Pub Date : 2024-11-12DOI: 10.1016/j.rhisph.2024.100991
Dinda Rista Anis Mufida , Ivan Permana Putra , Abdjad Asih Nawangsih , Ni Putu Ratna Ayu Krishanti , Aris Tri Wahyudi
Fusarium oxysporum, a phytopathogenic fungus responsible for fusarium wilt in more than 120 plant species, is primarily managed using synthetic fungicides, which pose environmental hazards. Therefore, alternative biological control methods are urgently needed. Actinobacteria isolated from maize rhizosphere, which produce β-1.3-glucanase enzymes that degrade fungal cell wall glucans, offer promising potential as biocontrol agents. This study aimed to evaluate glucanase activity, identify genes of actinobacteria, and assess their antifungal activity against F. oxysporum. Actinobacteria demonstrating glucanase production, Streptomyces sp. ARJ 22, Streptomyces tendae ARJ 42, Streptomyces sp. ARJ 44, and Streptomyces sp. ARJ 81, were selected. Streptomyces isolates exhibited activity values ranging from 10.38 to 24.08 U/mg of protein. The presence of the bglS gene, encoding endo-β-1.3-glucanase from glycoside hydrolase family 16, supports the production of glucanase. The amino acid sequence was constructed to 3D structural model. This model exhibited high similarity to endo-β-1.3-glucanase from Nocardiopsis sp. F96. In vitro assays demonstrated that all isolates inhibited hyphal growth of F. oxysporum. Direct inhibition assays showed an average inhibition of 26.18%, whereas the filtrate culture method showed 29.38% inhibition. Enzymes from Streptomyces sp. ARJ 44 was partially purified using acetone, resulting in a specific activity of 46.34 U/mg of protein and a purity increase of up to 1.92-fold. The purified enzyme inhibited the growth of F. oxysporum mycelia by 35.80%. This inhibition was confirmed by observing damage to F. oxysporum hyphae using scanning electron microscopy. The study concluded that the four Streptomyces sp. Strains producing β-1.3-glucanase enzymes have potential as biocontrol agents against F. oxysporum.
{"title":"Glucanase enzyme activity from rhizospheric Streptomyces spp. inhibit growth and damage the cell wall of Fusarium oxysporum","authors":"Dinda Rista Anis Mufida , Ivan Permana Putra , Abdjad Asih Nawangsih , Ni Putu Ratna Ayu Krishanti , Aris Tri Wahyudi","doi":"10.1016/j.rhisph.2024.100991","DOIUrl":"10.1016/j.rhisph.2024.100991","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em>, a phytopathogenic fungus responsible for fusarium wilt in more than 120 plant species, is primarily managed using synthetic fungicides, which pose environmental hazards. Therefore, alternative biological control methods are urgently needed. Actinobacteria isolated from maize rhizosphere, which produce β-1.3-glucanase enzymes that degrade fungal cell wall glucans, offer promising potential as biocontrol agents. This study aimed to evaluate glucanase activity, identify genes of actinobacteria, and assess their antifungal activity against <em>F. oxysporum</em>. Actinobacteria demonstrating glucanase production, <em>Streptomyces</em> sp. ARJ 22, <em>Streptomyces tendae</em> ARJ 42, <em>Streptomyces</em> sp. ARJ 44, and <em>Streptomyces</em> sp. ARJ 81, were selected. <em>Streptomyces</em> isolates exhibited activity values ranging from 10.38 to 24.08 U/mg of protein. The presence of the <em>bgl</em>S gene, encoding endo-β-1.3-glucanase from glycoside hydrolase family 16, supports the production of glucanase. The amino acid sequence was constructed to 3D structural model. This model exhibited high similarity to endo-β-1.3-glucanase from <em>Nocardiopsis</em> sp. F96. <em>In vitro</em> assays demonstrated that all isolates inhibited hyphal growth of <em>F. oxysporum</em>. Direct inhibition assays showed an average inhibition of 26.18%, whereas the filtrate culture method showed 29.38% inhibition. Enzymes from <em>Streptomyces</em> sp. ARJ 44 was partially purified using acetone, resulting in a specific activity of 46.34 U/mg of protein and a purity increase of up to 1.92-fold. The purified enzyme inhibited the growth of <em>F. oxysporum</em> mycelia by 35.80%. This inhibition was confirmed by observing damage to <em>F. oxysporum</em> hyphae using scanning electron microscopy. The study concluded that the four <em>Streptomyces</em> sp. Strains producing β-1.3-glucanase enzymes have potential as biocontrol agents against <em>F. oxysporum</em>.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100991"},"PeriodicalIF":3.4,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142698581","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}
Pub Date : 2024-11-09DOI: 10.1016/j.rhisph.2024.100990
Misagh Parhizkar , Mohammad Reza Nasiri
The flow depth is an important hydraulic parameter for calculating other hydraulic parameters of overland flow. There is notable changes in hydraulic parameter when the roots of a plant develop in the topsoil. A power regression equation between soil detachment capacity (Dc) and unit energy of cross section (UEC) was established in soils under Fraxinus excelsior L. species based on the Froude number. For measuring Dc, samples collected from soils under the studied species and subjected to five slopes (from 13.9 to 33.9%) and five water discharges (from 0.39 to 0.77 L m−1 s−1) by a hydraulic flume. Compared with the soil with absence of root, the soil with presence of root had lower Dc. The results showed a strong power relationship between the unit energy of cross section and Dc, suggesting that soil detachment rate in rill erosion can be estimated using this hydraulic parameter (R2 = 0.84). This finding is particularly relevant for hillslopes with slopes from 12% to 31%, where the proposed mathematical model could be applied to predict Dc. Overall, this investigation supports a broader use of native species (such as the european ash Fraxinus excelsior L.), as a useful eco-engineering conservation practice and an alternative technique instead of utilizing artificial and expensive conservation practices.
