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1.
J Phycol ; 60(2): 229-253, 2024 04.
Artigo em Inglês | MEDLINE | ID: mdl-38502571

RESUMO

Aero-terrestrial algae are ecologically and economically valuable bioresources contributing to carbon sequestration, sustenance of soil health, and fertility. Compared to aquatic algae, the literature on subaerial algae is minimal, including studies of distinctive habitats such as forest soils, agricultural fields, deserts, polar regions, specific subaerial zones, artificial structures, and tropical soils. The primary goal here was to identify the gaps and scope of research on such algae. Accordingly, the literature was analyzed per sub-themes, such as the "nature of current research data on terrestrial algae," "methodological approaches," "diversity," "environmental relationships," "ecological roles," and "economic significance." The review showed there is a high diversity of algae in soils, especially members belonging to the Cyanophyta (Cyanobacteria) and Chlorophyta. Algal distributions in terrestrial environments depend on the microhabitat conditions, and many species of soil algae are sensitive to specific soil conditions. The ecological significance of soil algae includes primary production, the release of biochemical stimulants and plant growth promoters into soils, nitrogen fixation, solubilization of minerals, and the enhancement and maintenance of soil fertility. Since aero-terrestrial habitats are generally stressed environments, algae of such environments can be rich in rare metabolites and natural products. For example, epilithic soil algae use wet adhesive molecules to fix them firmly on the substratum. Exploring the ecological roles and economic utility of soil and other subaerial algae could be helpful for the development of algae-based industries and for achieving sustainable soil management.


Assuntos
Clorófitas , Cianobactérias , Solo/química , Plantas/microbiologia , Ecossistema
2.
Mol Plant Microbe Interact ; 37(3): 347-353, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38114082

RESUMO

Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, including static content and rapid obsolescence. To address these challenges, we have developed a Web-based knowledge platform dedicated to xanthomonads, inspired by the concept of living systematic reviews. This platform offers a dynamic resource that encompasses bacterial virulence factors, plant resistance genes, and tools for diagnostics and genetic diversity studies. Our goal is to facilitate access for newcomers to the field, provide continuing education opportunities for students, assist plant protection services with diagnostics, provide valuable information to breeders on sources of resistance and breeding targets, and offer comprehensive expert knowledge to other stakeholders interested in plant-pathogenic xanthomonads. This resource is available for queries and updates at https://euroxanth.ipn.pt. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.


Assuntos
Melhoramento Vegetal , Xanthomonas , Humanos , Virulência/genética , Xanthomonas/genética , Fatores de Virulência/genética , Plantas/microbiologia , Doenças das Plantas/microbiologia
3.
New Phytol ; 240(5): 2035-2049, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37691273

RESUMO

Recent studies on root traits have shown that there are two axes explaining trait variation belowground: the collaboration axis with mycorrhizal partners and the conservation ('fast - slow') axis. However, it is yet unknown whether these trait axes affect the assembly of soilborne fungi. We expect saprotrophic fungi to link to the conservation axis of root traits, whereas pathogenic and arbuscular mycorrhizal fungi link to the collaboration axis, but in opposite directions, as arbuscular mycorrhizal fungi might provide pathogen protection. To test these hypotheses, we sequenced rhizosphere fungal communities and measured root traits in monocultures of 25 grassland plant species, differing in age. Within the fungal guilds, we evaluated fungal species richness, relative abundance and community composition. Contrary to our hypotheses, fungal diversity and relative abundance were not strongly related to the root trait axes. However, saprotrophic fungal community composition was affected by the conservation gradient and pathogenic community composition by the collaboration gradient. The rhizosphere AMF community composition did not change along the collaboration gradient, even though the root trait axis was in line with the root mycorrhizal colonization rate. Overall, our results indicate that in the long term, the root trait axes are linked with fungal community composition.


