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The rhizosphere microbiome plays a key role in plant protection against soil-borne pathogens. Plant breeding for resistance against soil-borne pathogens can alter the rhizosphere microbiome. However, most studies have focused on bacterial and fungal communities, leaving the role of the virus and viroids unassessed. Here, we tested the influence of resistance breeding on the composition of rhizosphere viruses and viroids. By analyzing metatranscriptomes from the rhizosphere of common bean (Phaseolus vulgaris) cultivars with varying resistance to the soil-borne pathogen Fusarium oxysporum, we recovered sequences representing 78 and 23 novel populations of viruses and viroids, respectively. We compared the abundances of these infectious agents across the different cultivars and found that the Fusarium-resistant cultivar harbored >1.2 times more viroids and a more different composition of viroids and viruses than less resistant plants. Given their role in interfering with host metabolism and their potential influence on plant-fungi associations, our study suggests that changes in the rhizosphere infectome are an important consideration in breeding for resistance against soil-borne pathogens.

This study focused on the effects of vinasse (V), a by-product of the sugar-ethanol industry, combined with mineral nitrogen fertilizer (N) and straw retention on the fungal community diversity, composition, and structure in a sugarcane-cultivated soil. The experiment consisted of a combination of V, mineral N and sugarcane-straw blanket. Soil samples were collected at 7, 157, and 217 days after planting, corresponding to maximum carbon dioxide emissions from soil after three repeated applications of fertilizers into the soil. Across 57 soil metagenomics datasets, it was revealed that the application the V in combination with N fertilizer and straw retention decreased the diversity, evenness and richness of fungi at the community level in soil. Analysis of the soil fungal community composition based on the 20 genera most abundant revealed decrease for Blastomyces, Melampsora, and Penicillium after the third application of V in combination with N fertilizer and straw blanket. An opposite response was revealed for Amauroascus, Cantharellus, Chrysosporium, Clavaria, Morchella, Puccinia, and Tuber in soil under this treatment. Shifts in fungal community composition were followed by increases in mycorrhizal and decomposers soil-borne fungi and decrease in potentially pathogenic fungi, but not by changes in community structure. Based on these results, it is possible to attest that repeated applications of V in combination with N fertilizer and sugarcane-straw blankets affect ecological aspects of the soil fungal community composition and potential functions played by fungi in sugarcane soil, which are essentials to ecosystem function and sustainable management of agricultural ecosystems.

O projeto foi desenvolvido na Embrapa Pecuária Sudeste (São Carlos/SP) e dividido em duas etapas. A primeira etapa consistiu em um experimento em campo, onde avaliou-se a influência da inoculação com rizóbios específicos, não específicos e fertilização nitrogenada no desenvolvimento inicial de duas linhagens de guandu. Os tratamentos foram representados por inoculação de sementes com estirpes de Bradyrhizobium SEMIA 6156, recomendada para guandu; estirpes de Bradyrhizobium SEMIA 5079 5080, recomendada para cultura da soja; fertilização nitrogenada na dose de 50 kg.ha-1 N; e tratamento testemunha, aplicados na linhagem g6-95 e cultivar BRS Mandarim. As plantas foram colhidas aos 40 dias após emergência, e avaliadas quanto aos parâmetros de crescimento e acúmulo de N na parte aérea. A segunda etapa foi representada por um experimento em casa de vegetação, com objetivo de avaliar as características relacionadas ao desenvolvimento vegetativo de duas linhagens de guandu sob influência de inoculação com rizóbios específicos, não específicos e doses de adubação nitrogenada combinadas ou não com a inoculação, e seus efeitos sobre a abundância de micro-organismos rizosféricos. Os tratamentos consistiram em duas linhagens de guandu, inoculadas com estirpes SEMIA 6156; estirpes SEMIA 5079 5080; doses de 10 kg.ha-1 N combinadas aos inoculantes; fertilização nitrogenada na dose de 50 kg.ha-1 N; e tratamento testemunha. As plantas foram avaliadas aos 90 dias após emergência, e avaliadas quanto aos parâmetros de crescimento e nodulação. Os resultados demonstraram que não houve diferença entre as linhagens e estirpes avaliadas, indicando as plantas inoculadas com