水流深度是计算陆地流其他水力参数的一个重要水力参数。当植物的根系在表土中生长时，水力参数会发生显著变化。根据弗劳德数，建立了 Fraxinus excelsior L. 树种下土壤的脱离能力（Dc）与横截面单位能量（UEC）之间的幂回归方程。为测量 Dc，从所研究树种下的土壤中采集了样本，并通过水槽对其进行了五次斜坡（从 13.9% 到 33.9%）和五次排水（从 0.39 到 0.77 L m-1 s-1）试验。与无根土壤相比，有根土壤的 Dc 值较低。结果表明，横截面单位能量与 Dc 之间存在很强的幂函数关系，这表明可以利用这一水力参数（R2 = 0.84）来估算碾压侵蚀中的土壤剥离率。这一发现尤其适用于坡度在 12% 到 31% 之间的山坡，在这些山坡上，所提出的数学模型可用于预测 Dc。总之，这项调查支持更广泛地使用本地物种（如欧洲白蜡树），将其作为一种有用的生态工程保护措施和替代技术，而不是使用人工和昂贵的保护措施。
{"title":"Modeling root effects on soil detachment capacity using critical flow depth and unit energy of cross section in soils under Fraxinus excelsior L. species","authors":"Misagh Parhizkar , Mohammad Reza Nasiri","doi":"10.1016/j.rhisph.2024.100990","DOIUrl":"10.1016/j.rhisph.2024.100990","url":null,"abstract":"<div><div>The flow depth is an important hydraulic parameter for calculating other hydraulic parameters of overland flow. There is notable changes in hydraulic parameter when the roots of a plant develop in the topsoil. A power regression equation between soil detachment capacity (D<sub>c</sub>) and unit energy of cross section (UEC) was established in soils under <em>Fraxinus excelsior</em> L. species based on the Froude number. For measuring D<sub>c</sub>, samples collected from soils under the studied species and subjected to five slopes (from 13.9 to 33.9%) and five water discharges (from 0.39 to 0.77 L m<sup>−1</sup> s<sup>−1</sup>) by a hydraulic flume. Compared with the soil with absence of root, the soil with presence of root had lower D<sub>c</sub>. The results showed a strong power relationship between the unit energy of cross section and D<sub>c</sub>, suggesting that soil detachment rate in rill erosion can be estimated using this hydraulic parameter (R<sup>2</sup> = 0.84). This finding is particularly relevant for hillslopes with slopes from 12% to 31%, where the proposed mathematical model could be applied to predict D<sub>c</sub>. Overall, this investigation supports a broader use of native species (such as the european ash <em>Fraxinus excelsior</em> L.), as a useful eco-engineering conservation practice and an alternative technique instead of utilizing artificial and expensive conservation practices.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100990"},"PeriodicalIF":3.4,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663391","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}
Mangrove forest is a unique wetland ecosystem that is highly productive and provides an environment for a variety of microorganisms. Endophytic fungi derived from mangrove plants provide the plants with protection from adverse environmental conditions, while also allowing the fungi to produce valuable bioactive compounds. The present study sampled 11 mangrove trees and isolated, screened, and identified the potent endophytic fungi and their bioactive substances showing anti-pathogenic, anti-mutagenic and antioxidant activities, while the endophytes were investigated for their enzymatic potential. In total, 47 endophytic fungi were isolated from the leaves (36) and stems (11) of the host plants and all isolates were tested for antagonistic activities against selected plant pathogens. Based on the results, isolates BgS-04 and BcL-05 had the highest anti-pathogenic activities against Curvularia sp., Fusarium sp., and Colletotrichum sp. Therefore, the ethyl acetate crude extracts from these two fungi were further investigated for their antioxidant and anti-mutagenic activities and their phenolic compound contents, based on phytochemical analysis. Based on the results, the crude extracts of BgS-04 and BcL-05 contained 5.24 and 4.8 mg gallic acid equivalent/g of total phenolic compounds, respectively, and had antioxidant activity (half maximal inhibitory concentration) levels of 7.4 and 4.26 mg/mL, respectively. The preliminary qualitative phytochemical analysis of the fungal crude extracts identified tannins and coumarins. The anti-mutagenic activity levels of BgS-04 and BcL-05 against the mutagenic compounds, Trp-P-1 and DMBA, were determined using the Ames test, which revealed that the crude extracts of BgS-04 and BcL-05 had moderate-to-high antimutagenic potential against TA98 and TA100.
