Community Structure In Rhizosphere Research Articles

Manure amendments and fungistasis, and relation with protection of wheat from Fusarium graminearum

Certain soils promote crop health because they are pathogen-suppressive (i.e., fungistatic) or disease-suppressive, but the effect of soil management on these properties is not fully understood. Here, we tested the hypothesis that manure could favor fungistasis by screening 26 manured or non-manured wheat fields from Serbia for their ability to control survival/growth of the fungal plant pathogen Fusarium graminearum Fg1. Quantitative PCR showed that the pathogen grew after inoculation in all 26 autoclaved soils. In absence of autoclaving, the pathogen was stable or grew in 16 soils (37 % manured) but declined in the 10 others (70 % manured). For most soils, there was no significant link between soil chemistry and fungistasis, except with Mionica in western/central Serbia. Mionica soils MI2 and MI3, which had received manure, exhibited higher levels of organic matter and potassium compared with soils MI4 and MI5, which had not received manure and were non-fungistatic. Using Mionica soils, we then tested the hypothesis that fungistatic (manured) soils rather than non-fungistatic (non-manured) soils would protect wheat from F. graminearum disease. Indeed, fungistatic soils were suppressive to wheat damping-off. Non-fungistatic soil MI4 was conducive, as expected, but non-fungistatic soil MI5 turned out to be suppressive. Metabarcoding showed that the structure of prokaryotic and fungal rhizosphere communities depended mostly on field location, with a significant effect of F. graminearum inoculation. In conclusion, our findings show that certain farming practices (here, manure amendments) may promote soil fungistasis towards F. graminearum. However, both fungistatic and non-fungistatic soils can be suppressive to F. graminearum disease in wheat, and their differences in rhizosphere microbiota suggest different phytoprotection mechanisms.

Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions

BackgroundRhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides.ResultsThe findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics.ConclusionsThe diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.

Enhancing the phytoextraction efficiency of heavy metals in acidic and alkaline soils by Sedum alfredii Hance: A study on the synergistic effect of plant growth regulator and plant growth-promoting bacteria

Plant growth regulators (PGR) and plant growth-promoting bacteria (PGPB) have the potential in phytoremediation of heavy metals (HMs) contaminated soils. However, their sole application may not yield the optimal results, thus necessitating the combined application. The present study aimed to enhance the phytoremediation efficiency of Sedum alfredii Hance (S. alfredii) in acidic and alkaline soils through the combination of PGR (Brassinolide, BR) and PGPB (Pseudomonas fluorescens, P. fluorescens). The combination of BR and P. fluorescens (BRB treatment) effectively increased the removal efficiency of S. alfredii for Cd, Pb, and Zn by 355.2 and 155.3 %, 470.1 and 128.9 %, and 408.4 and 209.6 %, in acidic and alkaline soils, respectively. Moreover, BRB treatment led to a substantial increase in photosynthetic pigments contents and antioxidant enzymes activities, resulting in a remarkable increase in biomass (86.71 and 47.22 %) and dry mass (101.49 and 42.29 %) of plants grown in acidic and alkaline soils, respectively. Similarly, BRB treatment significantly elevated the Cd (109.4 and 71.36 %), Pb (174.9 and 48.03 %), and Zn levels (142.8 and 104.3 %) in S. alfredii shoots, along with cumulative accumulation of Cd (122.7 and 79.47 %), Pb (183.8 and 60.49 %), and Zn (150.7 and 117.9 %), respectively. In addition, the BRB treatment lowered the soil pH and DTPA-HMs contents, while augmenting soil enzymatic activities, thereby contributing soil microecology and facilitating the HMs absorption and translocation by S. alfredii to over-ground tissues. Furthermore, the evaluation of microbial community structure in phyllosphere and rhizosphere after remediation revealed the shift in microbial abundance. The combined treatment altered the principal effects on S. alfredii HMs accumulation from bacterial diversity to the soil HMs availability. In summary, our findings demonstrated that synergistic application of BR and P. fluorescens represents a viable approach to strengthen the phytoextraction efficacy of S. alfredii in varying soils.

Phytophthora Infection Reorients the Composition of Rhizospheric Microbial Assembly in Khasi Mandarin (Citrus reticulata Blanco)

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin.

The accumulation of active ingredients of Polygonatum cyrtonema Hua is associated with soil characteristics and bacterial community.

