Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.

Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.

Tolerance and reduction of chromium by bacterial strains.

Bacteria have potential to tolerate and reduce metals. This study evaluated the potential of selected bacterial strains in tolerating and reducing chromium (Cr). Six bacterial strains (Rhizobium miluonense LCC01, LCC04, LCC05, and LCC69; Rhizobium pusense LCC43; and Agrobacterium deltaense LCC50) showed tolerance to Cr(VI) (16 and 32 µg mL-1), reduction potential of Cr(VI) (from 50 to 80%), and efficiency in producing exopolysaccharides. Rhizobium pusense LCC43 exhibited the highest tolerance (128 µg mL-1), reduction potential of Cr(VI) (from 80 to 100%), and efficiency in producing exopolysaccharides. These results suggested that this strain may have the potential to be used in the bioremediation of soils contaminated with Cr(VI).

Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere.

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.

Isolation and Characterization of Plant Growth-Promotion Diazotrophic Endophytic Bacteria Associated to Sugarcane (Saccharum officinarum L.) Grown in Paraíba, Brazil

Abstract: Sugarcane is an important Brazilian commodity, being usually cultivated in soils with low natural fertility. This study aimed to isolate diazotrophic endophytes from sugarcane tissues and evaluate the morphological and physiological characteristics of their colonies as well as their plant growth-promoting (PGP) traits in select diazotrophic endophytic bacteria. Fifty-six bacterial isolates were identified in the sugarcane tissues, and these isolates presented distinct morphological and physiological traits. A total of thirty-five bacterial isolates were biochemically evaluated. Overall, Bacillus was the dominant genus. Isolates of Methylobacterium spp. and Brevibacillus agri were present only in leaves, while Herbaspirillum seropedicae occurred only in stems. Except to IPA-CF45A, all isolates were nitrogenase positive. All endophytes exhibit production of indol 3-acetic acid. Over 50% of endophytes solubilize phosphate, release N-acyl homoserine lactones, and present the activity of 1-aminocyclopropane-1-carboxylic acid deaminase, catalase, lipase and protease. The network analysis showed that isolates belonged to Burkholderia, Herbaspirillum, and Methylobacterium interact with Bacillus. Bacterial endophytes exhibited distinct morphological, physiological, and PGP traits that are useful for sustainable agriculture, highlighting the isolates IPA-CC33, IPA-CF65, IPA-CC9 and IPA-CF27. Further studies on the effects of these diazotrophic endophytes and their potential for providing microbial inoculants for improving sugarcane fields will provide valuable information to maintain the sustainability and environment quality.

Dynamics of bacterial and archaeal communities along the composting of tannery sludge.

The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil.

Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

Inoculation of arbuscular mycorrhizal fungi as a strategy to improve annatto (Bixa orellana L. ) growth

This study aimed to assess the occurrence of arbuscular mycorrhizal fungi (AMF) in annatto (Bixa orellana L.) cultivars and their response to AMF inoculation using biometric parameters. The occurrence surveys were conducted in annatto fields in three municipalities from Pernambuco Forest Zone: Lagoa de Itaenga, Gloria de Goitá, and Vitoria de Santo Antão, and in four cultivars (Red Piave, Green Piave, Red Peruvian Paulista, and Green Peruvian Paulista). In a greenhouse, biometric parameters of annatto seedlings of Red Piave, Red Peruvian Paulista, Embrapa-36, and Embrapa-37 cultivars inoculated with AMF isolated from annatto fields. The Red Piave cultivar exhibited greater root colonization than the Green Peruvian Paulista in the Lagoa de Itaenga and Vitoria de Santo Antão municipalities. The cultivar Red Piave showed a more beneficial association with AMF in plants and soil than cultivar Green Peruvian Paulista did, in both Lagoa de Itaenga and Vitoria de Santo Antão. AMF inoculation was effective in promoting the growth of annatto plants, particularly those inoculants with S. heterogama and C. etunicatum.

Responses of soil microbial biomass and enzyme activity to herbicides imazethapyr and flumioxazin.

