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Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities

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Abstract

We studied the microbial communities in maize (Zea mays) rhizosphere to determine the extent to which their structure, biomass, activity and growth were influenced by plant genotype (su1 and sh2 genes) and the addition of standard and high doses of different types of fertilizer (inorganic, raw manure and vermicompost). For this purpose, we sampled the rhizosphere of maize plants at harvest, and analyzed the microbial community structure (PLFA analysis) and activity (basal respiration and bacterial and fungal growth rates). Discriminant analysis clearly differentiated rhizosphere microbial communities in relation to plant genotype. Although microorganisms clearly responded to dose of fertilization, the three fertilizers also contributed to differentiate rhizosphere microbial communities. Moreover, larger plants did not promoted higher biomass or microbial growth rates suggesting complex interactions between plants and fertilizers, probably as a result of the different performance of plant genotypes within fertilizer treatments, i.e. differences in the quality and/or composition of root exudates.

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... Regarding sugarcane, cultivars are developed by polyploidy via crossing two species, i.e., Saccharum spontaneum and Saccharum officinarum (Meng et al. 2018), thus embedding a unique chromosome combination (Grivet and Arruda 2002). Two sugarcane genotypes may vary in two genes, which encode different amounts of sugar in roots, resulting in a different activity and composition of rhizosphere fungi (Aira et al. 2010). Zhao et al. (2020) demonstrated that different genotypes of sugarcane developed diverse rhizosphere fungal communities due to variations in root exudates. ...
... Depending on species and genotype, the molecular signals produced by plants are likely to be specific components of root exudates, which may attract some rhizosphere microbial species (Merbach et al. 1999;Haichar et al. 2008). Two sugarcane genotypes vary in two genes that code for the quantity and sort of sugar in roots, as well as potentially the quantity and sort of sugar exuding to the rhizosphere, resulting in a rhizosphere microbial population of varying activity and composition (Aira et al. 2010). A similar observation was made using Arabidopsis variants or ecotypes that altered root phytochemical excretions, resulting in a significant shift in the structure and progression of the rhizosphere's fungal communities (Badri et al. 2009;Micallef et al. 2009). ...
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Sugarcane cultivars (Saccharum officinarum L.) are widely cultivated for both sugar and renewable energy in China. The response of rhizosphere fungal composition and diversity to different emerging sugarcane cultivars is limited. Therefore, utilizing high-throughput sequencing, we explored fungal communities’ structure in soils adhering to six sugarcane cultivars’ roots (Guitang 08–120, Regan14-62, Guitang 08–1180, Haizhe 22, Liucheng 05–136, Taitang 22) in Guangxi Province, China. Our results suggested that sugarcane varieties significantly altered rhizosphere soil attributes, with Haizhe 22 having substantially lower soil pH, organic matter (OM), available phosphorus (AP), and soil water contents (SWC) than others cultivars. Different sugarcane varieties did not substantially affected the Shannon fungal diversity index, but the apparent effect on fungal richness was significant. Beta diversity analysis revealed that “Haizhe 22” distinguished the fungal community from the other five cultivars. Soil pH, OM, cultivars, and soil moisture were crucial determinants in shaping soil fungal composition. The Haizhe 22 rhizosphere significantly enriched the operational taxonomic units (OTUs) assigned to two fungal genera (Cephalotheca and Sagenomella), while rhizosphere of other verities significantly enriched the OTUs assigned to four fungal genera (Chaetomium, Chaetosphaeria, Mortierella, and Talaromyces), suggesting their essential role in plant development, disease tolerance, and bioremediation. These findings may help in selecting or breeding innovative genotypes capable of supporting abundant rhizosphere fungi beneficial to plants that would likely improve crops’ agronomic potential and maintain soil ecosystem sustainability.
... Previous study on the phytoremediation has found that rhizosphere bacterial communities from distinct Sedum alfredii ecotypes were diverse (Hou et al., 2018), which was owing to the differences of rhizosphere micro-environments (Badri et al., 2009;Micallef et al., 2009). Each aquatic macrophyte differs in their respective root exudation in terms of quality and composition (Fig. 3 , Table S4); thus, the macrophytes differ in their influences on the assembly and composition of rhizosphere bacterial communities (Aira et al., 2010;Hu et al., 2021). ...
... It was interesting that the phytoremediation of both macrophytes potentially increased bacterial richness and diversity in highly Cd-contaminated sediments (Cd-50) (Fig. 2). Previous study found that rhizosphere carbon inputs from root exudation could notably increase microbial activities (Griffiths et al., 1999;Aira et al., 2010). Moreover, high oxygen levels and root exudation provide resource-enriched habitats for rhizosphere microbes, which favors the recruitment of more copiotrophic species than oligotrophic taxa (Hu et al., 2021). ...
Article
Aquatic macrophytes have been widely employed for in-situ phytoremediation of cadmium (Cd) polluted sediments. But, little is known about the responses of rhizosphere bacteria and their interspecific interactions to phytoremediation. In this study, the α-diversity, community composition, co-occurrence network and keystone species of sediment bacteria in rhizosphere zones of two typical macrophytes, Hydrilla verticillata and Elodea canadensis, were investigated using 16S rRNA gene high-throughput sequencing. The results showed that after fifty days of phytoremediation, a group of specialized sediment bacteria were assembled in the rhizosphere zones closely associated with different host macrophytes. Rhizosphere micro-environments, i.e., the increases of redox potential and organic matter and the decreases of pH, nitrogen and phosphorus, reduced bacterial α-diversity through niche-based species-sorting process, which in turn reduced interspecific mutualistic relationships. But meanwhile, benefiting from the nutrients supplied from macrophyte roots, more bacterial species survived in the highly Cd-contaminated sediments (50 mg kg⁻¹). In addition, the co-occurrence network revealed that both macrophytes harbored two same keystone bacteria with the high betweenness centrality values, including the family Pedosphaeraceae (genus_unclassified) and genus Parasegetibacter. Their relative abundances were up to 28-fold and 25-fold higher than other keystone species, respectively. Furthermore, these two keystone bacteria were metabolic generalists with vital ecological functions, which posed significant potentials for promoting plant growth and tolerating Cd bio-toxicity. Therefore, the identified keystone rhizobacteria, Pedosphaeraceae and Parasegetibacter, would be potential microbial modulations applied for the future optimization of phytoremediation in Cd-contaminated sediment.
... Microorganisms, including cyanobacteria possess the ability to colonise the rhizosphere and roots, thereby, develop tight linkages with the plant; this helps in better transport of nutrients made available by microbial activities and facilitates reciprocal signalling between plants and microorganisms (Bais et al., 2006;Di Salvo et al., 2018;Pagnani et al., 2020). However, each plant genotype often selects its own microbiome, and along with soil characteristics and fertilization conditions, represents important determinants in the selection of effective inoculants, as demonstrated by several researchers (Picard et al., 2008;Aira et al., 2010;Rodríguez--Blanco et al., 2015). Recent reports suggest that root-associated microbiota exhibit reproducible associations with plant genotype and specific microbial taxa respond to differences in host genotype, which can help in the construction of beneficial synthetic communities (Chen et al., 2019;Walters et al., 2018). ...
... Plants are known to release 5-21 % of their photosynthetically fixed carbon in the form of soluble sugars, amino acids, which nourish the microflora and fauna and the rhizosphere microbiome is shaped by genotype, root exudates and environment (Aira et al., 2010). Recent reports suggest that soil characteristics and the plant immune system can have an overwhelming effect and shape the root microbiomes of maize Table 3 Mean performance of grain yield (g/plot) among maize inbreds, as influenced by cyanobacterial inoculants. ...
Article
Microbe-mediated enrichment of crops has emerged as an environment-friendly intervention to tackle the problems of eroding soil fertility and malnutrition globally. The responses of a set of ten biofortified maize genotypes to three cyanobacterial inoculants (cyanobacterial consortium BF1-4, Anabaena sp.–Trichoderma sp. biofilm-An-Tr and Anabaena sp.+ Providencia sp. -CR1 + PR3) were evaluated over a period of two years. Significant genetic variation existed among the maize inbreds for all soil microbial parameters, soil macronutrients (N and P) and micronutrients (Mn and Zn), besides physiological and nutritional quality traits. Genotype x Inoculants interaction was more significant for soil glomalin (32 %), organic carbon (26 %), soil polysaccharides (20 %) and soil available N (18 %). Genotype x inoculants x environment (years) interactions significantly influenced available Zn (36 %), organic carbon (31 %), glomalin (30 %), available N (20 %) and polysaccharides (20 %). Promising genotype-inoculant combinations of PMI-Q2+ BF1-4 or An-Tr, PMI-PV2+BF1-4 or CR1 + PR3, HP-467-13 + BF 1-4 or An-Tr were identified, which can be evaluated across agro-ecologies. It was concluded that cyanobacterial inoculation can lead to N savings, improved soil fertility and enhanced crop vigor in maize.
... Consequently, the oxygen-and nutrient-rich conditions favor the recruitment of more copiotrophic bacterial groups (e.g., Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria) than oligotrophic bacterial groups (e.g., Acidobacteria, Nitrospirae, and Planctomycetes) (Nuccio et al. 2016;Bledsoe et al. 2020). Each plant genotype differs in their respective root exudates in terms of quality and composition; therefore, genotypes will differ in their effects on the assembly and composition of rhizosphere bacterial communities (Aira et al. 2010). Moreover, recent work using multivariate plant resource/defense phenotypes indicated an extensive genetic variation in the multidimensional traits of plants, including chemical defense, litter decomposition, productivity, fine root growth, and other geneticbased traits (Schweitzer et al. 2008;Grady et al. 2011;Lau et al. 2016). ...
... These traits and their differences contribute to the variability among genotypes in altering soil microbial communities. However, current advances associated with the contribution of plant genotype to the composition of the rhizosphere microbial community mainly focused on model and economic crops, including Arabidopsis thaliana (Micallef et al. 2009), Populus (Bonito et al. 2019), maize (Aira et al. 2010), rice (Edwards et al. 2015), wheat (Mahoney et al. 2017), and soybean (Zhong et al. 2019). Different habitats may select for specific bacterial taxa. ...
Article
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High oxygen levels and root exudates together provide a resource-enriched habitat for rhizosphere microbes that, in turn, foster plant growth and perform key ecological functions. Plant genotype is a main factor shaping rhizosphere bacterial communities; however, the influence of plant genotype on the rhizosphere bacterial community of aquatic macrophytes remains unknown. Here we collected samples of the rhizosphere and bulk sediments of two genotypes of the macrophyte Phragmites australis from the littoral areas of freshwater lakes in China. High-throughput sequencing of the 16S rRNA gene was used to characterize the rhizosphere bacterial community. We found that the rhizosphere recruited a distinct bacterial community relative to that of the bulk sediment. The rhizosphere microbial community was characterized by distinct community composition and core OTUs comprising a few dominant taxa involved in the regulation of plant fitness and nutrient cycling. These taxa included Arthrobacter, Pseudomonas, Trichococcus, and Ramlibacter. Network analysis showed distinct co-occurrence patterns and a genotype-specific preference for hub taxa within the rhizosphere bacterial communities of each genotype. Functional analysis revealed difference between the relative abundance of functional groups participating in C, N, and S cycling. Our results improve our understanding of the composition of the rhizosphere bacterial community of aquatic macrophytes and highlight the importance of a comprehensive consideration of plant genotype in plant bioremediation in aquatic ecosystems.