With the increasing demand for health products derived from Polygonati rhizoma (PR), people begin to artificially plant Polygonatum cyrtonema Hua (P. cyrtonema) in the middle and lower reaches of the Yangtze River. To promote P. cyrtonema cultivation and increase farmers' income, efforts are needed to understand the ways to obtain high-quality PR under artificial cultivation conditions. Rhizomes of artificial planting P. cyrtonema and rhizosphere soils were collected across five regions in Zhejiang Province, China. Subsequently, the contents of the main active ingredients of P. cyrtonema and soil properties were analyzed, and both rhizosphere and endophytic bacteria of P. cyrtonema were detected by 16S rDNA sequencing. The relationship between the active ingredients and soil properties, and the dominant bacteria were investigated by correlation analysis. The content of active ingredients of P. cyrtonema from the five regions varied significantly, especially polysaccharides and saponins. High-throughput sequencing demonstrated that Proteobacteria was the dominant bacterial phylum in all samples, and Burkholderia-Caballeronia-Paraburkholderia was the main endophytic bacterial genus in rhizome. In addition, the bacterial diversity and richness of rhizosphere soil samples were higher than those of rhizome samples. Soil physicochemical properties and enzyme activities were significantly different across regions, leading to notable variations in the community structures of rhizosphere and endophytic bacteria. Redundancy analysis (RDA) displayed that pH and urease (UE) were the major factors altering shifting rhizosphere bacteria community structure. Moreover, the composition and diversity of rhizome endophytic bacteria were principally affected by both soil physicochemical properties and soil enzyme activities. Soil properties and bacteria from rhizosphere soil and rhizome had a considerable impact on certain active ingredients in P. cyrtonema under artificial cultivation conditions after Pearson correlation analysis. Polysaccharides were significantly correlated with nutrient-rich soil and endophytic bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Ralstonia, and Bacillus. However, flavonoids were associated with nutrient-poor soil. Saponins were positively correlated with OM and available phosphorous (AP) and were significantly negatively affected by rhizosphere bacterial communities. The study demonstrated that bacterial microorganisms were involved in the accumulation of active ingredients of P. cyrtonema together with soil physicochemical properties and enzyme activities, which provided a theoretical basis for the scientific and effective artificial cultivation of high-quality P. cyrtonema.

D genome acquisition and breeding have had a significant impact on interaction of wheat with ACC deaminase producers in soil or ACC deaminase potential activity in the rhizosphere

Rhizosphere functioning depends on plant traits, but the underlying genotypic properties are poorly understood. Wheat has undergone several domestication events combined with genomic hybridization, including the acquisition by Triticum dicoccon (AABB genome) of the D genome from Aegilops tauschii, resulting into bread wheat Triticum aestivum (AABBDD genome). The D genome is likely to modulate the functioning of beneficial wheat-microbe interactions, but data are needed to substantiate this. Here, we tested the hypothesis that genome D is important for soil interactions of wheat with 1-aminocyclopropane-1-carboxylate (ACC) deaminase producers, a key microbial functional group that enhances plant performance by fine-tuning ethylene metabolism in roots. A range of wheat lines from T. aestivum (AABBDD), T. diccocon (AABB) and Ae. tauschii (DD) were compared based on abundance (qPCR on acdS gene marker), diversity (Illumina MiSeq) and potential ACC deaminase activity (colorimetric assays) of ACC deaminase producers in the rhizosphere. Results showed that the abundance of ACC deaminase producers was lower for D-genome wheats than D-negative T. dicoccon at 40 days, but ACC deaminase potential activity in the rhizosphere was lower for D-genome Ae. tauschii and T. aestivum landraces than T. aestivum cultivars (recent and old), while D-negative T. dicoccon was in between. Rhizosphere community structure of Ae. tauschii and T. dicoccon differed from that of T. aestivum, and differences occurred also between various genotype categories of T. aestivum. Overall, the acquisition of the D genome has had a negative impact on the ability of wheat to recruit ACC deaminase producers in soil, but bread wheats resulting from recent breeding displayed improved ACC deaminase activity in the rhizosphere.