All 47 endophytic isolates were assessed for their potential role in producing extracellular enzyme; they were capable of producing protease (53%), pectinase (28%), amylase (26%) and cellulase (19%) but none of them produced lipase. Among the isolates, RmL-01 derived from the leaves of Rhizophora mucronata had the significantly highest amylase production. Maximum amylase production (141.2 U/mL) was observed at 30 °C, pH 7.0 and 120 h of incubation time. Molecular identification of the isolates BgS-04, BcL-05 and RmL-01 using nuclear ribosomal DNA internal transcribed spacer sequences revealed that they were Pestalotiopsis parva, Collectotrichum perseae, and Aspergillus oryzae, respectively, with high bootstrap support. It was concluded that the distinct groups of mangrove endophytes were potential sources of novel and valuable bio-based compounds with impressive anti-plant pathogen, anti-mutagenic, and antioxidant activities and capable of producing multi-industrial enzyme cocktails that might be important and useful for biotechnological applications.
{"title":"Discovery of pharmaceutical compounds in endophytic fungi from mangrove trees","authors":"Siriluck Iamtham , Anyalak Wachirachaikarn , Kathawut Sopalun , Nongpanga Jarussophon","doi":"10.1016/j.rhisph.2024.100989","DOIUrl":"10.1016/j.rhisph.2024.100989","url":null,"abstract":"<div><div>Mangrove forest is a unique wetland ecosystem that is highly productive and provides an environment for a variety of microorganisms. Endophytic fungi derived from mangrove plants provide the plants with protection from adverse environmental conditions, while also allowing the fungi to produce valuable bioactive compounds. The present study sampled 11 mangrove trees and isolated, screened, and identified the potent endophytic fungi and their bioactive substances showing anti-pathogenic, anti-mutagenic and antioxidant activities, while the endophytes were investigated for their enzymatic potential. In total, 47 endophytic fungi were isolated from the leaves (36) and stems (11) of the host plants and all isolates were tested for antagonistic activities against selected plant pathogens. Based on the results, isolates BgS-04 and BcL-05 had the highest anti-pathogenic activities against <em>Curvularia</em> sp., <em>Fusarium</em> sp., and <em>Colletotrichum</em> sp. Therefore, the ethyl acetate crude extracts from these two fungi were further investigated for their antioxidant and anti-mutagenic activities and their phenolic compound contents, based on phytochemical analysis. Based on the results, the crude extracts of BgS-04 and BcL-05 contained 5.24 and 4.8 mg gallic acid equivalent/g of total phenolic compounds, respectively, and had antioxidant activity (half maximal inhibitory concentration) levels of 7.4 and 4.26 mg/mL, respectively. The preliminary qualitative phytochemical analysis of the fungal crude extracts identified tannins and coumarins. The anti-mutagenic activity levels of BgS-04 and BcL-05 against the mutagenic compounds, Trp-P-1 and DMBA, were determined using the Ames test, which revealed that the crude extracts of BgS-04 and BcL-05 had moderate-to-high antimutagenic potential against TA98 and TA100.</div><div>All 47 endophytic isolates were assessed for their potential role in producing extracellular enzyme; they were capable of producing protease (53%), pectinase (28%), amylase (26%) and cellulase (19%) but none of them produced lipase. Among the isolates, RmL-01 derived from the leaves of <em>Rhizophora mucronata</em> had the significantly highest amylase production. Maximum amylase production (141.2 U/mL) was observed at 30 °C, pH 7.0 and 120 h of incubation time. Molecular identification of the isolates BgS-04, BcL-05 and RmL-01 using nuclear ribosomal DNA internal transcribed spacer sequences revealed that they were <em>Pestalotiopsis parva</em>, <em>Collectotrichum perseae</em>, and <em>Aspergillus oryzae</em>, respectively, with high bootstrap support. It was concluded that the distinct groups of mangrove endophytes were potential sources of novel and valuable bio-based compounds with impressive anti-plant pathogen, anti-mutagenic, and antioxidant activities and capable of producing multi-industrial enzyme cocktails that might be important and useful for biotechnological applications.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100989"},"PeriodicalIF":3.4,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663390","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}
Pub Date : 2024-10-30DOI: 10.1016/j.rhisph.2024.100986
Yingying Wang , Gang Wang , Zhiming Zhang , Shangwen Xia , Xiaodong Yang
Revealing the assembly processes of plant rhizosphere microbial communities and the underlying influencing factors is essential for understanding the biodiversity and function of forest ecosystem. However, it remains unclear how deterministic and stochastic processes shape community structure and their relative importance in phosphorus-limited tropical environments. Here, we investigated the diversity, composition, and assembly processes of rhizosphere microbial communities of Ficus species in the Xishuangbanna region of southwest China, using methods such as high-throughput sequencing, variance partitioning analysis and null model analysis. We found that the community assembly processes of bacteria and fungi were primarily dominated by deterministic processes, with the fungal group being more deterministic than the bacteria group. Soil total phosphorus (TP) was the primary determinant of the composition and assembly of the rhizosphere microbial community, explaining 12.58% and 21.35% of the compositional variation in bacterial and fungal communities, respectively, and accounting for 14% of the microbial community assembly, but has a minor impact on their alpha diversity. This study highlights the distinct environmental driving factors of community composition and community assembly. The exposed positive relationship between soil TP and microbial deterministic process has inspiration for link of microbial community functions to soil function and sustainable forest management.