... There is evidence that rhizosphere microbes can contribute to the uptake of minerals (Bais et al. 2006), tolerance to drought (Kim et al. 2012) and salinity (Zhang et al. 2008;Fatima et al. 2019). Rhizosphere dynamics are complex (McCully 1999) and microbial communities change in response to many factors, including host plant genetics (Aira et al. 2010;Schmidt et al. 2016;Yu and Hochholdinger 2018). Thus, it is conceivable that as we gain more understanding of these factors, varieties can be bred to support a managed microbiome that improves resilience of the crop. ...
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In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the ‘hidden half’ of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.
... Soluble sugars and organic acids serve as important carbon sources and primary energy sources for rhizosphere microorganisms (Bais et al., 2006;Liu et al., 2016). Therefore, the available carbon in root exudates might be an important factor affecting microbial communities in wetland sediments and the extent of influence might vary depending on the plant species and environmental factors (Aira et al., 2010;Marschner et al., 2001). ...
Article
To understand the mechanisms by which emergent plants influence the microbial communities in wetland sediments, we analyzed the response of microbial composition, abundance, metabolic activity, and metabolic genes to three emergent plant species [Cyperus alternifolius L. (Cyp), Typha angustifolia L. (Typ), and Phragmites australis (Cav.) Trin. ex Steud. (Phr)], and determined the important physicochemical properties of the soils and root exudates in Zhaoniu River Constructed Wetland in northern China. We found the composition of both the microbial communities and the metabolic genes differed between rhizosphere and non-rhizosphere sediments. The rhizosphere microbial abundance in Phr in summer was significantly higher than in the other two plants and in the non-rhizosphere. The rates of microbial respiration and ammonia oxidation in rhizosphere sediments were significantly higher than those in non-rhizosphere sediments. Our statistical analyses showed that the total organic carbon (TOC) concentration in root exudates and the oxidation-reduction potential (ORP) significantly influenced the differences in the composition, abundance, and metabolic activities of the microbial community and metabolic genes between rhizosphere and non-rhizosphere sediments, suggesting that the secretion of root exudates and oxygen by emergent plants was the main mechanism affecting the composition and function of the microbial community. As the result of the high levels of TOC and the ORP, the rhizosphere sediments showed relatively high abundances of the genes related to biodegradation of xenobiotic compounds. By contrast, non-rhizosphere sediments showed relatively high abundances of genes related to carbon fixation and sulfate reduction, possibly due to the low levels of TOC and ORP. Plants with an enhanced ability to secrete root ex-udates and oxygen, such as Phr, should be preferred in constructed wetlands to increase the metabolic activity of sediment microbial communities. This study extends our understanding of the mechanisms by which the plant rhizosphere affects the ecological functions of wetlands.
... High-throughput sequencing technology enabled us to study plant-associated microbial communities at high resolution. Studies on rhizosphere microorganisms associated with plant roots have been conducted in Arabidopsis thaliana, Hordeum vulgare [15,16,34,35], corns, and soybeans [22,36]. Despite these fundamental studies, the truth is that there is a scarcity of research on the roots and rhizosphere microorganisms in commercial and nonmodel plants. ...
Article
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Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology , respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina se-quencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.
... Plant roots can promote or prevent the recruitment of rhizosphere microorganisms by secreting root exudates and volatile compounds (Berendsen et al. 2012;Schmidt et al. 2019). A variety of root exudates, including sugars and amino acids, as well as proteins, organic acids and various secondary metabolites, are released into the rhizosphere and thus become nutrients for rhizosphere microbes, affecting the composition and diversity of rhizosphere microbial communities (Aira et al. 2010;Babalola 2010). This effect might largely depend on the plant species or genotype (Rengel and Marschner 2005). ...
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AimsThere is an increasing awareness of the importance of root-associated bacteria and fungi to plant growth. At present, little is known about whether different ginseng cultivars affect the soil rhizosphere microbial community. Here, we examined the changes in the microorganismal diversity and composition of the rhizospheres of different ginseng cultivars.Methods The rhizosphere soil of four ginseng cultivars, namely CBGL (GAOLI ginseng), JYSH (COMMON ginseng) and SZSZ (SHIZHU ginseng) and TSBT (BIANTIAO ginseng) were obtained. The 16S rRNA genes and internal transcribed spacer (ITS) regions from the total ginseng rhizosphere microorganism community were analyzed to investigate the diversity and structure of the bacterial and fungal communities of the different ginseng cultivars.ResultsWe found that fungal communities were more influenced by the cultivars than bacterial communities, and we revealed differences in the microbial community composition and diversity among the different ginseng cultivars. We found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ, but, TSBT had the lowest bacterial and fungal diversity, which may be related to the agricultural management for BIANTIAO ginseng. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the long survival time of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium sp. agrAR069.Conclusion We conclude that the microbial diversity and community structures under different ginseng cultivars are significantly different and are related to the host cultivar. This result provides information that can be used for the breeding of Panax ginseng.
... In this regard, previous studies have reported that maize and its genotype can influence bacterial composition in the rhizosphere and the rhizoplane (Peiffer et al. 2013;Walters et al. 2018), correlating with the fact that the genetic distance between rhizobacterial communities correlates significantly with the phylogenetic distance between maize genotypes (Bouffaud et al. 2014). Similarly, maize lines with mutations affecting their carbon storage pattern have been shown to harbor distinct prokaryotic microbiomes in the rhizosphere (Aira et al. 2010). In contrast, the effect of maize and its genotype on shaping the eukaryotic community in soil remains poorly understood, even though eukaryotic communities play important roles in the rhizosphere as plant parasites, decomposers and bacterial predators, among others (Bailly et al. 2007;Couradeau et al. 2011;Asiloglu et al. 2015). ...
Article
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The microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.
... Multifunctionality is an essential biological and management concept that describes the ability of an ecosystem to maintain multiple ecological functions simultaneously [1,2,5]. As significant drivers of ecosystem functions, soil microbial communities can be regulated by plant diversity via changing the nutrient availability and microenvironmental conditions [6][7][8]. However, global climate changes and intensive anthropogenic activities have led to the loss of plant diversity in grassland ecosystems [2,[9][10][11]. ...
Article
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Loss in plant diversity is expected to impact biodiversity and ecosystem functioning (BEF) in terrestrial ecosystems. Soil microbes play essential roles in regulating ecosystem functions. However, the important roles and differences in bacterial and fungal diversity and rare microbial taxa in driving soil multifunctionality based on plant diversity remain poorly understood in grassland ecosystems. Here, we carried out an experiment in six study sites with varied plant diversity levels to evaluate the relationships between soil bacterial and fungal diversity, rare taxa, and soil multifunctionality in a semi-arid grassland. We used Illumina HiSeq sequencing to determine soil bacterial and fungal diversity and evaluated soil functions associated with the nutrient cycle. We found that high diversity plant assemblages had a higher ratio of below-ground biomass to above-ground biomass, soil multifunctionality, and lower microbial carbon limitation than those with low diversity. Moreover, the fungal richness was negatively and significantly associated with microbial carbon limitations. The fungal richness was positively related to soil multifunctionality, but the bacterial richness was not. We also found that the relative abundance of saprotrophs was positively correlated with soil multifunctionality, and the relative abundance of pathogens was negatively correlated with soil multifunctionality. In addition, the rare fungal taxa played a disproportionate role in regulating soil multifunctionality. Structural equation modeling showed that the shift of plant biomass allocation patterns increased plant below-ground biomass in the highly diverse plant plots, which can alleviate soil microbial carbon limitations and enhance the fungal richness, thus promoting soil multifunctionality. Overall, these findings expand our comprehensive understanding of the critical role of soil fungal diversity and rare taxa in regulating soil multifunctionality under global plant diversity loss scenarios.
... The majority of studies examining how plant developmental stage affects the plant's microbiome have focused on bacteria associated with the rhizosphere of annuals or herbaceous perennials such as maize (37,38), rice (28), sorghum (27,32), wheat (39), Arabidopsis (29), and Boechera (30). These important studies indicate that rhizosphere-associated microbiomes can shift in association with plant developmental stages in both domesticated and wild plants that have short-lived aboveground tissues. ...
Article
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Research at the forefront of plant microbiome studies indicates that plant-associated microbes can alter the timing of plant development (phenology). However, it is unclear if host phenological stage affects microbial community assembly.
... Chemical fertilizer treatment and the control group were not statistically different in the survival rate of C. obtusa seedlings ( Table 1). The use of chemical fertilizers increases the biomass of phytopathogens in the soil, which in turn increases the rate of seedling infection [52]. In the present study, B. velezensis CE 100 secreted cell wall-degrading enzymes such as β-1,3-glucanase and protease throughout the incubation period ( Figure 3). ...
Article
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Root rot diseases, caused by phytopathogenic oomycetes, Phytophthora spp. cause devastating losses involving forest seedlings, such as Japanese cypress (Chamaecyparis obtusa Endlicher) in Korea. Plant growth-promoting rhizobacteria (PGPR) are a promising strategy to control root rot diseases and promote growth in seedlings. In this study, the potential of Bacillus velezensis CE 100 in controlling Phytophthora root rot diseases and promoting the growth of C. obtusa seedlings was investigated. B. velezensis CE 100 produced β-1,3-glucanase and protease enzymes, which degrade the β-glucan and protein components of phytopathogenic oomycetes cell-wall, causing mycelial growth inhibition of P. boehmeriae, P. cinnamomi, P. drechsleri and P. erythoroseptica by 54.6%, 62.6%, 74.3%, and 73.7%, respectively. The inhibited phytopathogens showed abnormal growth characterized by swelling and deformation of hyphae. B. velezensis CE 100 increased the survival rate of C. obtusa seedlings 2.0-fold and 1.7-fold compared to control, and fertilizer treatment, respectively. Moreover, B. velezensis CE 100 produced indole-3-acetic acid (IAA) up to 183.7 mg/L, resulting in a significant increase in the growth of C. obtusa seedlings compared to control, or chemical fertilizer treatment, respectively. Therefore, this study demonstrates that B. velezensis CE 100 could simultaneously control Phytophthora root rot diseases and enhance growth of C. obtusa seedlings. View Full-Text Keywords: forest seedling production; antagonistic bacteria; lytic enzymes; phytopathogenic oomycetes; auxin; plant development; biocontrol agent
... For example, the phyllosphere and rhizosphere of rice were colonized by particular bacterial communities with physiological traits of differential importance, such as transport processes and stress responses were more conspicuous in the phyllosphere, whereas dinitrogenase reductase was exclusively identified in the rhizosphere (Knief et al., 2012). Individual microbial populations in the maize rhizosphere were strongly modified by the crop genotype (Aira et al., 2010). The dominant factors influencing microbial community composition in the wheat rhizosphere included both plant age and site (Donn et al., 2015). ...