Microbial inoculation alters rhizoplane bacterial community and correlates with increased rice yield

Microbial inoculants are recognized as environmentally friendly methods to promote plant growth and improve soil properties. However, the effects of inoculation on the rhizosphere and rhizoplane community structure of plants remain poorly documented and need further investigation. Rhodopseudomonas palustris (R. palustris) strain has nitrogen fixing ability and Bacillus subtilis (B. subtilis) strain is a plant growth-promoting rhizobacterium (PGPR). In this study, we investigated the effects of single and co-inoculation with R. palustris and B. subtilis on the increase of rice yield as well as on the microbial communities in the rhizosphere and rhizoplane of rice through potting experiments, respectively. The results showed that inoculation significantly increased rice yield and seed setting rate, with co-inoculation raising the yield by up to 13.7%. Inoculation influenced both rhizosphere and rhizoplane community structures and functions, amplifying the differences between them. The most significant changes were brought about by the combined inoculation treatment. Co-inoculation with R. palustris and B. subtilis had a synergistic effect. The profound alterations of rhizoplane bacterial community structures and functions were proved to be positively correlated with rice yield and seed setting rate (r = 0.59–0.76, p < 0.05). These results provide new ideas for the investigation of the potential microbiological mechanisms of microbial co-inoculation in practical agricultural applications.

Changes in Soil Chemistry and Microbial Communities in Rhizospheres of Planted Gastrodia elata on a Barren Slope and under a Forest

Continuous cropping of the important achlorophyllous medicinal orchid Gastrodia elata Blume causes an imbalance in soil microecology leading to soil-borne diseases. However, the impacts on different land covers remain largely unknown. Hence, this study aimed to investigate changes in the soil nutrient composition and the global microbial community structure in rhizospheres of G. elata cultivated on a barren slope (HPGJ) and under a forest (LXT) using integrated shotgun metagenomics and an analysis of soil chemical properties. High-throughput sequencing revealed an increase in the abundance of Proteobacteria, Actinobacteria, Mucoromycota, Basidiomycota, and Ascomycota, which drive N- and C-cycling genes in HPGJ and LXT. Notably, the fungal community was significantly improved in the HPGJ (from 0.17% to 23.61%) compared to the LXT (from 0.2% to 2.04%). Consequently, mineral cycling was enhanced in the HPGJ, resulting in a more improved soil nutrient composition than in the LXT. The soil chemical properties analysis unveiled a significant increase in the contents of the total nitrogen, NO3−-N, organic matter, total carbon, organic carbon, total sulfur, and total phosphorus in the HPGJ, while no changes were recorded in the LXT. It was noteworthy that the abundance of pathogenic microorganisms increased significantly in the HPGJ compared to the LXT. Our results provide supporting data to optimize G. elata cultivation on slopes.

Bacterial Community Structure in Rhizosphere of Barley at Maturity Stage

The crop rhizosphere is the main site of soil microbial activities. Understanding the structure and diversity of microbial communities in the crop rhizosphere will help us reveal interactions between rhizosphere microorganisms and plant growth. In this study, the rhizosphere soil was collected from 35 cultivated barley varieties at the mature stage. To investigate the structure and diversity of bacterial communities in the rhizosphere of different barley varieties, the 16S rDNA gene of microorganisms from the soil was sequenced using Illumina MiSeq next-generation high-throughput sequencing technology. The results showed that 13, 25, 49, and 59 bacterial flora with relative abundance &gt;1% were detected from 35 barley rhizosphere samples at the phylum, class, order, and family levels, respectively. The abundance of bacteria among varieties differed relatively little, but the abundance of the same bacteria in rhizospheres of different varieties was different. In addition, both the cluster analysis and principal component analysis (PCA) divided the 35 samples into three clusters at the phylum level. Groups III and IV showed significantly higher abundance than group II in Proteobacteria, while group II exhibited significantly higher abundance of Chloroflexi than groups III and IV. This finding provides a realistic basis for further using the relationship between barley rhizosphere microorganisms and barley growth to improve the resistance and quality of barley.

Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil.

In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.

Effects of maize and soybean intercropping on soil phosphorus bioavailability and microbial community structure in rhizosphere.