SEMIA 5079 5080, produzem tanto quanto as plantas inoculadas com rizóbio específico, e em condições de campo produzem o equivalente àquelas adubadas com fertilizante nitrogenado. O uso de 10 kg.ha-1 N nas plantas inoculadas possibilitou maior produção de massa seca e melhorou os teores de N da parte aérea. A cultivar BRS Mandarim, apresentou maior nodulação que a linhagem g6-95, no entanto se mostrou menos eficiente na absorção de N, o que pode estar relacionado aos diferentes padrões de exsudação radicular e interações com microbiota do solo rizosférico. No geral, o guandu apresentou baixa especificidade, resultando em índices de eficiência simbiótica elevada mesmo em solos sem inoculação. The project was developed at Embrapa South-East Cattle Research Center (São Carlos, SP, Brazil) and divided into two experiments. The first experiment consisted of a field experiment, where the influence of inoculation with specific and non-specific rhizobia and nitrogen fertilization on the initial development of two pigeonpea lines was evaluated. The treatments were represented by seed inoculation with Bradyrhizobium strains SEMIA 6156, recommended for pigeon pea; Bradyrhizobium strains SEMIA 5079 5080, recommended for soybean cultivation; nitrogen fertilization at a rate of 50 kg.ha-1 of N; and control treatment, applied to line g6-95 and BRS Mandarim. The plants were harvested 40 days after emergence and evaluated for growth parameters and shoot N accumulation. The second experiment was conducted in a greenhouse, with the objective of evaluating the characteristics related to the vegetative development of two pigeon pea lines under the influence of inoculation with specific and non-specific rhizobia, and nitrogen fertilization rates combined or not with inoculation and its effects on the abundance of rhizospheric microorganisms. The treatments consisted of two pigeon pea lines, inoculated with Bradyrhizobium strains SEMIA 6156; Bradyrhizobium strains SEMIA 5079 5080; nitrogen fertilization at a rate of 10 kg.ha-1 N combined with inoculants; nitrogen fertilization at a rate of 50 kg.ha-1 of N; and control treatment. The plants were evaluated 90 days after emergence and evaluated for growth and nodulation parameters. The results showed that there was no difference between the tested lines and strains evaluated, indicating that plants inoculated with SEMIA 5079 5080 produce as much as plants inoculated with specific rhizobia, and under field conditions they produce the equivalent of those fertilized with nitrogen fertilizer. The use of 10 kg.ha-1 of N in the inoculated plants allowed increase of production of dry mass and better levels of N in the shoot. The BRS Mandarim showed higher nodulation than line g6-95, but was less efficient in N uptake, which may be related to different patterns of root exudation and interactions with the rhizospheric soil organisms. In general, pigeonpea had low specificity, resulting in high rates of symbiotic efficiency even in soils without inoculation.

Soil microbiome is essential for providing ecosystem services. The relationship between microbial diversity and ecosystem services is well elucidated for soil microbiome collective functions (i.e. organic matter decomposition and carbon assimilation). However, this relationship remains poorly understood for more specific functions (pesticides and o other xenobiotics degradation). Here, the dilution-to-extinction approach, radiorespirometry and high-throughput sequencing of 16S rRNA gene were used to assess the role of bacterial diversity depletion in the dissipation of antibiotic sulfadiazine (SDZ) and herbicide atrazine (ATZ), which are widely used in pig farming and agriculture, respectively. SDZ microcosm was assembled using paralel soils without (S1) and with (S2) a long-term of swine manure application. While the ATZ microcosm was assembled using Pasture Soil (GS, without long- term of ATZ application) and Cultivated Soil (CS, with long-term of ATZ application). Swine manure application promoted increases in pH and organic carbon and macronutrient contents, as well as impacted the soil bacterial community structure and diversity. The bacterial diversity depletion reduced SDZ mineralization (14C-CO2) and non-extractable residue (NER) formation, but NER recovered after 42 d of incubation. Surprisingly, the non-manured soil ( treatment NS- S1) had a faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a large number of bacterial families involved in the main SDZ dissipation pathways (14C-CO2 and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae and Sphingobacteriaceae. Similarly, land use and the long-term of atrazine application promoted changes in the soil physico-chemical attributes, bacterial community structure, diversity and composition, as well as in its capacity to dissipate atrazine. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes and Gemmatimonadetes were the dominant phyla in both soils (GS and CS). Atrazine minerazation was reduced by 12-fold when compared to the worst scenarios of bacterial diversity depletion. Long-term atrazine application resulted in greater bacterial community efficiency in herbicide dissipation. Bacterial diversity depletion reflected in the reduction of complexity, classification of species (specialists, generalists and very rare), in addition to increases in the abundance of functions related to obtaining energy and nitrogen transformations. Twelve bacterial genera (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 and Crenobacter) correlated with atrazine mineralization, suggesting the selection of these genera as potential atrazine degraders. The NER formation was the SDZ primary dissipation route and had the greatest impact of the bacterial diversity depletion. While mineralization was the ATZ primary dissipation route in cultivated soil (CS). The bacterial diversity depletion resulted in simplified bacterial communities, greater imbalance in the niches occupation, as well as higher abundance of functions associated with obtaining energy. O microbioma do solo é essencial para o fornecimento de serviços ecossistêmicos. A relação entre diversidade microbiana e serviços ecossistêmicos é bem elucidada para funções coletivas do microbioma do solo (decomposição de matéria orgânica e assimilação de carbono). Contudo, esta relação ainda permanece pouco elucidada para funções mais específicas (degradação de pesticidas e outros xenobióticos). Aqui, foram utilizadas a abordagem da diluição para extinção, a radiorespirometria e o sequenciamento alto rendimento do gene 16S rRNA para avaliar o papel da depleção da diversidade bacteriana na dissipação do antibiótico sulfadiazina (SDZ) e herbicida atrazina (ATZ), que são amplamente usados na suinocultura e agricultura, respectivamente. O microcosmo da SDZ foi montado utilizando solos sem (S1) e com histórico de aplicação de esterco suíno (S2). Enquanto o microcosmo da ATZ foi montado usando Solo de Pastagem (GS, sem histórico de aplicação de ATZ) e Solo Cultivado (CS, com histórico de aplicação de ATZ). A aplicação de esterco promoveu aumentos no pH e nos teores de carbono orgânico e macronutrientes, bem como impactou a estrutura e diversidade da comunidade bacteriana do solo. A depleção da diversidade bacteriana reduziu a mineralização da SDZ (14C-CO2) e a formação de resíduo não extraível (NER), mas o NER se recuperou após 42 d de incubação. Surpreendentemente, o solo natural não adubado (NS-S1) apresentou taxa de dissipação da SDZ mais rápida (DT90 = 2.0 versus 21 d) e teve um grande número de famílias bacterianas envolvidas nas principais vias de dissipação da SDZ (14C-CO2 e principalmente NER), tais como Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae e Sphingobacteriaceae. De forma similar, o uso da terra e longo período de aplicação da atrazina promoveu mudanças nos atributos físicos e químicos do solo, na estrutura, diversidade e composição da comunidade bacteriana, bem como em sua capacidade para dissipar a atrazina. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes e Gemmatimonadetes foram os filos dominantes ambos os solos (GS e CS). A mineralização da atrazina foi reduzida em 12 vezes quando comparada aos piores cenários de perda da diversidade bacteriana. O longo histórico de aplicação de atrazina resultou em maior eficiência da comunidade bacteriana na dissipação do herbicida. A perda da diversidade bacteriana refletiu na redução da complexidade, classificação das espécies (especialistas, generalistas e muito raras), além de aumentos na abundância de funções relacionadas à obtenção de transformações de energia e nitrogênio. Doze gêneros bacterianos (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 e Crenobacter) se correlacionaram com a mineralização da atrazina, sugerindo a seleção desses gêneros como potenciais degradadores de atrazina. A formação de NER foi a rota primária de dissipação da SDZ e com maior impacto da depleção da diversidade bacteriana. Enquanto a mineralização foi a rota primária de dissipação da ATZ no solo cultivado (CS). A perda da diversidade bacteriana resultou em comunidades bacterianas simplificadas, maior desbalanço na ocupação de nichos, bem como maior abundância de funções associadas obtenção de energia.