Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class “Acidobacteriia”

Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated

Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf

Soil fungi are key players in the degradation of recalcitrant organic matter in terrestrial ecosystems. To examine the organisms and genes responsible for complex organic matter degradation in soil, we tracked changes in fungal community composition and expressed genes in soil adjacent to mesh bags containing maize leaves undergoing decomposition. Using high-throughput sequencing approaches, changes in fungal community composition were determined by targeting 18S rRNA gene sequences, whereas community gene expression was examined via a metatranscriptomic approach. The majority of the 93 000 partial 18S rRNA gene sequences generated, were affiliated with the Ascomycota and Basidiomycota. Fungal diversity was at least 224 operational taxonomic units at the 97% similarity cutoff level. During litter degradation, the relative proportion of Basidiomycota increased, with a decrease in Ascomycota : Basidiomycota ratios over time. The most commonly detected decomposition-associated fungi included Agaricomycetes and Tremellales as well as unclassified Mucoromycotina. The majority of protein families found in the metatranscriptomic data were affiliated to fungal groups described to degrade plant-derived cellulose, such as Mucoraceae, Chaetomiaceae, Sordariaceae, Sebacinaceae, Tremellaceae, Psathyrellaceae and Schizophyllaceae. The combination of high-throughput rRNA gene-based and metatranscriptomic approaches provided perspectives into the organisms and genes involved in complex organic matter in soi

Arbuscular mycorrhizal fungi originated from soils with a fertility gradient highlight a strong intraspecies functional variability

Characterization and selection of arbuscular mycorrhizal fungal (AMF) taxa to design inocula tailored to meet a spectrum of needs is a crucial first step to achieve specific beneficial agronomic functions. Commonly, commercial microbial inocula are based on generalist single AM fungal taxa, having low genetic variability and not offering efficiency and stability when applied in agroecosystems. In this study, we investigated the AMF functional variability at inter- and intra-species levels by characterizing colonization traits, host growth, and mineral uptake of single-spore AM fungi isolated from soils with a fertility gradient. Nineteen single-spore cultures, showing high spore density and AMF colonization, were phylogenetically assigned to different isolates of 3 AMF species (i.e. Entrophospora claroidea, Funneliformis mosseae and Archaeospora trappei). A higher functional variability in infectivity and effectiveness was detected among isolates within AMF species (25 % of total variance) than among AMF species. Most of AMF isolates of F. mosseae have a better outcome in terms of plant growth, although with a performance gradient, while the isolates of E. claroidea showed a variable functional pattern, and those of A. trappei a less variable pattern. Overall, isolates originating from the soil of the conventional arable field with higher pH and phosphorous availability promoted the uptake of plant nutrients, while those originating from soils with higher SOM and plant diversity promoted plant growth. On the contrary, the infectivity traits of the AM fungi were more conserved, as they were not affected by the environmental parameters of the soils of origin. Finally, we highlighted that soil pH played an important role in shaping the pattern of AMF functionality. Boosting the isolation and cultivation of AMF taxa, originating from agricultural and natural soils, is shown to be a key step in exploiting AMF diversity and designing the new generation of microbial inoculants

A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil

Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil (“MP kit”) and the DNeasy PowerSoil Pro Kit (“PowerSoil kit”). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642–37,805 16S rRNA gene sequence reads and 30,380–42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils

Current Challenges and Pitfalls in Soil Metagenomics

Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility

Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels

Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1–2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats

Caracterização citomorfológica, cultural, molecular e patogênica de Rhizoctonia solani Kühn associado ao arroz em Tocantins, Brasil.

O principal objetivo deste trabalho foi determinar o grupo de anastomose (AG) de isolados de R. solani associados ao arroz naquela região, testando a hipótese de que esses isolados pertencem ao grupo padrão de anastomose AG-1 IA, que também é o agente causal da mela em soja em áreas úmidas do Norte do Brasil. Todos os quatro isolados de arroz foram caracterizados, através de fusão de hifas, como AG-1 IA. A caracterização cultural, em função das temperaturas basais (mínimas, máximas e ótimas), evidenciou que os isolados de R. solani de arroz apresentaram perfis semelhantes aos padrões AG-1 IA, AG-1 IB e AG-1 IC. Os isolados de arroz foram caracterizados como autotróficos para tiamina assim como os isolados padrões AG-1 IA, IB, IC, AG-4 HGI e o isolado da mela da soja. O teste de patogenicidade em plantas de arroz cultivar IRGA-409 e de patogenicidade cruzada à cultivar IAC-18 de soja (suscetível à mela), indicou que além de causar a queima da bainha em arroz, esses isolados causam mela em soja. Da mesma forma, o isolado SJ-047 foi patogênico ao arroz. As seqüências de bases de DNA da região ITS-5.8S do rDNA dos isolados do arroz foram similares às seqüências do AG-1 IA, depositadas no GenBank® - NCBI. A filogenia do ITS-rDNA indicou um grupo filogenético comum formado pelos isolados do arroz, o isolado da soja e o isolado teste do AG-1 IA. Assim, com base em características citomorfológicas, culturais, filogenéticas e patogênicas, foi confirmada a hipótese de que os isolados de R. solani patógenos de arroz do Estado do Tocantins pertencem ao grupo de anastomose AG-1 IA, além da indicação de que esses isolados podem também causar a mela em soja

Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation

A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility