Defining the wheat microbiome: towards microbiome-facilitated crop production

Wheat is one of the world’s most important crops, but its production relies heavily on agrochemical inputs which are notoriously harmful to the environment. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production

Potencial de Pseudomonas sp. psicrotolerantes isoladas da Antártica no biocontrole de Botrytis cinerea.

Resumo: A Antártica, por ser um ambiente extremo, comporta micro-organismos que podem ter características interessantes, como crescimento a baixas temperaturas (psicrotolerância), além da produção de compostos antimicrobianos. Como também a possibilidade de aplicação desses micro-organismos no controle de fitopatogenos que se desenvolveu em baixas temperaturas, como é o caso de Botrytis cinerea, que ataca dezenas de culturas agrícolas em zonas temperadas. O morango, Fragaria vesca, é comumente atacado por este fungo, causando a doença conhecida como podridão cinzenta, principalmente durante a pós-colheita. Desta forma, o objetivo deste trabalho foi prospectar bactérias isoladas da Antártica e avaliar o potencial de inibição deste fitopatogeno. Assim foram testadas 56 bactérias sendo que 42% apresentaram melhor crescimento a 4°C. 4 dessas pertencentes ao gênero Pseudomonas, sendo que a linhagem 44-4 (Pseudomonas Syringae), foi capaz de controlar o desenvolvimento do fungo em morango (4°C). Demonstra-se, portanto, a possibilidade de prospecção de bactérias Psicrofilicas com potencial de reduzir o crescimento de fungos a baixa temperatura. Ensaios estão sendo feitos para elucidação dos compostos químicos responsáveis por este efeito. Abstract: Antarctica, being an extreme environment, includes micro-organisms that may have interesting features, such as growth at low temperatures (psicrotolerância), besides the production of antimicrobial compounds. As well as the possibility of application of these micro-organisms to control plant pathogens that developed at low temperatures, as is the case of Botrytis cinerea, attacking dozens of agricultural crops in temperate zones. The strawberry, Fragaria vesca, is commonly attacked by this fungus causing the disease known as gray mold, especially during post-harvest. Thus, the objective was to prospect for bacteria isolated from Antarctica and evaluate the potential inhibition of this pathogen. So were tested 56 bacteria and 42% showed better growth at 4°C. Four of these belonging to the genus Pseudomonas, and the line 44-4 (Pseudomonas syringae) was able to control the development of the fungus in strawberry (4°C). It is shown so the prospectivity of Psychrophilic bacteria with potential to reduce the fungal growth at low temperature. Tests are being made to elucidation of the chemical compounds responsible for this effect

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea

We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote⃝R fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture- dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies

Bacterial structure of agricultural soils with high and low yields.

The purpose of this study was to evaluate the structure of bacterial communities at two agricultural fields in Brazil (Paraná (PR) and Bahia (BA) states) with a history of high and low productivity of soybean. 16S rRNA gene amplicons revealed that plots with low yield of grains showed greater bacterial richness than plots with high yield. The phylum Acidobacteria was more abundant in soil samples from PR site. The rhizosphere of plants presented a similar bacterial community for both high and low yield plots. Soil samples from BA showed differences in the diversity between the plots with high and low productivity. The use of 16S rRNA amplicon sequencing allowed the assessment of differences between plots with different soybean yields. This might be useful in the future to harness plant microbiomes for increased crop productivity

Insights into the rhizosphere microbiome: past and future perspectives

Microorganisms associated to plants can promote plant growth and development through direct and/or indirect mechanisms in addition to enabling them to tolerate biotic and abiotic stresses. Several factors are responsible for shaping the microbiome associated with plants and understanding how they influence the structure and functions of microbial communities is crucial for the development of sustainable agriculture. Using culture-independent methods and soils from Rothamsted Research, I will describe the importance of different factors in determining the root microbiome structure and diversity in wheat. In addition, I will describe a culturedependent approach that led to the development of a microbial product for maize. I also discuss gaps and benefits of taking a multidisciplinary approach to explore the plant microbiome to generate microorganism-based solutions for sustainable intensification of crop production