SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

MENDES, L. W.; MENDES, R.; TSAI, S. M..

The rhizosphere is the narrow zone of soil around the living plant roots that is influenced by the activity of the plants. Many beneficial microorganisms in the rhizosphere provide plants with mineral nutrients, phytohormones, and also help to protect the plant against soil-borne pathogens. Microbiological studies are addressed to understand how rhizosphere microorganisms are recruited from soil and either benefit or harm plant growth, nutrition and health. Here, we aimed to identify potential microbial groups and functional traits correlated to the suppression of the soil borne pathogen Fusarium oxysporum, the causal agent of Fusarium wilt on common beans. We used shotgun metagenomics to investigate the rhizosphere microbiome of two common bean cultivars...

Back to the roots: revealing beneficial interactions between the rhizosphere microbiome and wild wheat.

Palavras-chave: Microbial ecology; Microbiome; Shotgun metagenomics; Soil born pathogen; Feijão; Fusarium oxysporum.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1036665

ROSSMANN, M.; PÉREZ-JARAMILLO, J. E.; CHIARAMONTE, J. B.; KAVAMURA, V. N.; DUMACK, K.; FIORE-DONNO, A. M.; MENDES, L. W.; BONKOWSKI, M.; MAUCHLINE, T.; RAAIJMAKERS, J. M.; MENDES, R..

Domestication of plants may have impacted the interactions between plants and their rhizosphere microbiome. Considering that plants rely on the rhizosphere microbiome for functions related with plant growth, nutrition and health, the objective of this work was to analyse the rhizosphere microbiome of wild relatives and modern varieties of wheat and to investigate whether wild relatives recruit a higher proportion of beneficial microbes than modern cultivars. By 16S-rRNA gene amplicon, ITS and 18SrRNA gene amplicon, we assessed the bacterial, fungal and cercozoa rhizosphere community composition of five modern cultivars and three wheat ancestors cultivated in forest and agricultural soils. Results revealed a pronounced soil type and rhizosphere effect on...

Breeding for resistance to soil-borne pathogen impacts rhizosphere microbiome functions in common bean.

Palavras-chave: Wild wheat; Trigo; Rizosfera; Rhizosphere; Wheat; Microbiome.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1103217

MENDES, L. W.; MENDES, R.; RAAIJMAKERS, J. M.; TSAI, S. M..

Over the past century, plant breeding programs have substantially improved plant growth and health, but have not yet considered the potential effects on the plant microbiome. Here, we conducted a metatranscriptome analysis to determine if and how breeding for resistance of common bean against the root pathogen Fusarium oxysporum (Fox) affected gene expression in the rhizobacterial community. Our data revealed that rhizobacterial community assembly of Fox-resistant and susceptible bean cultivars follows niche-based mechanisms, presenting lower diversity and distinct community structure compared to the bulk soil. The microbiome of the Fox-resistant bean cultivar presented a significantly higher expression of bacterial genes associated with nutrient...

Cross-kingdom similarities in microbiome ecology and biocontrol of pathogens.

Palavras-chave: Rizosfera; Feijão; Microbiome; Rhizosphere; Beans; Breeding.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1103238

BERG, G.; KRAUSE, R.; MENDES, R..

Abstract: The concept of "gut and root microbiota commonalities" was already presented by Ramírez-Puebla et al.(2013); they discussed a lot of similar functional traits, host-bacteria interactions as well as evolutionary trends but also several differences. Based on deeper insights obtained by omics technologies, Mendes and Raaijmakers (2015) recently presented their concept that the structure and function of rhizosphere and gut microbiomes showcross-kingdom similarities. In parallel, Hacquard et al. (2015) analyzed similarities of the microbiota composition across plant and animal kingdoms and found only little overlap comparing fish gut and plant root communities. They explained the differences by various start inoculants and abiotic, niche-specific...

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.

Palavras-chave: Ecological theories; Rizosfera; População microbiana; Bactéria; Controle biológico; Microbiome; Biological control agents; Rhizosphere; Pathogens.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1032834

PEREZ-JARAMILLO, J. E.; HOLLANDER, M. de; RAMÍREZ, C. A.; MENDES, R.; RAAIJMAKERS, J. M.; CARRIÓN, V. J..

Abstract: Background: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers oforigin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial communityassembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterialdiversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agriculturalsoil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 wereshared by all eight bean accessions grown in native and agricultural...

Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples

Palavras-chave: Common bean; Wild and modern accessions; Domestication; Rhizosphere; Core microbiome; Networks.; Feijão; Rizosfera; Phaseolus; Microbiome; Rhizosphere; Domestication.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115028

BJM

Hassan,Mariam; Essam,Tamer; Megahed,Salwa.

Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree)...

