ABSTRACT The nature of the soil is shaped by the presence of roots and the soil microbiota. Bacteria, archaea and fungi profoundly alter plant growth and, in turn, depend on root exudation of carbon-rich and energy-yielding compounds. The microbial communities act as facilitators of plant processes by secreting plant growth regulators, solubilizing minerals, providing N for plant growth, altering plant immune responses and competing with plant pathogens. Characterizing and engineering the processes driven by the multiple microbial taxa that make up a “plant growth-promoting soil” represents an ecologically friendly solution that may lead to unprecedented increases in agronomic efficiency. This review outlines the characteristics of soil-plant-microbiota interactions that would lead to enhanced plant growth and the importance of characterizing the soil microbial communities with metabarcoding and shotgun metagenomics allied to machine learning analytics. Although much is still needed to be understood about soil microbial ecology, it is possible to choose the best soil management practices to take advantage of beneficial microbial activity with our current knowledge.

Resumo Neste estudo, avaliou-se a qualidade da água e do sedimento de amostras coletadas em diferentes pontos de arrozais orgânicos (O1, O2, O3 e O4) e convencionais (C1, C2 e C3) pré-germinados em Viamão/RS. Indicadores de qualidade como fósforo, oxigênio dissolvido, manganês, ferro, turbidez e DBO5 reduziram a qualidade da água além das classes 3 e 4, conforme definido pela Resolução CONAMA 357/2005. Com base nos níveis de alumínio, as amostras de água coletadas em todos os pontos foram categorizadas como classe 4; além disso, o IQA classificou a qualidade das amostras de água dos pontos O4 e C1 como "ruim". A relação DQO/DBO foi alta, demonstrando que a fração biodegradável era consideravelmente baixa. A condutividade da água nos pontos O4, C1, C2 e C3, ultrapassou 100 µS/cm, conforme definido pela CETESB, indicativo de ambientes impactados. Os teores de zinco em C1 e níquel em O2, C2 e C3 no sedimento superaram os valores de referência de qualidade estabelecidos pela Portaria FEPAM 85/2014. De maneira geral, a mais baixa qualidade da água foi observada nas amostras coletadas nos pontos O2 e O4, e a mais baixa qualidade do sedimento foi observada nas amostras coletadas em todos os pontos nos arrozais convencionais e no ponto O2 nos arrozais orgânicos.

Abstract This study evaluated the water and sediment quality of samples collected from different points in organic (O1, O2, O3, and O4) and conventional (C1, C2, and C3) pre-germinated rice fields located in Viamão/RS. Quality indicators such as phosphorus, dissolved oxygen, manganese, iron, turbidity, and BOD5 reduced water quality beyond Classes 3 and 4, as defined by CONAMA Resolution 357/2005. Based on the aluminum levels, the water samples collected from all the points were categorized as Class 4; furthermore, the IQA classified the quality of water samples from Points O4 and C1 as “bad.” The COD/BOD ratio was high, demonstrating that the biodegradable fraction was considerably low. The conductivity of water at points O4, C1, C2, and C3, exceeded 100 µS/cm, as defined by CETESB, indicating impacted environments. The levels of zinc in C1 and nickel in O2, C2, and C3 in the sediment exceeded the quality reference values established by the FEPAM Ordinance 85/2014. In general, the lowest water quality was observed in the samples collected from Points O2 and O4, and the lowest sediment quality was observed in the samples collected from all points in the conventional rice fields and from Point O2 in the organic rice field.

Abstract In the pursuit of sustainable agriculture, bioinoculants usage as providers of a crop's needs is a method to limit environmental damage. In this study, a collection of cultivable putative plant growth promoting (PGP) bacteria associated with wheat crops was obtained and this bacterial sample was characterized in relation to the functional diversity of certain PGP features. The isolates were obtained through classical cultivation methods, identified by partial 16S rRNA gene sequencing and characterized for PGP traits of interest. Functional diversity characterization was performed using Categorical Principal Component Analysis (CatPCA) and Multiple Correspondence Analysis (MCA). The most abundant genera found among the 346 isolates were Pseudomonas, Burkholderia, and Enterobacter. Occurrence of PGP traits was affected by genus, niche, and sampling site. A large number of genera grouped together with the ability to produce indolic compounds; phosphate solubilization and siderophores production formed a second group related to fewer genera, in which the genus Burkholderia has a great importance. The results obtained may help future studies aiming prospection of putative plant growth promoting bacteria regarding the desired organism and PGP trait.