{"title":"Soil total phosphorus mediate the assembly processes of rhizosphere microbial communities of ficus species in a tropical rainforest","authors":"Yingying Wang , Gang Wang , Zhiming Zhang , Shangwen Xia , Xiaodong Yang","doi":"10.1016/j.rhisph.2024.100986","DOIUrl":"10.1016/j.rhisph.2024.100986","url":null,"abstract":"<div><div>Revealing the assembly processes of plant rhizosphere microbial communities and the underlying influencing factors is essential for understanding the biodiversity and function of forest ecosystem. However, it remains unclear how deterministic and stochastic processes shape community structure and their relative importance in phosphorus-limited tropical environments. Here, we investigated the diversity, composition, and assembly processes of rhizosphere microbial communities of <em>Ficus</em> species in the Xishuangbanna region of southwest China, using methods such as high-throughput sequencing, variance partitioning analysis and null model analysis. We found that the community assembly processes of bacteria and fungi were primarily dominated by deterministic processes, with the fungal group being more deterministic than the bacteria group. Soil total phosphorus (TP) was the primary determinant of the composition and assembly of the rhizosphere microbial community, explaining 12.58% and 21.35% of the compositional variation in bacterial and fungal communities, respectively, and accounting for 14% of the microbial community assembly, but has a minor impact on their alpha diversity. This study highlights the distinct environmental driving factors of community composition and community assembly. The exposed positive relationship between soil TP and microbial deterministic process has inspiration for link of microbial community functions to soil function and sustainable forest management.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100986"},"PeriodicalIF":3.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142571535","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}
Pub Date : 2024-10-30DOI: 10.1016/j.rhisph.2024.100987
Ying Ren , Yinli Bi , Jiapeng Kang
Sodium sulfate (Na2SO4) is one sodium salt extensively found in saline soils; in certain regions, it is the dominant salt present. Dark septate endophytes (DSE) are competent in enhancing plants’ resistance to stressed environments. Nevertheless, little is known about the role of DSE in enhancing plant tolerance to Na2SO4. This study examined DSE growth and its impacts on alfalfa plants exposed to varying Na2SO4 concentrations (0%, 0.15%, 0.3%, and 0.45% (w/w)). Our findings revealed that DSE can thrive even in salt-stress environments. On the 8th day of cultivation, their biomass reached the highest level under 0.45% salt concentration. Moreover, DSE successfully colonized alfalfa roots and significantly enhanced plant growth and development across the various salt gradients. Notably, DSE made the highest contribution 68% to the total biomass of alfalfa at 0.45% salt concentration. Meanwhile, DSE significantly decreased the presence of root’s Na+ across varying salt gradients. Additionally, DSE significantly increased catalase (CAT) activity at salt concentrations of 0.3% and 0.45%. Our study also revealed strong positive correlations of plant biomass with the root index, root’s K+ content, and K+/Na+ ratio, and strong negative correlations of plant biomass with root’s Na+ content and soil’s Na+ and SO42− contents. Structural equation modeling (SEM) demonstrated that DSE indirectly enhanced plant’s shoot biomass under various salt stresses via increasing root length, decreasing root’s Na+ content, and raising CAT activity, while salt indirectly reduced plant’s shoot weight via reducing root length or increasing root’s Na+ content or exerted a direct negative effect on plant shoot biomass. Thus, DSE are instrumental in bolstering the salt tolerance of plants, which holds strategic importance for the management of saline-alkali soils.
