed in the endosphere, rhizosphere, and bulk soil. The dominant factor that affected the fungal community structural changed in the endosphere, rhizosphere, and bulk soil was SOM. Therefore, we conclude that soil microbial community changes under the drought stress-rotation patterns are mainly influenced by soil SOM and microbial biomass content.

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health

The increasing impacts of global climate change on crop performance pose a significant threat to global food security. The rhizosphere microbiomes intimately interact with the plant and can largely facilitate plants in growth promotion and stress resistance via multiple mechanisms. This review focuses on approaches for harnessing the rhizosphere microbiomes to produce beneficial effects toward enhanced crop productivity, including the use of organic and inorganic amendments, and microbial inoculants. Emerging methods, such as the utilization of synthetic microbial consortia, host-mediated microbiome engineering, prebiotics made from specific plant root exudates, and crop breeding to promote beneficial plant-microbiome interactions, are highlighted. Updating our knowledge in this field is critical for understanding and improving plant-microbiome interactions, thereby enhancing plant adaptiveness to changing environmental conditions.

Potential of Medicago sativa and Perilla frutescens for overcoming the soil sickness caused by ginseng cultivation

There are serious soil sickness in ginseng cultivation. Crop rotation is an effective agricultural management to improve soil sustainability and reduce soil sickness. To explore an appropriate ginseng rotation system, Medicago sativa (alfalfa) and Perilla frutescens (perilla) were planted on ginseng cultivation soil for 1 year to evaluate the improvement effect of both. Through chemical analysis and high-throughput sequencing technology, we found that after alfalfa and perilla cultivation for one-year, various nutrients and enzyme activities in ginseng cultivation soil were significantly improved. In addition, perilla significantly increased the diversity and richness of soil fungal communities. Cultivation of alfalfa and perilla significantly changed the composition of soil bacterial and fungal communities and significantly reduced the abundance of the potentially pathogenic fungi Ilyonectria. Further pot experiments also showed that the improved soil could significantly increase root activity of ginseng plant after two plants were planted. It should be noted that, unlike alfalfa, perilla decreased soil electrical conductivity, increased soil organic matter, soil urease, and may significantly improve the diversity and richness of soil fungal community. Moreover, in the pot experiment, the root fresh weight of ginseng cultured in perilla treated soil increased significantly. This study highlights that perilla may have better soil improvement effect than alfalfa and it has the potential to be used in the soil improvement of ginseng cultivation.

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.)

Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.

Effects of planting of two common crops, Allium fistulosum and Brassica napus, on soil properties and microbial communities of ginseng cultivation in northeast China

Background

Long-term cultivation of ginseng can cause severe crop disorders and soil sickness. Crop rotation is an effective agricultural management measure to improve soil sustainability and decrease pathogens. However, the suitable ginseng rotation system and the changes in soil microbial community and soil characteristics under the rotation system need to be further explored.

Methods

To explore suitable ginseng crop rotation systems and improve soil utilization, Allium fistulosum and Brassica napus were planted on ginseng cultivation soil for one year. The effects of the two crops on the chemical properties and enzyme activities of the ginseng cultivation soil were evaluated by chemical analysis. In addition, amplicon sequencing targeting 16 s rDNA genes of bacteria and ITS of fungi has been used to characterize the functional and compositional diversity of microbial communities.

Results

The results elucidated that the levels of available phosphorus (AP) and available potassium (AK) in the soil increased significantly after one year of cultivation for both crops and Allium fistulosum cultivation may also have reduced soil salinity. In addition, the effects of the two crops on the activities of key soil enzymes were different. Catalase (CAT), urease (URE), and acid phosphatase (A-PHO) activities were significantly reduced and sucrase (SUC), and laccase (LAC) activities were significantly increased after Allium fistulosum planting. While A-PHO activity was significantly increased and LAC activity was significantly decreased after Brassica napus planting. Allium fistulosum significantly reduced the abundance of soil fungal communities. The cultivation of Allium fistulosum and Brassica napus significantly altered the composition of soil bacterial and fungal communities, where changes in the abundance of dominant microorganisms, such as Ascomycota, and Mortierellomycota, etc., were closely related to soil chemistry and enzyme activity. Moreover, both significantly reduced the abundance of the pathogenic fungus Ilyonectria.

Conclusions

Our study clarified the effects of Allium fistulosum and Brassica napus on the microbial community and physicochemical properties of ginseng cultivated soil and provides a basis for the sustainable application of ginseng cultivation soil and the development of ginseng crop rotation systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02592-0.

Biochar fertilization effects on soil bacterial community and soil phosphorus forms depends on the application rate