The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.

O manejo, em termos de preparo e sistemas de culturas, exerce forte influência sobre as propriedades do solo; e essas, por sua vez, condicionam o seu potencial supressivo a doenças de plantas. Nesse contexto, a fungistase é um dos componentes da supressividade, sendo um processo mediado pela microbiota do solo. Este trabalho teve como objetivo avaliar a influência de diferentes sistemas de manejo sobre a fungistase ao fungo fitopatogênico Fusarium graminearum, a sua relação com o perfil bacteriano do solo e os possíveis mecanismos de ação envolvidos no processo. As avaliações foram realizadas a partir de amostras de um Argissolo Vermelho distrófico, coletadas em um experimento de manejo de longa duração, conduzido sob plantio direto e preparo convencional e cultivado com os sistemas de culturas aveia + vica/milho + caupi, vica/milho e aveia/milho. A fungistase do solo foi avaliada em termos de redução do crescimento radial do fungo testado. O perfil bacteriano foi avaliado pelo polimorfismo do espaço intergênico do 16S rRNA (RISA). Foram obtidos 120 isolados bacterianos, que foram avaliados quanto à antibiose e à produção de compostos voláteis e de sideróforos. As amostras provenientes de plantio direto apresentaram maior fungistase a F. graminearum, reduzindo acentuadamente o desenvolvimento do patógeno. Também foi observada maior inibição do patógeno nas amostras de solo cultivadas sob o sistema aveia + vica/milho + caupi, enquanto o sistema aveia/milho foi o menos antagonista. O perfil genético bacteriano do solo também foi influenciado pelos sistemas de manejo, havendo semelhança entre os sistemas mais antagonistas. Embora não tenha sido identificada uma relação entre os sistemas de manejo e as características dos isolados, pode-se concluir que a antibiose e a produção de sideróforos foram os mecanismos que mais contribuíram para a fungistase.

Soil management, in terms of tillage and cropping systems, strongly influences the biological properties of soil involved in the suppression of plant diseases. Fungistasis mediated by soil microbiota is an important component of disease-suppressive soils. We evaluated the influence of different management systems on fungistasis against Fusarium graminearum, the relationship of fungistasis to the bacterial profile of the soil, and the possible mechanisms involved in this process. Samples were taken from a long-term experiment set up in a Paleudult soil under conventional tillage or no-tillage management and three cropping systems: black oat (Avena strigose L.) + vetch (Vicia sativa L.)/maize (Zea mays L.) + cowpea (Vigna sinensis L.), black oat/maize, and vetch/maize. Soil fungistasis was evaluated in terms of reduction of radial growth of F. graminearum, and bacterial diversity was assessed using ribosomal intergenic spacer analysis (RISA). A total of 120 bacterial isolates were obtained and evaluated for antibiosis, and production of volatile compounds and siderophores. No-tillage soil samples showed the highest level of F. graminearum fungistasis by sharply reducing the development of this pathogen. Of the cropping systems tested, the vetch + black oat/maize + cowpea system showed the highest fungistasis and the oat/maize system showed the lowest. The management system also affected the genetic profile of the bacteria isolated, with the systems from fungistatic soils showing greater similarity. Although there was no clear relationship between soil management and the characteristics of the bacterial isolates, we may conclude that antibiosis and the production of siderophores were the main mechanisms accounting for fungistasis.