To investigate the effect of maize/soybean intercropping on rhizosphere soil microbial communities and phosphorus (P) bioavailability, we examined the changes of soil bioavailable P fractions and microbial community characteristics in the monoculture and intercropping systems based on high-throughput sequencing. The results showed that maize/soybean intercropping increased the contents of rhizosphere soil organic matter (SOM), available phosphorus (AP), microbial biomass phosphorus (MBP), and aboveground biomass. The increase of AP was mainly related to the increasing enzyme extracted phosphorus (Enzyme-P) and hydrochloric acid extracted phosphorus (HCl-P) contents. The dominant bacterial phyla under each treatment were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, while the dominant bacterial genera were Nocardioides, Solirubacter, Sphingomonas and Arthrobacter, with Proteobacteria and Sphingomonas having the highest relative abundance. The relative abundance of Proteobacteria and Sphingomonas in intercropping maize rhizosphere soil was significantly higher than that in monoculture, and that of Proteobacteria in intercropping soybean rhizosphere soil was significantly higher than monoculture. Soil properties and P fractions were closely related to the rhizosphere soil microbial composition. In all, maize/soybean intercropping could affect the rhizosphere soil P bioavailability by altering the structure of rhizosphere microbial communities.

Microdiversity sustains the distribution of rhizosphere-associated bacterial species from the root surface to the bulk soil region in maize crop fields.

Over the years, the microbial community of maize (Zea mays) rhizosphere has been extensively studied; however, the role of microdiversity sustain rhizosphere-associated microbial species distribution from root surface to bulk soil in mature maize is still unclear. Although operational taxonomic units (OTUs) have been used to classify species, amplicon sequence variants (ASVs) have been shown to be effective in representing microdiversity within OTUs at a finer genetic scale. Therefore, the aim of this study was to examine the role of microdiversity in influencing the distribution of rhizosphere-associated microbial species across environmental gradients from root surface to bulk soil at the OTU and ASV levels. Here, the microbial community structures of bulk, loosely bound, and tightly bound soil samples from maize rhizosphere were examined at OTU and ASV levels. The results showed that OTU and ASV methods exhibited similar microbial community structures in rhizosphere. Additionally, different ecotypes with varying distributions and habitat preferences were observed within the same bacterial OTU at the ASV level, indicating a rich bacterial microdiversity. In contrast, the fungal community exhibited low microdiversity, with no significant relationship between fungal microdiversity and persistence and variability. Moreover, the ecotypes observed within the bacterial OTUs were found to be positively or negatively associated with environmental factors, such as soil organic carbon (SOC), NO3 --N, NH4 +-N contents, and pH. Overall, the results showed that the rich microdiversity could sustain the distribution of rhizosphere-associated bacterial species across environmental gradients from root surface to bulk soil. Further genetic analyses of rhizosphere-associated bacterial species could have considerable implications for potential mediation of microdiversity for sustainable crop production.

Effects of Male and Female Strains of Salix linearistipularis on Physicochemical Properties and Microbial Community Structure in Saline-Alkali Soil.

The woody plant gender difference may lead to alteration in rhizosphere microbial communities and soil physicochemical properties. In this study, we investigated the differences in rhizosphere soil properties and microbial community structures of S. linearistipularis. Rhizosphere microorganisms were analyzed by high-throughput sequencing technology. The results showed that there were significant differences in rhizosphere soil nutrition between male and female S. linearistipularis plants in saline-alkali soil. The female S. linearistipularis plants significantly reduce soil pH values and significantly increase the soil water content (SWC), available total nitrogen (TN), soil organic matter (SOM), and soil urease activity (S-UE) compared to the male plant. The ACE, Chao, and Shannon index of the female plant was significantly higher than that of the male strain. At the level of Bacteriophyta, the relative abundance of Actinobacteriota in male and female S. linearistipularis was the highest, with 34.26% and 31.03%, respectively. Among the named bacterial genera, the relative abundance of Defluviicoccus of male and female plants was the highest, with 2.67% and 5.27%, respectively. At the level of Eumycophyta, the relative abundance of Ascomycetes in male and female plants was the highest, with 54.93% and 52.10%, respectively. Among the named fungi genera, the relative abundance of male and female plants of Mortierella was the highest, with 6.18% and 9.31%, respectively. In addition, soil pH, SOM, SWC, and S-UE activities were the main driving factors of soil microbial community structures. In the process of restoring saline-alkali land in the Songnen Plain, we may prioritise the planting of female S. linearistipularis, which also provides a theoretical basis for the microorganisms restoration of saline-alkali land in the Songnen plain.

