Short-term continuous monocropping reduces peanut yield mainly via altering soil enzyme activity and fungal community.

Continuous monocropping can lead to soil sickness and increase of soil-borne disease, which finally reduces crop yield. Microorganisms benefit plants by increasing nutrient availability, participating in auxin synthesis, and defending against pathogens. However, little is known about the influence of short-term successive peanuts cropping on soil properties, enzyme activities, its yield, plant-associated microbes, and their potential correlations in peanut production. Here, we examined the community structure, composition, network structure and function of microbes in the rhizosphere and bulk soils under different monocropping years. Moreover, we assessed the impact of changes in the soil micro-environment and associated soil microbes on peanut yield. Our results showed that increase of monocropping year significantly decreased most soil properties, enzyme activities and peanut yield (p < 0.05). Principal co-ordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated that monocropping year significantly influenced the fungal community structure in the rhizosphere and bulk soils (p < 0.01), while had no effect on the bacterial community. With the increase of continuous monocropping year, peanut selectively decreased (e.g., Candidatus_Entotheonella, Bacillus and Bryobacter) or increased (e.g., Nitrospira, Nocardioides, Ensifer, Gaiella, and Novosphingobium) the abundance of some beneficial bacterial genera in the rhizosphere. Continuous monocropping significantly increased the abundance of plant pathogens (e.g., Plectosphaerella, Colletotrichum, Lectera, Gibberella, Metarhizium, and Microdochium) in the rhizosphere and negatively affected the balance of fungal community. Besides, these species were correlated negatively with L-leucine aminopeptidase (LAP) activity. Network co-occurrence analysis showed that continuous monocropping simplified the interaction network of bacteria and fungi. Random forest and partial least squares path modeling (PLS-PM) analysis further showed that fungal community, pathogen abundance, soil pH, and LAP activity negatively affected peanut yield. In conclusion, short-term continuous monocropping decreased LAP activity and increased potential fungal pathogens abundance, leading to reduction of peanut yield.

Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress.

Waterlogging in soil can limit the availability of nitrogen to plants by promoting denitrification and reducing nitrogen fixation and nitrification. The root-associated microorganisms that determine nitrogen availability at the root-soil interface can be influenced by plant genotype and soil type, which potentially alters the nitrogen uptake capacity of plants in waterlogged soils. In a greenhouse experiment, two soybean genotypes with contrasting capacities to resist waterlogging stress were grown in Udic Argosol and Haplic Alisol soils with and without waterlogging, respectively. Using isotope labeling, high-throughput amplicon sequencing and qPCR, we show that waterlogging negatively affects soybean yield and nitrogen absorption from fertilizer, atmosphere, and soil. These effects were soil-dependent and more pronounced in the waterlogging-sensitive than tolerant genotype. The tolerant genotype harbored more ammonia oxidizers and less nitrous oxide reducers. Anaerobic, nitrogen-fixing, denitrifying and iron-reducing bacteria such as Geobacter/Geomonas, Sphingomonas, Candidatus Koribacter, and Desulfosporosinus were proportionally enriched in association with the tolerant genotype under waterlogging. These changes in the rhizosphere microbiome might ultimately help the plant to improve nitrogen uptake under waterlogged, anoxic conditions. This research contributes to a better understanding of the adaptability of soybean genotypes under waterlogging stress and might help to formulate fertilization strategies that improve nitrogen use efficiency of soybean. Schematic representation of the effects of waterlogging on nitrogen uptake and rhizosphere microbiota in dependence of soil type and soybean genotype.

Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield.

The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.

Transgenic soybean of GsMYB10 shapes rhizosphere microbes to promote resistance to aluminum (Al) toxicity.