Microrganismos que habitam o interior e a superfície podem fornecer substancias essenciais ao crescimento das plantas, como fitormônios e nutrientes essenciais. O presente trabalho teve como objetivo isolar e caracterizar as bactérias da filosfera, do ambiente endofítico e a água de tanque associadas à Vriesea gigantea e Tillandsia aeranthos. As bactérias foram submetidas a testes de verificação de produção de sideróforos e de ácido indol acético (AIA), solubilização de fosfatos, e a presença do gene nif H. A diversidade genética dos isolados bacterianos foi analisada por rep-PCR. Sessenta e oito microrganismos foram isolados de 3 microambientes distintos de V. gigantea e de 2 microambientes de T. aeranthos. A maioria das bactérias isoladas foram bacilos formadores de esporos, gram-positivos. Todos os isolados produziram AIA in vitro na presença de quantidades pequenas de triptofano. Mais de 70% das bactérias analisadas produziram sideróforos, solubilizaram fosfatos e possuíam o gene nif H. Não foi possível distinguir grupos definidos de microrganismos baseados no microhabitat e na espécie de bromélia de onde foram isolados usando rep-PCR. A água do tanque apresentou maior diversidade microbiana quando comparada com a filosfera e o ambiente endofítico, provavelmente devido à alta concentração de nutrientes, que promove um ambiente favorável para o desenvolvimento de comunidades microbianas complexas.

Microorganisms that live inside and around a plant can supply it with essential substances, such as phytohormones and essential nutrients. The present investigation aimed to isolate and characterize the phyllosphere, the endophytic, and the water tank bacteria associated with Vriesea gigantea and Tillandsia aeranthos. The bacteria were tested for siderophore and indole-3-acetic acid (IAA) production, phosphate solubilization, and presence of the nif H gene. Genetic diversity of the bacterial isolates was evaluated by rep-PCR. Sixty-eight bacterial strains were isolated from 3 different microhabitats of V. gigantea and from 2 microhabitats of T. aeranthos bromeliad plants. Gram-positive, spore-forming bacilli comprised most bacterial isolates. All isolates produced IAA in vitro in presence of very low amounts of tryptophan. More than 70% of the evaluated bacteria presented the ability of siderophore production and phosphate solubilization, and possessed the nif H gene. It was not possible to distinguish well-defined groups of isolates based on the bromeliad species and microhabitat they inhabit using genetic characterization by rep-PCR. Water tanks presented the most abundant diversity compared with phyllosphere and endophytes, probably due to the high nutrient concentration, which promotes an ideal environment for complex microbial communities.

Bacteria that colonize plant roots and promote plant growth are referred to as plant growth-promoting rhizobacteria (PGPR). PGPR are highly diverse and in this review we focus on rhizobacteria as biocontrol agents. Their effects can occur via local antagonism to soil-borne pathogens or by induction of systemic resistance against pathogens throughout the entire plant. Several substances produced by antagonistic rhizobacteria have been related to pathogen control and indirect promotion of growth in many plants, such as siderophores and antibiotics. Induced systemic resistance (ISR) in plants resembles pathogen-induced systemic acquired resistance (SAR) under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. Both types of induced resistance render uninfected plant parts more resistant to pathogens in several plant species. Rhizobacteria induce resistance through the salicylic acid-dependent SAR pathway, or require jasmonic acid and ethylene perception from the plant for ISR. Rhizobacteria belonging to the genera Pseudomonas and Bacillus are well known for their antagonistic effects and their ability to trigger ISR. Resistance-inducing and antagonistic rhizobacteria might be useful in formulating new inoculants with combinations of different mechanisms of action, leading to a more efficient use for biocontrol strategies to improve cropping systems.

Duas linhagens bacterianas que apresentaram amplificação de parte do gene nifH, RP1p e RP2p, pertencentes aos gêneros Enterobacter e Serratia, foram isoladas do rizoplano de Lupinus albescens. Essas bactérias são Gram-negativas, com formato de bastonete, móveis, anaeróbias facultativas e apresentam multiplicação rápida, com colônias alcançando diâmetros de 3-4 mm em 24 h de incubação a 28 ºC. RP1p e RP2p também foram capazes de multiplicação em temperaturas elevadas, como 40 ºC, na presença de alta concentração de NaCl (2-3 % v/v) e em valores de pH que variaram de 4 a 10. A linhagem RP1p foi capaz de utilizar 10 das 14 fontes de carbono avaliadas, enquanto a linhagem RP2p utilizou nove. Os isolados produziram sideróforos e compostos indólicos, mas foram incapazes de solubilizar fosfatos. A inoculação de L. albescens com as linhagens RP1p e RP2p resultou em aumento significativo do peso das plantas secas, o que demonstra que essas bactérias apresentam propriedades que favorecem o crescimento vegetal.

