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Saline‐alkali soils cover an area of more than 900 million ha and pose an acute threat to global food security. Rice cultivation is an effective method of saline‐sodic soil amelioration in the Songnen Plain in northeastern China. However, the changes in soil microbial communities that follow rice cultivation are largely unknown. In this study, soil bacterial and fungal communities were investigated using high‐throughput sequencing along a chronosequence of rice paddies cultivated in saline‐sodic soils. The results showed that soil fungi and bacteria become more diverse and abundant after rice cultivation compared with uncultivated saline‐sodic soil, in combination with the decreased pH and increased soil organic matter, indicating the amelioration of saline‐sodic soil. The processes of microbial succession following rice cultivation can be divided into two stages: shorter than and longer than 10 years. Moreover, soil fungi and bacteria exhibited distinct variation patterns as they were dominated by different influential factors. The results indicated that bacteria were more strongly dominated by soil properties than fungi, while the latter were more dependent on vegetation. As rice cultivation continued, fungi exhibited better adaptation and faster succession than bacteria in response to environmental shifts after rice cultivation. Therefore, measures that can enhance plant–microbe interactions may be a viable approach for promoting saline‐sodic soil amelioration. This study provided novel insights into the microbial assembly processes following rice cultivation on saline‐sodic lands. [ABSTRACT FROM AUTHOR]

The barriers caused by continuous tillage have had a negative impact on the crop and soil environment. Black soils are economically important as a valuable natural resource in Northeast China, but limited soil resources have led to continuous planting of major food crops and medicinal plants. At present, the extent to which two different types of plants—grains and medicinal plants that are successively grown on the same soil—have an impact on soil quality and microbiology is not known. In this study, we investigated the effects of different types of long-term continuous cropping on soil and soil microbial communities by determining the physicochemical properties, the soil community composition and function of grain crops and medicinal-plant soils with more than five years of continuous cropping, as well as fallow soils. The results showed that long-term continuous cropping reduced the pH of different types of soils, but there was no significant difference in the content of AK. The relative abundance of beneficial dominant phyla, such as Actinomycetes, Acidobacteria, and Green Campylobacter decreased and the relative abundance of pathogenic genera such as Alternaria and Didymellaceae, increased after the long-term continuous cropping of DM (grain crops) and DG (medicinal plants). Specifically, continuous cropping increased the relative abundance of fungi with pathogenic potential, such as Sordariomycetes, Dothideomycetes, Saccharomycetes, and Mucoromycetes in grain soils and Agaricostilbomycetes in herb soils. Among the soil physicochemical properties, NH4+-N and pH were the most important factors contributing to changes in the composition of bacterial and fungal communities, respectively. Continuous cropping of different types of plants altered the diversity of the microbial communities, with the most significant effect from the continuous cropping of food crops. Our findings provide a scientific and theoretical basis for future agricultural research to improve soil microbial activity, mitigate continuous-cropping barriers, and increase productivity. [ABSTRACT FROM AUTHOR]

Soil physicochemical properties and fungal communities are pivotal factors for continuous cropping of American ginseng (Panax quinquefolium L.). However, the response of soil physicochemical properties and fungal communities to replant disease of American ginseng has not yet been studied. High-throughput sequencing and soil physicochemical analyses were undertaken to investigate the difference of soil fungal communities and environmental driver factors in new and old ginseng fields; the extent of replant disease in old ginseng fields closely related to changes in soil properties and fungal communities was also determined. Results indicated that fungal communities in an old ginseng field were more sensitive to the soil environment than those in a new ginseng field, and fungal communities were mainly driven by soil organic matter (SOM), soil available phosphorus (AP), and available potassium (AK). Notably, healthy ginseng plants in new and old ginseng fields may influence fungal communities by actively recruiting potential disease suppressive fungal agents such as Amphinema, Cladophialophora, Cadophora, Mortierella, and Wilcoxina. When these key groups and members were depleted, suppressive agents in the soil possibly declined, increasing the abundance of pathogens. Soil used to grow American ginseng in the old ginseng field contained a variety of fungal pathogens, including Alternaria, Armillaria, Aphanoascus, Aspergillus, Setophoma, and Rhexocercosporidium. Additionally, micro-ecological factors affecting disease outbreaks in the old ginseng field included a strengthening in competition relationships, a weakening in cooperation relationships, and a change of trophic strategies among fungal communities. [ABSTRACT FROM AUTHOR]