The use of herbicides is important for controlling weeds in crops. However, they can present impacts on soil properties, such as biological properties. In this study, we evaluated the responses of soil microbial biomass and enzymes activity to the application of the herbicides imazethapyr and flumioxazin and their mixture in an experiment under laboratory conditions, using soils with a different history of use. Soil microbial biomass C (MBC) decreased, while microbial biomass N (MBN) was not affected after the application of the herbicides as compared to the control. Soil respiration, respiratory quotient, and dehydrogenase (DHA) activity increased significantly after the application of the herbicides compared to the control. The hydrolysis of fluorescein diacetate (FDA) was not significantly different between the control and the herbicide treatments. The principal response curve showed the largest initial effects for the flumioxazin, followed by imazethapyr and their mixture. Flumioxazin had a different influence on soil respiration and respiratory quotient than imazethapyr and their mixture. Finally, the effects of herbicides on soil microbial biomass and enzymes are short-term as we observed recovery in the biological parameters over time.

Dynamics of archaeal community in soil with application of composted tannery sludge.

Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7th year by using different rates (0, 2.5, 5, 10 and 20 ton ha-1). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.

Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado.

Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.

Less abundant bacterial groups are more affected than the most abundant groups in composted tannery sludge-treated soil.

The application of composted tannery sludge (CTS) has promoted shifts in soil chemical properties and, therefore, can affect the soil bacterial community. This study assessed the effect of the CTS on the soil bacterial community over time. The CTS was applied at five rates (0, 2.5, 5, 10 and 20 t/ha), and the bacterial community was evaluated for 180 days. The principal curve response (PRC) analysis showed that the most abundant phyla were not influenced by the CTS rates over time, while the analysis of the bacterial community showed that some of the less abundant phyla were influenced by the CTS rates. Similarly, the PRC analysis for the bacterial classes showed the significant effect of the CTS rates. The redundancy analyses for the bacterial phyla and classes showed the relationship between the significant chemical properties and the bacterial community of the soil after the CTS amendment over time. Therefore, there was a shift in the bacterial community over time with the application of the composted tannery sludge. Our study has shown that the less abundant bacterial groups were more influenced by the CTS than the most abundant bacterial groups and that these bacterial groups were driven by soil chemical properties, primarily chromium (Cr) and the soil pH.

Bacillus subtilis improves maize tolerance to salinity / Bacillus subtilis melhora a tolerância do milho a salinidade

ABSTRACT: The aim of this study was to evaluate the biochemical responses of maize, under saline stress, inoculated with Bacillus subtilis. Four levels of salinity were assessed: 0mM, 50mM, 100mM, and 200mM of sodium chloride (NaCl). Saline conditions influenced negatively maize growth. However, the inoculation of B. subtilis improved the plant growth at highest level of NaCl. Chlorophyll content decreased while proline increased in inoculated plants submitted to highest salt levels. Also, B. subtilis increased the relative water content in leaves. B. subtilis improves the plant growth under salinity and ameliorates the biochemical damages in maize.

RESUMO: O objetivo do estudo foi avaliar a resposta bioquímica do milho, sob stresse salino, inoculado com Bacillus subtilis. Quatro níveis de salinidade foram avaliados: 0mM, 50mM, 100mM e 200mM de cloreto de sódio (NaCl). Condições salinas influenciaram negativamente o crescimento do milho. Entretanto, a inoculação com B. subtilis melhorou o crescimento das plantas no maior nível de NaCl. O teor de clorofila decresceu enquanto que a prolina aumentou em plantas submetidas aos níveis salinos e inoculadas com B. subtilis. B. subtilis também aumentou o conteúdo de agua foliar. A inoculação com B. subtilis promove melhor crescimento das plantas sob salinidade e atenua os danos bioquímicos no milho.

Interrelationship of Bradyrhizobium sp. and plant growth-promoting bacteria in cowpea: survival and symbiotic performance.

The objective of this study was to evaluate the survival of cowpea during bacterial colonization and evaluate the interrelationship of the Bradyrhizobium sp. and plant growth-promoting bacteria (PGPB) as a potential method for optimizing symbiotic performance and cowpea development. Two experiments using the model legume cowpea cv. "IPA 206" were conducted. In the first experiment, cowpea seeds were disinfected, germinated and transferred to sterilized Gibson tubes containing a nitrogen-free nutritive solution. The experimental design was randomized blocks with 24 treatments [Bradyrhizobium sp. (BR 3267); 22 PGPB; absolute control (AC)] with three replicates. In the second experiment, seeds were disinfected, inoculated according to their specific treatment and grown in Leonard jars containing washed and autoclaved sand. The experimental design was randomized blocks with 24 treatments [BR 3267; 22 BR 3267 + PGPB; AC] with three replicates. Scanning electron microscopy demonstrated satisfactory colonization of the roots of inoculated plants. Additionally, synergism between BR 3267 and PGPB in cowpeas was observed, particularly in the BR 3267 + Paenibacillus graminis (MC 04.21) and BR 3267 + P. durus (C 04.50), which showed greater symbiotic performance and promotion of cowpea development.