Plant resistance genes could affect rhizosphere microbiota, which in turn enhanced plant resistance to stresses. Our previous study found that overexpression of the GsMYB10 gene led to enhanced tolerance of soybean plants to aluminum (Al) toxicity. However, whether GsMYB10 gene could regulate rhizosphere microbiota to mitigate Al toxicity remains unclear. Here, we analyzed the rhizosphere microbiomes of HC6 soybean (WT) and transgenic soybean (trans-GsMYB10) at three Al concentrations, and constructed three different synthetic microbial communities (SynComs), including bacterial, fungal and cross-kingdom (bacteria and fungi) SynComs to verify their role in improving Al tolerance of soybean. Trans-GsMYB10 shaped the rhizosphere microbial communities and harbored some beneficial microbes, such as Bacillus, Aspergillus and Talaromyces under Al toxicity. Fungal and cross-kingdom SynComs showed a more effective role than the bacterial one in resistance to Al stress, and these SynComs helped soybean resist Al toxicity via affecting some functional genes that involved cell wall biosynthesis and organic acid transport etc. Overall, this study reveals the mechanism of soybean functional genes regulating the synergistic resistance of rhizosphere microbiota and plants to Al toxicity, and also highlights the possibility of focusing on the rhizobial microbial community as a potential molecular breeding target to produce crops.

Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence.

Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.

Silicon Application Modulates the Growth, Rhizosphere Soil Characteristics, and Bacterial Community Structure in Sugarcane.

Silicon (Si) deficiency, caused by acidic soil and rainy climate, is a major constraint for sugarcane production in southern China. Si application generally improves sugarcane growth; however, there are few studies on the relationships between enhanced plant growth, changes in rhizosphere soil, and bacterial communities. A field experiment was conducted to measure sugarcane agronomic traits, plant nutrient contents, rhizosphere soil enzyme activities and chemical properties, and the rhizosphere bacterial community diversity and structure of three predominant sugarcane varieties under two Si treatments, i.e., 0 and 200 kg of silicon dioxide (SiO2) ha-1 regarded as Si0 and Si200, respectively. Results showed that Si application substantially improved the sugarcane stalk fresh weight and Si, phosphorus (P), and potassium (K) contents comparing to Si0, and had an obvious impact on rhizosphere soil pH, available Si (ASi), available P (AP), available K (AK), total phosphorus (TP), and the activity of acid phosphatase. Furthermore, the relative abundances of Proteobacteria showed a remarkable increase in Si200, which may be the dominant group in sugarcane growth under Si application. Interestingly, the AP was noticed as a major factor that caused bacterial community structure differences between the two Si treatments according to canonical correspondence analysis (CCA). In addition, the association network analysis indicated that Si application enriched the rhizosphere bacterial network, which could be beneficial to sugarcane growth. Overall, appropriate Si application, i.e., 200 kg SiO2 ha-1 promoted sugarcane growth, changed rhizosphere soil enzyme activities and chemical properties, and bacterial community structures.

Rhizosphere Soil Bacterial Communities of Continuous Cropping-Tolerant and Sensitive Soybean Genotypes Respond Differently to Long-Term Continuous Cropping in Mollisols.

The continuous planting of soybeans leads to soil acidification, aggravation of soil-borne diseases, reduction in soil enzyme activity, and accumulation of toxins in the soil. Microorganisms in the rhizosphere play a very important role in maintaining the sustainability of the soil ecosystem and plant health. In this study, two soybean genotypes, one bred for continuous cropping and the other not, were grown in a Mollisol in northeast China under continuous cropping for 7 and 36years in comparison with soybean-maize rotation, and microbial communities in the rhizosphere composition were assessed using high-throughput sequencing technology. The results showed that short- or long-term continuous cropping had no significant effect on the rhizosphere soil bacterial alpha diversity. Short-term continuous planting increased the number of soybean cyst nematode (Heterodera glycines), while long-term continuous planting reduced these numbers. There were less soybean cyst nematodes in the rhizosphere of the tolerant genotypes than sensitive genotypes. In addition, continuous cropping significantly increased the potential beneficial bacterial populations, such as Pseudoxanthomonas, Nitrospira, and Streptomyces compared to rotation and short-term continuous cropping, suggesting that long-term continuous cropping of soybean shifts the microbial community toward a healthy crop rotation system. Soybean genotypes that are tolerant to soybean might recruit some microorganisms that enhance the resistance of soybeans to long-term continuous cropping. Moreover, the network of the two genotypes responded differently to continuous cropping. The tolerant genotype responded positively to continuous cropping, while for the sensitive genotype, topology analyses on the instability of microbial community in the rhizosphere suggested that short periods of continuous planting can have a detrimental effect on microbial community stability, although this effect could be alleviated with increasing periods of continuous planting.