Impact of plant domestication on rhizosphere microbiome assembly and functions.

Palavras-chave: Bioinformatics; Method; Microbiome; Next-generation sequencing; QIIME.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000500001

PÉREZ-JARAMILLO, J. E.; MENDES, R.; RAAIJMAKERS, J. M..

Abstract: The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how...

Impacto da domesticação do trigo em sua interação com bactérias benéficas da rizosfera.

Palavras-chave: Rhizosphere microbiome; Plant domestication; Wild relatives; Plant-microbe interactions; Rizosfera; Bactéria; Rhizosphere bacteria; Microbiome; Crops; Domestication.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1042651

Inorganic nitrogen application affects both taxonomical and predicted functional structure of wheat rhizosphere bacterial communities.

CARVALHO, J. C. de; COSTA, L. S. A. S.; CHIARAMONTE, J. B.; ROSSMANN, M.; MENDES, R..

Resumo: O processo de domesticação do trigo, como outras espécies cultivadas, está relacionado à formação de civilizações sedentárias. A domesticação consiste na seleção de caracteres fenotípicos úteis para uso humano. A transição do ambiente natural para sistemas de produção modernos geram diversas mudanças no ambiente que podem acarretar em impactos na microbiota do solo cultivado. As plantas vivem em associação com microrganismos que auxiliam em funções como defesa, saúde e crescimento da planta, e esta associação deve-se a um longo processo de coevolução. Assumindo que existe a dependência dessa microbiota, acredita-se que cultivares modernos perderam algumas características para recrutar microrganismos específicos do hospedeiro durante o processo de...

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: Domesticação de plantas; Microbioma da rizosfera; Interação planta-microbioma; Trigo; Rizosfera; Microbiome; Domestication; Wheat; Soil-plant interactions.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1105014

KAVAMURA, V. N.; HAYAT, R.; CLARK, I. M.; ROSSMANN, M.; MENDES, R.; HIRSCH, P. R.; MAUCHLINE, T. H..

The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks). Phylogenetic and 16S rRNA gene-predicted functional analyses were performed....

Is Malassezia nana the main species in horses’ ear canal microbiome?

Palavras-chave: Nitrogênio inorgânico; Trigo; Fertilizante nitrogenado; Impacto ambiental; Rizosfera; Wheat; Rhizosphere; Microbiome; Nitrogen fertilizers; Environmental impact; Bacterial communities; Functional diversity; Sustainable agricultural intensification.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1105404

BJM

Aldrovandi,Ana Lúcia; Osugui,Lika; Coutinho,Selene Dall’ Acqua.

ABSTRACT The objective of this study was to characterize genotypically Malassezia spp. isolated from the external ear canal of healthy horses. Fifty-five horses, 39 (70.9%) males and 16 (29.1%) females, from different breeds and adults were studied. External ear canals were cleaned and a sterile cotton swab was introduced to collect cerumen. A total of 110 samples were cultured into Dixon medium and were incubated at 32 °C for up to 15 days. Macro- and micromorphology and phenotypic identification were performed. DNA was extracted, strains were submitted to polymerase chain reaction technique, and the products obtained were submitted to Restriction Fragment Length Polymorphism using the restriction enzymes BstCI and HhaI. Strains were sent off to genetic...

Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat.

Palavras-chave: Malassezia nana; Malassezia slooffiae; Microbiome; Horses; Ear canal.

Ano: 2016

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000300770

KAVAMURA, V. N.; ROBINSON, R. J.; HAYAT, R.; CLARK, I. M.; HUGHES, D.; ROSSMANN, M.; HIRSCH, P. R.; MENDES, R.; MAUCHLINE, T. H..

Abstract: Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the...

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling

Palavras-chave: Endosphere; Rizosfera; População Microbiana; Manejo do Solo; Trigo; Semente; Rhizosphere; Microbiome; Wheat; Seeds.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115412

ArchiMer

Dubé, Caroline; Ky, Chin-long; Planes, Serge.

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland,...

Tipo: Text

Palavras-chave: Pearl oyster; Microbiome; Tissue-specific bacterial communities; 16S rRNA gene sequencing; Functional profiling prediction.

Ano: 2019

URL: https://archimer.ifremer.fr/doc/00505/61670/65589.pdf

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.

CAMARGO, A. P.; SOUZA, R. S. C. de; COSTA, P. de B.; GERHARDT, I. R.; DANTE, R. A.; TEODORO, G. S.; ABRAHÃO, A.; LAMBERS, H.; CARAZZOLLE, M. F.; HUNTEMANN, M.; CLUM, A.; FOSTER, B.; FOSTER, B.; ROUX, S.; PALANIAPPAN, K.; VARGHESE, N.; MUKHERJEE, S.; REDDY, T. B. K.; DAUM, C.; COPELAND, A.; CHENM U, M. A.; IVANOVA, N. N.; KYRPIDES, N. C.; PENNACCHIO, C.; ELOE-FADROSH, E. A.; ARRUDA, P.; OLIVEIRA, R. S..