Article
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Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we investigated endophytic bacterial communities in wheat leaves and roots under different long-term fertilization regimes, including NPK chemical fertilizer and NPK chemical fertilizer combined with wheat straw, pig manure, or cow manure. Endophytic bacterial community composition considerably differed in leaves and roots. Although different fertilization treatments did not affect the endophytic bacterial species richness or phylogenetic diversity in either leaves or roots, the community composition was significantly altered, particularly in roots. The endophytic bacterial co-occurrence network in leaves was more complex and stable than that in roots. Furthermore, many of the keystone species that were identified by their topological positions in the co-occurrence networks of leaves and roots were involved in plant growth and fitness. The total relative abundance of keystone species was the highest in the NPK plus cow manure treatment in both leaves and roots. Overall, our results suggest that different fertilization regimes can strongly affect endophytic bacterial communities, and the combination of NPK fertilizer and cow manure promoted the relative abundance of the key endophytic bacterial microbiota in both leaves and roots, which might be beneficial for plants in agroecosystems.
... Average root growth in maize was shown to proceed at a rate of 2 cm d −1 for primary roots, 0.75 cm d −1 for first and second order lateral roots, and 3 cm d −1 for the seminal roots and the shoot born crown roots (de Moraes et al., 2019). Because only a part of bulk soil microorganisms (e.g., the fast-growing, "copiotrophic" microorganisms) possess the physiological prerequisites to exploit the transient resource pulses from rhizodeposits (Ho et al., 2017), the rhizosphere microbiota are generally characterized by a lower alpha diversity and evenness compared to bulk soil communities (Gomes et al., 2001;Haichar et al., 2008;Aira et al., 2010;Peiffer et al., 2013;Ofek et al., 2014;Walters et al., 2018). ...
Article
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Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
... Likewise, plant genotypic variation has been shown to modulate the soil microbial community structure in rice [7][8][9]22] and other crops such as maize [23][24][25]. Many studies examined the plant genotype effect on soil microbe interactions using one or a few genetically diverse cultivars, whereas other studies used plants possessing a single gene mutation that modifies a trait of interest. ...
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Plant–soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizosphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Two plant developmental stages were studied, heading and physiological maturity, based on root and shoot biomass growth patterns across the selected genotypes. We used partial least squares (PLS) regression analysis to examine plant trait-driven microbial populations and identify microbial species, functions, and genes corresponding to root and shoot biomass as well as developmental stage patterns. Species identified correlated with increases in either root or shoot biomass were widely present in soil and included species involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocella avoryzae), as well as known endophytes (Bradyrhizobium spp.). Additionally, PLS analysis allowed us to explore the relationship of developmental stage with species, microbial functions, and genes. Many of the community functions and genes observed during the heading stage were representative of cell growth (e.g., carbohydrate and nitrogen metabolism), while functions correlated with physiological maturity were indicative of cell decay. These results are consistent with the hypothesis that microbial communities exist whose metabolic and gene functions correspond to plant biomass traits.
... Most significant among these antimicrobials are cyclic-lipopeptides (CLPs) constituting iturins, fengycins, and surfactins that are pivotal in root colonization by Bacillus spp. (Aira et al., 2010;Carvalhais et al., 2013). ...
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Bacillus spp. are well-characterized as efficient bioinoculants for sustainable plant growth promotion and biocontrol of phytopathogens. Members of this spp. exhibit the multifaceted beneficial traits that are involved in plant nutrition and antimicrobial activities against phytopathogens. Keeping in view their diverse potential, this study targeted the detailed characterization of three root-colonizing Bacillus strains namely B. amyloliquefaciens, B. subtilis, and B. tequilensis, characterized based on 16S rRNA sequencing homology. The strains exhibited better plant growth promotion and potent broad-spectrum antifungal activities and exerted 43–86% in-vitro inhibition of growth of eight fungal pathogens. All strains produced indole acetic acid (IAA) in the range of 0.067–0.147 μM and were positive for the production of extracellular enzymes such as cellulase, lipase, and protease. Ultra-performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry (UPLC-ESI-MS/MS) analysis revealed the production of antifungal metabolites (AFMs) such as surfactins, iturins, fengycins, macrolactins, bacillomycin-D, and catechol-based siderophore bacillibactin which were further confirmed by amplifying the genes involved in the biosynthesis of these antimicrobial lipopeptides. When compared for the amounts of different cyclic-peptides produced by three Bacillus strains, B. amyloliquefaciens SB-1 showed the most noticeable amounts of all the antifungal compounds. Plant experiment results revealed that inoculation with phytohormone producing Bacillus spp. strains demonstrated substantial growth improvement of wheat biomass, number of spikes, and dry weight of shoots and roots. Results of this study indicate the biocontrol and biofertilizer potential of Bacillus spp. for sustainable plant nutrient management, growth promotion, and effective biocontrol of crop plants, particularly cultivated in the South Asian region.
... These influence varies from plant to plant and is achieved through roots exudation and modifications of soil environmental conditions (water, minerals and temperature) (Denef et al. 2009; Dini-Andreote and van Elsas 2013). The rhizosphere microbial communities can be altered by the specific genotype of the plants growing in the soil (Aira et al. 2010;Lawal and Babalola 2014), which may support Enebe and Babalola AMB Expr (2021) 11:24 microbial biomass formation and metabolic activities that will be inherent in the soil. These interactions at the rhizosphere generally control important biogeochemical cycling involved in carbon cycle, emission of greenhouse gases and cycling of other nutrients. ...
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Soil microbes perform important functions in nitrogen and carbon cycling in the biosphere. Microbial communities in the rhizosphere enhance plants’ health and promote nutrient turnover and cycling in the soil. In this study, we evaluated the effects of soil fertilization with organic and inorganic fertilizers on the abundances and distribution of carbon and nitrogen cycling genes within the rhizosphere of maize plants. Our result showed that maize plants through rhizosphere effects selected and enriched the same functional genes glnA, gltB , gudB involved in nitrogen cycle as do high compost and low inorganic fertilizer treatments. This observation was significantly different from those of high doses of inorganic fertilizer and low compost manure treated soil. Only alpha amylase encoding genes were selectively enriched by low compost and high inorganic fertilized soil. The other treatments only selected xynB (in Cp8), lacZ (Cp4), bglA , pldB , trpA (N2), uidA (N1) and glgC , vanA (Cn0) carbon cycling genes in the rhizosphere of maize. Also Actinomycetales are selected by high compost, low inorganic fertilizer and control. The control was without any fertilization and the soil was planted with maize. Bacillales are also promoted by low compost and high inorganic fertilizer. This indicated that only microbes capable of tolerating the stress of high dose of inorganic fertilizer will thrive under such condition. Therefore, soil fertilization lowers nitrogen gas emission as seen with the high abundance of nitrogen assimilation genes or microbial anabolic genes, but increases carbon dioxide evolution in the agricultural soil by promoting the abundance of catabolic genes involve in carbon cycling.
... The microbes inhabiting rhizosphere soil are beneficial for the host plants, particularly in terms of nutrient availability, stress resistance, and defense against soil-borne pathogens [4,5]. Studies have shown that rhizosphere microbes are influenced by soil nutrients, plant species, and the application of fertilizers [6][7][8]. In terrestrial agro-ecosystems, changes in the composition of soil microorganisms are powerful indicators of soil bioactivity and crop productivity [9,10]. ...
Article
This study was conducted to investigate the effect of biofertilizers on the structure and diversity of the rhizosphere bacterial community of maize. Different biofertilizers were applied to maize. The physical and chemical properties of rhizosphere soil samples were analyzed and the rhizosphere bacteria were analyzed by 16S amplicon sequencing. The results showed that treatment with Bacillus licheniformis and B. amyloliquefaciens as biofertilizers increased the soil organic matter (SOM), total nitrogen, total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents, indicating that the plant growth-promoting rhizobacteria in the biofertilizers might help the host plant to produce root exudates that, in return, recruit beneficial communities due to available sugars, amino acids, organic acids, vitamins, and polymers. The rhizosphere of maize treated with B. subtilis biofertilizer had the highest diversity and richness. However, the rhizosphere treated with the combined bacterial strains had the lowest diversity and richness, which might be due to the directional increase of the abundance of some bacteria with special functions, but the decrease of the overall bacterial community diversity in the soil. The dominant bacterial phyla were Proteobacteria (32.2%-34.6%), Acidobacteria (15.0%-21.0%), Actinobacteria (13.1%-17.2%), and Gemmatimonadetes (9.0%-10.8%), and the dominant bacterial species were Aciditerrimonas ferrireducens JCM 15389 (4.3%-5.2%), Gemmatimonas aurantiaca (3.2%-4.1%), and Pyrinomonas methylaliphatogenes (2.1%-4.8%). The significantly enriched bacterial functions were associated with amino acid metabolism, sugar metabolism, and energy metabolism pathways. The results of a redundancy analysis showed that SOM, TP, and AK were the main factors affecting the microbial community structure in the maize rhizosphere. In conclusion, the application of biofertilizers increased the diversity and richness of the bacterial community in the maize rhizosphere soil. However, combined strain treatment was failed and not an ideal strategy due to the lowest abundance and diversity.
... There is growing evidence that plant influences on soil microbial communities, and the functions they undertake, vary not only between plant species but also between individual genotypes within a single plant species. For example, studies by Aira et al. (2010), Bouffaud et al. (2012), Peiffer et al. (2013) and Walters et al. (2018) suggest that rhizosphere microbial community composition under maize is related to plant genotype. In barley, our previous findings (Mwafulirwa et al. 2016(Mwafulirwa et al. , 2017 and those of Pausch et al. (2016) are indicative that soil microbial activity and, in turn, the decomposition of SOM are also impacted by plant genotype. ...
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Purpose Rhizodeposition shapes soil microbial communities that perform important processes such as soil C mineralization, but we have limited understanding of the plant genetic regions influencing soil microbes. Here, barley chromosome regions affecting soil microbial biomass-C (MBC), dissolved organic-C (DOC) and root biomass were characterised. Methods A quantitative trait loci analysis approach was applied to identify barley chromosome regions affecting soil MBC, soil DOC and root biomass. This was done using barley Recombinant Chromosome Substitution Lines (RCSLs) developed with a wild accession (Caesarea 26-24) as a donor parent and an elite cultivar (Harrington) as recipient parent. Results Significant differences in root-derived MBC and DOC and root biomass among these RCSLs were observed. Analysis of variance using single nucleotide polymorphisms genotype classes revealed 16 chromosome regions influencing root-derived MBC and DOC. Of these chromosome regions, five on chromosomes 2H, 3H and 7H were highly significant and two on chromosome 3H influenced both root-derived MBC and DOC. Potential candidate genes influencing root-derived MBC and DOC concentrations in soil were identified. Conclusion The present findings provide new insights into the barley genetic influence on soil microbial communities. Further work to verify these barley chromosome regions and candidate genes could promote marker assisted selection and breeding of barley varieties that are able to more effectively shape soil microbes and soil processes via rhizodeposition, supporting sustainable crop production systems.
... Generally, genetic based-interactions among genotypes are complex and have been recently gaining attention (Rasche et al., 2006;Xu et al., 2009;Aira et al., 2010;Ýnceoglu et al., 2012;Cheng et al., 2020), and even minor genotype differences as between genetically modified and parental lines are believed to affect the microbial colonization of plant, particularly in vegetatively propagated crop. The seed stem-associated bacterial communities, independently of the genotypes and the soil type, is also a possible factor determining the specificity of the bacterial community in the tuber root system compartments. ...
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Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
... Additionally, conventional tillage also can imprint shifts in the rhizosphere as well as in the bulk soil (Hartman et al., 2018;Mathew et al., 2012;Wattenburger et al., 2019). In the last decade, many studies assessing the changes in the microbiome of the bulk soil under no-tillage and conventional tillage have been published (Aira et al., 2010;Fuka et al., 2015), specifically studies focusing on metagenomics (Carbonetto et al., 2014;Yin et al., 2017). ...
Article
Soil management systems are a set of farming techniques and practices used to avoid degradation, erosion, and depletion of the soil. This study proposes an evaluation of two of the several management techniques: no-tillage and fallow system. No-tillage is a tropical management system which improves soil quality by adding organic matter in the form of straw covering, which also maintains the soil's friability and structure due to reducing mechanization. On the other hand, a fallow system is the resting state of soil for several vegetative cycles, which allows the soil to recover and store organic matter while retaining moisture and disrupting the life cycles of pathogens through natural soil microbiota. In both techniques, the soil microbiota is an important parameter that is affected by the management system. The rhizosphere microbiota, in particular, is highly affected. Thus, this study aimed to characterize the corn rhizosphere microbial community of soils under the no-tillage (NT) and fallow soil (FS) management systems, correlating the data with soil chemicals and productivity parameters. Bacterial networks were also checked to get the main taxa in each soil management system. As a result, the diversity of the rhizosphere community in FS was significantly higher than in the NT system, with Proteobacteria, Actinobacteria and Acidobacteria being the more abundant phyla in both systems. The estimated productivity showed a weak correlation to the bacterial community. In addition, the Verrumicrobia and Cyanobacteria phyla were exclusive to FS, while the Actinobacteria, Firmicutes and Chlamydiae phyla were exclusive to NT. The main bacterial genera that were able to distinguish soil management were DA101 (Verrucomicrobia) in FS, and Geodermatophilus in NT. These results show that different soil management systems lead to significant shifts in the microbiota of the rhizosphere.
... Plant genotypes and soil have specific effects on the wheat rhizosphere microbial community [76]. The effect of plant genotypes on the inter-root microbial community of maize showed that the two genotypes had a significant effect on the inter-root microbial community of maize [77]. Lamit investigated different cottonwood genotypes supporting different aboveground fungal communities [78]. ...
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In recent years, host–microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.
... As the common phyla in soil under agricultural management, Table 1 showed that the relative abundances of Firmicutes, Verrucomicrobia, Spirochaetes, and Kiritimatiellaeota were higher in indica soils, while Bacteroidetes, Proteobacteria, and Planctomycetes were relatively more abundant in japonica soils, which might have an influence on rice NUE (Janssen, 2006;Muller et al., 2016;Fiard et al., 2022). As shown in different cultivars of potato, maize, and Arabidopsis plants, the nitrogen uptake activity and NUE of different plant cultivars are closely related to distinct microbial species recruited by their root systems because of the variability of the root exudates (Mansouri et al., 2002;Weinert et al., 2011;Aira et al., 2010;Badri et al., 2009). ...
Article
Rice cultivars, fertilizer types, and irrigation modes can affect soil bacterial communities and thus influence nitrogen utilization by soil microorganisms and plants. However, the combined effects of these three factors on soil bacterial communities and nitrogen productivity in rice plants remain unknown. Here, we examined the response of rhizosphere bacteria and nitrogen productivity to different combinations of cultivar (japonica or indica), fertilization (organic plus chemical or chemical), and irrigation (controlled or shallow-frequent). The results demonstrated the interactive effects of cultivars with fertilizers and irrigation on rhizosphere bacterial communities, nitrogen accumulation, and grain yield. These significant interactive effects were related to differences in the response to soil environment (soil inorganic nitrogen concentration and moisture condition) between diverse rhizosphere bacteria recruited by indica and japonica. We found that rhizosphere bacterial communities recruited by indica were more active in soil fertilized with organic plus chemical nitrogen, while those recruited by japonica were suitable for living in soil fertilized with chemical nitrogen. Rhizosphere bacteria diversity positively correlated with soluble inorganic nitrogen in soil, suggesting that more diverse bacterial communities and greater contents of NH4+-N might favor nitrogen accumulation in rice plants under shallow-frequent irrigation. The combinations of cultivars, fertilizer types, and irrigation greatly affected rhizosphere bacterial communities, thus triggering a significant difference in soil inorganic nitrogen content, which could play an essential role in affecting nitrogen productivity.
... While the role of plant-associated microbes for crop disease resistance is well recognized (e.g., Mendes et al. 2011;Berendsen et al. 2012;Pieterse et al. 2016), host regulatory mechanisms that shape a beneficial or detrimental plant microbiome remain largely underutilized. There is increasing evidence for an exploitable genetic base for plant responsiveness to native soil microbiomes that plays a significant part in driving root-associated microbial community composition and activity (Aira et al. 2010;Bulgarelli et al. 2015;Walters et al. 2018;Wille et al. 2019). More specifically, genotypic differences in the regulation of beneficial plant-microbe interactions of various crops were shown for microbe-mediated resistance by individual strains (Sefloo et al. 2019) or entire communities (Elhady et al. 2018), responsiveness to soil microbial feedbacks (Hu et al. 2018), and microbe-induced resistance priming (Shrestha et al. 2019). ...
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Crop root-associated microbiomes have been heralded for their potential to improve plant health and productivity. Optimizing beneficial interactions with rhizosphere microorganisms has been proposed to reduce reliance on external inputs, increase pathogen resistance, and alleviate abiotic stresses. Producers of Theobroma cacao, the economically important tropical perennial whose pods are used to produce chocolate, are faced with numerous challenges to sustainable production and rising demand. Cacao further provides an interesting case study to complement the extensive plant microbiome research on annual crops in temperate regions. However, current knowledge of the cacao root-associated microbiome is limited. Characterizing the factors that influence the composition and functions of microbial communities associated with cacao roots is a key first step to developing microbiome-targeted interventions for improved agricultural sustainability in cacao agroecosystems. These rhizosphere engineering approaches can be understood within the framework of provisioning, regulating, and supporting ecosystem services. Here we review the potential of cacao root-associated microbiomes to solve current challenges to production by increasing provisioning of ecosystem services. The major points are the following: (1) We describe factors affecting the cacao root-associated microbiome by expanding the traditional model of genotype-by-environment (G × E) interactions to include agricultural management (G × E × M) and discuss the unique aspects of this model in cacao agroforestry systems. (2) We then highlight how specific breeding targets and management practices can be optimized to enhance the ecosystem services mediated by the cacao root-associated microbiome. Such optimizations of ecosystem services will alleviate the reliance on external inputs and, eventually, contribute to more sustainable cacao production systems.
... The rhizosphere soil of L. chinensis was collected by the "shaken off" method to detect the AMF spore density and soil chemical properties (Aira et al. 2010). The rhizosphere soil of each sample was passed through a 2-mm sieve and divided into two parts. ...
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Aims Rapid spread and growth of plants that are poisonous to animals produces large amounts of plant litter in degraded grasslands. Nitrogen (N) input may promote the growth of these poisonous plants and alter the rhizosphere microbes and arbuscular mycorrhizal fungi (AMF) in particular. However, it is unclear how poisonous plant litter affects the growth of palatable plants and their associated AMF in the rhizosphere and whether and how N deposition may mediate these effects. Methods In a meadow steppe in northeast China, a greenhouse experiment was performed to test the combined effects of litter addition of a poisonous plant, S. chamaejasme, and N addition on the growth of a dominant grass, L. chinensis, AMF characteristics, and soil properties. Important Findings Litter addition significantly increased the ramet number and aboveground biomass of L. chinensis and soil available phosphorous (AP) and decreased the spore density of AMF. However, the interaction of both treatments had no significant effects on the traits of L. chinensis and the properties of AMF. S. chamaejasme litter positively affected L. chinensis by increasing AP and negatively affected AMF by combining soil nutrient balance changes and litter-induced allelopathic compositions. Higher N addition may alleviate soil N limitation and inhibit litter decomposition, thus overriding the litter's effects on L. chinensis and AMF. These findings imply that it is necessary to objectively and comprehensively evaluate the ecological functions of poisonous plants beyond their harmful effects on livestock. Simultaneously, N deposition should be an indispensable factor in predicting the relationships between poisonous plants and edible plants in degraded grasslands.
... For example, a comparison of root microbiomes in wheat, sorghum, and maize revealed that these plants had diverse community compositions (Bouffaud et al., 2014). Several studies have investigated the plant microbiome and their functionality in both model and crop plants such as Arabidopsis thaliana (Bulgarelli et al., 2012), Oryza sativa (Edwards et al., 2015), Zea mays (Aira et al., 2010), Glycine max (Rascovan et al., 2016), Triticum aestivum (Donn et al., 2015;Chen et al., 2019), and Populus trichocarpa (Shakya et al., 2013), which provides several opportunities to further explore their potential for sustainable agriculture. To date, most of the beneficial traits from microbes for crop improvement were based on individual or combined microbial inoculation which has attained limited success; hence, there is a need to explore plant microbiome and develop an elite microbial consortium with beneficial traits using next-generation technologies and synthetic biology tools to enhance crop productivity and stress resilience for sustainable agriculture. ...
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Heavy metal toxicity has become an impediment to agricultural productivity, which presents major human health concerns in terms of food safety. Among them, arsenic (As) a non-essential heavy metal has gained worldwide attention because of its noxious effects on agriculture and public health. The increasing rate of global warming and anthropogenic activities have promptly exacerbated As levels in the agricultural soil, thereby causing adverse effects to crop genetic and phenotypic traits and rendering them vulnerable to other stresses. Conventional breeding and transgenic approaches have been widely adapted for producing heavy metal resilient crops; however, they are time-consuming and labor-intensive. Hence, finding new mitigation strategies for As toxicity would be a game-changer for sustainable agriculture. One such promising approach is harnessing plant microbiome in the era of ‘omics’ which is gaining prominence in recent years. The use of plant microbiome and their cocktails to combat As metal toxicity has gained widespread attention, because of their ability to metabolize toxic elements and offer an array of perquisites to host plants such as increased nutrient availability, stress resilience, soil fertility, and yield. A comprehensive understanding of below-ground plant-microbiome interactions and their underlying molecular mechanisms in exhibiting resilience towards As toxicity will help in identifying elite microbial communities for As mitigation. In this review, we have discussed the effect of As, their accumulation, transportation, signaling, and detoxification in plants. We have also discussed the role of the plant microbiome in mitigating As toxicity which has become an intriguing research frontier in phytoremediation. This review also provides insights on the advancements in constructing the beneficial synthetic microbial communities (SynComs) using microbiome engineering that will facilitate the development of the most advanced As remedial tool kit in sustainable agriculture.
... Although the grain of our classification is coarse, it gives us hints on the divergent nature of community assembly for the different plant types, and in turn of potentially divergent biogeochemical/metabolic dynamics regarding nutrient cycling processes such as C MIN . Previous studies have documented various mechanisms through which plants influence microbial community assembly in soil and rhizosphere (Berg and Smalla 2009;Aira et al. 2010;Philippot et al. 2013). A very well established mechanism is the chemical nature of the root exudates of plants, which can vary phylogenetically and even at the genotype level of the same plant species (Miethling et al. 2000;Bais et al. 2006;Huang et al. 2014;Lakshmanan, Selvaraj and Bais 2014). ...
Article
Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts in soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil functioning, is relevant to assess such impacts. We evaluate the effect that plant type change in semiarid ecosystems has for microbial diversity and composition, and how this is related to carbon mineralization (CMIN) as a proxy for soil functioning. We followed a mesocosms experiment during two years within the Biosphere 2 facility in Oracle, Arizona, USA. Two temperature regimes were established with two types of plants (grass or mesquite). Soil samples were analyzed for physicochemical and functional parameters, as well as microbial community composition using 16S rRNA amplicon metagenomics (MiSeq Illumina). Our results show the combined role of plant type and temperature regime on CMIN, where CMIN in grass has lower values in elevated temperatures compared with the opposite trend in mesquite. We also found a strong correlation of microbial composition with plant type but not with temperature regime. Overall, we provide evidence of the major effect of plant type in the specific composition of microbial communities as a potential result of the shrub encroachment.
... The influence of plants on soil microbial activity and soil aggregation has been widely documented on maize (Aira et al. 2010), wheat (Kaci et al. 2005) and sunflower (Alami et al. 2000). Phenotyping of pearl millet lines for rhizospheric soil aggregation potential reveled contrasted lines. ...
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Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with several plants and play a key role in improving plant growth, tolerance to abiotic and biotic stresses as well as the soil structure. This work aimed at elucidating the AMF temperature stress modulating impact on four pearl millet lines plant growth and soil aggregation. Experimental trials were carried out in both greenhouse and growth chamber to determine the response of the four millet lines to inoculation with two AMF strains (Rhizophagus aggregatus and Funneliformis mosseae) under heat and non-stress conditions. We first investigated the mycorrhizal colonization (MC) and the mycorrhizal growth response (MGR) of millet lines in relation with their soil aggregation potential (root adhering soil/root biomass, MAS/RB) in the greenhouse. Secondly, the four millet lines were grown in two separated growth chambers and subjected to a day/night temperature of 32/28 °C as the control treatment and 37/32 °C as the temperature stress treatment. Plant growth, mycorrhization rate and several physiological, mycorrhizal and soil parameters were measured. Results showed that the mycorrhization rates of millet lines were low and not significantly different. Funneliformis mosseae (31.39%) showed higher root colonization than Rhizophagus aggregatus (22.79%) and control (9.79%). The temperature stress reduced the mycorrhizal colonization rate, shoot and root biomass, and the soil aggregation for all tested lines. L220 and L132 showed more MC rate and MGR than the other lines under control and high-temperature treatment. The MGR was significantly better under temperature stress conditions than in the control. Under the temperature stress conditions, inoculation with R. aggregatus and F. mosseae increased chlorophyll concentration, root dry weight and shoot dry weight as compared to non-inoculated plants. AMF inoculation, particularly with F. mosseae had a positive influence on the tolerance of millet lines to temperature stress. This study demonstrates that AMF play an important role in the response of these four millet lines to temperature stress. AMF is therefore an important component in the adaptation of crops to climatic variations in Sub-Saharan Africa.
... Our results have demonstrated that two tea varieties determine changes of the microbial community of rhizosphere soils under the same environmental conditions, which are similar with the study reported by Aira et al. (2010). Sequence analyses revealed that Proteobacteria, Acidobacteria, Ascomycota, and Basidiomycota were the most abundant phyla. ...
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Pu-erh tea is one of the most popular teas in China due to its health benefits. However, there is little research into the microbial community among the rhizosphere soils from medium-small-leaf variety and small-leaf variety (an ancient tea tree "Mansong tea") of Camellia sinensis used to produce Pu-erh tea. This is the first report on characterization of the microbial communities in the rhizosphere soils from both tea varieties by means of high-throughput sequencing. The results indicated that diverse bacteria and fungi were present in the tea tree rhizosphere soils, and Proteobacteria, Acidobacteria, Ascomycota, and Basidiomy-cota were the dominant phyla. The composition of bacterial and fungal communities composition in the rhi-zosphere soils of two tea varieties was markedly different. This study may result in improving our understanding of differentiating tea varieties and development of specific microbial communities in the tea orchards.
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El ecosistema está constituido por las interrelaciones de los factores bióticos y abióticos, en la cual se sostiene la vida. Las leguminosas y otras plantas, viven de forma simbiótica con bacterias que proliferan en el suelo y son capaces de fijar nitrógeno atmosférico (N₂), elemento vital, para la nutrición de las plantas. Las bacterias del género Rhizobium y las de diazótrofos tienen la capacidad de fijar N₂ convirtiendo este a una forma asimilable por las plantas. Las bacterias promotoras del crecimiento en plantas, (PGPB) por sus siglas en inglés son importantes en diferentes ecosistemas donde se presentan adversidades de sequía, baja fertilidad de los suelos cultivables y bajo rendimiento de la producción. La distribución, identificación y predicción de las funciones de la diversidad microbiana ayuda al manejo productivo e incrementa el rendimiento en cultivos agrícolas. Este artículo de revisión estudia la fijación biológica del nitrógeno a través de la interacción y simbiosis de plantas-bacterias.
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Plants have their microbiomes that live on the surface or within them. Microbiomes coexist with plants, play a key role in Nature's food cycle, and help assimilate nutrients; they play an important role in improving crops; protecting against heat, drought, and pathogenic organisms; and conserving endangered species. The rhizosphere that exists around the root is very significant for the development of microorganisms. Root‐associated bacteria are essential for plant growth and health. Understanding the combination and role of root microbiota is crucial toward agricultural methods that are less dependent on chemical fertilizers that have been identified to have negative effects on the ecosystem and human health. It has been estimated based on a common approach that less than 1% of the total microbial population in drylands has been successfully isolated in pure culture. Therefore, the analysis of complex microbiomes associated with plants is technically limited. But using next‐generation sequencing methods and phospholipid‐derived fatty acids allows the identification of microbial populations in different ecosystems. This chapter attempts to investigate the role of emerging biotechnology and metagenomics techniques in identifying microbial populations and microbial engineering in the recovery of the rhizosphere .
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Both atmospheric nitrogen (N) deposition and soil microbial legacy (SML) can affect plant performance, the activity of soil N-cycling functional microbes and the relative abundance of N-cycling functional genes (NCFGs). In the grassland vegetation successional process, how the interaction of SML and N deposition affects the performance of dominant grass and NCFGs remains unclear. Therefore, we planted Leymus chinensis, a dominant grass in the Songnen grassland, in the soil taken from the early, medium, late, and stable successional stages. We subjected the plants to soil sterilization and N addition treatments and measured the plant traits and NCFG abundances (i.e., nifH, AOB amoA, nirS, and nirK). Our results showed the biomass and ramet number of L. chinensis in sterilized soil were significantly higher than those in non-sterilized soil, indicating that SML negatively affects the growth of L. chinensis. However, N addition increased the plant biomass and the AOB amoA gene abundance only in sterilized soils, implying that SML overrode the N addition effects because SML buffered the effects of increasing soil N availability on NCFGs. Therefore, we emphasize the potential role of SML in assessing the effects of N deposition on dominant plant performance and NCFGs in the grassland vegetation succession.
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Purpose: Atractylodes lancea is a medicinal plant used to treat rheumatic diseases, digestive disorders, night blindness, and influenza. However, the microbiome associated with A. lancea remains unclear. In this study, we assess the role of microorganisms in the roots of A. lancea in regulating plant growth and secondary metabolites, and investigate the microbial composition of the root of A. lancea. Methods: The roots of A. lancea were inoculated with 10% soil suspension at different temperatures. Thereafter, the biological indices, major volatile oils, chemical properties of the rhizosphere soil, and the diversity of root endophytic and rhizosphere bacterial communities of A. lancea were assessed. Results: Soil microorganisms could attenuate the damage of high-temperature to A. lancea and significantly promote the growth and accumulation of volatile oil. A. lancea recruited endogenous plant growth-promoting bacteria (PGPBs) from soil, including Burkholderia-Caballeronia-paraburkholderia, Bradyrhizobium, Paenibacillus, Bacillus and Rhodococcus. These bacteria were positively correlated with four volatile oils. In the rhizosphere, PGPBs such as Novosphingobium are recruited. Conclusions: Soil microorganisms promote the growth and development of A. lancea, improve the plant’s ability to resist high temperature stress, and accelerate secondary metabolite accumulation. Most importantly, A. lancea could recruit and enrich specialized PGPBs from the soil. The PGPBs were significantly and positively correlated with A. lancea secondary metabolite and soil nutrient content, and can be used as ideal biological material in A. lancea cultivation and quality improvement.
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The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co2+, Fe3+, Mo2 +, V5+, Zn2+), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.
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Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants’ metabolisms and activation of plants’ responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.
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Sustainable practices are key to the improvement of soil fertility and quality in apple (Malus ×domestica Borkh.) orchards. Rootstock genotype and fertilizer inputs can both alter soil biology, as well as aboveground traits including nutrient acquisition. In this study, a factorial design was used to assess the interaction between two apple rootstocks, ‘Geneva® 41’ (‘G.41’) and ‘Malling 9’ (‘M.9’) with four fertilizer treatments (chicken‐litter compost, yardwaste compost, fertigation using calcium nitrate, and an unamended control). The bacterial community in the rhizosphere was assessed for its impact on both plant and soil properties for each rootstock × fertilizer treatment combination. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Planctomycetes, but Verrucomicrobia and Chloroflexi were the most responsive to the fertilizer treatments. The Chicken Litter and Yardwaste treatments had a greater effect on bacterial community structure than the Control. Yardwaste, in particular, was associated with increased relative abundance of Chloroflexi which was correlated with soil nutrient concentrations. ‘Malling 9’ had a greater bacterial diversity than ‘G.41’, but the rootstock treatment had no independent effect on the rhizosphere community structure. There was; however, a strong interaction between the rootstock and fertilizer treatments. Carbon cycling was the most prominent functional change associated with the soil bacterial community. These results suggest that compost amendments have a more positive effect on soil bacterial activity and nutrient availability than calcium nitrate. Our work shows that waste‐stream amendments can lead to multiple positive responses, such as increasing aboveground tree biomass, thus potentially improving orchard productivity. This article is protected by copyright. All rights reserved Organic and inorganic fertilizer treatments supported different rhizosphere bacteriomes Soil bacteriome change and organic composts were positively associated with tree growth Positive feedbacks can explain bacteriome change with greater apple growth Results justify the need to test mechanisms of apple‐compost‐bacteriome feedbacks
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Despite the lower reactivity of natural phosphates compared to soluble fertilizers, their P bioavailability can increase over the cultivation years, due to the physicochemical processes and the activity of soil microbiota. Therefore, this work aimed to evaluate the α and β diversity of the rhizosphere microbiota of maize and sorghum genotypes grown under different sources and doses of phosphate fertilizers. Four commercial maize and four sorghum genotypes were grown under field conditions with three levels of triple superphosphate (TSP) and two types of rock phosphate sources: phosphorite (RockP) and bayóvar (RP) during two seasons. Maize and sorghum presented a significant difference on the genetic β diversity of both rhizosferic bacterial and arbuscular mycorrhizal fungi. Moreover, P doses within each phosphate source formed two distinct groups for maize and sorghum, and six bacterial phyla were identified in both crops with significant difference in the relative abundance of Firmicutes and Proteobacteria. It was observed that RockP fertilization increased Firmicutes population while Proteobacteria was the most abundant phylum after TSP fertilization in maize. In sorghum, a significant impact of fertilization was observed on the Acidobacteria and Proteobacteria phyla. TSP fertilization increased the Acidobacteria population compared to no fertilized (P0) and RockP while Proteobacteria abundance in RockP was reduced compared to P0 and TSP, indicating a shift toward a more copiotrophic community. Our results suggested that the reactivity of P source is the predominant factor in bacterial community' structures in the maize and sorghum rhizosphere from the evaluated genotypes, followed by P source.
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This contribution (forthcoming as a chapter in an edited volume with Cambridge University Press) critically considers how underlying assumptions in international IP treaties reflect, as well as impact upon, realities. International IP treaties, and more broadly, international agreements which set minimum standards and so harmonize and co-ordinate norm-setting among and within states, frequently codify underlying assumptions about the social, economic, cultural or environmental utility of the standards they aim to globalize. While these assumptions may be correct in particular territorial, historical and socio-economic contexts, once they are engrained in international standards that are cast into the stones of international treaty law, they become global norms that are at best difficult, and at times even factually impossible to implement, amend or adapt. In worst case scenarios, the habitual implementation of such laws can lead to significant socio-economic, cultural, as well as environmental dystrophy. Whenever an implementation of such standards does not materialize the underlying assumptions, the global norms ultimately become redundant, more broadly challenging their legitimacy. Using the international protection of plant varieties as an example, this contribution critically reviews the assumptions built into the UPOV treaty regime and whether they are supported by science and empirical research on biodiversity, food security, nutrition and seed sovereignty. Contrary to expectations, this redundancy may extend beyond the context of biodiversity-rich countries of the Global South into countries of the Global North that are also (and perhaps more severely) struggling with biodiversity losses and climate change.
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The present chapter deals with inference of finite population parameters under super population model when variates are subject to measurement error. I have given some models to find measurement error from the finite super population model. Following Royall (1970, 71), and Royall and Herson (1973a, 1973b) approach, estimators of the finite population total under error-in-variables super population model have been developed. This study has been extended by various authors viz. Fuller (1975), Mukhopadhyay (1994), Manas et al. (1994), Bolfarine (1991), Battese et al. (1988), Eltinge (1994), Stefanski (2000), Ghosh and Sinha (2007), Ma and Li (2010), West (2010), Arima et al. (2012) etc. Keywords: super population model, measurement error, inference
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Roots are near‐ubiquitous components of soils globally but have often been regarded as separate from the soil rather than a substantial factor in determining what soil is and how it functions. The start of rapid soil formation commenced about 400 million years ago with the emergence of vascular plants and the evolution of roots and associated microbes. Roots and associated microorganisms contribute significantly to soil formation by altering rocks and soil minerals through a variety of biogeochemical processes and supply carbon to a depth that can have long residence times. Living root inputs of carbon via rhizodeposits are more efficient than shoot and root litter inputs in forming slow‐cycling, mineral‐associated soil organic carbon pools. The current functionality of soils in providing food and fuel and fibres, supplying plant nutrients, filtering water and flood regulation, and disease suppression are all dependent on the activities of plant roots. Roots are actively communicating and collaborating with other organisms for mutual benefit, and the signals underlying this modulation of the rhizosphere microbiome are being identified. In this review I examine how plant roots (an organ not an organism) affect soil formation and function and conclude that, from several perspectives, roots are not just “in” soil but “of” it and that definitions of soil should recognise this. A possible definition is: “Soils are altered surficial rock or sediment, composed of organic matter, minerals, fluids, and organisms whose formation and functionality are influenced by biogeochemical weathering and interactions of these components with plant roots.” Paleoclimatic and paleosoil research shows the key role of roots and mycorrhiza in soil formation. Deep roots and living root inputs are substantial contributors to long‐term C storage. Root/microbe signalling facilitates mutualistic symbioses, nutrient uptake and disease suppression. Definitions of soil should explicitly include roots as an important component of the soil system.
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The forest pathology paradigm that one disease is caused by one pathogen is shifting toward a consideration of the complex ecological interactions among pathogens, microbial communities, tree host, and environment. Currently, rapidly evolving technologies have increasing potential to provide a wealth of novel information on complex ecological interactions that can enhance or suppress plant disease; however, these technologies and the resulting ecological information are not yet well developed for application to forest pathology and related microbial processes. This chapter explores a recently developed concept of the soil microbiome and provides current information on interpreting the myriad of interactions among host, soil-borne pathogens, soil microbial community, and soil environments in relation to forest diseases. Because studies on the interactions among the soil microbiome and forest pathosystems are in their initial stages, examples of applications are drawn from agricultural and/or cropping systems.
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Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology impacts microbial community assembly. Microbiome studies in annuals or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis , retain leaves for years allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction.
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A field experiment involving cry1Ab transgenic rice (GM) and its parental non-cry1Ab rice (M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16S rRNA-based Illumina MiSeq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted UniFrac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted UniFrac distance, indicated that the above separations between line GM and cultivar M were statistically significant (P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina MiSeq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amoA gene, archaeal amoA gene and denitrifying bacterial nirK gene significantly increased (P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.
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Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report , we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis , the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.
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Microbes in the rhizosphere influence plant growth, productivity, susceptibility, and resistance to biotic and abiotic stresses. Various studies have been reported to show diversity and activity of microbes are as high in plants as in endophytes and rhizosphere. The roots harbor more diverse microbes than any other part of the plant. The soil type and its management also influence the microbial diversity. The microbial communities can enhance and facilitate pathogen defense and their role in environmental remediation through different mechanisms. Metagenomics is a growing field that helps understand the genomes in the microbial communities. The high resolution of uncultured microbes and the correlation of the function with the environment can be achieved using functional metagenomics. New emerging subdisciplines of metagenomics are Metatranscriptomics and Metaproteomics, which provide further functional analysis of microbial communities. Integrative metagen“omics” approach results in comprehensive information for the community from genes to RNA to proteins and metabolites. In this chapter, we discuss the plant rhizosphere; types of metagenomics analysis such as 16S (for bacteria), whole metagenomics, and 18S/ITS (for fungus); and application of metagenome associated with rhizosphere and endophytes.
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Sweet potatoes are an alternative source of carbohydrates that have high nutritional content. Development of sweet potato cultivation methods needs to be done to overcome the decrease of productive agricultural land due to land conversion. This study aimed to test the effect of differences in the composition of the growing media on the growth, yield, and quality of sweet potato. This study was a pot experiment using a Randomized Block Design (RBD) with 7 treatments and 5 replications. The types of treatments tested were P0: 100% soil + inorganic fertilizer; P1: 50% soil + 50% cow manure; P2: soil 50% + vermicompost 50%; P3: soil 50% + biochar rice husk 25%, cow manure 25%, P4: soil 50% + biochar rice husk 25% + vermicompost 25%, P5: soil 50% + cocopeat 25% + cow manure 25%, P6: soil 50% + cocopeat 25% + vermicompost 25%. The research results showed that the composition of the growing medium significantly affected plant growth and yield. The results of the statistical analysis showed that the treatments of P4 and P6 gave the highest growth, while the high yield of fresh weight of tubers per pot were found in the treatments P1, P2, P3, and P4 by 165.59 g, 143.38 g, 171.56 g, and 144.80 g, respectively. The highest number of tubers was found in treatment P6 by 7.66 tubers. The highest yield of dry matter was also found in treatments P1, P2, P3, and P4 by 59.91 g, 51.73 g, 59.02 g, and 48.59 g, respectively. Based on the research results, it can be recommended that the cultivation of sweet potato plants in pots can be carried out using porous growing media in a container that is sufficient and available balanced nutrients for the development of plant tubers.Keywords: Vermicompost, composition of growing media, Sweet Potatoes, Yield, Quality
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Nutrient enrichment impacts ecosystems globally. Population history, especially past resource environments, of numerically‐dominant plant species may affect their responses to subsequent changes in nutrient availability. Eutrophication can also alter plant‐microbe interactions via direct effects on associated microbial communities or indirect effects on dominant species’ biomass production/allocation as a result of modified plant‐soil interactions. We combined a greenhouse common garden and a field reciprocal transplant of a salt marsh foundation species (Spartina alterniflora) within a long‐term, whole‐ecosystem, nutrient‐enrichment study to determine whether enrichment affects plant production and microbial community structure differently depending on plant population history. For the greenhouse portion, we collected 20 S. alterniflora genotypes – 10 from an enriched creek that had received elevated nutrient inputs for 10 years and 10 from an unenriched reference creek – and reared them in a common garden for one year. For the field portion, we conducted a two‐year, fully‐crossed reciprocal transplant experiment with two gardens each at the enriched and unenriched sites; we examined the effects of source site (i.e., population history), garden site, and plant genotype. After two years, plants in enriched gardens had higher aboveground biomass and altered belowground allocation compared to plants in unenriched gardens. However, performance also depended on plant population history: plants from the enriched site had decreased aboveground and rhizome production compared to plants from the unenriched site, most notably in unenriched gardens. In addition, almost all above‐ and below‐ground traits varied depending on plant genotypic identity. Effects of nutrient enrichment on the associated microbial community were also pronounced. Following one year in common garden, microbial community structure varied by plant population history and S. alterniflora genotypic identity. However, at the end of the reciprocal transplant, microbial communities differed primarily between enriched and unenriched gardens. Synthesis: Nutrient enrichment can impact plant foundation species and associated soil microbes in the short‐term. Most importantly, nutrient enrichment can also have long‐lasting effects on plant populations and associated microbial communities that potentially compromise their ability to respond to changing resource conditions in the future.
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The composition of rhizospheric microbial community may be shaped by plant genotype. Forty five melon (Cucumis melo L.) and seven snake melon (Cucumis melo var. flexuosus) genotypes were tested for their growth and yield parameters compared to a commercial melon cultivar “Star plus”. To estimate the microbial community in the rhizospheric soil of these genotypes, soil dilution plating technique on specific agar medium was used and compared to control. The majority of melon genotypes showed significantly comparable height, fruit weight and fruit yield per plant as “Star plus”. The fruit yield per plant varied significantly depending on tested genotypes. The total bacterial population in the rhizosphere of ten melon and two snake melon genotypes was significantly 59 to 68% higher than control soil. For most tested genotypes, a significant increase in the culturable rhizospheric actinomycetes, about 28.5 to 92.6%, was recorded comparatively to control soil. Fungal population counts in the rhizosphere of tested genotypes were significantly comparable to control. The genotypic difference in melon and snake melon reflects the quantum and diversity of their microbiomes that melon breeders could benefit when seeking at the holobiont concept to include associated microbiomes in breeding programs.
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It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.
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Vermicomposting, a very efficient method of converting solid organic waste into an environmentally-friendly, useful and valuable resource, is an accelerated process that involves bio-oxidation and stabilization of the waste as a result of the interactions between some species of earthworms and microorganisms. Although microorganisms are the main agents for biochemical decomposition of organic matter, earthworms are critical in the process of vermicomposting. Complex interactions among the organic matter, microorganisms, earthworms and other soil invertebrates result in the fragmentation, bio-oxidation and stabilization of the organic matter.
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The cell content of 12 bacterial phospholipid fatty acids (PLFA) was determined in bacteria extracted from soil by homogenization/centrifugation. The bacteria were enumerated using acridine orange direct counts. An average of 1.4010-17 mol bacterial PLFA cell-1 was found in bacteria extracted from 15 soils covering a wide range of pH and organic matter contents. With this factor, the bacterial biomass based on PLFA analyses of whole soil samples was calculated as 1.0–4.8 mg bacterial C g-1 soil C. The corresponding range based on microscopical counts was 0.3–3.0 mg bacterial C g-1 soil C. The recovery of bacteria from the soils using homogenization/centrifugation was 2.6–16% (mean 8.7%) measured by PLFA analysis, and 12–61% (mean 26%) measured as microscopical counts. The soil content of the PLFA 18:26 was correlated with the ergosterol content (r=0.92), which supports the use of this PLFA as an indicator of fungal biomass. The ratio 18:26 to bacterial PLFA is therefore suggested as an index of the fungal:bacterial biomass ratio in soil. An advantage with the method based on PLFA analyses is that the same technique and even the same sample is used to determine both fungi and bacteria. The fungal:bacterial biomass ratio calculated in this way was positively correlated with the organic matter content of the soils (r=0.94).
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The effect of transgenic Bt 176 maize on the rhizosphere bacterial community has been studied with a polyphasic approach by comparing the rhizosphere of Bt maize cultivated in greenhouse with that of its non transgenic counterpart grown in the same conditions. In the two plants the bacterial counts of the copiotrophic, oligotrophic and sporeforming bacteria, and the community level catabolic profiling, showed no significant differences; differences between the rhizosphere and bulk soil bacterial communities were evidenced. Automated ribosomal intergenic spacer analysis (ARISA) showed differences also in the rhizosphere communities at different plant ages, as well as between the two plant types. ARISA fingerprinting patterns of soil bacterial communities exposed to root growth solutions, collected from transgenic and non transgenic plants grown in hydroponic conditions, were grouped separately by principal component analysis suggesting that root exudates could determine the selection of different bacterial communities.
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We have studied the effects of factorial combinations of lime and N additions on soil microbial biomass, respiration rates and phosphatase activity of an upland grassland. We also used an Agrostis capillaris seedling bioassay to assess the effect of the treatments on the activity of arbuscular-mycorrhizal (AM) fungi and root surface phosphatase enzymes and the concentrations of N and P in the bioassay plant shoots. In the F and H horizons, soil microbial biomass carbon (Cmic) decreased in response to the liming, while addition of lime and N together reduced basal respiration rates. In the Ah horizon, Cmic was unaffected by the treatments but basal respiration rates decreased in the plots receiving nitrogen. Soil phosphatase activity decreased only in the Ah horizon in plots receiving lime, either in combination with N or alone. The mass of root fwt. colonized by AM fungi increased in response to the treatments in the order nitrogenR2=28.7%, P=0.004). The results demonstrate the sensitivity of both free-living heterotrophic microorganisms and symbiotic mycorrhizal fungi to short-term (2years) applications of lime and N to long-term upland grassland, particularly in relation to the key P cycling activities undertaken by these organisms.
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The population size of diazotrophic bacteria naturally associated with the maize rhizosphere can be affected by biotic and environmental factors. In this work we have evaluated the effect of two genotypes of maize, with and without nitrogen fertilization, on the population dynamics and distribution of diazotrophic bacteria associated with maize plants over different plant ontogenic stages. The study was carried out in a field experiment with and without nitrogen fertilization, using two maize cultivars (Santa Helena 8447 and Santa Rosa 3063) previously selected from 32 maize cultivars for the lowest and highest response to nitrogen fertilization, respectively. Microbiological and molecular approaches were used to characterize the diazotrophic bacterial population structure. Bacterial population was assessed by the most probable number using semi-solid N-free media, and by DNA isolation from soil and plant tissue followed by amplification of nifH gene fragments using nested PCR, and by RFLP analysis using the restriction endonucleases TaqI and HaeIII. The dynamics of the diazotrophic bacterial population were affected by the ontogenic stage of the maize plants, but not by the cultivar type. Roots were the preferred site of colonization, independent of cultivar type and growth stage. During the first stage of maize growth, addition of nitrogen fertilizer negatively affected the diazotrophic bacterial population.
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An understanding of the environmental factors affecting size and composition of rhizosphere microbial populations is important when introducing exogenous microorganisms in the rhizosphere of crop plants for plant growth promotion. The influence of plant development, cultivar and soil characteristics on the total rhizosphere microbial population and community structure of maize plants was investigated using the concept of r/K strategy. During maize growth microbial population density did not vary significantly, whereas the microbial community structure changed markedly in the early stages of plant growth but afterwards remained stable. Comparisons of the rhizosphere microflora of several maize cultivars, showing differential susceptibility to Fusarium, revealed that different cultivars support similar numbers of indigenous bacteria. Moreover the bacterial community structures of different maize cultivars did not show any significant difference. On the contrary, soil type had a marked influence on the microbial population of maize rhizosphere. Indeed the rhizosphere microbial density and community structure varied significantly among the different sampling sites. In conclusion, plant development and soil type have a marked influence on the rhizosphere microflora of maize, whereas cultivar type does not have a role.
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Soil communities dominated by fungi such as those of no-tillage (NT) agroecosystems are often associated with greater soil organic matter (SOM) storage. This has been attributed in part to fungi having a higher growth yield efficiency (GYE) compared to bacteria. That is, for each unit of substrate C utilized, fungi invest a greater proportion into biomass and metabolite production than do bacteria. The assumption of higher fungal efficiency may be unfounded because results from studies in which fungal and bacterial efficiencies have been characterized are equivocal and because few studies have measured microbial GYE directly. In this study, we measured microbial GYE in agricultural soils by following 13C-labeled glucose loss, total CO2–C, and 13CO2–C evolution at 2 h intervals for 20 h in two experiments (differing in N amendment levels) in which the fungal:bacterial biomass ratios (F:B) were manipulated. No differences in efficiency were observed for communities with high versus low F:B in soils with or without added inorganic N. When calculated using 13CO2–C (in contrast to total CO2–C) evolution, growth yield efficiencies of soils having high and low F:B were 0.69±0.01 and 0.70±0.01, respectively. When soils were amended with N, soils with high and low F:B had growth yield efficiencies of 0.78±0.01 and 0.76±0.01, respectively. Our experiments do not support the widely held assumption that soil fungi have greater growth efficiency than soil bacteria. Thus, claims of greater fungal efficiency may be unsubstantiated and should be evoked cautiously when explaining the mechanisms underlying greater C storage and slower C turnover in fungal-dominated soils.
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The interface between living plant roots and soils (the rhizosphere) is a central commodities exchange, where organic carbon flux from roots fuels decomposers that, in turn, can make nutrients available to roots. This ongoing exchange operates in the path of vast, transpiration-driven water flow. How the spatio-temporal patterning in resource availability around plant roots affects rhizosphere community composition, activity, and nutrient cycling remains unknown. This review considers how molecular approaches contribute to the exploration of rhizosphere resource exchange, highlighting several recently developed methods linking microbial identity with substrate uptake and gene expression. In particular, strengths and weaknesses of genetically engineered bioreporters are discussed, because currently they alone provide in situ spatio-temporal information at scales of rhizosphere organisms. The soil spatial context is an emerging frontier in ecological soils research. We conclude with parallels linking empirical investigation in the rhizosphere with the quest for understanding general rhizosphere function in Earth’s diverse ecosystems.
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The effect of cattle activity on pastures can be subdivided into three categories of disturbances: herbage removal, dunging and trampling. The objective of this study was to assess separately or in combination the effect of these factors on the potential activities of soil microbial communities and to compare these effects with those of soil properties and plant composition or biomass. Controlled treatments simulating the three factors were applied in a fenced area including a light gradient (sunny and shady situation): (i) repeated mowing; (ii) trampling; (iii) fertilizing with a liquid mixture of dung and urine. In the third year of the experiment, community level physiological profiles (CLPP) (Biolog Ecoplates¿) were measured for each plots. Furthermore soil chemical properties (pH, total organic carbon, total nitrogen and total phosphorus), plant species composition and plant biomass were also assessed. Despite differences in plant communities and soil properties, the metabolic potential of the microbial community in the sunny and in the shady situations were similar. Effects of treatments on microbial communities were more pronounced in the sunny than in the shady situation. In both cases, repeated mowing was the first factor retained for explaining functional variations. In contrast, fertilizing was not a significant factor. The vegetation explained a high proportion of variation of the microbial community descriptors in the sunny situation, while no significant variation appeared under shady condition. The three components of cattle activities influenced differently the soil microbial communities and this depended on the light conditions within the wooded pasture. Cattle activities may also change spatially at a fine scale and short-term and induce changes in the microbial community structure. Thus, the shifting mosaic that has been described for the vegetation of pastures may also apply for below-ground microbial communities.
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Plant health depends, in part, on associations with disease-suppressive microflora, but little is known about the role of plant genes in establishing such associations. Identifying such genes will contribute to understanding the basis for plant health in natural communities and to new strategies to reduce dependence on pesticides in agriculture. To assess the role of the plant host in disease suppression, we used a genetic mapping population of tomato to evaluate the efficacy of the biocontrol agent Bacillus cereus against the seed pathogen Pythium torulosum. We detected significant phenotypic variation among recombinant inbred lines that comprise the mapping population for resistance to P. torulosum, disease suppression by B. cereus, and growth of B. cereus on the seed. Genetic analysis revealed that three quantitative trait loci (QTL) associated with disease suppression by B. cereus explained 38% of the phenotypic variation among the recombinant inbred lines. In two cases, QTL for disease suppression by B. cereus map to the same locations as QTL for other traits, suggesting that the host effect on biocontrol is mediated by different mechanisms. The discovery of a genetic basis in the host for interactions with a biocontrol agent suggests new opportunities to exploit natural genetic variation in host species to enhance our understanding of beneficial plant-microbe interactions and develop ecologically sound strategies for disease control in agriculture.
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An understanding of agroecosystems is key to determining effective farming systems. Here we report results from a 21-year study of agronomic and ecological performance of biodynamic, bioorganic, and conventional farming systems in Central Europe. We found crop yields to be 20% lower in the organic systems, although input of fertilizer and energy was reduced by 34 to 53% and pesticide input by 97%. Enhanced soil fertility and higher biodiversity found in organic plots may render these systems less dependent on external inputs.
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Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.
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Crop nutrition is frequently inadequate as a result of the expansion of cropping into marginal lands, elevated crop yields placing increasing demands on soil nutrient reserves, and environmental and economic concerns about applying fertilizers. Plants exposed to nutrient deficiency activate a range of mechanisms that result in increased nutrient availability in the rhizosphere compared with the bulk soil. Plants may change their root morphology, increase the affinity of nutrient transporters in the plasma membrane and exude organic compounds (carboxylates, phenolics, carbohydrates, enzymes, etc.) and protons. Chemical changes in the rhizosphere result in altered abundance and composition of microbial communities. Nutrient-efficient genotypes are adapted to environments with low nutrient availability. Nutrient efficiency can be enhanced by targeted breeding through pyramiding efficiency mechanisms in a desirable genotype as well as by gene transfer and manipulation. Rhizosphere microorganisms influence nutrient availability; adding beneficial microorganisms may result in enhanced availability of nutrients to crops. Understanding the role of plant-microbe-soil interactions in governing nutrient availability in the rhizosphere will enhance the economic and environmental sustainability of crop production.