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium , Lecythophora , and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions. [ABSTRACT FROM AUTHOR]

Rice cultivation is widely used to improve saline-sodic soils in Northeast China. However, the chronological effect of rice cultivation on soil fungal communities has not been studied. Therefore, this study investigated the variation of soil fungal communities in different rice cultivation years. Compared with the blank area, the rice cultivation for 20 years significantly decreased the pH and electrical conductivity by 16.6% and 70.1%, while significantly increased the soil organic carbon and available phosphorus by 90.6% and 17.4 times, respectively. Meanwhile, the relative abundance of Ascomycota and Basidiomycota significantly decreased and increased after rice cultivation, respectively. Moreover, some genera of arbuscular mycorrhizal fungi (AMF), e.g. Corymbiglomus, Glomus, and Rhizophagus, and pathogenic fungi (Thanatephorus cucumeris) disappeared, while Dentiscutata (one genus of AMF) appeared after rice cultivation. In addition, the fungal richness significantly increased when the rice cultivation less than 15 years and the fungal communities were similar between 15 and 20 years. Our findings showed that rice cultivation improved the nutrient availability and reduced salinity-alkalinity stress of sodic soils. After the rice cultivation for 15 years, the soil fungal community tended to be stable. [ABSTRACT FROM AUTHOR]

To understand the mechanisms of soil ameliorants affecting microbial communities is important for saline-sodic soils reclamation. High-throughput sequencing was used to characterize the fungal community in soils amended with four types of ameliorants over an 8-year period. Besides a control without any additional ameliorant (CK), other four treatments including 1) amendment with sandy soil (SS), 2) amendment with desulfurization gypsum (DG), 3) amendment with farm manure (FM), and 4) amendment with a mixture of SS, DG, and FM (M) were analyzed. Soil pH and electrical conductivity significantly decreased with the addition of soil ameliorants, whereas the soil organic carbon (SOC), total nitrogen (TN), and SOC/TN ratio (C/N) significantly increased in the FM and M treatments compared with the CK treatment. Fungal richness increased significantly with the mixed ameliorants addition (M). Distinct fungal community structures were observed in the treatments with soil ameliorants. The fungal community composition was significantly associated with the SOC, C/N, aggregate content with a diameter > 0.25 mm and geometric mean diameter. The changes in these soil characteristics were highly correlated with the ameliorants additions, suggesting that the impacts of ameliorants on the soil fungal community occurred indirectly as a result of alterations to soil physiochemical properties. [ABSTRACT FROM AUTHOR]

The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops. [ABSTRACT FROM AUTHOR]

Peatlands in the Sanjiang Plain could be more vulnerable to global warming because they are located at the southernmost boundary of northern peatlands. Unlike bacteria, fungi are often overlooked, even though they play important roles in substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding of fungal community structure and diversity in the peatlands. In this study, high-throughput Illumina sequencing was used to study the fungal communities in three fens in the Sanjiang Plain, located at the southern edge of northern peatlands. Peat soil was collected from the three fens which developed during different periods. A total of 463,198 fungal ITS sequences were obtained, and these sequences were classified into at least six phyla, 21 classes, more than 60 orders and over 200 genera. The fungal community structures were distinct in the three sites and were dominated by Ascomycota and Basidiomycota. However, there were no significant differences between these three fens in any α-diversity index (p > 0.05). Soil age and the carbon (C) accumulation rate, as well as total carbon (TC), total nitrogen (TN), C/N ratio, and bulk density were found to be closely related to the abundance of several dominant fungal taxa. We captured a rich fungal community and confirmed that the dominant taxa were those which were frequently detected in other northern peatlands. Soil age and the C accumulation rate were found to play important roles in shaping the fungal community structure. [ABSTRACT FROM AUTHOR]

The farmland residual film pollution caused by traditional PE film has an adverse impact on crops and the environment. Polypropylene carbonate (PPC) film is a fully biodegradable film that can alleviate "white pollution". In this study, the soil physicochemical properties and the composition and function of the soil community of FM (PPC film mulching) and CK (no film) treatments were determined to explore the effect of PPC film mulching on soil and the soil microbial community. Furthermore, the microorganisms at different time periods during the degradation of PPC mulch film were also analyzed. The results showed that film mulching increased soil pH but decreased the contents of EC and SOC, and there was no significant difference in the contents of AP and AK. The relative abundance of the phyla Acidobacteria was increased with film mulching, and the relative abundance of the genera MB_A2_108 also increased in the film mulched soil. Among the soil physicochemical properties, pH and SOC were the most important factors leading to changes in the composition of the bacterial and fungal communities. PPC film mulching had no significant effect on soil microbial community abundance and diversity. In addition, Pseudomonas, Flavobacterium, and Rhizobacter were dominant in the degradation of PPC film. Our research results provide a scientific theoretical basis for soil safety and the large-scale use of PPC biodegradable mulching films and a research foundation for the degradation of PPC plastics. [ABSTRACT FROM AUTHOR]

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice. [ABSTRACT FROM AUTHOR]

Rice is a staple food for the world's population. However, the straw produced by rice cultivation is not used sufficiently. Returning rice straw to the field is an effective way to help reduce labor and protect the soil. This study focused on the effect of water-covered depth with the freeze–thaw cycle on rice straw decomposition and the soil fungal community structure in a field in Northeast China. The field and controlled experiments were designed, and the fungal ITS1 region was tested by high-throughput sequencing for analyzing the fungal communities in this study. The results showed that water coverage with the freeze–thaw cycle promoted the decomposition of rice straw and influenced the fungal community structure; by analyzing the network of the fungal communities, it was found that the potential keystone taxa were Penicillium, Talaromyces, Fusarium, and Aspergillus in straw decomposition; and the strains with high beta-glucosidase, carboxymethyl cellulase, laccase, lignin peroxidase, and manganese peroxidase could also be isolated in the treated experiment. Furthermore, plant pathogenic fungi were found to decrease in the water-covered treatment. We hope that our results can help in rice production and straw return in practice. [ABSTRACT FROM AUTHOR]

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community. [ABSTRACT FROM AUTHOR]

• Strigolactone (SL) phytohormones determine the rhizomicrobiome in rice. • SL-mediated metabolic pathways are likely to be responsible for the regulation of rhizomicrobiome in rice. • Genetic modulation of rice SL biosynthesis and/or signaling may promote the abundance of specific beneficial bacterial taxa. The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter , were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice. [ABSTRACT FROM AUTHOR]

• Biochar application significantly decreased the diversity of microbial community. • Biochar application enhanced the microbial interaction in the megaaggregates. • B10 and B30 treatments increased the interactions between microbial communities. • B50 treatment decreased the interactions between microbial communities. Soil microbial community diversity and composition are responsive to biochar application. However, the impacts of biochar application on soil microbial community structure and interactions in different aggregate fractions are poorly understood. We conducted a 3-year field trial involving biochar application to black soil in northeastern China. Four biochar treatments were applied: 0 (B0, control), 10 (B10), 30 (B30) and 50 (B50) t ha−1 biochar. Compared to the B0 treatment, biochar application significantly decreased the diversity of bacterial and fungal communities. In addition, biochar application significantly increased the relative abundances (RAs) of Bacteroidetes and Proteobacteria and significantly decreased those of Actinobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia. Moreover, the B30 and B50 treatments significantly increased and decreased the RA of Nitrospirae, respectively. Moreover, the RA trends of Acidobacteria, Nitrospirae and Planctomycetes among different aggregate fractions was mega-aggregates (ME; > 2 mm) > macroaggregates (MA; 0.25–2 mm) > microaggregates (MI; < 0.25 mm); the RAs of Basidiomycota and Glomeromycota in ME were higher than those in MA and MI. The RA of Ascomycota in MI was the highest among the different aggregate fractions. The co-occurrence networks showed that the B30 treatment enhanced microbial interactions in terms of the number of links, average degree, and modularity, while the B50 treatment reduced these interactions. Additionally, co-inertia analysis demonstrated that the microbial interactions in ME were enhanced by biochar application. Thus, an appropriate biochar application (e.g., 30 t ha−1 used in the present study area) can enhance soil microbial interactions, especially in ME. [ABSTRACT FROM AUTHOR]