Resposta da co-inoculação de bactérias promotoras de crescimento em plantas e Bradyrhizobium sp. em caupi / Co-inoculation response of growth promoting bacterias in plants and Bradyrhizobium sp. in cowpea

Para a região árida e semi-árida do Nordeste brasileiro, o cultivo do caupi (Vigna unguiculata [L.] Walp.) vem se destacando por ser uma cultura adaptável as condições da região. Devido à capacidade do caupi de, em simbiose com o rizóbio, realizar a FBN, a co-inoculação rizóbio e bactérias promotoras de crescimento em plantas (BPCP's) poderá optimizar a fixação do N2 atmosférico dependendo da combinação e compatibilidade das estirpes envolvidas. O objetivo do trabalho foi avaliar a resposta da co-inoculação de BPCP's e Bradyrhizobium sp. como alternativa para optimizar a performance simbiótica e o desenvolvimento do caupi em condições de casa-de-vegetação. O experimento foi instalado em casa de vegetação, utilizando como substrato areia lavada e autoclavada em vasos de Leonard. Os tratamentos foram: 22 estirpes de BPCP's comparadas com a estirpe padrão (BR 3267), no caupi cv. "IPA 206". A colheita foi efetuada aos 35 dias após o plantio (DAP) e foram avaliados as seguintes variáveis: altura de planta (AP) aos 15, 25 e 35 dias, comprimento da raiz (CR), matéria seca da parte aérea (MSPA), matéria seca da raiz (MSR), matéria seca do nódulo (MSN), nodulação específica (NE) e nitrogênio acumulado na parte aérea (Nac). Os resultados mostram que a cultura do caupi respondeu significativamente a inoculação de estirpes de Bacillus, Brevibacillus e Paenibacillus co-inoculados com a estirpe de Bradyrhizobium sp. (BR 3267). A interação dos micro-organismos estudados não influenciou as variáveis, nodulação específica e matéria seca dos nódulos no caupi cv. IPA 206. A estirpe de Paenibacillus graminis (MC 04.21) co-inoculada com Bradyrhizobium sp. (BR 3267) foi superior em relação às demais estirpes avaliadas na produção de nitrogênio acumulado na matéria seca da parte aérea, proporcionando uma melhor performance simbiótica.

In the arid and semi-arid northeastern Brazil, the cultivation of cowpea has stood out for being an adaptable culture conditions in the region. Because of the ability of cowpea, in symbiosis with rhizobia carry out the FBN, the co-inoculation Rhizobium and growth promoting bacteria in plants can optimize the fixation of atmospheric N2 depending on the combination and compatibility of the strains involved. The objective of this study was to evaluate the response of the inoculation BPCP's and Bradyrhizobium sp. as an alternative to optimize performance and development of symbiotic cowpea under conditions of green-house. The experiment was conducted in a greenhouse, using as substrate washed and sterilized sand in Leonard jars. The treatments were: 22 strains BPCP's compared with the strain (BR 3267), on cowpea cv. IPA 206. At harvest 35 days after planting (DAP) and the following variables were evaluated: plant height (AP) 15, 25 and 35 days, root length (CR), shoot dry matter (MSPA), root dry matter (MSR), nodule dry matter (MSN), specific nodulation (NE) and nitrogen accumulated in shoots (Nac). The results show that the culture of cowpea responded significantly to inoculation of strains of Bacillus, Brevibacillus and Paenibacillus co-inoculated with the strain of Bradyrhizobium sp. (BR 3267). The interaction of microorganisms studied non-influenced the variables specific nodulation and dry matter of nodules in cowpea cv. IPA 206. The strain of Paenibacillus graminis (MC 04/21) coinoculated with Bradyrhizobium sp. (BR 3267) was higher compared to other strains tested in the production of nitrogen accumulated in shoot dry matter, providing a better performance symbiotic.