{"title":"The overlooked salt: Impact of dark septate endophytes on alfalfa at varying sodium sulfate levels","authors":"Ying Ren , Yinli Bi , Jiapeng Kang","doi":"10.1016/j.rhisph.2024.100987","DOIUrl":"10.1016/j.rhisph.2024.100987","url":null,"abstract":"<div><div>Sodium sulfate (Na<sub>2</sub>SO<sub>4</sub>) is one sodium salt extensively found in saline soils; in certain regions, it is the dominant salt present. Dark septate endophytes (DSE) are competent in enhancing plants’ resistance to stressed environments. Nevertheless, little is known about the role of DSE in enhancing plant tolerance to Na<sub>2</sub>SO<sub>4</sub>. This study examined DSE growth and its impacts on alfalfa plants exposed to varying Na<sub>2</sub>SO<sub>4</sub> concentrations (0%, 0.15%, 0.3%, and 0.45% (w/w)). Our findings revealed that DSE can thrive even in salt-stress environments. On the 8<sup>th</sup> day of cultivation, their biomass reached the highest level under 0.45% salt concentration. Moreover, DSE successfully colonized alfalfa roots and significantly enhanced plant growth and development across the various salt gradients. Notably, DSE made the highest contribution 68% to the total biomass of alfalfa at 0.45% salt concentration. Meanwhile, DSE significantly decreased the presence of root’s Na<sup>+</sup> across varying salt gradients. Additionally, DSE significantly increased catalase (CAT) activity at salt concentrations of 0.3% and 0.45%. Our study also revealed strong positive correlations of plant biomass with the root index, root’s K<sup>+</sup> content, and K<sup>+</sup>/Na<sup>+</sup> ratio, and strong negative correlations of plant biomass with root’s Na<sup>+</sup> content and soil’s Na<sup>+</sup> and SO<sub>4</sub><sup>2−</sup> contents. Structural equation modeling (SEM) demonstrated that DSE indirectly enhanced plant’s shoot biomass under various salt stresses via increasing root length, decreasing root’s Na<sup>+</sup> content, and raising CAT activity, while salt indirectly reduced plant’s shoot weight via reducing root length or increasing root’s Na<sup>+</sup> content or exerted a direct negative effect on plant shoot biomass. Thus, DSE are instrumental in bolstering the salt tolerance of plants, which holds strategic importance for the management of saline-alkali soils.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100987"},"PeriodicalIF":3.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586309","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}
Pub Date : 2024-10-30DOI: 10.1016/j.rhisph.2024.100988
Cristina M. Troya , Lucas W. Mendes , Marileide M. Costa , Everlon Cid Rigobelo , Ludwig H. Pfenning , Victor Hugo Buttros , Joyce Dória
This study explores the dynamics of bacterial communities in the bulk soil, rhizosphere, and endosphere of banana plants, focusing on variations among cultivars with differing levels of genetic resistance to Fusarium wilt. Four banana cultivars were examined: one resistant (P), one moderately susceptible (PT), and two susceptible (W and M). Using 16S rDNA sequencing, we analyzed the bacterial community structures in these habitats. Results showed significant differences in bacterial communities across the three habitats and among the cultivars, with the endosphere communities being the most distinct. The rhizosphere and bulk soil communities exhibited more similarities, likely due to the soil microbiome's influence on the rhizosphere. Resistant cultivars (PT and P) displayed unique bacterial communities, with notable taxa such as Burkholderia, Leifsonia, and Marmoricola in the rhizosphere, known for their antagonistic properties against Fusarium oxysporum. Although the most abundant taxa are not the only ones influencing disease suppression, the susceptible cultivars (W and M) were dominated by genera such as Reyranella and Mucilaginibacter, which are yet to be described as potential biocontrol agents against Fusarium wilt. The endosphere of resistant cultivars also featured beneficial genera like Amycolatopsis and Achromobacter, known for their roles in plant growth promotion and disease resistance. The findings underscore the importance of plant genotype and soil type in shaping the rhizosphere microbiome, with specific microbial taxa associated with resistance to Fusarium. These insights suggest a potential for developing targeted microbial-based strategies to enhance disease resistance and overall plant health. The study highlights key microbial players that could be leveraged for biological control and improved management of Fusarium wilt in banana cultivation. This research advances our understanding of plant-microbe interactions and their implications for sustainable agriculture, particularly in combating soilborne pathogens.
{"title":"Genetic resistance to Fusarium wilt shapes rhizospheric beneficial microbiota in four banana cultivars","authors":"Cristina M. Troya , Lucas W. Mendes , Marileide M. Costa , Everlon Cid Rigobelo , Ludwig H. Pfenning , Victor Hugo Buttros , Joyce Dória","doi":"10.1016/j.rhisph.2024.100988","DOIUrl":"10.1016/j.rhisph.2024.100988","url":null,"abstract":"<div><div>This study explores the dynamics of bacterial communities in the bulk soil, rhizosphere, and endosphere of banana plants, focusing on variations among cultivars with differing levels of genetic resistance to <em>Fusarium</em> wilt. Four banana cultivars were examined: one resistant (P), one moderately susceptible (PT), and two susceptible (W and M). Using 16S rDNA sequencing, we analyzed the bacterial community structures in these habitats. Results showed significant differences in bacterial communities across the three habitats and among the cultivars, with the endosphere communities being the most distinct. The rhizosphere and bulk soil communities exhibited more similarities, likely due to the soil microbiome's influence on the rhizosphere. Resistant cultivars (PT and P) displayed unique bacterial communities, with notable taxa such as <em>Burkholderia</em>, <em>Leifsonia</em>, and <em>Marmoricola</em> in the rhizosphere, known for their antagonistic properties against <em>Fusarium oxysporum</em>. Although the most abundant taxa are not the only ones influencing disease suppression, the susceptible cultivars (W and M) were dominated by genera such as <em>Reyranella</em> and <em>Mucilaginibacter</em>, which are yet to be described as potential biocontrol agents against <em>Fusarium</em> wilt. The endosphere of resistant cultivars also featured beneficial genera like <em>Amycolatopsis</em> and <em>Achromobacter</em>, known for their roles in plant growth promotion and disease resistance. The findings underscore the importance of plant genotype and soil type in shaping the rhizosphere microbiome, with specific microbial taxa associated with resistance to <em>Fusarium</em>. These insights suggest a potential for developing targeted microbial-based strategies to enhance disease resistance and overall plant health. The study highlights key microbial players that could be leveraged for biological control and improved management of <em>Fusarium</em> wilt in banana cultivation. This research advances our understanding of plant-microbe interactions and their implications for sustainable agriculture, particularly in combating soilborne pathogens.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100988"},"PeriodicalIF":3.4,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142698582","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}