Soybean is considered as one of the most important food for both humans and animals; unfortunately, it faces soil-borne diseases caused by bacteria or fungi, leading to severe yield losses. Hybridization has helped the soybean to obtain beneficial genes from wild species that can resist some adverse conditions. However, the influences of hybridization on the rhizosphere microbiomes of wild and cultivated soybeans have not been much elucidated until now. In this article, we investigated the influences of hybridization of wild and cultivated soybeans on the rhizosphere microbiomes using four soybean genotypes: the cultivated soybean (C), the wild soybean (W), the first hybridization generation (F1) and the second hybridization generation (F2). Results indicated that there had significant differences in both the fungal and bacterial communities in all four groups. More specifically, bacterial and fungal communities were more similar between the F2 generation and wild soybean groups. The relative abundances of Glomeromycota in wild soybean and F2 generation were significantly higher than those in C and F1 groups. Furthermore, the network analysis showed that the wild soybean had more complicated bacterial and fungal connections than other genotypes, which might help wild soybean maintain the beneficial traits of resistance to adverse conditions. Results of this study can provide a theoretical basis for recognizing the different members of the rhizosphere bacterial and fungal communities of wild and cultivated soybeans, as well as their offspring. Additionally, our findings will hopefully provide a practical guide for screening useful microbial resources from the wild soybean rhizomicrobiome. • Hybridization of wild and cultivated soybeans influences the structure of rhizosphere microbiomes. • Wild soybean has more complicated bacterial and fungal connections. • The relative abundances of Glomeromycota in the wild soybean and F2 generation were significantly higher than those in the cultivated soybean and F1 generation. [ABSTRACT FROM AUTHOR]

Soil type and domestication are the main factors that contribute to the determination of root-associated bacterial communities in soybean; however, to what extent these factors influence root-associated fungal communities remains unclear. Here, we grew wild soybean (Glycine soja) and cultivated soybean (Glycine max) in three soil suspensions (black, red and saline-sodic soil) and analyzed the soybean rhizosphere fungal internal transcribed spacer 1 (ITS1) region by high-throughput sequencing technology. The results showed that the fungal communities had significantly different richness and alpha-diversity indexes in the three soil suspensions; however, there was no marked difference in the rhizosphere fungal communities between the two wild and cultivated soybean varieties. Furthermore, soil type was a main factor in determining the distribution of arbuscular mycorrhizal fungi (AMF; Paraglomus and Rhizophagus) and soybean pathogenic fungi (Fusarium and Rhizoctonia). In addition, the abundant rhizosphere fungi from wild soybean exhibited diverse potential functions, while the functions of rhizosphere fungi from cultivated soybean were mainly related to plant nutrient uptake. The diversity and structure of the soybean rhizosphere fungal communities were mainly affected by soil type rather than soybean variety, and domestication caused wild and cultivated soybeans to recruit different rhizosphere fungi. Accordingly, a thorough understanding of soybean fungal communities and their influencing factors is important for improving the health and harvest of soybean. • Soil type and wild and cultivated soybean varieties induced rhizosphere fungi shifts. • Soil type had a decisive influence on the distribution of pathogenic fungi and AMF. • More diverse potential functions in wild than cultivated soybean rhizosphere fungi [ABSTRACT FROM AUTHOR]

Continuous cropping of soybean often causes significant declines in yields of soybean because of the outbreaks of soil-borne fungal diseases. It has been reported that wild crops often harbour a unique microbiome to benefit the host plants. Thus, it is necessary to find the different community structures of the rhizomicrobiomes associated with cultivated and wild soybeans in their continuous cropping. In this study, we simulated monocropping of cultivated and wild soybeans under greenhouse conditions to investigate the rhizomicrobiomes of both soybeans. Results indicated that the bacterial community structure still maintained a changing trend after four continuous planting seasons, while fungal community structure showed a stable trend as indicated by the high similarity in the fungal community structure between the third and fourth planting rotations in both soybeans. In addition, by comparing the continuous cropping of the two soybeans, we found different fungal groups in their rhizospheres between the wild and cultivated soybeans following each passage. Spizellomycetaceae was more highly enriched in the rhizosphere following cultivation of the cultivated soybean, while Chaetomiaceae and Orbiliaceae were more highly enriched in the rhizosphere of wild soybean. Taken together, results of this study suggested that although there was the same trend of stabilized fungal development in the rhizospheres of both soybeans, wild soybean rhizosphere had different fungal groups compared with that of cultivated soybean following their continuous cropping. The findings of this study may provide useful information for the farmers with regard to planting soybean, especially when they consider growing soybean in monoculture. [ABSTRACT FROM AUTHOR]