Diversity and structure of bacterial communities in saline and non-saline rice fields in Cilacap Regency, Indonesia

Abstract Increased concerns for sustainable agriculture have led to increased use of beneficial rhizobacteria as biofertilizers. Soil bacteria play a significant role in the nutrient cycle of soil, but their presence can be affected by abiotic stress, such as salinity. This study aimed to compare the chemical characteristics of slightly saline and non-saline rice soil and examine the bacterial community structure in both rhizosphere and bulk soil. We utilized 16SrRNA gene sequencing and performed arithmetic means clustering, a type of hierarchical clustering, on the samples collected from the rice fields of Cimrutu and Rawaapu Village in Cilacap Regency, Indonesia. Although the nutrient content was similar in both soils, there was a noticeable difference in their electrical conductivity (EC) despite the two locations being less than 4 km apart. The EC value in the Cimrutu soil suggests that it is non-saline, while the Rawaapu soil exhibits a low salinity level. The study found that Proteobacteria was the most prevalent phylum in saline rhizospheric soil. In contrast, Firmicutes was the most abundant group in saline bulk soil and non-saline rhizospheric and bulk soil. Additionally, Halothiobacillus, Thioalkalispira-Slvurivermis, and Acidothermus genera dominated the saline rhizospheric soil, suggesting that halotolerant microbes play a significant role as plant growth-promoting rhizobacteria in saline soil. The study provides valuable insights into cultured or uncultured bacterial populations and structure in saline and non-saline soil to develop future strategies related to salinity by introducing beneficial microbes.

Phosphorus addition modifies the bacterial community structure in rhizosphere of Achnatherum inebrians by influencing the soil properties and modulates the Epichloë gansuensis-mediated root exudate profiles

Phosphorus addition modifies the bacterial community structure in rhizosphere of Achnatherum inebrians by influencing the soil properties and modulates the Epichloë gansuensis-mediated root exudate profiles

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.

Effects of Microplastic High-density Polyethylene on Cotton Growth, Occurrence of Fusarium wilt, and Rhizosphere Soil Bacterial Community

Plastic mulch, especially polyethylene mulch, is widely used in agricultural production in China, but the microplastics formed by its degradation gradually have accumulated in soil, causing a series of environmental problems. At present, there have been many reports on the environmental biological effects of microplastics in farmland soil, but studies on the effects of microplastics on crop growth, disease occurrence, and rhizosphere soil bacterial communities are still lacking. In the previous study, it was found that 1% high-density polyethylene (HDPE, 500 mesh) could increase the incidence rate of cotton Fusarium wilt (33.3%) and inhibit growth, but this phenomenon was not found after soil sterilization. It was speculated that HDPE could affect the growth and occurrence of Fusarium wilt by regulating the soil microbial community. Therefore, high-throughput sequencing technology, combined with network and FAPROTAX function analysis, were used to investigate the effects of HDPE on the bacterial community structure, interaction network, and soil function in cotton rhizosphere in order to analyze the mechanism of HDPE. NovaSeq sequencing showed that the bacterial community of HDPE-treated cotton rhizosphere soil was composed of 54 phyla and 472 genera; the number of phyla and genera was higher than that in untreated soil. The α and β diversity and ANOSIM/Adonis analyses showed that HDPE significantly reduced the richness of the bacterial community and changed the composition of the community structure. Based on a T-test species difference analysis, HDPE significantly reduced the relative abundance of bacteria with biological control, pollutant degradation, and antifungal drug synthesis (such as Kribbella, Massiliam, Hailiangium, and Ramlibacter).The change in the bacterial community will lead to the change in soil bacterial function. Further analysis of FAPROTAX function revealed that HDPE weakened some biochemical functions of bacteria in the cotton rhizosphere soil, such as aerobic chemoheterotrophy, fermentation, and nitrate reduction. The correlation network at the genus level showed that HDPE treatment weakened the interaction between rhizosphere bacteria, reduced the number of positive correlation connections, increased the number of negative correlation connections, simplified network structure, and changed the key flora. The above results showed that HDPE could reduce the cotton growth and the occurrence of Fusarium wilt by changing the bacterial community, interaction, and functional metabolism in rhizosphere soil, which can provide guidance for evaluating the ecological risk of polyethylene microplastics and the remediation of contaminated soil.

Plant growth stages covered the legacy effect of rotation systems on microbial community structure and function in wheat rhizosphere.