Two bacterial strains that amplified part of the nifH gene, RP1p and RP2p, belonging to the genus Enterobacter and Serratia, were isolated from the rhizoplane of Lupinus albescens. These bacteria are Gram-negative, rod-shaped, motile, facultative anaerobic, and fast-growing; the colonies reach diameters of 3-4 mm within 24 h of incubation at 28 ºC. The bacteria were also able to grow at temperatures as high as 40 ºC, in the presence of high (2-3 % w/v) NaCl concentrations and pH 4 -10. Strain RP1p was able to utilize 10 of 14 C sources, while RP2p utilized nine. The isolates produced siderophores and indolic compounds, but none of them was able to solubilize phosphate. Inoculation of L. albescens with RP1p and RP2p strains resulted in a significant increase in plant dry matter, indicating the plant-growth-promoting abilities of these bacteria.

Nas últimas décadas, o uso de rizobactérias promotoras de crescimento de plantas tem se mostrado uma alternativa para aumentar a produção vegetal. Rhizobium leguminosarum biovar trifolii está entre as mais promissoras rizobactérias e tem sido usada também em não leguminosas. O presente trabalho analisou in vitro a ocorrência de características de promoção de crescimento vegetal em isolados de R. leguminosarum biovar trifolii nativos de solos do Rio Grande do Sul. Os isolados foram obtidos de 11 localidades e avaliados quanto à produção de ácido indolacético, produção de sideróforos e solubilização de fosfato. Dez isolados foram também caracterizados molecularmente e testados com relação a antagonismo a um fungo fitopatogênico e promoção de crescimento em plântulas de arroz. De um total de 252 isolados, 59 produziram ácido indolacético, 20 produziram sideróforos e 107 solubilizaram fosfato. Todos os isolados apresentaram algum grau de antagonismo a Verticillium sp., reduzindo o crescimento micelial em meio líquido. O isolado AGR-3 destacou-se por aumentar o crescimento radicular das plântulas de arroz, enquanto o isolado ELD-18, além de aumentar o comprimento das raízes em comparação com o controle não inoculado, também aumentou o índice de velocidade de germinação, o comprimento da parte aérea e a massa das plântulas secas. Esses resultados confirmam o potencial de R. leguminosarum biovar trifolii como rizobactéria promotora de crescimento de plantas.

In the last decades, the use of plant growth-promoting rhizobacteria has become an alternative to improve crop production. Rhizobium leguminosarum biovar trifolii is one of the most promising rhizobacteria and is even used with non-legume plants. This study investigated in vitro the occurrence of plant growth-promoting characteristics in several indigenous R. leguminosarum biovar trifolii isolated from soils in the State of Rio Grande do Sul, Brazil. Isolates were obtained at 11 locations and evaluated for indoleacetic acid and siderophore production and inorganic phosphate solubilization. Ten isolates were also molecularly characterized and tested for antagonism against a phytopathogenic fungus and for plant growth promotion of rice seedlings. Of a total of 252 isolates, 59 produced indoleacetic acid, 20 produced siderophores and 107 solubilized phosphate. Some degree of antagonism against Verticillium sp. was observed in all tested isolates, reducing mycelial growth in culture broth. Isolate AGR-3 stood out for increasing root length of rice seedlings, while isolate ELD-18, besides increasing root length in comparison to the uninoculated control, also increased the germination speed index, shoot length, and seedling dry weight. These results confirm the potential of some strains of R. leguminosarum biovar trifolii as plant growth-promoting rhizobacteria.