Biochar plays a key role in soil phosphorus (P) forms and distribution by affecting soil biochemical characteristics with relevant effects on the microbial community. In this study, we aimed to study the role of biochar in the variation of microbial community and P forms, and the relationships between soil properties, microbial community, and P forms. Here, we conducted a five-year field experiment NPK minerally fertilized with different application rates of biochar; control (B0, 0 kg ha^-1 yr^-1), low rate (B1500, 1500 kg ha^-1 yr^-1), medium rate (B3000, 3000 kg ha^-1 yr^-1), high rate (B6000, 6000 kg ha^-1 yr^-1). Our study showed that the highest increases in bacterial diversity and abundances coincided with increases in P forms typically retained in bacterial cells (β-glucosidase, adenosine monophosphate-AMP, choline phosphate, and glucose-6 phosphate) and occurred at medium application rates. At low application rates, N₂-fixing and P solubilizing and mineralizing bacteria (Sphingomonas, Haliangium, and Bradyrhizobium) increased. P forms retained in bacterial cells decreased at the highest application rates while the most stable forms such as DNA and inositol hexaphosphate (IHP), steadily increased. Stereoisomers of IHP derived from soil microbes (scyllo-IHP and D-chiro-IHP) accounted for the total IHP increases at high application rates. pH and available P and K and total P were highest at high biochar application rates whereas the proportion of organic P was reduced. The most relevant genus in such soils was Gemmatimonas, a polyphosphate accumulating and pyrogenic material degrading bacterium. Therefore, it appears that applying biochar at higher rates reduced the abundance of plant growth promoting bacteria while enhancing the abundance of P accumulating and pyrogenic degrading types.

Comparative physiological and soil microbial community structural analysis revealed that selenium alleviates cadmium stress in Perilla frutescens

Cadmium (Cd) toxicity not only affects plant growth and development, but also affects human health through the food chain. Several studies have demonstrated that Selenium (Se) alleviates Cd stress in plants; however, whether and how Se-alleviated Cd stress by regulating the structure of soil microbial community remain largely unclear. Here, we investigated the alleviating effects of exogenous applied Se (foliar spraying or root application) on plant growth under Cd stress in perilla (Perilla frutescens L.) by measuring the biomass, photosynthetic fluorescence parameters, root cell wall components and soil microbial community structure and diversity. Under Cd stress, perilla seedlings supplemented with Se increased chlorophyll content. Foliar spraying Se increased the levels of relative chlorophyll content (ΦII), photosynthetic system II (Φ_PSII) and electron transport rate (ETR) in perilla leaves under Cd stress; while, root application of Se increased the levels of photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), water use efficiency (WUE) and stomatal limitation value (Ls) under Cd stress. Compared with Cd toxicity alone, root application of Se increased the contents of hemicellulosic 1 and hemicellulosic 2 in the cell wall of perilla roots. Cd toxicity or root application of Se did not affect soil bacterial community diversity. Root application of Se increased the relative abundance of Proteobacteria, Bacteroidetes, Fibrobacteres, Sphingomonas and Nitrosospira in Cd-contaminated soil, and thereby improving soil microbial community structure, finally promoting the growth of perilla seedlings.

Rhizosphere element circling, multifunctionality, aboveground productivity and trade-offs are better predicted by rhizosphere rare taxa

Microbes, especially abundant microbes in bulk soils, form multiple ecosystem functions, which is relatively well studied. However, the role of rhizosphere microbes, especially rhizosphere rare taxa vs. rhizosphere abundant taxa in regulating the element circling, multifunctionality, aboveground net primary productivity (ANPP) and the trade-offs of multiple functions remains largely unknown. Here, we compared the multiple ecosystem functions, the structure and function of rhizosphere soil bacterial and fungal subcommunities (locally rare, locally abundant, regionally rare, regionally abundant, and entire), and the role of subcommunities in the Zea mays and Sophora davidii sole and Z. mays/S. davidii intercropping ecosystems in subtropical China. Results showed that intercropping altered multiple ecosystem functions individually and simultaneously. Intercropped Z. mays significantly decreased the trade-off intensity compared to sole Z. mays, the trade-off intensity under intercropped S. davidii was significantly higher than under intercropped Z. mays. The beta diversities of bacterial and fungal communities, and fungal functions in each subcommunity significantly differed among groups. Network analysis showed intercropping increased the complexity and positive links of rare bacteria in Z. mays rhizosphere, but decreased the complexity and positive links of rare bacteria in S. davidii rhizosphere and the complexity and positive links of fungi in both intercropped plants rhizosphere. Mantel test showed significant changes in species of locally rare bacteria were most strongly related to nitrogen-cycling multifunctionality, ANPP and trade-offs intensity, significant changes in species of locally rare fungus were most strongly related to carbon-cycling multifunctionality, phosphorus-cycling multifunctionality, and average ecosystem multifunctionality. This research highlights the potential and role of rare rhizosphere microorganisms in predicting and regulating system functions, productivity, and trade-offs.

Interspecific Neighbor Stimulates Peanut Growth Through Modulating Root Endophytic Microbial Community Construction

Plants have evolved the capability to respond to interspecific neighbors by changing morphological performance and reshaping belowground microbiota. However, whether neighboring plants influence the microbial colonization of the host's root and further affect host performance is less understood. In this study, using 16S rRNA high-throughput sequencing of peanut (Arachis hypogaea L.) roots from over 5 years of mono- and intercropping field systems, we found that neighbor maize can alter the peanut root microbial composition and re-shape microbial community assembly. Interspecific maize coexistence increased the colonization of genera Bradyrhizobium and Streptomyces in intercropped peanut roots. Through endophytic bacterial isolation and isolate back inoculation experiments, we demonstrated that the functional potentials of available nutrient accumulation and phytohormones production from Bradyrhizobium and Streptomyces endowed them with the ability to act as keystones in the microbial network to benefit peanut growth and production with neighbor competition. Our results support the idea that plants establish a plant-endophytic microbial holobiont through root selective filtration to enhance host competitive dominance, and provide a promising direction to develop modern diversified planting for harnessing crop microbiomes for the promotion of crop growth and productivity in sustainable agriculture.