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing...

Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome

Palavras-chave: Microbioma de plantas; Campos rupestres brasileiros; Sequenciamento genético; Condições extremas; Solos; Stressful environments; DNA sequencing; Soils; Microrganismo; Velloziaceae; Microorganisms; Microbiome.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1111238

ArchiMer

Clerissi, Camille; De Lorgeril, Julien; Petton, Bruno; Lucasson, Aude; Escoubas, Jean Michel; Gueguen, Yannick; Dégremont, Lionel; Mitta, Guillaume; Toulza, Eve.

Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from...

Tipo: Text

Palavras-chave: Holobiont; Microbiome; Metabarcoding; Fitness; Bacteria.

Ano: 2020

URL: https://archimer.ifremer.fr/doc/00621/73332/72500.pdf

Mining of the endophytic microbiome for novel biosynthetic genes and antifungal metabolites.

CARRION, V. J.; PÉREZ-JARAMILLO, J.; CORDOVEZ, V.; HOLLANDER, M. de; TRACANNA, V.; MENDES, L. W.; MENDES, R.; MEDEMA, M. H.; RAAIJMAKERS, J. M..

Endophytic microbes have been proposed to contribute to a range of plant support functions, including nutrient acquisition and disease protection. To date, the molecular mechanisms underlying disease protection in the endosphere have only been studied for individual culturable organisms. Here, we conducted a systematic microbiome-wide perspective on the taxonomic diversity and functional potential of the endophytic microbiome of plants grown in an agricultural soil that is naturally suppressive to damping-off disease caused by the fungal root pathogen Rhizoctonia solani. Metagenomic analyses showed an enrichment of Burkholderiaceae, Chitinophagaceae and Xanthomonadaceae in the endosphere of plants grown in disease-suppressive soil challenged with the...

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach.

Palavras-chave: Microbiome; Antifungal agents; Metagenomics.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1103500

SOUZA, R. C.; CANTAO, M. E.; NOGUEIRA, M. A.; VASCONCELOS, A. T. R.; HUNGRIA, M..

Abstract: The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the...

Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Palavras-chave: Metagenome; Manejo do Solo; Plantio Direto; Microbiologia do Solo; Soil management; Soil enzymes; No-tillage; Metagenomics; Microbiome.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1100838

BJM

Souza,Renata Carolini; Cantão,Maurício Egídio; Nogueira,Marco Antonio; Vasconcelos,Ana Tereza Ribeiro; Hungria,Mariangela.

ABSTRACT The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the...

Physiological adaptations of ruminants and their potential relevance for production systems

Palavras-chave: Metagenome; Microbiome; Soil enzymes; Soil management; No-tillage.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000400723

R. Bras. Zootec.

Clauss,Marcus; Hummel,Jürgen.

ABSTRACT Herbivores face the dilemma that the level of feed intake is negatively related to factors that determine digestive efficiency, such as thoroughness of ingesta comminution by chewing, and retention of digesta in the digestive tract. Ruminants have evolved particular adaptations to solve this dilemma. Most ruminants share the characteristic of “digesta washing”: fluid moves through their digestive tract faster than particles, thus effectively washing very fine particles, such as bacteria, out of the digesta plug. As the forestomach is followed by auto-enzymatic digestion, this allows a continuous, increased harvest of microbes from the forestomach. True rumination only evolved twice, in the camelids and the true ruminants. These both evolved a...

Presence of Enterobacteriaceae and Clostridiaceae in thte soil according to the use of biofertilizers of feces from goats and sheep.

Palavras-chave: Cattle; Digesta washing; Foregut fermenter; Microbial harvest; Microbiome.

Ano: 2017

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982017000700606

ROSA, D. S.; OLIVEIRA, J. F. da S.; COSTA, M. M. da; MELO, A. M. Y. de; GOUVEIA, J. J. de S.; MALAGO JUNIOR, W.; REGITANO, L. C. de A.; GOUVEIA, G. V..

The use of biofertilizers appears as an alternative to the use of chemical fertilizers and use of residues generated by animal production. However, the presence of possible pathogens belonging to the families Enterobacteriaceae and Clostridiaceae in biofertilizers from feces can lead to sanitary and ecological problems.

Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome.

Palavras-chave: Inoculant; RRNA 16S; Bioinformatics; Microbiome.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1118441

MENDES, L. W.; CHAVES, M. G. de; FONSECA, M. de C.; MENDES, R.; RAAIJMAKERS, J. M.; TSAI, S. M..

Abstract: The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher...