Genes In Rhizosphere Research Articles

Chemotaxis mediates nitrogen acquisition of maize under long-term nitrogen input

Chemotaxis is a process that enables motile bacteria to move along nutrient gradients, thereby exploring nutrient hotspots, and potentially playing important biogeochemical roles in agricultural ecosystems. In this study, a 36-year field experiment of nitrogen (N) input was conducted, along with the use of a synthetic community (SynCom) inoculation, to confirm the role of chemotaxis in the cycling of N. The chemotaxis genes abundances of N+ treatments were 97.2% and 95.3% higher than that of N- treatments in bulk soil and rhizosphere, respectively, indicating a significant increase in chemotaxis genes under long-term N input. Positive correlations between chemotaxis genes and N metabolism genes in N+ treatments suggested an important role of chemotaxis in N cycling. The chemotaxis genes abundance was 3.6 times higher in rhizosphere than in bulk soil, and chemotaxis genes showed the most complex correlations with N metabolism genes in rhizosphere under N input, suggesting a key role of chemotaxis in plant N uptake. To assess the potential function of chemotactic bacteria, a SynCom consisting of 10 bacterial strains isolated from in situ N-input soils and capable of chemotaxis, was applied to the maize rhizosphere. The promotion of N acquisition in maize plants through inoculation was confirmed by about 30% greater N content in the shoots of SynCom inoculated soil than in the control. Long-term N input enhanced the functions related to metabolite transport and energy metabolism in the bacterial community, particularly in the rhizosphere. Thus, plants may provide bacteria that migrate to the rhizosphere via chemotaxis with more root metabolites as nutrients. In summary, this study provides novel ecological and molecular insights into chemotaxis-mediated biogeochemical cycling in agricultural ecosystems.

Function of CAZymes encoded by highly abundant genes in rhizosphere microbiome of Moringa oleifera

Metagenomic analysis referring to CAZymes (Carbohydrate-Active enZymes) of CAZy classes encoded by the most abundant genes in rhizosphere versus bulk soil microbes of the wild plant Moringa oleifera was conducted. Results indicated that microbiome signatures and corresponding CAZy datasets differ between the two soil types. CAZy class glycoside hydrolases (GH) and its α-amylase family GH13 in rhizobiome were proven to be the most abundant among CAZy classes and families. The most abundant bacteria harboring these CAZymes include phylum Actinobacteria and its genus Streptomyces and phylum Proteobacteria and its genus Microvirga. These CAZymes participate in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway “Starch and sucrose metabolism” and mainly use the “double displacement catalytic mechanism” in their reactions. We assume that microbiome of the wild plant Moringa oleifera is a good source of industrially important enzymes that act on starch hydrolysis and/or biosynthesis. In addition, metabolic engineering and integration of certain microbes of this microbiomes can also be used in improving growth of domestic plants and their ability to tolerate adverse environmental conditions.

Adaptation of bacterial community in maize rhizosphere for enhancing dissipation of phthalic acid esters in agricultural soil.

Rhizospheric degradation is a green and in situ strategy to accelerate dissipation of organic pollutants in soils. However, the mechanism on microbial degradation of phthalic acid esters (PAEs) in rhizosphere is still unclear. Here, the bacterial community and function genes in bulk and rhizospheric soils of maize (Zea mays L.) exposed to gradient concentrations of di-(2-ethylhexyl) phthalate (DEHP) were analyzed with 16S rRNA, metagenomic sequencing and quantitative PCR (qPCR). Maize rhizosphere significantly increased the dissipation of DEHP by 4.02-11.5% in comparison with bulk soils. Bacterial community in rhizosphere exhibited more intensive response and shaped its beneficial structure and functions to DEHP stress than that in bulk soils. Both rhizospheric and pollution effects enriched more PAE-degrading bacteria (e.g., Bacillus and Rhizobium) and function genes in rhizosphere than in bulk soil, which played important roles in degradation of PAEs in rhizosphere. The PAE-degrading bacteria (including genera Sphingomonas, Sphingopyxis and Lysobacter) identified as keystone species participated in DEHP biodegradation. Identification of PAE intermediates and metagenomic reconstruction of PAE degradation pathways demonstrated that PAE-degrading bacteria degraded PAEs through cooperation with PAE-degrading and non-PAE-degrading bacteria. This study provides a comprehensive knowledge for the microbial mechanism on the superior dissipation of PAEs in rhizosphere.

