Rhizosphere最新文献

{"title":"Locomotion of Bacillus subtilis SL-44 mediated by root exudate and carrier in Cr(OH)3-modified porous media","authors":"","doi":"10.1016/j.rhisph.2024.100964","DOIUrl":"10.1016/j.rhisph.2024.100964","url":null,"abstract":"<div><div>Plant growth promoting rhizobacteria (PGPR) have a remediation effect on Cr-contaminated soil; however, the remediation scope is only within a small area around the bacteria. Hence, the remediation effect depends on the migration ability of bacteria in the soil. Root exudates enhance the chemotaxis and locomotion of <em>Bacillus subtilis</em> SL-44 by reducing its adhesion coefficient <em>k</em>_att and hydrodynamic dispersion coefficient <em>D</em>. The locomotion capacity was enhanced by 7.84%–20.00%. Among the root exudates, proline and sucrose remarkably improved the motility of SL44. Biochar and bentonite increased the <em>k</em>_att and <em>D</em> of SL-44, inhibited bacterial locomotion, and improved the retention rate on the carrier surface. Bacterial locomotion was reduced by biochar and bentonite by 57.99% and 50.42%, respectively. These reductions were caused by macropore. SL-44 locomotion was positively correlated with the concentration of environmental root exudate (R² = 0.88−0.92). The results of the simulated soil study were validated in actual agricultural Cr-contaminated soils through qPCR.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142322541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrate Over Ammonium: Limited inorganic N niche partitioning between wheat and weeds regardless of fertilization treatment","authors":"","doi":"10.1016/j.rhisph.2024.100962","DOIUrl":"10.1016/j.rhisph.2024.100962","url":null,"abstract":"<div><div>Fertilization is a crucial agricultural practice that influences biogeochemical cycles and ecosystem functions, and it plays a central role in widespread wheat and weed coexistence. However, it remains unclear how wheat and weeds coexist under N-limited conditions and how plant N uptake strategy change after N fertilization. Wheat (<em>Triticum aestivum</em> L.), and two weeds (wild oats (<em>Avena fatua</em>), and barnyard grass (<em>Echinochloa crusgalli</em>)) were selected as targeted plant species. We grew them alone, and after about seven months, we labeled these plants with ¹⁵NH₄Cl or ¹⁵KNO₃ for 2 h to quantify their NH₄⁺ and NO₃⁻ uptake, and measured root length, root area, specific root length, specific root area, specific root volume, and root tissue density. We found that fertilization led to a more resource-acquisitive nutrient acquisition traits in wheat (i.e., increased specific root area and specific root volume (<em>P</em> &lt; 0.05)), without altering weed root traits. Across three species, the increased NH₄⁺ and NO₃⁻ uptake after fertilization were not mediated by root traits, but by the direct effect of fertilization. Additionally, both wheat and weeds predominantly preferred NO₃⁻ than NH₄⁺ regardless of fertilization or not, indicating a limited niche differentiation for wheat-weed coexistence. These findings can improve our understanding of the mechanisms of species coexistence in agricultural systems, particularly with regards to N uptake strategies among crops and weeds.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecology of arbuscular mycorrhizal association in coconut (Cocos nucifera L.) palms: Analysis of factors influencing AMF in fields","authors":"","doi":"10.1016/j.rhisph.2024.100961","DOIUrl":"10.1016/j.rhisph.2024.100961","url":null,"abstract":"<div><div>This study is the first thorough ecological analysis of arbuscular mycorrhizal fungal (AMF) diversity in randomly selected traditional coconut fields across Kerala, South India. We conducted a critical analysis of AMF diversity, percentage root length colonization (PRLC), and mean spore density (MSD) across 248 sites, taking into account variations in plant, environmental, and soil factors like coconut varieties, palm health conditions, agroclimatic zones, soil types, and seasons in the region. A total of 23 AMF species from seven genera (Acaulospora, Archaeospora, Funneliformis, Glomus, Sclerocystis, Septoglomus, and Scutellospora) were identified, with <em>Acaulospora scrobiculata</em> being the dominant species in all studied fields. A critical analysis of diversity indices, including the Shannon-Weiner Index, Simpson's diversity index, and Gini-Simpson index, concerning variables indicated that soil series influences AMF diversity in specific fields. Correlational and principal component analyses highlighted the interrelationships between specific soil types and quality parameters affecting AMF characteristics, underscoring their crucial role in coconut palm growth. The study also revealed the ecological amplitudes of indigenous AMF species related to specific soil fertility parameters. Overall, this research serves as a model for identifying root- and soil-specific AMF in agricultural fields and provides valuable ecological insights for utilizing indigenous AMF species as ecotechnological tools for sustainable coconut cultivation.