Pub Date : 2024-10-29DOI: 10.1016/j.rhisph.2024.100985
Xuedong Chen , Ying Zhu , Lin Tang , Kongyang Wu , Jiayi Liu , Yihan Yang
In order to investigate the impact of Pb smelter pollution on bacterial community structure, diversity and function at the microenvironment scale, the maize rhizosphere soils subjected to long-term (over 20 years) Pb smelter pollution were collected, and bacterial communities and putative functions in different aggregate-size fractions were identified by 16S rRNA sequencing, KEGG and FAPROTAX. The results showed that Pb pollution significantly diminished bacterial diversity, and prompted a shift in the bacterial communities toward more oligotrophic taxa, including Firmicutes, Chloroflexi, and Gemmatimonadetes. Furthermore, the functional subcategories related to cell motility and energy metabolism, as well as the functional groups involved in carbon (C), nitrogen (N), and sulfur (S) cycles, exhibited a marked decline under Pb pollution. At the aggregate scale, distinct differences were observed in the composition of bacterial communities across silt and clay (<250 μm), micro-aggregates (250–1000 μm), and macro-aggregates (1000–2000 μm and >2000 μm) in uncontaminated soils. However, Pb pollution disrupted these original distinctions among bacterial communities in various aggregate-size fractions, with a decreased abundance of dominant Proteobacteria and an increased abundance of Firmicutes in large aggregates. While the differences in bacterial functional groups in aggregate-size fractions were also detected. The functional groups associated with C and N cycles were significantly enriched in the macro-aggregates (1000–2000 μm) in uncontaminated soils. However, similar with the change of bacterial community structure, most functional groups (except for chemoheterotrophy) in aggregate-size fractions exhibited no significant differences under Pb exposure. Our results suggested that Pb pollution altered bacterial community structure and predicted functions at the aggregate level, and showed greater negative effects on bacterial functions in macro-aggregates (1000–2000 μm). This study can provide a new perspective for the influence of Pb smelter pollution on soil aggregate microenvironment.
{"title":"Pb pollution altered bacterial community assembly and predicted functions in aggregate-size fractions of agricultural soil near a smelter","authors":"Xuedong Chen , Ying Zhu , Lin Tang , Kongyang Wu , Jiayi Liu , Yihan Yang","doi":"10.1016/j.rhisph.2024.100985","DOIUrl":"10.1016/j.rhisph.2024.100985","url":null,"abstract":"<div><div>In order to investigate the impact of Pb smelter pollution on bacterial community structure, diversity and function at the microenvironment scale, the maize rhizosphere soils subjected to long-term (over 20 years) Pb smelter pollution were collected, and bacterial communities and putative functions in different aggregate-size fractions were identified by 16S rRNA sequencing, KEGG and FAPROTAX. The results showed that Pb pollution significantly diminished bacterial diversity, and prompted a shift in the bacterial communities toward more oligotrophic taxa, including Firmicutes, Chloroflexi, and Gemmatimonadetes. Furthermore, the functional subcategories related to cell motility and energy metabolism, as well as the functional groups involved in carbon (C), nitrogen (N), and sulfur (S) cycles, exhibited a marked decline under Pb pollution. At the aggregate scale, distinct differences were observed in the composition of bacterial communities across silt and clay (<250 μm), micro-aggregates (250–1000 μm), and macro-aggregates (1000–2000 μm and >2000 μm) in uncontaminated soils. However, Pb pollution disrupted these original distinctions among bacterial communities in various aggregate-size fractions, with a decreased abundance of dominant Proteobacteria and an increased abundance of Firmicutes in large aggregates. While the differences in bacterial functional groups in aggregate-size fractions were also detected. The functional groups associated with C and N cycles were significantly enriched in the macro-aggregates (1000–2000 μm) in uncontaminated soils. However, similar with the change of bacterial community structure, most functional groups (except for chemoheterotrophy) in aggregate-size fractions exhibited no significant differences under Pb exposure. Our results suggested that Pb pollution altered bacterial community structure and predicted functions at the aggregate level, and showed greater negative effects on bacterial functions in macro-aggregates (1000–2000 μm). This study can provide a new perspective for the influence of Pb smelter pollution on soil aggregate microenvironment.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100985"},"PeriodicalIF":3.4,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663392","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}
Pub Date : 2024-10-26DOI: 10.1016/j.rhisph.2024.100980
Suriya Prakash Ganesan , David Boldrin , Anthony Kwan Leung
Plant acclimation to drought involves morphological changes such as leaf shrinkage and root elongation. We sought correlations between drought acclimated plant morphological traits and water potential of leaf () and root (), which are limitedly available. Leaves and roots of Chrysopogon zizanioides L. (vetiver) grown for different periods (3, 4 and 5 months) in biochar amended sandy soil were sampled at a soil water potential () representing drought condition. Morphological traits including leaf area, root diameter and root length were determined to correlate with and . Leaf area and root length increased with increasing growth period, but root diameter remained largely constant. Leaf area and was positively and linearly correlated. Root diameter and root length displayed a contrasting response with ; lower was measured in larger root diameters and shorter root lengths. Vetiver grass avoided the drought stress by increasing their root length, which will benefit the use of this species for soil bioengineering. The proliferation of roots to deeper soil depths could stabilise soil sliding and at the same time survive under drought conditions.