Legume-based crop rotation is conducive to improve soil multifunctionality, but how the legacy effect of previous legumes influenced the rhizosphere microbial community of the following crops along withgrowth stages remains unclear. Here, the wheat rhizosphere microbial community was assessed at the regreening and filling stages with four previous legumes (mungbean, adzuki bean, soybean, and peanut), as well as cereal maize as a control. The composition and structure of both bacterial and fungal communities varied dramatically between two growth stages. The differences in fungal community structure among rotation systems were observed at both the regreening and filling stages, while the difference in bacterial community structureamong rotation systems was observed only at the filling stage. The complexity and centrality of the microbial network decreased along with crop growth stages. The species associations were strengthened in legume-based rotation systems than in cereal-based rotation system at the filling stage. The abundance of KEGG orthologs (KOs) associated with carbon, nitrogen, phosphorus, and sulfur metabolism of bacterial community decreased from the regreening stage to the filling stage. However, there was no difference in the abundance of KOs among rotation systems. Together, our results showed that plant growth stages had a stronger impact than the legacy effect of rotation systems in shaping the wheat rhizosphere microbial community, and the differences among rotation systems were more obvious at thelate growth stage. Such compositional, structural, and functional changes may provide predictable consequences of crop growth and soil nutrient cycling.

Comparative Insights into the Microbial Diversity and Community Structure of Striga hermonthica-Infested Maize Rhizosphere

The damaging competition between crops and parasitic weeds has a negative impact on agricultural productivity; however, the impact of disturbance on the soil’s microbial community has received less attention. Hence, this study investigates the microbial composition and diversity of the maize rhizosphere infected with Striga hermonthica using a shotgun sequencing approach from two maize-growing fields (Eruwa, Nigeria and Mbuzini, South Africa). The rhizosphere soil DNA was extracted from infested soil using a Nucleospin soil genomic DNA extraction kit and sequenced on an Illumina platform. The dominant phyla were Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Acidobacteria, Chloroflexi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Chlorobi, Proteobacteria, Firmicutes, Nitrospirae, Thermotogae, Synergistetes, Ascomycota, Euryarchaeota, and Crenarchaeota. Bacteria phyla were observed to be of higher proportion in the rhizosphere soil samples obtained from Striga-infested maize field in Eruwa (Es) than those recovered from Mbuzini (Ms). The alpha diversity of microbial communities indicated insignificance differences (p &gt; 0.05) between the five taxonomical groups (phylum, class, order, family, and genus), while the beta diversity produced a significant (p = 0.01, R = 0.52) difference in the microbial diversity of the infested soil. In summary, the study sheds light on the diversity and composition of the microbiome of Striga hermonthica-infested soil, which influences the microbial functions in the management and sustenance of plant health against parasitic weeds.

Structural diversity of bacterial communities in two divergent sunflower rhizosphere soils

PurposeFarming practices on farmlands aim to improve nutrients in the fields or crops, soil quality and functions, as well as boost and sustain crop yield; however, the effect of loss of ecological diversity and degradation have impacted ecosystem functions. The beneficial rhizosphere-microorganism network and crop rotation may enhance a stable ecosystem. The use of next-generation sequencing technique will help characterize the entire bacterial species in the sunflower rhizosphere compared with the nearby bulk soils. We investigated the potential of the bacterial community structure of sunflower rhizosphere and bulk soils cultivated under different agricultural practices at two geographical locations in the North West Province of South Africa.MethodsDNA was extracted from rhizosphere and bulk soils associated with sunflower plants from the crop rotation (rhizosphere soils from Lichtenburg (LTR) and bulk soils from Lichtenburg (LTB) and mono-cropping (rhizosphere soils from Krayburg (KRPR) and bulk soils from Krayburg (KRPB) sites, and sequenced employing 16S amplicon sequencing. Bioinformatics tools were used to analyse the sequenced dataset.ResultsProteobacteria and Planctomycetes dominated the rhizosphere, while Firmicutes and Actinobacteria were predominant in bulk soils. Significant differences in bacterial structure at phyla and family levels and predicted functional categories between soils (P < 0.05) across the sites were revealed. The effect of physicochemical parameters was observed to influence bacterial dispersal across the sites.ConclusionThis study provides information on the predominant bacterial community structure in sunflower soils and their predictive functional attributes at the growing stage, which suggests their future study for imminent crop production and management for enhanced agricultural yields.