Responses of Soil PhoC and PhoD Gene Microbial Communities to the Combined Application of Biochar with Chemical Fertilizers and Organic Fertilizers

Soil microorganisms have an important influence on the transformation of soil nutrients. As functional genes encoding phosphatase, phoC and phoD provide effective means for detecting the types, abundance, and community structure of microorganisms in the environment, and studying the changes in the diversity of phoC and phoD gene microbial communities in the rhizosphere and non-rhizosphere soil of the plant rhizosphere and non-rhizosphere soil under the treatment of chemical fertilizer and organic fertilizer combined with biochar can provide a scientific basis for the agricultural utilization of biochar. In this study, corn stalks and rice husk stalks were used as test materials, and the pot experiment method was used to set the following treatments:control (CK), traditional fertilization (F), chemical fertilizer+20 t·hm-2 rice husk biochar (FP), chemical fertilizer+10 t·hm-2 rice husk biochar+10 t·hm-2 corn biochar (FPM), organic fertilizer+20 t·hm-2 rice husk biochar (PP), and fresh organic fertilizer+20 t·hm-2 rice husk biochar (NPP). The community structure of phoC and phoD genes in rhizosphere and non-rhizosphere soil was analyzed by using T-RFLP and fluorescence quantitative PCR technology to clarify the response characteristics of phoC and phoD genes to the addition of biochar. The results showed that:① In rhizosphere soil and non-rhizosphere soil, the phoD gene community structure was more complicated than that of phoC, and the number of end restriction fragments of the phoC gene increased after chemical fertilizer and organic fertilizer were combined with biochar. ② The combined application of biochar with chemical fertilizer and organic fertilizer reduced the copy number of the phoC gene in non-rhizosphere soil compared with that in the CK. Compared with that in the CK, the copy number in the FP, FPM, PP, and NPP treatments decreased by 9.18%, 11.46%, 10.97%, and 13.76%, respectively. Organic fertilizer combined with biochar increased the copy number of the phoD gene in rhizosphere soil by 2.48% and 5.16% in the PP and NPP treatments, respectively, compared with that in the CK. ③ Total phosphorus in the soil was the main factor affecting the phoC gene microbial community structure in non-rhizosphere soil (P<0.01), whereas the phoC gene microbial community structure in rhizosphere soil was regulated by a variety of environmental factors. pH was the most critical factor affecting the phoD gene copy number, and the copy number of phoD gene was significantly correlated with soil nitrate nitrogen and pH. The combined application of biochar with chemical fertilizers and organic fertilizers can promote the growth and reproduction of microorganisms that function in soil phosphorus conversion, which is of great significance for improving the utilization of phosphorus fertilizers.

Phytoremediation of Cadmium-Contaminated Mining Soil Enhanced by Rhizobial Inoculation: Responses of Rare and Abundant Microbial Communities and Nitrogen-Cycling Genes in Rhizosphere

Phytoremediation of Cadmium-Contaminated Mining Soil Enhanced by Rhizobial Inoculation: Responses of Rare and Abundant Microbial Communities and Nitrogen-Cycling Genes in Rhizosphere

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories.

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere

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.

Nitrogen removal and abundances of associated functional genes in rhizosphere and non-rhizosphere of a vertical flow constructed wetland in response to salinity

It investigated the nitrogen removal performance and the abundances of nitrogen functional genes in the rhizosphere and non-rhizosphere when vertical flow constructed wetland (VFCW) was used to treat brackish eutrophic water. The results demonstrated that both total nitrogen (TN) and ammonia nitrogen (NH4-N) removal efficiencies decreased with the salinity increasing from 0.05% to 1.0%. However, the removal efficiency of nitrate nitrogen (NO3-N) remained more than 93%. It was found by quantitative real-time polymerase chain reaction (qPCR) that abundances of amoA, nosZ, napA, nirK and nirS were greater in the rhizosphere than in the non-rhizosphere at the salinities of 0.05%, 0.5% and 1.0%. As the salinity increased, the abundance of amoA reduced. It indicated that the salinity inhibited the growth of ammonia oxidizing bacteria (AOB) and further hindered the nitrification, which resulted in the deterioration of TN removal performance. The abundances of nosZ, napA, nirK and nirS in the rhizosphere and non-rhizosphere were the highest at 1.0% salinity. The denitrifying bacteria might adapt to the salinity stress, which guaranteed high NO3-N removal efficiency.

Phosphorus regulates As uptake by rice via releasing As into soil porewater and sequestrating it on Fe plaque

Phosphorus (P) application rate can affect the As uptake by rice, but its mechanism lacks systematic studies. In this study, P fertilizers with different dosages (0, 75, 150, and 300 mg P2O5 kg−1 soil) were used to investigate the effects of P on As release in soil porewater, As sequestration on Fe plaque and the change of abundance and communities of aioA and arsC genes in rhizosphere, and then explore its effect on As uptake by rice. Our results indicated that As content in brown rice under P0 and P75 treatments was 14.3–28.6% lower than that under P150 treatment. The total accumulation of As in brown rice under P0 treatment (1.51 μg plant−1) was significantly lower than that under P150 treatment (2.17 μg plant−1). Compared to P150 treatment, P0 treatment decreased the total As content in porewater but increased the proportion of As(V) to total As in porewater. The activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) in rice roots and the Fe and As contents in Fe plaque were significantly higher under P0 treatment than under P150 treatment. Most of As (80.3–82.9%) sequestered by Fe plaque was in the form of arsenate (As(V)), and the associated As(V) on Fe plaque was 11.0% higher under P0 treatment than under P150 treatment. In addition, the abundance of aioA gene was 73.5% higher under P0 treatment than under P150 treatment, and the dominant aioA at genus level was Rhizobium and Rhodoferax. In general, P0 treatment led to higher root oxidation activity, which improved the formation of Fe plaque; and P0 treatment also improved the abundance of aioA gene in rhizosphere, thus increased the oxidation of As; so, P0 treatment indirectly enhanced As sequestration on Fe plaque, and that in turn reduced As accumulation in brown rice.

Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere

In water-scarce regions, alternate-furrow irrigation (AFI)—alternately wetting half of the plant roots—has proven to be an effective water-saving approach without compromising yield. However, the extent to which AFI with wastewater affects N cycling genes remains poorly studied. We aimed to investigate changes in main N transformation processes, bacterial and fungal community composition, as well as relative abundance of N cycle-associated genes in soil receiving AFI with swine wastewater. The experimental plan included three irrigation rates, irrigating pepper plants with 50%, 65%, and 80% of the amount of water required under conventional furrow irrigation to prevent the crop suffering water stress. Each treatment had a groundwater irrigation control. We measured edaphic factors, microbial community composition, and relative abundance of genes in rhizosphere and bulk soils. Altering water use in AFI did not exert a significant effect on bacterial and fungal communities. By increasing the irrigation rate of wastewater, relative abundances of nifH, bacterial and archaeal amoA and nosZ genes decreased, whereas those of nirK and nirS genes increased in the rhizosphere soil; nitrification rate did not decrease and the denitrification rate remained unchanged in both rhizosphere and bulk soil, implying that appropriate increase of wastewater use by AFI can improve N use efficiency.

Arsenic and phosphate rock impacted the abundance and diversity of bacterial arsenic oxidase and reductase genes in rhizosphere of As-hyperaccumulator Pteris vittata

Microbially-mediated arsenic (As) transformation in soils affects As speciation and plant uptake. However, little is known about the impacts of As on bacterial communities and their functional genes in the rhizosphere of As-hyperaccumulator Pteris vittata. In this study, arsenite (AsIII) oxidase genes (aroA-like) and arsenate (AsV) reductase genes (arsC) were amplified from three soils, which were amended with 50mgkg−1 As and/or 1.5% phosphate rock (PR) and grew P. vittata for 90 d. The aroA-like genes in the rhizosphere were 50 times more abundant than arsC genes, consistent with the dominance of AsV in soils. According to functional gene alignment, most bacteria belonged to α-, β- and γ-Proteobacteria. Moreover, aroA-like genes showed a higher biodiversity than arsC genes based on clone library analysis and could be grouped into nine clusters based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Besides, AsV amendment elevated aroA-like gene diversity, but decreased arsC gene diversity. Redundancy analysis indicated that soil pH, available Ca and P, and AsV concentration were key factors driving diverse compositions in aroA-like gene community. This work identified new opportunities to screen for As-oxidizing and/or -reducing bacteria to aid phytoremediation of As-contaminated soils.

Diversity and distribution of 16S rRNA and phenol monooxygenase genes in the rhizosphere and endophytic bacteria isolated from PAH-contaminated sites.

This is the first investigation of the diversity and distribution of 16S rRNA and phenol monooxygenase (PHE) genes in endophytic and rhizosphere bacteria of plants at sites contaminated with different levels of PAHs. Ten PAHs at concentrations from 34.22 to 55.29 and 45.79 to 97.81 mg·kg−1 were measured in rhizosphere soils of Alopecurus aequalis Sobol and Oxalis corniculata L., respectively. The diversity of 16S rRNA and PHE genes in rhizosphere soils or plants changed with varying PAH pollution levels, as shown based on PCR-DGGE data. Generally, higher Shannon-Weiner indexes were found in mild or moderate contaminated areas. A total of 82 different bacterial 16S rRNA gene sequences belonging to five phyla; namely, Acfinobacteria, Proteobacteria, Chloroflexi, Cyanophyta, and Bacteroidetes, were obtained from rhizosphere soils. For the 57 identified PHE gene sequences, 18 were excised from rhizosphere bacteria and 39 from endophytic bacteria. The copy numbers of 16S rRNA and PHE genes in rhizosphere and endophytic bacteria varied from 3.83 × 103 to 2.28 × 106 and 4.17 × 102 to 1.99 × 105, respectively. The copy numbers of PHE genes in rhizosphere bacteria were significantly higher than in endophytic bacteria. Results increase our understanding of the diversity of rhizosphere and endophytic bacteria from plants grown in PAH-contaminated sites.