{"title":"Correlation between plant morphological traits and water potential exhibits drought avoidance in Chrysopogon zizanioides","authors":"Suriya Prakash Ganesan , David Boldrin , Anthony Kwan Leung","doi":"10.1016/j.rhisph.2024.100980","DOIUrl":"10.1016/j.rhisph.2024.100980","url":null,"abstract":"<div><div>Plant acclimation to drought involves morphological changes such as leaf shrinkage and root elongation. We sought correlations between drought acclimated plant morphological traits and water potential of leaf (<span><math><mrow><msub><mi>ψ</mi><mi>L</mi></msub></mrow></math></span>) and root (<span><math><mrow><msub><mi>ψ</mi><mi>R</mi></msub></mrow></math></span>), which are limitedly available. Leaves and roots of <em>Chrysopogon zizan</em><em>i</em><em>oides</em> L. (vetiver) grown for different periods (3, 4 and 5 months) in biochar amended sandy soil were sampled at a soil water potential (<span><math><mrow><msub><mi>ψ</mi><mi>S</mi></msub></mrow></math></span>) representing drought condition. Morphological traits including leaf area, root diameter and root length were determined to correlate with <span><math><mrow><msub><mi>ψ</mi><mi>L</mi></msub></mrow></math></span> and <span><math><mrow><msub><mi>ψ</mi><mi>R</mi></msub></mrow></math></span>. Leaf area and root length increased with increasing growth period, but root diameter remained largely constant. Leaf area and <span><math><mrow><msub><mi>ψ</mi><mi>L</mi></msub></mrow></math></span> was positively and linearly correlated. Root diameter and root length displayed a contrasting response with <span><math><mrow><msub><mi>ψ</mi><mi>R</mi></msub></mrow></math></span>; lower <span><math><mrow><msub><mi>ψ</mi><mi>R</mi></msub></mrow></math></span> was measured in larger root diameters and shorter root lengths. Vetiver grass avoided the drought stress by increasing their root length, which will benefit the use of this species for soil bioengineering. The proliferation of roots to deeper soil depths could stabilise soil sliding and at the same time survive under drought conditions.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100980"},"PeriodicalIF":3.4,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554867","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}
Pub Date : 2024-10-25DOI: 10.1016/j.rhisph.2024.100984
Ameni Ben Zineb , Mariem Zakraoui , Imane Bahlouli , Fatma Karray , Asma Ben Salem , Ahmed Mliki , Stephan Declerck , Mahmoud Gargouri
In the field of innovative challenges, it is essential to incorporate microorganisms into agricultural practices that promote and improve plant growth and health, particularly under conditions of salinity stress. This work elucidated the response of two Opuntia ficus-indica cultivars (spiny, Gialla and spineless, Rossa) inoculated inland with a coastal cactus rhizospheric soil (Opuntia littoralis) under NaCl treatment. The two cultivars reacted differently to salinity stress. The cladodes and roots of the Rossa cultivar were sensitive to salinity and accumulated both Na+ and Cl−. In contrast, the Gialla cultivar showed Na + exclusion from the cladodes and root growth was unaffected by salinity. The diversity, richness, and correlation networks of root compartments bacterial communities were mainly determined while the cactus cultivar was subjected to salinity stress. Different subsets of key soil bacteria taxa were selected by the root systems of each cultivar after exposure to salinity. Our results highlight the importance of the rhizosphere of endemic coastal plants in improving plant resistance to salinity stress, particularly in the spiny cultivar compared to the spineless cultivar. The microbiome networks provide solid evidence that each cultivar adapts its bacterial community composition and interactions in response to salinity.