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungal secondary metabolite gliotoxin enhances enzymatic activity in soils by reshaping their microbiome","authors":"","doi":"10.1016/j.rhisph.2024.100960","DOIUrl":"10.1016/j.rhisph.2024.100960","url":null,"abstract":"<div><p>Gliotoxin (GT) is a sulfur-containing epidithiodioxopiperazine produced by various filamentous fungi, including those used in biological plant protection (<em>Trichoderma virens</em>). The pronounced antimicrobial effect of GT on a variety of fungi and bacteria makes it a promising agent for controlling phytopathogens in agricultural systems. In this study, we aim to investigate the microbiological properties of the soil microbiome after the introduction of GT. GT was applied at doses of 10, 25, 50, 100 and 500 μM kg⁻¹ soil. Soil sampling was carried out after 1, 7, 14, 30, 60 and 90 days of incubation. It was found that GT significantly stimulated the respiratory activity of soil microorganisms and maintained this activity throughout the experiment. Carbon of microbial biomass, on the contrary, decreases under the influence of GT and is restored at the end of the experiment only in microcosms with 10 and 25 μM GT. Separate estimates of bacterial and fungal biomass showed that the bacterial community increased in biomass on day 14, while fungal biomass increased on day 30 after the treatment. Under the influence of GT, the activity of soil enzymes involved in the carbon (CB, βG, βX), nitrogen (NAG, LAP) and phosphate (AP) cycles significantly increased. High-throughput amplicon sequencing of the ITS and 16S rDNA markers revealed that the soil fungal community is more susceptible to GT than the bacterial community. This was reflected in changes in alpha-diversity indices and in the pattern of changes in the abundance of some microbial genera. Thus, on the one hand, the data obtained provides insight into the biological effects of GT on the soil microbial community. On the other hand, it sets the direction for further research into the ecological role of antibiotics produced by soil and rhizosphere microorganisms.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive characterization of the rhizosphere metabolome: A novel method for non-targeted analysis of Lotus japonicus root exudates","authors":"","doi":"10.1016/j.rhisph.2024.100957","DOIUrl":"10.1016/j.rhisph.2024.100957","url":null,"abstract":"<div><p>Plant root exudates play a pivotal role in shaping soil dynamics and the microbial community in the rhizosphere. The chemical composition of root exudates includes primary and secondary metabolites, including amino acids, organic acids, flavonoids, and small peptides. Comprehensive characterization of root exudates will allow for a better understanding of rhizosphere processes and interactions, but analysis of root exudates is hindered by complicated collection setups, time-consuming sample preparation, and a lack of definitive annotations within metabolomics. We present a method optimized for non-targeted analysis of primary and secondary metabolites in root exudate samples using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry. The method was tested on root exudates from <em>Lotus japonicus</em>, collected using distinct and well-established sampling methods: a hydroponic-soil-hybrid approach, as well as a modification of a soil-leaching method, thus exemplifying the versatility of the analysis method. The method allows for non-targeted screening of plant metabolites, and provides low detection limits (0.002–0.05 μg/mL) and high recoveries (78 <span><math><mrow><mo>±</mo></mrow></math></span> 30%), though a matrix effect was observed for certain plant metabolites. Detection of a large number of features was achieved (670–2785) of which the majority could be putatively annotated at the compound class level. Of these, 14 features were putatively annotated to a specific structure with high confidence, three of which were confirmed with analytical reference standards. The method can be used for investigation of the overall change in root exudation, as well as for investigating significant changes in metabolites in response to intraenous and extraneous parameters.