Assuntos
Micorrizas , Rizosfera , Raízes de Plantas/microbiologia , Pradaria , Micorrizas/fisiologia , Plantas/microbiologia , Fungos/fisiologia , Microbiologia do Solo , Solo
4.
Molecules ; 28(15)2023 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-37570772

RESUMO

One trend in agriculture is the replacement of classical pesticides with more ecofriendly solutions, such as elicitation, which is a promising approach consisting of stimulating the natural immune system of a plant to improve its resistance to pathogens. In this fashion, a library of p-coumaric-based compounds were synthesized in accordance with as many principles of green chemistry as possible. Then, these molecules were tested for (1) the direct inhibition of mycelium growth of two pathogens, Botrytis cinerea and Sclerotinia sclerotiorum, and (2) plasma membrane destabilization in Arabidopsis and rapeseed. Finally, the protective effect was evaluated on an Arabidopsis/B. cinerea pathosystem. Total inhibition of the growth of both fungi could be achieved, and significant ion leakage was observed using dihydroxylated fatty p-coumarate esters. A direct effect on plants was also recorded as a ca. three-fold reduction in the necrosis area.


Assuntos
Antifúngicos , Arabidopsis , Antifúngicos/química , Arabidopsis/metabolismo , Plantas/microbiologia , Membrana Celular , Botrytis , Doenças das Plantas/prevenção & controle , Doenças das Plantas/microbiologia
5.
J Basic Microbiol ; 63(7): 690-708, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-36998101

RESUMO

Medicinal plants are an important source of bioactive compounds and have been used to isolate various bioactive compounds having industrial applications. The demand for plants derived bioactive molecules is increasing gradually. However, the extensive use of these plants to extract bioactive molecules has threatened many plant species. Moreover, extracting bioactive molecules from these plants is laborious, costly, and time-consuming. So, some alternative sources and strategies are urgently needed to produce these bioactive molecules similar to that of plant origin. However, the interest in new bioactive molecules has recently shifted from plants to endophytic fungi because many fungi produce bioactive molecules similar to their host plant. Endophytic fungi live in mutualistic association within the healthy plant tissue without causing disease symptoms to the host plant. These fungi are a treasure house of novel bioactive molecules having broad pharmaceutical, industrial, and agricultural applications. The rapid increase in publications in this domain over the last three decades proves that natural product biologists and chemists are paying great attention to the natural bioactive products from endophytic fungi. Though endophytes are source of novel bioactive molecules but there is need of advanced technologies like clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) and epigenetic modifiers to enhance the production of compounds having industrial applications. This review provides an overview of the various industrial applications of bioactive molecules produced by endophytic fungi and the rationale behind selecting specific plants for fungal endophyte isolation. Overall, this study presents the current state of knowledge and highlights the potential of endophytic fungi for developing alternative therapies for drug-resistant infections.


Assuntos
Anti-Infecciosos , Produtos Biológicos , Endófitos/metabolismo , Fungos/metabolismo , Plantas/microbiologia , Simbiose , Anti-Infecciosos/metabolismo , Indústria Farmacêutica , Produtos Biológicos/metabolismo
6.
J Gen Virol ; 102(12)2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34850675

RESUMO

An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.


Assuntos
Micovírus/genética , Fusarium/virologia , Micovírus/classificação , Micovírus/ultraestrutura , Fusarium/isolamento & purificação , Genoma Viral/genética , Paquistão , Filogenia , Doenças das Plantas/microbiologia , Plantas/microbiologia , Vírus de RNA/classificação , Vírus de RNA/genética , Vírus de RNA/ultraestrutura , RNA Viral/genética , Proteínas Virais/genética , Viroma/genética
7.
OMICS ; 25(8): 484-494, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34255557

RESUMO

Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.


Assuntos
Biovigilância/métodos , DNA/isolamento & purificação , Técnicas Microbiológicas , Vigilância em Saúde Pública/métodos , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Técnicas Genéticas/economia , Humanos , Técnicas Microbiológicas/economia , Plantas/microbiologia
8.
Nat Commun ; 12(1): 4431, 2021 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-34290234

RESUMO

Experiments showed that biodiversity increases grassland productivity and nutrient exploitation, potentially reducing fertiliser needs. Enhancing biodiversity could improve P-use efficiency of grasslands, which is beneficial given that rock-derived P fertilisers are expected to become scarce in the future. Here, we show in a biodiversity experiment that more diverse plant communities were able to exploit P resources more completely than less diverse ones. In the agricultural grasslands that we studied, management effects either overruled or modified the driving role of plant diversity observed in the biodiversity experiment. Nevertheless, we show that greater above- (plants) and belowground (mycorrhizal fungi) biodiversity contributed to tightening the P cycle in agricultural grasslands, as reduced management intensity and the associated increased biodiversity fostered the exploitation of P resources. Our results demonstrate that promoting a high above- and belowground biodiversity has ecological (biodiversity protection) and economical (fertiliser savings) benefits. Such win-win situations for farmers and biodiversity are crucial to convince farmers of the benefits of biodiversity and thus counteract global biodiversity loss.