{"title":"Differential recruitment of root bacterial community by inoculated inland spiny and spinless cactus in response to salinity stress","authors":"Ameni Ben Zineb , Mariem Zakraoui , Imane Bahlouli , Fatma Karray , Asma Ben Salem , Ahmed Mliki , Stephan Declerck , Mahmoud Gargouri","doi":"10.1016/j.rhisph.2024.100984","DOIUrl":"10.1016/j.rhisph.2024.100984","url":null,"abstract":"<div><div>In the field of innovative challenges, it is essential to incorporate microorganisms into agricultural practices that promote and improve plant growth and health, particularly under conditions of salinity stress. This work elucidated the response of two <em>Opuntia ficus-indica</em> cultivars (spiny, <em>Gialla</em> and spineless, <em>Rossa</em>) inoculated inland with a coastal cactus rhizospheric soil (<em>Opuntia littoralis</em>) under NaCl treatment. The two cultivars reacted differently to salinity stress. The cladodes and roots of the <em>Rossa</em> cultivar were sensitive to salinity and accumulated both Na<sup>+</sup> and Cl<sup>−</sup>. In contrast, the <em>Gialla</em> cultivar showed Na <sup>+</sup> exclusion from the cladodes and root growth was unaffected by salinity. The diversity, richness, and correlation networks of root compartments bacterial communities were mainly determined while the cactus cultivar was subjected to salinity stress. Different subsets of key soil bacteria taxa were selected by the root systems of each cultivar after exposure to salinity. Our results highlight the importance of the rhizosphere of endemic coastal plants in improving plant resistance to salinity stress, particularly in the spiny cultivar compared to the spineless cultivar. The microbiome networks provide solid evidence that each cultivar adapts its bacterial community composition and interactions in response to salinity.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100984"},"PeriodicalIF":3.4,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142538773","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}
Pub Date : 2024-10-24DOI: 10.1016/j.rhisph.2024.100981
Maria Tartaglia, Monica Labella-Ortega, Maria Maisto, Antonello Prigioniero, Daniela Zuzolo, Carmine Guarino
This study examined rhizosphere soil samples from vineyards located in Sannio area, (Campania, Italy) with different management practices to assess the microbiota's functionality through a metatranscriptomic analysis. The analysis provided a comprehensive taxonomic characterization, gene expression insights, and predictive functional analyses. The experiment included 18 samples from three management-based groups (green manure, periodic hoeing, burying pruning) each with six biological replicates from two vineyards, yielding 316 Gb of data (17.5 Gb/sample). In the vineyards in which a green manure mix of Brassicaceae and Fabaceae was practised, the predominant bacterial phyla are Actinomycetota (with predominant families Conexibacteraceae and Nocardioidaceae), and Pseudomonadota (predominantly Nitrobacteraceae and Methylobacteriaceae). As regards the phylum Streptophyta, as expected, there is a greater abundance of transcripts from Vitaceae and Brassicaceae. About fungi, the most abundant phylum Ascomycota has predominantly Pyronemataceae and Pleosporaceae. Of particular interest related to this type of managment is the abundance of viral transcripts, with the most abundant phylum Pisuviricota and the families Secoviridae and Dicistroviridae. The most significantly up-regulated genes in these vineyards belonged to GO classes involved in viral infections and plant stress responses. In vineyards where regular tilling is carried out, a similar pattern but higher percentages of Actinobacteria and Lenarviricota were observed. In these samples, genes involved in phytohormone pathways (Jasmonic acid, Gibberellin, Salicylic acid) and root system development were up-expressed. Vineyards with a discordant taxonomic profile were those where pruning waste was routinely buried. This management practice was correlated with a marked increase in Nematoda transcripts. Gene expression and pathway enrichment analyses identified significant metabolic and signal transduction pathways associated with differentially expressed genes, highlighting how the rhizosphere is influenced by agricultural practices.
{"title":"Management impacts rhizosphere composition and gene expression in vineyards","authors":"Maria Tartaglia, Monica Labella-Ortega, Maria Maisto, Antonello Prigioniero, Daniela Zuzolo, Carmine Guarino","doi":"10.1016/j.rhisph.2024.100981","DOIUrl":"10.1016/j.rhisph.2024.100981","url":null,"abstract":"<div><div>This study examined rhizosphere soil samples from vineyards located in Sannio area, (Campania, Italy) with different management practices to assess the microbiota's functionality through a metatranscriptomic analysis. The analysis provided a comprehensive taxonomic characterization, gene expression insights, and predictive functional analyses. The experiment included 18 samples from three management-based groups (green manure, periodic hoeing, burying pruning) each with six biological replicates from two vineyards, yielding 316 Gb of data (17.5 Gb/sample). In the vineyards in which a green manure mix of Brassicaceae and Fabaceae was practised, the predominant bacterial phyla are Actinomycetota (with predominant families Conexibacteraceae and Nocardioidaceae), and Pseudomonadota (predominantly Nitrobacteraceae and Methylobacteriaceae). As regards the phylum Streptophyta, as expected, there is a greater abundance of transcripts from Vitaceae and Brassicaceae. About fungi, the most abundant phylum Ascomycota has predominantly Pyronemataceae and Pleosporaceae. Of particular interest related to this type of managment is the abundance of viral transcripts, with the most abundant phylum Pisuviricota and the families Secoviridae and Dicistroviridae. The most significantly up-regulated genes in these vineyards belonged to GO classes involved in viral infections and plant stress responses. In vineyards where regular tilling is carried out, a similar pattern but higher percentages of Actinobacteria and Lenarviricota were observed. In these samples, genes involved in phytohormone pathways (Jasmonic acid, Gibberellin, Salicylic acid) and root system development were up-expressed. Vineyards with a discordant taxonomic profile were those where pruning waste was routinely buried. This management practice was correlated with a marked increase in Nematoda transcripts. Gene expression and pathway enrichment analyses identified significant metabolic and signal transduction pathways associated with differentially expressed genes, highlighting how the rhizosphere is influenced by agricultural practices.</div></div>","PeriodicalId":48589,"journal":{"name":"Rhizosphere","volume":"32 ","pages":"Article 100981"},"PeriodicalIF":3.4,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142528596","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}
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