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452219824001125/pdfft?md5=344047754caa486524941f7232a08475&pid=1-s2.0-S2452219824001125-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142238935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rice night-time thirst: Genotype nutrient needs reflected in nocturnal transpiration","authors":"","doi":"10.1016/j.rhisph.2024.100956","DOIUrl":"10.1016/j.rhisph.2024.100956","url":null,"abstract":"<div><p>To enhance rice grain protein content, understanding strategies to improve nitrogen uptake is crucial. While the impact of transpiration on nitrogen flux is known in trees, its role in rice is unclear due to inconsistent results. Our study used a phenomics facility for real-time transpiration measurements during the entire crop growth period. We hypothesized that genotypes respond differently to transpiration regulation based on nitrogen needs. This study investigates the morphological responses and grain protein content (GPC) of two genotypes of rice, GEN-RIC_784 and GEN-RIC_384, under varying light and nitrogen conditions. GEN-RIC_784 exhibited lower reductions in biomass and total leaf area under limiting nitrogen and light compared to GEN-RIC_384. Both genotypes showed comparable reduction in biomass and leaf area when low nitrogen was combined with low light (LN + LL) condition. GEN-RIC_784 flowered early under low light, while GEN-RIC_384 did so only in LN + LL conditions. GEN-RIC_384 experienced significant yield reductions under all treatments except LN + LL, while maintaining high GPC compared to control. In contrast, GEN-RIC_784 showed a &gt;50% reduction in GPC under low nitrogen conditions. Cumulative water transpired decreased notably only under LN + LL for both genotypes. GEN-RIC_384 had higher daytime transpiration declines across treatments and increased nighttime transpiration in CN + LL and LN + AL treatments. Daytime transpiration rates per leaf area were higher across treatments compared to controls. Water use efficiency decreased in both genotypes, most prominently under LN + LL. Across growth stages, transpiration trends varied, with notable increases under LN + AL and LN + LL. GEN-RIC_784 showed higher transpiration during vegetative stages, while GEN-RIC_384 showed higher nocturnal transpiration under CN + LL. Nitrogen supplementation affected shoot growth and chlorophyll content, particularly in GEN-RIC_384, with notable reductions when nitrogen was withheld at night. The study underscores the complex genotype-light-nitrogen interactions in rice, offering insights for enhancing rice productivity and grain quality under diverse environmental conditions.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insight into the differential response of functional denitrifiers to novel formulated organic amendments in soybean agroecosystem","authors":"","doi":"10.1016/j.rhisph.2024.100954","DOIUrl":"10.1016/j.rhisph.2024.100954","url":null,"abstract":"<div><p>Fertilizer application has been known to cause substantial changes in the microbial composition of agricultural soil. Therefore, there is a need for more fertilizer management practices that will improve nitrogen (N) content, which is the key restrictive factor for microbial growth. To elucidate the characteristics of these fertilizers in the soil, samples were collected from a soybean field of control (S0) with no addition of organic amendment, biochar made from rice straw (S1), compost made from cattle manure and maize straw at a ratio of 5:1 (S2), composting S2 + 10 % S1 (S3), and mixture of S2 + 10 % S1 without composting (S4). The soil functional denitrifiers (<em>nirS</em> and <em>nirK</em>) were unravelled using Illumina high-throughput sequencing. It was observed that S3 (66.56 %) and S4 (61.14 %) increased the NO₃⁻-N, while S2 increased the total Kjeldahl nitrogen (TKN) by 15.79 % compared to S0. OTU847__{<em>norank_p_environmental_samples</em>} in <em>nirS</em> and OTU112__{<em>unclassified_f_Bradyrhizobiaceae</em>} in <em>nirK</em> were the most abundant genera in S1-S4 while S2 and S3 had the highest unique OTUs in <em>nirK</em> and <em>nirS</em> communities, respectively. The canonical correspondence analysis (CCA) showed that NO₂⁻-N and nitrate reductase (NIR) enzyme-shaped <em>nirS</em> and <em>nirK</em> denitrifiers. Also, from the structural equation model (SEM), TKN showed a higher negative significant effect on <em>nirK</em> alpha and beta diversities, while S4 showed the lowest positive network in <em>nirS</em> and <em>nirK</em>- denitrifiers. Meanwhile, <em>Bradyrhizobium</em> was observed as a common genus in the multivariate co-occurrence network in <em>nirS-</em> and <em>nirK</em>-type denitrifiers. This study provides the theoretical basis and technical support that single and combined fertilizers could influence <em>nirS</em> and <em>nirK</em> denitrifiers in soybean-grown soil.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142148140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution of tetracycline resistance genes within an organic fertilizer-amended soil–rice continuum","authors":"","doi":"10.1016/j.rhisph.2024.100955","DOIUrl":"10.1016/j.rhisph.2024.100955","url":null,"abstract":"<div><p>The transmission of antibiotic resistance genes (ARGs) to humans through the consumption of plants grown in manure-amended soils is a critical concern. However, the effect of manure application on the profiles of tetracycline resistance genes (TRGs) within the soil–rice continuum remains unclear. In this study, tetracycline (TC) content, bacterial communities, abundance of 8 TRGs, and class 1 integron (<em>int</em>I1) were characterized using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), Illumina sequencing, and quantitative PCR (qPCR) in rhizosphere soils, roots, and grains of rice exposed to pig manure (PM), rapeseed cake (RC), and chemical fertilizer (CF), respectively. Our findings indicate that the type of sample was the primary determinant of TRGs abundance variation within the soil-rice continuum, with a consistent decline from rhizosphere soils to roots to grains. Furthermore, fertilization type significantly influenced TRGs abundance, with the highest levels observed in PM treatment. <em>Tet</em>Z and <em>tet</em>X were predominant, constituting over 90% of total TRGs abundance across all samples. In addition, the mechanism of TRGs profile formation varies with sample types. Bacterial communities-TC content-<em>int</em>I1 interactions determined the change in TRGs abundance in rhizosphere soils, and bacterial communities constituted the most important factor affecting TRGs abundance within the roots. However, bacterial communities and/or <em>int</em>I1 poorly explained the change in TRGs abundance within the grains. Our study attempts to explore the underlying mechanism for the profiles of TRGs in soil–rice continuums exposed to manure, as well as provides a theoretical basis for controlling the spread of endogenous antibiotic resistance within rice grown in soil receiving pig manure.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142148139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inside Front Cover - Editorial Board Page","authors":"","doi":"10.1016/S2452-2198(24)00113-7","DOIUrl":"10.1016/S2452-2198(24)00113-7","url":null,"abstract":"","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452219824001137/pdfft?md5=2a23d1de14842e56a3db937d085a8eb3&pid=1-s2.0-S2452219824001137-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of Bacillus subtilis sub sp. subtilis GEB5 reveals its genetic assets for nematicidal and plant growth promoting mechanisms","authors":"","doi":"10.1016/j.rhisph.2024.100953","DOIUrl":"10.1016/j.rhisph.2024.100953","url":null,"abstract":"<div><p>The immense benefit of chemical nematicides in controlling plant parasitic nematodes in high-value crops is counterbalanced by the development of resistance in nematodes due to their overuse. <em>Bacillus subtilis</em> is a promising bacterium that not only confers resistance against plant parasitic nematodes but also promotes plant growth through nutrient acquisition. Considering the multifaceted action of <em>B. subtilis</em> attempts were made to sequence the whole genome of endophytic <em>B. subtilis</em> GEB5 to find the genome complexity of the potential bio-control agent isolated from the guava. The results confirmed the isolate as <em>B. subtilis</em> sub sp. <em>subtilis</em> with a circular genome of 8,341,276 bp (8.3 Mb) length and 41.8% GC content. The results of genome annotation revealed the presence of 8209 coding sequences (CDS) genes, 136 transfer RNA (tRNA) genes, and 6 ribosomal RNA (rRNA) genes. Nonribosomal peptide synthetase (NRPS) gene clusters in the genome of GEB5 included fengycin, bacillaene, plipastatin, subtilin, subtilosin A, bacilysin, surfactin, sporulation killing factor, bacillibactin. Moreover, the GEB5 genome assembly had 21 homologs corresponding to nematode-virulent proteases. Furthermore, the results of greenhouse experiments showcased that GEB5 quenched the population of <em>M. enterolobii</em> (72% reduction) and also boosted the plant growth of guava. A plurality of the putatively encoded nematode virulence protease and its ability to boost plant growth suggests its environmentally robust bio-control potential in protecting plants against invading plant parasitic nematodes.</p></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142136572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}