Assuntos
Agricultura/métodos , Biodiversidade , Pradaria , Fósforo/metabolismo , Agricultura/economia , Biomassa , Fertilizantes/economia , Análise de Classes Latentes , Micorrizas/classificação , Micorrizas/metabolismo , Fósforo/análise , Fósforo/economia , Plantas/classificação , Plantas/metabolismo , Plantas/microbiologia , Solo/química , Microbiologia do Solo
9.
Toxins (Basel) ; 13(4)2021 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-33921591

RESUMO

Zearalenone (ZEA) is a harmful secondary fungal metabolite, produced primarily by plant pathogenic fungi mostly belonging to the genus Fusarium. It is involved in reproductive disorders in animals since its structure is similar to the estrogen hormone. This induces precocious pubertal changes, fertility problems, and hyper estrogenic disorders. The main objectives of this study were to evaluate the ZEA removal capacity of plant-derived lactic acid bacteria (LAB) and to investigate the possible components and mechanisms involved in the removal of ZEA by physically and chemically treated plant-derived LAB. The bacterial cells were characterized using scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), and the analysis of zeta potential, and hydrophobic index. Results revealed that 17 out of 33 plant-derived LAB exhibited ZEA removal from liquid medium. The percentage of removal ranged from 0.5-23% and Lactobacillus plantarum BCC 47723, isolated from wild spider flower pickle (Pag-sian-dorng), exhibited the highest removal. The alteration of proteins on L. plantarum BCC 47723 structure by Sodium dodecyl sulphate (SDS) treatment was positively affected on ZEA removal, whereas that of lipids on ZEA removal was negatively observed. Heat treatment influenced the higher ZEA adsorption. SEM images showed that the morphologies of modified bacterial cells were distinctly deformed and damaged when compared with untreated control. FTIR analysis indicated that the original functional groups, which included amide (C=O, C-N), carboxyl (C=O, C-O, O-H), methylene (C=C), and alcohol (O-H) groups, were not changed after ZEA adsorption. The zeta potential indicated that electrostatic interaction was not involved in the ZEA removal, while hydrophobicity was the main force to interact with ZEA. These findings can conclude that adsorption by hydrophobicity is the main mechanism for ZEA removal of plant-derived L. plantarum BCC 47723. The alteration of bacterial cell structure by heat treatment enhanced the efficiency of L. plantarum BCC 47723 for ZEA reduction. Its activity can be protected by the freeze-drying technique. Hence, plant-derived L. plantarum BCC 47723 can be considered as an organic adsorbent for ZEA reduction in food and feedstuff.


Assuntos
Agentes de Controle Biológico/metabolismo , Fungos/metabolismo , Lactobacillus plantarum/metabolismo , Plantas/microbiologia , Zearalenona/metabolismo , Adsorção , Interações Hidrofóbicas e Hidrofílicas , Lactobacillus plantarum/isolamento & purificação , Metabolismo Secundário
10.
Environ Microbiol ; 23(1): 316-326, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33185929

RESUMO

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.


Assuntos
Bactérias/genética , Biodiversidade , Fungos/genética , Animais , Bactérias/classificação , Bactérias/isolamento & purificação , Fungos/classificação , Fungos/isolamento & purificação , Metagenoma , Metagenômica , Microbiota , Micobioma , Plantas/microbiologia
11.
Arch Microbiol ; 203(3): 1211-1219, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33231748