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Sweet corn (Zea mays L.) is one of the most popular vegetables in the USA and its popularity is increasing in Asia and Europe. In the USA, the farm value of sweet corn for processing ranks second only to tomatoes. Approximately 40% of the corn for processing is frozen and the remainder is canned. Among vegetables for fresh consumption, sweet corn ranks sixth in value in the USA. The USA ranks number one in sweet corn production followed by Japan, Canada, France, and Taiwan. Sweet corn is also grown in South America and Australia. Sweet corn is neither a race nor a subspecies of the Z. mays L. species. It is differentiated from other types of corn by the presence of a gene or genes that affect starch synthesis in the endosperm and its use as a vegetable. At present, at least seven other genes that affect endosperm carbohydrate synthesis are being used either singly or in combination in sweet corn varieties. Sweet corn is defined by its use as a vegetable and the presence of one or more simply inherited genes that alter the carbohydrate composition of the endosperm. This chapter provides an overview of cytology, genetics, germplasm resources, and reproductive biology of sweet corn. The chapter focuses on the breeding objectives and breeding methods of sweet corn. It also discusses the application of biotechnology in the sweet corn breeding along with the future prospects in the sweet corn industry.
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Most cultivated soils in temperate regions support earthworms. Population densities vary widely and the species present differ in relation to climatic conditions, soil type and cropping. Cultivation by mechanical disturbance completely changes the environment in which earthwormslive, destroying the habitat and changing the soil temperature and moisture and the availability of food. All these factors influence the size of earthworm populations, their species diversity, dominance and vertical distribution (Fig. 10. I).
Article
Methods are available in the literature for the measurement of instantaneous growth rates in field samples of photosynthetic microbes and procaryotic saprotrophic microbes, but there has been no such method for eucaryotic saprotrophic microbes (members of the kingdom Fungi). We have devised a technique for estimating instantaneous growth rates for ergosterol-containing fungi in field material, and preliminarily applied the technique to estimation of fungal productivities and throughputs in two types of standing-dead grass (one saltwater, one freshwater), obtaining plausible values (e.g., conversion efficiencies, total fungal production divided-by leaf mass loss, were calculated to be 36-64%). This method is based on measuring rates of radiolabeled acetate incorporation into ergosterol. We examined several potential problem areas for use of radiolabeled precursors in measurement of microbial molecular syntheses, and its extrapolation to microbial productivity. Key findings were: (a) 5 mmol/L added acetate (required for maximization of detection of rates) had positive or neutral impact on 48-h fungal growth, and no shift-up (sudden upward change in rate) or lag in incorporation of acetate into ergosterol occurred between 0.25 and 1.25 h of incubation of naturally decaying leaf (Spartina alterniflora) samples with 5 mmol/L acetate; (b) bacterial assemblages on leaves did not contribute radioactivity to the ergosterol fraction after incubation with radioacetate (as opposed to > 30 Bq per centimetre length of leaf containing fungal mycelium); (c) the average empirical factor for conversion from nanomoles C-14-acetate incorporated to micrograms organic fungal mass produced was 8.2-mu-g/nmol (coefficient of variation, 27%). We tentatively conclude that the acetate-to-ergosterol method is tenable for measurement of natural fungal productivity.
Article
This study describes the effects of balanced versus nutrient-deficiency fertilization on soil microbial biomass, activity, and bacterial community structure in a long-term (16 years) field experiment. Long-term fertilization greatly increased soil microbial biomass C and dehydrogenase activity, except that the P-deficiency fertilization had no significant effect. Organic manure had a significantly greater (P<0.05) impact on the biomass C and the activity, compared with mineral fertilizers. Microbial metabolic activity (dehydrogenase activity per microbial biomass C) was significantly higher (P<0.05) under balanced fertilization than under nutrient-deficiency fertilization. General bacterial community structure was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) targeting eubacterial 16S rRNA gene. Mineral fertilization did not affect the DGGE banding pattern, while specific DGGE band was observed in organic manure-fertilized soils. Phylogenetic analysis showed that the change of bacterial community in organic manure-fertilized soil might not be because of the direct influence of the bacteria in the compost, but because of the promoting effect of the compost on the growth of an indigenous Bacillus sp. in the soil. We emphasize the importance of balanced-fertilization, as well as the role of P, in maintaining soil organic matter, and promoting the biomass and activity of microorganisms.
Article
Nutrient solution culture and quartz sand amended with or without rock phosphate, were used to compare the short-term responses to phosphorus (P) deficiency of two contrasting maize hybrids, L3x228-3 (P-efficient) and HS 2841x5046 (P-inefficient). In solution-grown seedlings, the rapid P deficiency-induced enhancement of root growth and of the root/shoot ratio was a sign of P deficiency stress rather than of P efficiency. In sand culture, uptake of P from sparingly soluble rock phosphate was higher in P-efficient plants than in P-inefficient maize. In the variety L3-228-3, P efficiency seemed due to enhanced P acquisition rather than to an enhanced P use efficiency. In sand, but not in solution culture, higher citrate concentrations were detected in the rhizosphere of P-efficient than of P-inefficient maize. Quartz sand amended with rock phosphate was a better substrate than nutrient solution for revealing the varietal differences in P acquisition efficiency in short-term experiments.
Article
Lack of carbon has been assumed to be the most common limiting factor for bacterial growth in soil, although there are reports of limitation by other nutrients, e.g. nitrogen and phosphorus. We have studied which nutrient(s) limited instantaneous growth rates of bacteria in 28 Swedish soils using the thymidine or leucine incorporation technique to measure increased growth rate after adding different combinations of organic carbon (glucose), nitrogen and phosphorus. The soils ranged in pH between 3.1 and 8.9, in organic matter content between 1% and 91% and in soil C/N ratio between 10 and 28. We also tested the effect of adding different amounts of carbon on the bacterial change in growth rate for two soils with different organic matter content. We found that bacterial growth in most of the 28 soils was limited by a lack of carbon, indicated by an increased bacterial growth rate 48 h after adding glucose. In some soils, adding carbon together with nitrogen increased the bacterial growth rates even further. In three soils no effects were seen upon adding nutrients separately, but adding carbon and nitrogen together increased bacterial growth rates. Nitrogen addition tended to decrease bacterial growth rates, while phosphorus addition had little effect in most soils. No correlations were found between the soil C/N ratio, ammonium or nitrate content in soil and bacterial growth limitation, indicating that even soils with a C/N ratio of 28 could be carbon limited. Although the interpretation of the effects of a single limiting nutrient was in most cases straightforward, an interaction between the amount of carbon added and the organic matter content of the soil confounded the interpretation of the extent of a second limiting nutrient.
Article
Genotypes affect the survival of mutant genes in segregating populations. This study elucidates the effect of different maize genetic backgrounds on variation in gene frequency in sweet corn, sugary1 (su1) and sugary enhancer1 (se1), and supersweet corn, shrunken2 (sh2). Four sweet corn inbred lines and a supersweet synthetic were crossed to six field corn inbreds from diverse heterotic groups. The crosses were self-pollinated and the F2 population was recombined twice. Gene frequencies were calculated from grain frequencies. Variation of su1 frequency differed significantly from random drift and a significant linear reduction was observed for half of the su1su1Se1Se1Sh2Sh2 × Su1Su1Se1Se1Sh2Sh2 crosses. The su1 and sh2 frequencies suffered a significant linear reduction for most su1su1se1se1Sh2Sh2 × Su1Su1Se1Se1Sh2Sh2 and Su1Su1Se1Se1sh2sh2 × Su1Su1Se1Se1Sh2Sh2 crosses, respectively. Also, the residual sums of squares, due to deviations from the linear trend, were significant for some crosses due to frequency-dependent selection and genotypic interactions. Viability of su1 and sh2 depended on the specific sweet × field corn genotype combination but was not related to field corn heterotic groups. The se1 gene could have a detrimental effect on su1 viability.
Article
The incorporation of [14C]-leucine into protein by soil organisms was measured both in soil slurries and for bacteria extracted from soil by homogenization-centrifugation. The result was compared with thymidine incorporation. Using a soil slurry, 9.110-10 mol leucine h-1g-1 dry weight of soil was incorporated into protein, with a calculated leucine: thymidine ratio (mol:mol) of about 34. Non-specific labelling of macromolecules other than protein was observed with both the soil slurry and the homogenization-centrifugation method. With the latter, 46.5% of the total incorporation was found in the protein fraction (hot-acid insoluble). The incorporation of leucine was linear with time for at least 4 h for extracted bacteria. Even at 2000 nM, [14C]-leucine did not saturate incorporation into protein. Isotope dilution plots indicated that with 750 nM leucine, the degree of participation of the labelled substance in protein synthesis was 0.59. With this value, the ratio of leucine:thymidine incorporation into total macromolecules was calculated as 41 for extracted bacteria. On the basis of incorporation into protein (leucine) and incorporation into DNA (thymidine) only, the leucine:thymidine ratio was calculated as 117. The mean turnover time of bacteria at 22C, calculated using conversion factors from published studies and leucine incorporation into protein of extracted bacteria, was 4.3 days.
Article
A technique to estimate fungal growth rates in field samples was tested in soil. The technique is based on the addition of 14C-acetate to a soil slurry and the subsequent uptake and incorporation of the labelled acetate into the fungus specific substance ergosterol by the fungi. The addition of fungal inhibitors decreased acetate incorporation rates, while bacterial inhibitors did not. Fungus-free soil exhibited no incorporation of acetate into ergosterol, indicating that the method was specific for measuring fungal activity. Incorporation rates were linear up to 18 h after the addition of acetate indicating that changing the conditions (adding acetate as a solution to a soil slurry) did not affect the incorporation rate. Problems associated with saturation of the incorporation of the added acetate were encountered, which together with uncertain conversion factors made calculations of absolute growth rates difficult. However, for relative comparisons the technique worked well. This was exemplified by measuring the relationship between temperature and growth rate of the soil fungal community, where an optimum temperature between 25 and 30°C and an apparent minimum temperature for fungal growth of −11°C were found. The technique was also used to indicate which nutrients limited instantaneous fungal growth in soil by adding carbon, nitrogen and phosphorus in different combinations and measuring the rate of acetate incorporation into ergosterol 2 days later. Carbon appeared to be the limiting nutrient for fungal growth in both an agricultural soil and a forest humus soil.
Article
Bacterial densities, metabolic signatures and genetic structures were evaluated to measure the impact of soil enrichment of soluble organic carbon on the bacterial community structures. The exudates chosen were detected in natural maize exudates (glucose, fructose, saccharose, citric acid, lactic acid, succinic acid, alanine, serine and glutamic acid) and were used at a rate of 100 μg C g−1 day−1 for 14 days. Moreover two synthetic solutions with distinct carbon/nitrogen ratios (20.5 and 40.1), obtained by varying carboxylic and amino acids concentrations, were compared in order to evaluate the potential role of organic N availability. The in vitro experiment consisted of applying exudate solutions to bulk soil. In the case of the control, only distilled water was added. Both solutions significantly increased bacterial densities and modified the oxidation pattern of Biolog® GN2 plates with no effect of the C/N ratio on these two parameters. Genetic structure, measured by means of ribosomal intergenic spacer analysis (RISA), was also consistently modified by the organic amendments. N availability levels led to distinct genetic structures. In a second experiment, one of the previous exudate solutions (C/N 20.5) was applied to 15-day-old maize plants to determine the structural influence of exudates on the rhizosphere microbial community (in situ experiment). Bacterial densities were significantly increased, but to a lesser extent than had been found in the in vitro experiment. Metabolic potentials and RISA profiles were also significantly modified by the organic enrichment.