RESUMO

This study aimed to compare the fungal rhizosphere communities of Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex, and the gut mycobiota of Poekilocerus bufonius (Orthoptera, Pyrgomorphidae, "Usherhopper"). A total of 164,485 fungal reads were observed from the five plant rhizospheres and Usherhopper gut. The highest reads were in S. italica rhizosphere (29,883 reads). Species richness in the P. bufonius gut was the highest among the six samples. Ascomycota was dominant in all samples, with the highest reads in E. desvauxii (26,734 reads) rhizosphere. Sordariomycetes and Dothideomycetes were the dominant classes detected with the highest abundance in C. colocynthis and E. desvauxii rhizospheres. Aspergillus and Ceratobasidium were the most abundant genera in the R. stricta rhizosphere, Fusarium and Penicillium in the E. desvauxii rhizosphere and P. bufonius gut, Ceratobasidium and Myrothecium in the C. colocynthis rhizosphere, Aspergillus and Fusarium in the S. italica rhizosphere, and Cochliobolus in the Z. simplex rhizosphere. Aspergillus terreus was the most abundant species in the R. stricta and S. italica rhizospheres, Fusarium sp. in E. desvauxii rhizosphere, Ceratobasidium sp. in C. colocynthis rhizosphere, Cochliobolus sp. in Z. simplex rhizosphere, and Penicillium sp. in P. bufonius gut. The phylogenetic results revealed the unclassified species were related closely to Ascomycota and the species in E. desvauxii, S. italica and Z. simplex rhizospheres were closely related, where the species in the P. bufonius gut, were closely related to the species in the R. stricta, and C. colocynthis rhizospheres.


Assuntos
Biodiversidade , Fungos/genética , Metagenômica , Micobioma/genética , Plantas/microbiologia , Rizosfera , Microbiologia do Solo , Clima Desértico , Fungos/classificação , Filogenia , Raízes de Plantas/microbiologia
12.
New Phytol ; 225(1): 461-473, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31408907

RESUMO

Arbuscular mycorrhizal fungi (AMFs) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine the effects of the surrounding plant community, of the host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 wk, and AMFs in their roots were quantified. Additionally, we characterized the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMFs, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonization intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.


Assuntos
Pradaria , Interações Hospedeiro-Patógeno , Micobioma , Micorrizas/fisiologia , Plantas/microbiologia , Contagem de Colônia Microbiana , Funções Verossimilhança , Método de Monte Carlo , Análise Multivariada , Micorrizas/crescimento & desenvolvimento , Filogenia , Solo/química
13.
Sci Rep ; 9(1): 17961, 2019 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-31784634

RESUMO

Agrobacterium-mediated plant galls are often misdiagnosed as nematode-mediated knots, even by experts, because the gall symptoms in both conditions are very similar. In the present study, we developed biosensor strains based on agrobacterial opine metabolism that easily and simply diagnoses Agrobacterium-induced root galls. Our biosensor consists of Agrobacterium mannitol (ABM) agar medium, X-gal, and a biosensor. The working principle of the biosensor is that exogenous nopaline produced by plant root galls binds to NocR, resulting in NocR/nopaline complexes that bind to the promoter of the nopaline oxidase gene (nox) operon and activate the transcription of noxB-lacZY, resulting in readily visualized blue pigmentation on ABM agar medium supplemented with X-gal (ABMX-gal). Similarly, exogenous octopine binds to OccR, resulting in OoxR/octopine complexes that bind to the promoter of the octopine oxidase gene (oox) operon and activate the transcription of ooxB-lacZY, resulting in blue pigmentation in the presence of X-gal. Our biosensor is successfully senses opines produced by Agrobacterium-infected plant galls, and can be applied to easily distinguish Agrobacterium crown gall disease from nematode disease.


Assuntos
Agrobacterium tumefaciens/fisiologia , Técnicas Biossensoriais/métodos , Nematoides/fisiologia , Tumores de Planta/microbiologia , Tumores de Planta/parasitologia , Animais , Plantas/microbiologia , Plantas/parasitologia
14.
Proc Natl Acad Sci U S A ; 116(46): 23163-23168, 2019 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-31659035

RESUMO

Mycorrhizal fungi are critical members of the plant microbiome, forming a symbiosis with the roots of most plants on Earth. Most plant species partner with either arbuscular or ectomycorrhizal fungi, and these symbioses are thought to represent plant adaptations to fast and slow soil nutrient cycling rates. This generates a second hypothesis, that arbuscular and ectomycorrhizal plant species traits complement and reinforce these fungal strategies, resulting in nutrient acquisitive vs. conservative plant trait profiles. Here we analyzed 17,764 species level trait observations from 2,940 woody plant species to show that mycorrhizal plants differ systematically in nitrogen and phosphorus economic traits. Differences were clearest in temperate latitudes, where ectomycorrhizal plant species are more nitrogen use- and phosphorus use-conservative than arbuscular mycorrhizal species. This difference is reflected in both aboveground and belowground plant traits and is robust to controlling for evolutionary history, nitrogen fixation ability, deciduousness, latitude, and species climate niche. Furthermore, mycorrhizal effects are large and frequently similar to or greater in magnitude than the influence of plant nitrogen fixation ability or deciduous vs. evergreen leaf habit. Ectomycorrhizal plants are also more nitrogen conservative than arbuscular plants in boreal and tropical ecosystems, although differences in phosphorus use are less apparent outside temperate latitudes. Our findings bolster current theories of ecosystems rooted in mycorrhizal ecology and support the hypothesis that plant mycorrhizal association is linked to the evolution of plant nutrient economic strategies.


Assuntos
Micorrizas , Nitrogênio/metabolismo , Fósforo/metabolismo , Plantas/metabolismo , Plantas/microbiologia , Clima , Ecossistema , Fixação de Nitrogênio
15.
Sci Rep ; 9(1): 3753, 2019 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-30842590

RESUMO

A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.


Assuntos
Bactérias/genética , Biologia Computacional/métodos , Micorrizas/genética , Análise de Sequência de DNA/métodos , Algoritmos , Bactérias/isolamento & purificação , Análise por Conglomerados , DNA Ribossômico/genética , Lógica Fuzzy , Cadeias de Markov , Micorrizas/isolamento & purificação , Filogenia , Plantas/microbiologia
16.
Brief Bioinform ; 20(1): 274-287, 2019 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-29028906

RESUMO

The identification of plant-pathogen protein-protein interactions (PPIs) is an attractive and challenging research topic for deciphering the complex molecular mechanism of plant immunity and pathogen infection. Considering that the experimental identification of plant-pathogen PPIs is time-consuming and labor-intensive, computational methods are emerging as an important strategy to complement the experimental methods. In this work, we first evaluated the performance of traditional computational methods such as interolog, domain-domain interaction and domain-motif interaction in predicting known plant-pathogen PPIs. Owing to the low sensitivity of the traditional methods, we utilized Random Forest to build an inter-species PPI prediction model based on multiple sequence encodings and novel network attributes in the established plant PPI network. Critical assessment of the features demonstrated that the integration of sequence information and network attributes resulted in significant and robust performance improvement. Additionally, we also discussed the influence of Gene Ontology and gene expression information on the prediction performance. The Web server implementing the integrated prediction method, named InterSPPI, has been made freely available at http://systbio.cau.edu.cn/intersppi/index.php. InterSPPI could achieve a reasonably high accuracy with a precision of 73.8% and a recall of 76.6% in the independent test. To examine the applicability of InterSPPI, we also conducted cross-species and proteome-wide plant-pathogen PPI prediction tests. Taken together, we hope this work can provide a comprehensive understanding of the current status of plant-pathogen PPI predictions, and the proposed InterSPPI can become a useful tool to accelerate the exploration of plant-pathogen interactions.


Assuntos
Proteínas de Plantas/metabolismo , Plantas/metabolismo , Plantas/microbiologia , Mapeamento de Interação de Proteínas/métodos , Algoritmos , Arabidopsis/genética , Arabidopsis/metabolismo , Arabidopsis/microbiologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/imunologia , Proteínas de Arabidopsis/metabolismo , Biologia Computacional/métodos , Bases de Dados de Proteínas/estatística & dados numéricos , Perfilação da Expressão Gênica/estatística & dados numéricos , Ontologia Genética , Interações Hospedeiro-Patógeno/genética , Interações Hospedeiro-Patógeno/imunologia , Aprendizado de Máquina , Modelos Biológicos , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Imunidade Vegetal/genética , Proteínas de Plantas/genética , Proteínas de Plantas/imunologia , Plantas/genética , Mapeamento de Interação de Proteínas/estatística & dados numéricos
17.
Sci Rep ; 8(1): 13828, 2018 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-30218023

RESUMO

The uniformity of crop yield is extremely important for consumers and of as much relevance to the grower as overall yield. However, size inequality within a plant population is rarely measured and has never before been considered in relation to the use of beneficial microbes for yield enhancement. For the first time, we show that addition of soil bacteria to calabrese plants significantly increased size inequality. These effects were usually more apparent in above-ground biomass. This was caused by some (but not all) plants growing very large when inoculated with bacteria, while control plants were mostly small. We suggest that the main reason is the incompatibility of the inoculated bacteria with those already present in the rhizosphere. In some cases the inoculum matched the indigenous community, providing a benefit to plant growth, while often it did not and plants remained relatively small. We conclude that analyses of size inequality should be an integral part of experiments using microbial soil amendments. These analyses can help to inform the production of more effective microbial products and to ensure that the integration of beneficial microbes into sustainable production systems does not impair uniformity in yield.


Assuntos
Brassica/crescimento & desenvolvimento , Rhizobiaceae/metabolismo , Rizosfera , Bacillus/metabolismo , Bacillus/patogenicidade , Brassica/microbiologia , Desenvolvimento Vegetal/fisiologia , Raízes de Plantas/microbiologia , Plantas/microbiologia , Solo , Microbiologia do Solo
18.
Gene ; 676: 219-226, 2018 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-29981422

RESUMO

The genus Fusarium contains some of the most studied and important species of plant pathogens that economically affect world agriculture and horticulture. Fusarium spp. are ubiquitous fungi widely distributed in soil, plants as well as in different organic substrates and are also considered as opportunistic human pathogens. The identification of specific enzymes essential to the metabolism of these fungi is expected to provide molecular targets to control the diseases they induce to their hosts. Through applications of traditional techniques of sequence homology comparison by similarity search and Markov modeling, this report describes the characterization of enzymatic functionalities associated to protein targets that could be considered for the control of root rots induced by Fusarium oxysporum. From the analysis of 318 F. graminearum enzymes, we retrieved 30 enzymes that are specific of F. oxysporum compared to 15 species of host plants. By comparing these 30 specific enzymes of F. oxysporum with the genome of Arabidopsis thaliana, Brassica rapa, Glycine max, Jatropha curcas and Ricinus communis, we found 7 key specific enzymes whose inhibition is expected to affect significantly the development of the fungus and 5 specific enzymes that were considered here to be secondary because they are inserted in pathways with alternative routes.


Assuntos
Proteínas Fúngicas/genética , Fusarium/enzimologia , Proteínas de Plantas/genética , Plantas/enzimologia , Fusarium/genética , Regulação Enzimológica da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Cadeias de Markov , Doenças das Plantas/microbiologia , Raízes de Plantas/genética , Plantas/genética , Plantas/microbiologia , Homologia de Sequência de Aminoácidos , Especificidade da Espécie
19.
Syst Appl Microbiol ; 41(6): 629-640, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30055880

RESUMO

Plants are chronically associated with microorganisms, residing all tissues. Holonomic analysis of diversity of established rhizobacteria in uncultivated plants is scarce. Thus, the present study was conducted to access the root-associated bacterial diversity of 6 crops (maize, canola, soybean, reed canarygrass, alfafa, and miscanthus) and 20 uncultivated plant species in the region of Sainte-Anne-de-Bellevue, Québec, Canada, using pure-culture methods. Based on 16S rRNA gene sequence analysis, 446 bacterial isolates were distributed onto four phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes), 32 families and 90 genera. Proteobacteria constituted the largest group of isolates (240), 40% of ectophytic and 61% of endophytic bacteria. Representatives of the genera Bacillus and Pseudomonas dominated in rhizosphere soil; Microbacterium and Pseudomonas were the predominant endophytes. Some genera were associated with specific plant species, such as Stenotrophomonas, Yersinia, Labrys and Luteibacter. Several endophytes were occasionally observed in the rhizosphere, and vice versa. This is the first survey of culturable endophytic bacteria associated with uncultivated plants in Québec. The culturable bacterial community studied herein are assumed to represent a portion of the entire phytomicrobiome of the evaluated plants. Results confirmed that the crops and uncultivated plants of Québec represent an extremely rich reservoir of diverse rhizobacteria.


Assuntos
Bactérias/classificação , Endófitos/classificação , Raízes de Plantas/microbiologia , Rizosfera , Bactérias/isolamento & purificação , Técnicas de Tipagem Bacteriana , Biodiversidade , Produtos Agrícolas/microbiologia , DNA Bacteriano/genética , Endófitos/isolamento & purificação , Filogenia , Plantas/microbiologia , Quebeque , RNA Ribossômico 16S/genética , Microbiologia do Solo
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